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ISSN: 1907-1094

AgroBiogenJ U R N A L

Akreditasi Nomor: 614/AU3/P2MI-LIPI/03/2015

Balai Besar Penelitian dan Pengembangan Bioteknologi dan Sumber aya Genetik Pertanian DBadan Penelitian dan Pengembangan Pertanian

PertanianKementerian

Volume Nomor 2012 2, Desember 16

J. Agro Biogen Vol. 12 No. 2 hlm. 63–130

Bogor Desember 6201

ISSN 1907-1094

Jurnal AgroBiogen Vol. 12, No. 2, Desember 2016

Kata Pengantar Jurnal AgroBiogen Volume 12 Nomor 2 berisi enam naskah primer dan satu naskah tinjauan. Naskah primer terdiri atas eksplorasi lokus yang berperan dalam penangkapan P (Pup1) pada plasma nutfah padi, deteksi keberadaan kimera berdasarkan analisis jumlah salinan transgen padi Nipponbare transforman T0, kekerabatan beberapa aksesi padi lokal tahan hama penyakit, keragaman lima belas aksesi jeruk fungsional Indonesia berdasarkan karakter morfologis dan marka molekuler, konservasi tanaman Belitung (Xanthosoma sagittifolium [L.] Schott) dengan metode pertumbuhan minimal, teknik organogenesis dan krioterapi untuk mengeliminasi Sugarcane streak mosaic virus pada tanaman tebu. Naskah tinjauan mengenai studi kasus gen NBS-LRR pada kedelai.

SK Kepala LIPI Nomor 335/E/2015, Tanggal 15 April 2015

Penanggung Jawab Kepala Balai Besar Penelitian dan Pengembangan Bioteknologi dan Sumber Daya Genetik Pertanian

Dewan Redaksi Asadi Pemuliaan dan Genetika Tanaman Iswari Saraswati Dewi Bioteknologi Pertanian I Made Tasma Bioteknologi Pertanian Chaerani Hama dan Penyakit Dwinita Wikan Utami Bioteknologi Pertanian Yadi Suryadi Mikrobiologi Ika Roostika Kultur Jaringan

Mitra Bestari Sugiyono Kultur In Vitro Tumbuhan, Fisiologi Tumbuhan Universitas Jenderal Soedirman Miftahudin Fisiologi dan Biologi Molekuler Tumbuhan Institut Pertanian Bogor Sri Hendrastuti Hidayat Virologi Institut Pertanian Bogor Bahagiawati Bioteknologi Pertanian Balai Besar Penelitian dan Pengembangan Bioteknologi dan Sumber Daya Genetik Pertanian Sutrisno Bioteknologi Pertanian Balai Besar Penelitian dan Pengembangan Bioteknologi dan Sumber Daya Genetik Pertanian

Redaksi Pelaksana Joko Prasetiyono Kusumawaty Kusumanegara Ida N. Orbani

Alamat Penerbit Balai Besar Penelitian dan Pengembangan Bioteknologi dan Sumber Daya Genetik Pertanian Jalan Tentara Pelajar 3A, Bogor 16111, Indonesia E-mail: [email protected] Telepon: (0251) 8339793, 8337975 Faksimili: (0251) 8338820

Kala Terbit Dua kali per tahun

mailto:[email protected]

Jurnal AgroBiogen Vol. 12 No. 2, Desember 2016

Daftar Isi

Eksplorasi Lokus Pup1 pada 55 Genotipe Padi Berdasarkan Analisis Marka Molekuler dan Sekuensing (Exploration of the Pup1 Locus on 55 Rice Genotypes Based on Molecular Marker and Sequencing Analysis)

Tasliah, Ma’sumah, dan Joko Prasetiyono 63–72

Keragaman Jumlah Salinan Transgen Galur T0 Padi Kultivar Nipponbare Berdasarkan Analisis qPCR dengan Penanda Gen hptII (Diversity of Transgene Copy Number on T0 Rice Lines of Nipponbare Based on qPCR Analysis Using hptII Gene Marker)

Aqwin Polosoro dan Wening Enggarini 73–80

Kekerabatan Beberapa Aksesi Padi Lokal Tahan Hama Penyakit Berdasarkan Analisis Polimorfisme Marka SSR (Phylogeny of Some Local Paddy Accession Tolerant to Host Pest Based on Polymorphism Analysis of SSR Markers)

Wage R. Rohaeni, Untung Susanto, Nani Yunani, N. Usyati, dan Satoto 81–90

Keragaman Jeruk Fungsional Indonesia Berdasarkan Karakter Morfologis dan Marka RAPD (Variability of Indonesian Functional Citrus Based on Morphological Characters and RAPD Markers)

Farida Yulianti, Norry E. Palupi, dan Dita Agisimanto 91–100

Multiplikasi Tunas dan Konservasi In Vitro Tanaman Belitung (Xanthosoma sagittifolium [L.] Schott) dengan Metode Pertumbuhan Minimal (In Vitro Shoot Multiplication and Conservation of Belitung [Xanthosoma sagittifolium {L.} Schott] using Minimal Growth Conservation Method)

Muhamad Sabda dan Nurwita Dewi 101–108

Organogenesis dan Krioterapi Tebu untuk Mengeliminasi Sugarcane Streak Mosaic Virus (Organogenesis and Cryotherapy Techniques of Sugarcane to Eliminate Sugarcane Streak Mosaic Virus)

Ika Roostika, Sedyo Hartono, dan Deden Sukmadjaja 109–118

Gene Duplication to Reveal Adaptation Clue of Plant to Environmental Stress: A Case Study of NBS-LRR Genes in Soybean (Duplikasi Gen Mengungkap Petunjuk Adaptasi Tanaman terhadap Cekaman Lingkungan: Studi Kasus Gen NBS-LRR pada Kedelai)

Puji Lestari, Suk-Ha Lee, I Made Tasma, and Asadi 119–130

J. AgroBiogen Vol. 12 No. 2 hlm. 63-130

Bogor Desember 2016

ISSN 1907-1094

Gene Duplication to Reveal Adaptation Clue of Plant to Environmental Stress: A Case Study of

NBS-LRR Genes in Soybean (Duplikasi Gen Mengungkap Petunjuk Adaptasi Tanaman terhadap

Cekaman Lingkungan: Studi Kasus Gen NBS-LRR pada Kedelai)

Puji Lestari1*, Suk-Ha Lee2, I Made Tasma1, and Asadi1 1Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development, Jl. Tentara Pelajar 3A, Bogor 16111 Indonesia

Phone (+62-251) 8337975; Fax. (+62-251) 8338820; *E-mail: [email protected] 2Department of Plant Science, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea

Submitted: 4 August 2016; Revised: 30 September 2016; Accepted: 15 November 2016

ABSTRAK

Gen responsif terhadap cekaman lingkungan yang bertahan setelah mengalami duplikasi genom skala kecil merupakan bagian dari duplikasi genom. Namun demikian, informasi duplikasi gen yang berpengaruh terhadap sifat adaptif tanaman terhadap perubahan lingkungan masih terbatas. Ulasan ini menyajikan gambaran peristiwa duplikasi dalam genom tanaman yang berdampak terhadap duplikasi gen yang berkaitan dengan perubahan lingkungan, informasi duplikasi gen yang merupakan bagian dari mekanisme adaptasi, kasus duplikasi gen nucleotide-binding site-leucine-rich repeat (NBS-LRR) pada kedelai, dan implementasi informasi duplikasi gen terhadap pemuliaan kedelai di Indonesia. Peristiwa duplikasi genom menghasilkan duplikasi gen dan berperan terhadap evolusi adaptasi pada perubahan lingkungan. Informasi umum tentang tanaman yang beradaptasi dengan cekaman lingkungan memungkinkan untuk meningkatkan pemahaman kita tentang duplikasi gen sebagai mekanisme adaptasi. Gen-gen NBS-LRR yang terduplikasi diketahui berasosiasi dengan QTL terkait ketahanan penyakit dan ekspresi diferensialnya membuktikan kontribusi gen tersebut pada ketahanan kedelai terhadap cekaman biotik. Model yang diusulkan dari proses gen duplikasi NBS-LRR dapat membantu dalam memahami respons gen tersebut terhadap perubahan lingkungan. Duplikasi gen ketahanan terhadap hama/penyakit, NBS-LRR khususnya, memberi-kan informasi penting dalam pemilihan tetua pemuliaan dan pengembangan marka molekuler terkait ketahanan penyakit untuk memperbaiki kedelai di Indonesia secara genetik. Karena itu, sangat mungkin untuk meningkatkan program pemuliaan yang menargetkan gen ketahanan terhadap cekaman biotik/abiotik dan memberikan dasar molekuler sebagai strategi per-lindungan tanaman terhadap cekaman dan pengembangan kultivar kedelai khusus untuk lingkungan ekstrim.

Kata kunci: Cekaman lingkungan, duplikasi gen, hama/penyakit, kedelai, NBS-LRR.

ABSTRACT

Genes responsive to the environmental stresses which are retained after small scale duplication are part of plant genome duplication. However, information of duplicated genes that could be adaptive to environmental changes in plant is limited. This review presents an overview of duplication events in plant genomes which impact to gene duplication in relation to environmental changes, gene duplication as an adaptation mechanism, a case of duplicated nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes in soybean, and the gene duplication implementation for soybean plant breeding in Indonesia. Notably, genome duplication events generate gene duplication and contribute to adaptive evolution against environmental changes. Generalization of plants adaptation to the stressful conditions also probably improves our understanding of gene duplication as a mechanism of adaptation. Several recently duplicated NBS-LRR genes in soybean retain disease resistance QTL and the differential expression convince their contribution to biotic stress resistance in soybean. Proposed models of NBS-LRR genes duplication process may help to understand these genes response to the environmental changes. The duplication of genes resistant to pest/disease, particularly NBS-LRR, provides important information for breeding parents selection and developing molecular markers related to desease resistance to genetically improve soybean in Indonesia. Overall, it may therefore be possible to enhance breeding programs which target on genes tolerant/resistant to biotic/abiotic stresses and provide a molecular basis for crop-stress protection strategy and improve soybean cultivars specified for harsh environment.

Keywords: Environmental stress, gene duplication, soybean, pest/disease, NBS-LRR.

Hak Cipta © 2016, BB Biogen

Jurnal AgroBiogen 12(2):119–130

mailto:[email protected]

JURNAL AGROBIOGEN VOL. 12 NO. 2, DESEMBER 2016:119–130 120

INTRODUCTION

Climate change affects many aspects of plant architecture and represents a serious obstacle for developing sustainable agriculture. To cope with climate change, plants have evolved various molecular programs for adaptation. Consequently, plant adaptive strategies to environmental stresses have been a subject to great interest. Recent physiological and molecular programs have been identified in plants which could be relevant to global changes (Meehl and Stocker, 2007; Winning et al., 2009). However, more efforts are still needed due to less ability to encounter the stress challenges, especially to breed crops with enhanced resistance to multiple environmental stresses. The broad range of genes associated with resistance to the environmental stresses in many plants species has been progressed and may assist to develop new plant cultivars (Ahuja et al., 2010). The interlinked genetic and genomic features would make the improved crops achievable to encounter environmental stresses (Mochida and Shinozaki, 2010).

Advanced genomics and molecular biology have impacted to speed the identified genetic regions associated with quantitative trait loci (QTL) that increase opportunities for extensive breeding programs. Since the entire genome of many plant species has been published, the detailed genomic resources facilitate to easily identify desired traits. Whole genome duplication (WGD) forming polyploidy and small-scale duplication (SSD) provide a crucial understanding of genome relationship among plant species with close ancestry. Moreover, these duplication events which impact to genome structure and duplicated genes could be useful as a basis information for the interspecific breeding of plant with at least diploid or higher ploidy level that usually results in the appearance of new ploidy allele, such as allotetraploid in Brassica, wheat, maize, cotton, etc. (Renny-byfield and Wendel, 2014; Ziolkowski et al., 2012). Such genome structure with its impact to genes also is beneficial resource for breeding strategy in the corresponding crops, especially challenging with unpredictable climate. In addition to substantial study of the gene divergence and evolution associated with cycles of polyploidization, deeper information of agricultural useful genes and QTLs are able to be explored, including those related to resistance to biotic and abiotic stresses. Evolution of resistance genes has been reported to be implication of genome duplication and gene duplication events (Guo et al., 2004; Hanada et al., 2008).

Gene duplication is considered the main source of functional diversity on genotypic level. After duplication, each copy could evolve independently and diversify the effects, leading to functional novelty. Gene copies of various degree of divergence exist in genomes. Since any mutation, a duplication event may result on organism’s fitness. Thus, gene duplication affects gene dosage which is in turn to affect fitness. The fitness effects of a gene duplication that lies mainly in the arisen copy number cause an increase in protein dosage (Kondrashov, 2012), while other mechanisms can lead to adaptive response (Innan and Kondrashow, 2010). Particularly, an environmental adaptation can be the driving force in the fixation of gene duplication. Even some genes are clearly fixed during evolution by positive selection which plays an important role in the fixing of fraction of gene duplication. Genomic approach may identify the action of selection on specific gene duplication including adaptive gene duplications (Kondrashov, 2012).

Unlike the rich data shown by numerous publications from microbiological community suggesting adaptive impact of gene duplication under certain environmental conditions (Kondrashov, 2012), the information of genome and gene duplications in plants are still limited to support the adaptation to the environmental changes. Reports showed that some stress-responsive genes in plants were as tandem array, which might have been duplicated (Hanada et al., 2008; Zhang, 2003). Also, genes related to biotic stress response in A. thaliana (Maere et al., 2005) and disease resistance genes containing domain of a nucleotide-binding site and a leucine-rich repeat in soybean (Glycine max) (Kang et al., 2012; Shin et al., 2008) were well retained after the SSD and large scale duplication (LSD), suggesting their roles of adaptive evolution against environmental conditions.

We highlighted an overview based on genome resources focusing on plant genome duplication which impacted to gene duplication with their related aspects to environmental changes. This review also presented an information of gene duplication as an adaptation mechanism, a case of duplicated nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes in soybean to support a view of these gene relation to biotic stress, and the prospect and challenges of gene duplication implemented on soybean breeding for resistance/tolerance to biotic/ abiotic stress in Indonesia.

2016 Gene Duplication to Reveal Adaptation Clue of Plant: P. LESTARI ET AL.

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GENOME AND GENE DUPLICATIONS IN PLANTS

In the lineage of plants, genome duplications involving entire genome duplication (WGD) and SSD have occurred. WGD and SSD are more frequent in plants in comparison to other eukaryotes, as demonstrated in angiosperms as an outstanding model for genome and gene duplications elucidation. Many angiosperms have undergone multiple WGDs with certain mechanisms (Carretero-Paulet and Fares, 2012; Wang et al., 2012). The first angiosperm that has its genome sequenced, A. thaliana, evidenced at least three duplication rounds during its evolutionary history, of which two were recent WGDs. Moreover, cereals and legumes appear to experience different numbers of WGDs and reveal their shared duplications with other relative species and their ancient (Freeling, 2009). In the case of legume crops (e.g. soybean), in general they have undergone two rounds of duplications. Mungbean genome, however, demonstrated the exception of legume duplication phenomena that its genome has experienced only one round of duplication event (Kang et al., 2014). Unlike WGD that involves large scale duplication (LSD) leading to a dramatic risen in duplicated genes number, SSD is more restricted only involving one or few genes. Both WGD and SSD contribute significantly to the genome composition and gene duplication (Guo et al., 2004).

Considering its potency to result in novel functions, gene duplication is believed to relate with diverse evolutionary importance. Consequently, new genes and gene function play a role in performing phenotypic diversity of plants (Guo et al., 2004). One duplicated gene is predicted to be retained the ancestral function and another one evolves neutrally and free from selective constrains, indicating the divergence of the duplicated genes. For example, as a result of genome and gene duplications, two main branches of angiosperms, namely eudicots and monocots were estimated to diverge between 125 to 140 million years ago (Mya) and 170 to 235 Mya, respectively (Davis et al., 2004). Million years ago red clover, Medicago truncatula, soybean, and common bean were diverged from each other and from A. thaliana. Between two legume members, M. truncatula and alfalfa, syntenic and chromosome relationships of both genomes were also indicated, supporting their ancient duplication histories (Kim et al., 2015).

Genetic mechanism underlying duplication events can be different to result in duplicated genes. Several modes of gene duplication are distinguishable such as WGD/segmental, tandem, DNA-based

transposed duplications, etc. Gene families expansion possibly is enriched with particular modes of gene duplication events. Recent genome duplication also revealed homologous retention and chromosomal rearrangement (Schmuts et al., 2010). Homeologous blocks such as QTLs related to protein and oil content along with the corresponding genes have been identified in duplicated segments on the twenty chromosomes of soybean genome as depicted in Figure 1A (Lestari et al., 2013). DNA-based transposed duplications are enriched in disease resistance gene homologs in A. thaliana (Figure 1B) and WGS duplications are enriched in the C2H2 zinc finger protein in rice (Figure 1C).

Orthologous and paralogous relationships were also found in the genomic regions harboring soybean nematode resistance genes in the genomes of soybean and M. truncatula (Wang et al., 2013). These phenomena suggest that gene family member is likely to have common pattern of origin in different evolutionary lineages. Thus, duplicated genomes and genes can facilitate materials for evolutionary and functional divergence. The gene duplication is attributable to increase functional diversity and the increased expression divergence in duplicated genes can substantially contribute to phenotypic diversifications (Wang et al., 2012).

PLANT GENOME DUPLICATION IN RELATION TO ENVIRONMENTAL CHANGES

Duplicated genes, performing a key role in generating phenotypic variation and speciation to distinct species, are less preserved and remain unbalance via the SSD than LSD (Lynch, 2007). Notably, a region of older sister paralogs suggests that ancient SSD may occur before WGD in some crops. The SSDs are thought to be undergone continuously after WGD. Thus, the footprint of most recently duplicated genes should be left behind in the SSD in addition to LSD during its evolution (Guo et al., 2004).

Many non-overlapping duplicated regions show a conserved gene order and orientation in plants (Guo et al., 2004; Peterson et al., 2003). Genes are created by LSD to dramatic increase the duplicated genes numbers, however, these genes are easily decayed after SSD (Severin et al., 2011). Interestingly, most of genes in genome belonging to a gene family are found through continual SSD events. The SSD event, tandem gene duplication accounts for a significant contribution of the increased gene family size, in relative to the LSD depending on plant species (AGI, 2000; Goff et al., 2002).


LSD like “polyploidy episode” is thought to be one of the survival mechanisms of plants that may often coincide with the occurrence of extreme environments (Fawcett et al., 2009). That adaptive selection is suggested to possibly play a role in fixing pale-polyploidy in a plant species. Not only polyploidy event, the SSDs in plant genome might be also as a response to environmental changes which is likely to associate with environmental selection (Guo, 2013; Guo et al., 2004). The continuous mode of the SSD results in high rate of gene birth and decay in comparison to LSD. The duplication events may have consequences on the plant fitness, thus any mutation and/or selection could be undergone on the redundant gene copies against environmental changes for providing adaptation (Kandrashov, 2012).

Gene duplication leading to genetic redundancy would implicate to functional buffering. Partial redundancy by knocking out of either duplicate generates in more mitigated phenotypic changes than acting of both copies. Furthermore, functional compensation by duplicated genes for severe phenotypic effects is likely to be preserved longer than for a less severe effect by natural selection (Wang et al., 2013). Thus, differential gene

duplication which contributes to on-going process in genome evolution in geographically isolated plant populations also could cause reproductive isolation and particular adaptation (Magadum et al., 2013).

GENE DUPLICATION AS AN ADAPTATION MECHANISM

The duplicated genes may evolutionary acquire new functions, but how these changes occur and can adapt to different environments are still under investigation as many scientists suspects. Gene duplication as a form of adaptation to various environmental conditions is not a rare mechanism. Adaptive duplication seems to involve the genes which their products interact with molecules associated with variable environments and how rapidly/constantly they are produced at high level (Kondrashov, 2012). Furthermore, some logic hypothesis propose that fixed gene duplication playing an adaptive role in dosage response to environmental stresses are thought to be the functions of gene duplication with characterized adaptive roles (Flagel and Wendel, 2009). It is also instructive to predict the gene categories/types

Figure 1. Circular maps showing homologous relationships among chromosomes after genome and gene duplications in the genomes of soybean, A. thaliana, and rice. A = QTLs associated with protein and oil content in recently duplicated regions on twenty chromosomes of soybean (Lestari et al., 2013), B = disease resistance gene homologs in A. thalilana (Wang et al., 2011), C = C2H2 zinc finger gene family in rice (Wang et al., 2011). Chr1–Chr20, AT1–AT5, and OS1–OS12 in each circus denote the shown chromosome number of the corresponding plant genomes. Several colored ribbons represent duplicated regions which are grouped as bundles.

A

B C


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possibly conferring an adaptation in certain or various environments based on the functional repertoire of the gene duplication in genome (Kang et al., 2012; Kondrashov, 2012). Current accumulated studies demonstrated that new gene copy number may affect function. Many copy number variations (CNVs), including their association with diseases, are selected in the genome, which has to increase in gene dosage (Kondrashov and Kondrashov, 2006; Lupski, 2007). It appears that a gene duplication which is adaptive under a stressful environment comes as fitness cost in a benign environment (Kondrashov and Kondrashov, 2006).

Adaptive gene duplications could be categorized according to organism responses, such as nutrients transport, protection to heat, cold, and salt, heavy metals, adaptation to domestication, etc. A clear example of a gene duplication conferring an adaptation to nutrient limitation was demonstrated by the yeast hexose transporter genes. Under low glucose, the appearance of a new hybrid copy from two very closely related gene paralogues, namely HXT6 and HXT7, arose the expression level of hexose transporter gene and the glucose transport rate into the cells (Brown et al., 1998). Another example, adaptation to heat stress was shown via gene duplication of several stress-related genes in Escherichia coli (Riehle et al., 2001). Then, similar observation was also performed in yeast, revealing an increase propensity for chromosomal segmental duplications (James et al., 2008). Other examples included a study of the genome-wide expression and the corresponding copy numbers convinced an evidence for cold adaptations in Antartic cod (James et al., 2008).

Polyploidy events were observed to play an important role in adaptation in yeast and plant. A consistent polyploidy of yeast strains was observed to play an important role in adaptation. Similarly in plant, polyploidy has been linked to resistance to high salt concentrations in citrus (Saleh et al., 2008) and

sorghum (Ceccarelli et al., 2006), suggesting that polyploidy is likely a general physiological adaptive response to osmotic stress (Dhar et al., 2011). Duplication-induced metal resistance in different plant species might be related to export of the cations outside cell (Kondrashov and Kondrashov, 2006). At present, duplicated genes are associated with recent domestication-related phenotypic characters such as characters controlling milk proteins and the proteins themselves (Liu et al., 2009; Bickhart et al., 2012).

Even though studies of adaptive gene duplication in microorganism seem more than those in plants species, some adaptive gene duplication studies have been reported in plants. A number of adaptive gene duplications in plant species to encounter various environmental conditions are presented in Table 1. A gene encoding 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase in common bean, soybean, and tobacco (Nicotiana tabacum) was identified to function in the herbicide glyphosate induction (Shaner et al., 2012; Widholm et al., 2001). Some gene copies resulting from duplication events in A. thaliana were found related to tolerance to high temperature (DeBolt, 2010). Duplication of genes involved in pathogens resistance suggest the role of gene duplication involved in rapid coevolution between the host and the symbiont or pathogens (Hanada et al., 2008). Six duplicated gene pairs were clustered in specific regions on chromosome 6 and 13 with high homology level of around 80–90%. Syntenic QTL regions identified between the two chromosomes of soybean indicate an association of the QTL with homeologous chromosomal regions in the genome. Well predicted QTLs and candidate genes for stress tolerance may reveal novel mechanism of adaptation in soybean (Lestari et al., 2014). As a result of recent genome duplication, gene duplication could contribute not only to environmental adaptation but also affect other agronomical important traits in soybean such as seed protein/oil content (Lestari and Lee, 2014; Lestari et al., 2013).

Table 1. Few examples of adaptive gene duplication events found in several plant families/species.

Gene Function Plant family/species Environmental condition Evidence References

Prolamine-coding genes

Storage proteins Poaceae Nutrient storage in seeds

Indirect inference from large number of copies

Xu and Messing (2009)

IRI-like gene family Ice recrystallisation inhibition

Pooideae Low temperature Gene family expansion in cold-tolerant lineage

Sandve et al. (2008)

COR 15 Cold tolerance-related protein

Brassicaceae Low temperature Several independent duplications

Zhou et al. (2009)

EPSPS 5–enolpyruvyl shikimate–3–phosphate synthase

Amaranthus palmeri, Medicago sativa, Glycine max, Nicotiana tabacum, other species

Glyphosate Field studies, experimental evidence

Gaines et al. (2010, 2011); Shaner et al. (2012)


The developed gene families or clusters with related functions are still uncertain whether chromosome duplication itself has adaptive values. Even though the evolutionary forces involve in adaptation to a changing environments, both positive selection and the relaxation of the selective pressures maintaining an old function are equally important. In addition to the chromosome number in the genome, gene duplication events can function not only as an evolutionary mechanism, but also as a form of genetic variation to preserve plants (Kondrashov, 2012; Ramsey, 2011).

AN EXAMPLE: STUDY OF ASSOCIATION BETWEEN NBS-LRR GENES AND RESISTANCE TO BIOTIC

STRESS IN SOYBEAN

Resistance (R) genes with their functional sources against biotic and abiotic stresses could be used to gain improved crops with adaptation (Ahuja et al., 2010). Even though lack studies of R genes in diverse diseases in soybean, some promising NBS-LRR genes are reported to be associated with important traits related to disease resistance and tolerance to abiotic stresses. CC-NBS-LRR especially ADR1 along with EDS1 and ABI1 is involved in drought tolerance enhancement (Chini et al., 2004). LRR protein was found only in the aluminum treated library suggesting that the TIR-NBS-LRR protein probably takes part in a regulating pathway involved in the recognition of biotic and abiotic stresses. The cleavage of the TIR-NBS-LRR protein under aluminum stress might result in the disruption of the immune system, which might increase the susceptibility of the plant to other stresses (Zeng et al., 2012). NBS-LRR genes show a high association with resistance to various diseases such as disease caused by Pseudomonas syringae pv. glycinea, sudden death syndrome and rust diseases, and nodulation in soybean (Ashfield et al., 2003; Zhu et al., 2010). We described an example of correlation between the NBS-LRR and disease resistance QTL, functional redundancy of disease resistance in soybean on recently duplicated regions harboring these genes as reported by Kang et al. (2012).

A total of 314 NBS-LRR genes was located across twenty soybean chromosomes (Table 2) and five NBS-LRR were in scaffolds. Of the total NBS-LRR genes detected based on their N-terminal domains using homology analyses to the A. thaliana NBS-LRR genes, 116 TIR-NBS-LRRs, 20 CC-NBS-LRRs, and 183 other NBS-LRR were classified (Kang et al., 2012). A significant correlation was shown between the

numbers of NBS-LRR genes and the disease resistance QTLs within the NBS-LRR-flanked 2 Mb region supporting the common feature of association between the NBS-LRRs and the loci/QTL for biotic stress in plants. Disease resistance QTL for multiple pathogens tend to be positioned near the highly cluster regions harboring NBS-LRRs. The cluster was to be associated with duplication events during evolution with possibly driving forces of tandem duplication and mobile DNA-like transposase and integrase (Ream and Neidle, 2004; Roth et al., 1996).

To prove duplication events, it was notable that the distribution of NBS-LRR genes in the soybean was biased and clustered on certain chromosomes (Chr 3, 6, 13, 15, 16, and 18), and more than half were existed on these six chromosomes. The clusters were a result of duplication events on the chromosomal location of the NBS-LRR genes as was depicted on a circle genome map (Figure 2) (Kang et al., 2012). A number of NBS-LRR genes resides within recently duplicated genomic regions where the duplicated disease resistance QTLs also exist, suggesting specific copy number variations of NBS-LRR genes in the duplications. Kang et al. (2012) identified that most of NBS-LRR genes on the recently duplicated regions seem to be in the position of QTLs related to Sclerotinia stem rot, sudden death syndrome, brown stem rot, bacterial leaf pustule (BLP), Phytophthora sojae, and soybean cyst nematode infection. Duplicated regions containing the QTLs showed distinctive specificities for divergent diseases. Some duplicated NBS-LRR genes in a homeologous pair indicate the probability of the NBS-LRR genes to retain their biotic resistance functions and/or acquiring their novel specificities. However, recently duplicated regions contain biased number of NBS-LRR genes including tandem duplicated genes and several disease resistance QTLs located on several chromosome locations segregated (Table 2). The functional redundancy between duplicated regions was reported for several traits in soybean including the BLP resistance (Kim et al., 2009) and the recently NBS-LRR duplicated regions controlling several disease resistance phenotypes (Kang et al., 2012).

R genes contain abundant copies throughout genomes, possibly produced by unequal crossing over (Meyers et al., 2003). Three models were proposed explaining the duplication process of NBS-LRR genes (Kang et al., 2012). Model 1 explained the tandem duplication occurred prior to the recent duplication (e.g. ID 10176678) and Model 2, the recent duplication copied genes/regions to another chromosome, then the tandem duplication occurred


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independently (e.g. ID 18934088). The mixed model described that the tandem duplication events occurred prior to the recent duplication and the independent tandem duplications underwent after the recent duplication as they can be seen on chromosomes 13 and 15 (e.g. ID 18159398). Based on the possibility of a combination of tandem and inter-chromosomal duplications among the proposed model scenarios, the duplication history of NBS-LRR genes can be one of the factors involved in the diversifying QTLs for disease resistance phenotypes and in a more general, QTLs related to biotic stress.

Transcriptome analysis (Kang et al., 2012) demonstrates a significant fold-change in these NBS-LRR genes that seem to work either strain-specific or broad spectrum of pathogens, in line with the previous studies which observed against various diseases invasions and cyst nematode damage (Brechenimacher et al., 2008; Calla et al., 2009). Thus, it is likely that the duplicated NBS-LRR genes associated with disease resistance could contribute to the adaptation to cope with biotic stresses in soybean. Further investigation of these duplicated genes in genome in relation to abiotic stress will support the broad adaptation of soybean against environmental changes.

PROSPECTS AND CHALLENGES ON THE APPLICATION OF GENE DUPLICATION

PHENOMENON ON SOYBEAN BREEDING FOR PEST/DISEASE RESISTANCE IN INDONESIA

Comparative and collinear analyses between soybean and other legumes on their respective duplicated regions have been performed to assist soybean improvement for pest/disease resistance. Orthologous and paralogous relationships of the genomic regions between soybean and M. truncatula harbored soybean nematode resistance genes, rhg1 and rhg4 (Mudge et al., 2005). A total of 1,273 tandem duplicated genes with categories of defense response in adzuki bean (Kang et al., 2014) could also be useful in soybean breeding program. Higher significant QTLs related to 114 traits including the ones for pest/disease resistance were detected to have high phenotypic variation in soybean than those in mungbean, mainly as a result of two rounds of genome duplication events which have occurred in soybean. Synteny blocks consisting of QTLs responsible for bruchid resistance matched soybean synteny blocks locating SSR markers associated with nematode resistance QTLs (Kim et al., 2015). More than 1100 QTLs and 60,000 protein-coding loci are beneficial to reveal stress-response genes, which

Table 2. The NBS-LRR genes, disease resistance QTLs and disease resistance QTLs located within the 2-Mb flanking regions of NBS-LRR genes selected in recently duplicated regions in soybean chromosomes (Kang et al., 2012).

Chr No. NBS-LRR genes

No. QTLs

No. QTLs within 2-Mb flanking region of NBS-LRR genesa)

No. disease resistance QTLs in recently duplicated regionsb)

No. NBS-LRR loci in recently duplicated regions

Chr A Chr A’ Chr A Chr A’

1 20 8 4 SCN (4), Sclero (4) Sclero (2), SDL (1), Phytoph (1), Bra (1)

7 loci 7 loci

2 10 9 5* - - - - 3 36 7 7* Sclero (1), SDS (1) Sclero (4), Bra (1), OCS

(2), LMG (1) 2 loci 5 loc

5 5 3 3* - - - - 6 23 8 7* - - - - 8 15 10 9* Sclero (4), OCS (1), SCN

(5) Sclero (3), LMG (1) 1 locus 1 locus

9 11 9 9* Sclero (5) BSR (13), SCN (6), Sclero (5), Mi (5)

2 loci 17 loci

12 14 3 2* - - - - 13 22 15 12 - - - - 14 11 5 3* - - - - 15 25 4 4* Ma (1) Sclero (5), Ma (1), Mj (1) 13 loci 14 loci 17 6 9 4 Sclero (3) SCN (2) 2 loci 2 loci 20 13 2 1 OCS (1), SDL (1), SDS (1) SCN (2), Bra (1), Sclero

(14) 3 loci 3 loci

a)Regression analyses were done between the number of NBS-LRR genes and the number of QTLs within the 2-Mb flanking region of NBS-LRR genes. b)Fungal resistance QTLs: Sclerotinia stem rot (Sclero), sudden death syndrome (SDS), brown stem rot (BSR), Phytophthora sojae infection (Phytoph); Nematode resistance QTLs: soybean cyst nematode (SCN), peanut root-knot nematode (Ma), southern root-knot nematode (Mi), Javanese root-knot nematode (Mj); bacterial leaf pustule (BLP) resistance QTLs: OCS-G, SDL2178, 8ra, OCS-F, LMG7403. More than half of the disease resistance QTLs colocalized with NBS-LRR genes within the 2-Mb flanking region. Chromosome A (origin) and A’ (duplicate) represent the recently duplicated regions.


have been built into soybean databases (www.phytozome.net/soybean; http://soybase.org) and elucidated for their syntenies within duplication regions in soybean and with other legumes (Kang et al., 2012, 2014, 2015, 2016; Kim et al., 2015; Lestari et al., 2013). Syntenic QTL regions have been detected between chromosome pairs in soybean genome, showing duplicated genes clustered in homeologous QTLs to be possibly associated with environmental specific regulation as demonstrated in chromosomes 6 and 13 (Lestari et al., 2014). QTLs and candidate NBS-LRR genes corresponding to pest/disease resistance in duplication regions were also well predicted (Kang et al., 2012).

Eight Indonesian soybean genotypes with distinctive genetic background were resequenced and provided unique genome resources (Lestari et al., 2016; Satyawan et al., 2014) containing a number of SNPs with their descriptive genes related to defense systems (http://genom.litbang.pertanian. go.id). To date, however, studies on QTLs and

predicted genes in duplication regions in soybean genome are very limited in Indonesia. Therefore, this information provides a valuable starting point to identify genes controlling pest/disease resistance and develop their corresponding markers in soybean.

Breeding program of soybean, the third important food crop in Indonesia just after rice and maize, is still challenging to face pests and diseases that can significantly decline its quality and yield. In addition to abiotic stress, biotic stress (pest and disease) influences the production of soybean subjected to the changes of unpredictable climate. Prominent pests/diseases in soybean have been found in several areas in Indonesia and cause significant economic losses. As observed in Java, eleven important pests, two viral diseases vectors, and sixteen important diseases were distributed according to location as a result of cropping system, local weather, and host existence. According to disease intensity and area distribution, leaf rust, downy mildew, leaf blight, Sclerotium rolfsii, and BLP

Figure 2. The circular genome map depicting the locations of recently duplicated regions with NBS-LRR genes, transcription levels of NBS-LRR genes after BLP treatment, locations of disease resistance QTL, and significantly expressed NBS-LRR genes. Minimum values to maximum values of expression are denoted with black, grey, red, orange, yellow, lime, green, blue, and purple (Kang et al., 2012).

http://www.phytozome.net/soybean;

http://soybase.org)

http://genom.litbang.pertanian.


127

have been considered to be important diseases and put in a high priority to be controlled (www.balitkabi.litbang.pertanian.go.id). Thus, the genetically improved soybean cultivars are preferred to be highly adaptive to biotic/abiotic stress, high yielding, and high grain quality in Indonesia. Since, conventional breeding of soybean in Indonesia has long been a common way, with the advantages of genome and gene duplications clue implementing to marker-assisted breeding, improving soybean cultivars resistant to pests and diseases could be accelerated.

Special interest would be addressed on duplicated R genes such as NBS-LRR genes that have expectedly led to make more efficient soybean breeding using marker-assisted selection (MAS). As an initial clue, there is a number of duplicated NBS-LRR genes (Kang et al., 2012) to be known to control several soybean diseases existing in Indonesia including bacterial leaf rust, leaf pustule, Sclerotinia stem rot, etc. Given that the developed near isogenic lines (NILs) showed contrast expression between resistance and susceptible for BLP caused by Xanthomonas axonopodis pv. glycines (Xag) (Kang et al., 2012), similar model of NILs could be developed to identify recently duplicated NBS-LRR gene expression, more convincing the functional relevance of the disease resistance in Indonesia.

Molecular markers for NBS-LRR domains should be developed possibly by integrating several disease resistance genes to generate elite Indonesian soybean cultivars which are capable of resisting diverse range of pathogens. In addition, deeper analysis of gene duplication among Indonesian soybean genotypes could give clearer information of NBS-LRR. Most importantly, this gene duplication that implicates genetic resources with different mechanism is important for breeding materials. Taken together, these pest and disease obstacles in Indonesia should be controlled and managed using integrated technologies and interdisciplinary fields related to genomics, computational biology, and related-omics into useful and systematic soybean breeding programs. This, at the end, should in part help the national food self-sufficiency and food security programs in Indonesia.

CONCLUSIONS

WGD and SSD contribute significantly to gene duplication events in plants. Gene duplication leads to genetic redundancy that would implicate to functional buffering and is a form of adaptation to

various environmental conditions. To understand the adaptation of plant species to environmental stresses, it would be advisable to consider taking a closer look at the gene duplication from the recently duplicated regions. Gene duplication phenomenon which affects phenotypes, would prospectively direct researchers and breeders to select candidate genes and informative genetic markers for traits of interest. Developing biotic and abiotic stress resistance crops could be performed in cultivated gene pool for R genes. As an alternative, molecular markers corresponding to NBS-LRR domains are integrated with biotic stress against broad range of pests/ diseases to generate improved and well-adapted crop cultivars. The integrating knowledge of gene duplication phenomenon should promote research and is prospectively implemented in breeding programs to develop new soybean cultivars capable of encountering various environmental stresses in Indonesia.

ACKNOWLEDGEMENTS

Authors are grateful to Dr. Yang Jae Kang and Dr. Sutrisno for their constructive comments on this manuscript. We also thank the reviewers for their thorough reviews and useful comments.

REFERENCES

Arabidopsis Genome Initiative. 2000. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796–815.

Ahuja, I., H. de Vos Ric, A.M. Bones, and R.D. Hall. 2010. Plant molecular stress responses face climate change. Trends Plant Sci. 15:664–674.

Ashfield, T., A. Bocian, D. Held, A.D. Henk, L.F. Marek, D. Danesh, S. Penuela, K. Meksem, D.A. Lightfoot, Y.D. Young, R.C. Shoemaker, and R.W. Innes. 2003. Genetic and physical localization of the soybean Rpg1–b disease resistance gene reveals a complex locus containing several tightly linked families of NBS-LRR genes. MPMI 16:817–826.

Bickhart, D.M., Y. Hou, S.G. Schroeder, C. Alkan, M.F. Cardone, L.K. Matukumali, J. Song, R.D. Schnabel, M. Ventura, J.F. Taylor, J.F. Garcia, C.P. Van Tassel, T.S. Sonstegard, E.E. Eichler, and G.E. Liu. 2012. Copy number variation of individual cattle genomes using next-generation sequencing. Genome Res. 22:778–790.

Brechenimacher, L., M.Y. Kim, M. Benitez, M. Li, T. Joshi, B. Calla, M.P. Lee, M. Libault, L.O. Vodkin, D. Xu, S.H. Lee, S.J. Clough, and G. Stacey. 2008. Transcription profiling of soybean nodulation by Bradyrhizobium japonicum. MPMI 21:631–645.

http://www.balitkabi.litbang.pertanian.go.id).


Brown, C.J., K.M. Todd, and R.F. Rosenzweig. 1998. Multiple duplications of yeast hexose transport genes in response to selection in a glucose-limited environment. Mol. Biol. Evol. 15:931–942.

Calla, B., O. Radwan, T. Vuong, S.J. Clough, and G.L. Hartman. 2009. Gene expression profiling soybean stem tissue early response to Sclerotinia sclerotiorum and in silico mapping in relation to resistance markers. Plant Genome 2:149–166.

Carretero-Paulet, L. and M.A. Fares. 2012. Evolutionary dynamic and functional specialization of plant paralogs formed by whole and small-scale genome duplications. Mol. Biol. Evol. 29(11):3541–3551.

Ceccarelli, M., E. Santantonio, F. Marmottini, G.N. Amzallag, and P.G. Cionini. 2006. Chromosome endore duplication as a factor of salt adaptation in Sorghum bicolor. Protoplasma 227:113–118.

Chini, A., J.J. Grant, M. Seki, K. Shinozaki, and G.J. Loake. 2004. Drought tolerance established by enchanced expression of the CC-NBS-LRR gene, ADR1, requires salicylic acid, EDS1 and ABI1. Plant J. 38:810–822.

Davis, J.C. and D.A. Petrov. 2004. Preferential duplication of conserved proteins in eukaryotic genomes. PLoS Biol. 2(3): e55. doi:10.1371/journal.pbio.0020055.

DeBolt, S. 2010. Copy number variation shapes genome diversity in Arabidopsis over immediate family generational scales. Genome Biol. Evol. 2:441–453.

Dhar, R., R. Sägesser, C. Weikert, J. Yuan, and A. Wagner. 2011. Adaptation of Saccharomyces cerevisiae to saline stress through laboratory evolution. J. Evol. Biol. 24:1135–1153.

Fawcett, J.A., S. Maere, and Y. Van de Peer. 2009. Plants with double genomes might have had a better chance to survive the Cretaceous-Tertiary extinction event. Proc. Natl. Acad. Sci. USA 106:5737–5742.

Flagel, L.E. and J.F. Wendel. 2009. Gene duplication and evolutionary novelty in plants. New Phytol. 183:557–564.

Freeling, M. 2009. Bias in plant gene content following different sorts of duplication: Tandem, whole-genome, segmental, or by transposition. Annu. Rev. Plant Biol. 60:433–453.

Gaines, T.A., D.L. Shaner, S.M. Ward, J.E. Leach, C. Preston, and P. Westra. 2011. Mechanism of resistance of evolved glyphosate-resistant Palmer amaranth (Amaranthus palmeri). J. Agric. Food. Chem. 59:5886–5889.

Gaines, T.A., W. Zhang, D. Wang, B. Bukun, S.T. Chisholm, D.L. Shaner, S.J. Nissen, W.L. Patzoldt, P.J. Tranel, A.S. Culpepper, T.L. Grey, T.M. Webster, W.K Vencill, R.D. Sammons, J. Jiang, C. Preston, J.E. Leach, and P. Westra. 2010. Gene amplification confers glyphosate resistance in Amaranthus palmeri. Proc. Natl. Acad. Sci. USA 107:1029–1034.

Goff, S.A., D. Ricke, T.H. Lan, G. Presting, R. Wang, M. Dunn, J. Glazebrook, A. Sessions, P. Oeller, H.

Varma, D. Hadley, D. Hutchison, C. Martin, F. Katagiri, B.M. Lange, T. Moughamer, Y. Xia, P. Budworth, J. Zhong, T. Miguel, U. Paszkowski, S. Zhang, M. Colbert, W.L. Sun, L. Chen, B. Cooper, S. Park, T. Wood, L. Mao, P. Quail, R. Wing, R. Dean, Y. Yu, A. Zharkikh, R. Shen, S. Sahasrabudhe, A. Thomas, R. Cannings, A. Gutin, D. Pruss, J. Reid, S. Tavtigian, J. Mitchell, G. Eldredge, T. Scholl, R.M. Miller, S. Bhatnagar, N. Adey, T. Rubano, N. Tusneem, R. Robinson, J. Feldhaus, T. Macalma, A. Oliphant, and S. Briggs. 2002. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296:92–100.

Guo, Y.L. 2013. Gene family evolution in green plants with emphasis on the origination and evolution of Arabidopsis thaliana genes. Plant J. 73:941–951.

Guo, X.Y., G.H. Xu, Y. Zhang, W.M. Hu, and L.J. Fan. 2004. Small scale duplications play a significant role in rice genome evolution. Rice Sci. 12:173–178.

Hanada, K., C. Zhou, M.D. Lehti-Shiu, K. Shinozaki, and S.H. Shiu. 2008. Importance of lineage-specific expansion of plant tandem duplicates in the adaptive response to environmental stimuli. Plant Physiol. 148:993–1003.

Innan, H. and F. Kondrashov. 2010 The evolution of gene duplications: Classifying and distinguishing between models. Nat. Rev. Genet. 11:97–108.

James, T.C., J. Usher, S. Campbell, and U. Bond. 2008 Lager yeasts possess dynamic genomes that undergo rearrangements and gene amplification in response to stress. Curr. Genet. 53:139–152.

Kang, Y.J., S.K. Kim, M.Y. Kim, P. Lestari, K.H. Kim, B.K. Ha, T.H. Jun, W.J. Hwang, T. Lee, J. Lee, S. Shim, M.Y. Yoon, Y.E. Jang, K.S. Han, P. Taeprayoon, N. Yoon, P. Somta, P. Tanya, K.S. Kim, J.G. Gwag, J.K. Moon, Y.H. Lee, B.S. Park, A. Bombarely, J.J. Doyle, S.A. Jackson, R. Schafleitner, P. Srinives, R.K. Varshney, and S.H. Lee. 2014. Genome sequence of mungbean and insights into evolution within Vigna species. Nat. Commun. 5:5443. doi:10.1038/ncomms-6443.

Kang, Y.J., K.H. Kim, S. Shim, M.Y. Yoon, S. Sun, M.Y. Kim, K. Van, and S.H. Lee. 2012. Genome-wide mapping of NBS-LRR genes and their association with disease resistance in soybean. BMC Plant Biol. 12:39. doi:10.1186/1471-2229-12-139.

Kang, Y.J., T. Lee. J. Lee, S. Shim, H. Jeong, D. Satyawan, M.Y. Kim, and S.H. Lee. 2016. Translational genomics for plant breeding with genome sequence explosion. Plant Biotechnol. J. 14:1057–1069.

Kang, Y.J., D. Satyawan, S. Shim, T. Lee, J. Lee, W.J. Hwang, S. Kim, P. Lestari, K. Laosatit, K.H. Kim, T.J. ha, A. Chitikineni, M.Y. Kim, J.M. Ko, J.G. Gwag, J.K. Moon, Y.H. Lee, B.S. park, R.K. Varshney, and S.H. Lee. 2015. Draft genome sequence of adzuki bean, Vigna angularis. Sci. Rep. 5:8069. doi:10.1038/srep-08069.


129

Kim, S.K., R.M. Nair, J. Lee, and S.H. Lee. 2015. Genomic resource in mungbean for breeding programs. Front. Plant Sci. 6:626. doi:10.3389/fpls.2015.00626.

Kim, K.D., J.H. Shin, K. Van, D.H. Kim, and S.H. Lee. 2009. Dynamic rearrangements determine genome organization and useful traits in soybean. Plant Physiol. 151:1066–1076.

Kondrashov, F.A. 2012. Gene duplication as a mechanism of genomic adaptation to a changing environment. Proc. R. Soc. 279:5048–5057.

Kondrashov, F.A. and A.S. Kondrashov. 2006. Role of selection in fixation of gene duplications. J. Theor. Biol. 239:141–151.

Lestari, P. and S.H. Lee. 2014. Toward the characterization a major gene for seed protein content in soybean. In: G.K. Gupta, O.P. Joshi, A.N. Sharma, B.U. Dupare, and P. Sharma, editors, Proceedings of SOYCON-2014, International Soybean Research Conference on Mitigating Productivity Constrains in Soybean for Sustainable Agriculture. India, 22–24 February 2014. p. 52–56.

Lestari, P., Y.J. Kang, K. Mulya, I.M. Tasma, and S.H. Lee. 2016. Genome-wide SNP identification in Indonesian soybean using Illumina Hiseq. In: M. Sabran, P. Lestari, K. Kusumanegara, and J. Prasetiyono, editors, Pre-breeding and gene discovery for food and renewable energy security. Abstracts of oral presentation. IAARD Press, Jakarta. p. 151.

Lestari, P., Sutrisno, and I.M. Tasma. 2014. QTL study to reveal soybean response on abiotic and biotic stresses. J. AgroBiogen 10:109–114.

Lestari, P., K. Van, J. Lee, Y.J. Kang, and S.H. Lee. 2013. Gene divergence of homeologous regions associated with a major seed protein content QTL in soybean. Front. Plant Sci. 4:1–8.

Liu, G.E., M. Ventura, A. Cellamare, L. Chen, Z. Cheng, B. Zhu, C. Li, J. Song, and E.E. Eichler. 2009. Analysis of recent segmental duplications in the bovine genome. BMC Genomics 10:571. doi:10.1186/1471-2164-10-571.

Lupski, J.R. 2007. An evolution revolution provides further revelation. Bioassays 29:1182–1184.

Lynch, M. 2007. The region of genome architecture. Sinauer Associates, Sunderland, MA, USA.

Maere, S., S. De Bodt, J. Raes, T. Casneuf, M. Van Montagu, M. Kuiper, and Y. Van de Peer. 2005. Modeling gene and genome duplications in eukaryotes. Proc. Natl. Acad. Sci. USA 102:5454–5459.

Magadum, S.U. Banerjee, P. Murugran, D. Gangapur, and R. Ravikesavan. 2013. Gene duplication as a major force in evolution. J. Genet. 92:155–161.

Meehl, G.A. and T.F. Stocker. 2007. Global climate projections. In: S. Solomon, D. Qin, M. Manning, Z. Chen, M. Marquis, K.B. Averyt, M. Tignor, and H.L. Miller, editors, Climate change 2007: The physical

science basis. Contribution of Working Group I to the Fourth Assessment Report of the Intergovernmental Panel on Climate Change. Cambridge University Press, Cambridge, UK and New York, NY, USA. p. 749–845.

Meyers, B.C., A. Kozik, A. Griego, H.H. Kuang, and R.W. Michelmore. 2003. Genome-wide analysis of NBS-LRR-encoding genes in Arabidopsis. Plant Cell 15(4):809-834.

Mochida, K. and K. Shinozaki. 2010. Genomics and bioinformatics resources for crop improvements. Plant Cell Physiol. 51:497–523.

Mudge, J., S.B. Cannon, P. Kalo, G.E. Oldroyd, B.A. Roe, C.D. Town, and N.D. Young. 2005. Highly syntenic regions in the genomes of soybean, Medicago truncatula, and Arabidopsis thaliana. BMC Plant Biol. 5:15. doi:10.1186/1471-2229-5-15.

Paterson, A.H., J.F. Bowers, D.G. Peterson, J.C. Estill, and B.A. Chapman. 2003. Structure and evolution of cereal genomes. Curr. Opin. Genet. Dev. 13:644–650.

Ramsey, J. 2011. Polyploidy and ecological adaptation in wild yarrow. Proc. Natl. Acad. Sci. USA. 108(17):7096–7101.

Reams, A.B. and E.L. Neidle. 2004. Selection for gene clustering by tandem duplication. Annu. Rev. Microbiol. 58:119–142.

Renny-Byfield, S. and J.F. Wendel. 2014. Doubling down on genomes: Polyploidy and crop plants. Am. J. Bot. 101:1711–1725.

Riehle, M.M., A.F. Bennett, and A.D. Long. 2001. Genetic architecture of thermal adaptation in Escerichia coli. Proc. Natl. Acad. Sci. USA. 98:525–530.

Roth, J.R., N. Benson, T. Galitski, K. Haack, J.G. Lawrence, and L. Miesel. 1996. Rearrangements of the bacterial chromosome: Formation and application. In: F.C. Neidhardt, R. Curtiss III, J.L. Ingraham, E.C.C. Lin, K.B. Low, B. Magasanik, W.S. Reznikoff, M. Riley, M. Schaechter, and H.E. Umbarger, editors, Escherichia coli and Salmonella: Cellular and molecular biology. 2nd ed. ASM Press, Washington, D.C., USA. p. 2256–2276.

Saleh, B., T. Allario, D. Dambier, P. Ollitrault, and R. Morillon. 2008. Tetraploid citrus rootstocks are more tolerant to salt stress than diploid. C.R. Biol. 331:703–710.

Sandve, S.R., H. Rudi, T. Asp, and O.A. Rognli. 2008 Tracking the evolution of a cold stress associated gene family in cold tolerant grasses. BMC Evol. Biol. 8:245. doi:10.1186/1471-2148-8-245.

Satyawan, D., H. Rijzaani, and I.M. Tasma. 2014. Characterization of genomic variation in Indonesia soybean (Glycine max) varieties using next-generation sequencing. Plant Genet. Res. 12(S1):S109–S113.

Schmutz, J., S.B. Cannon, J. Schlueter, J. Ma, T. Mitros, W. Nelson, D.L. Hyten, Q. Song, J.J. Thelen, J. Cheng, D. Xu, U. Hellsten, G.D. May, Y. Yu, T. Sakurai, T.


Umezawa, M.K. Bhattacharyya, D. Sandhu, B. Valliyodan, E. Lindquist, M. Peto, D. Grant, S. Shu, D. Goodstein, K. Barry, M. Futrell-Griggs, B. Abernathy, J. Du, Z. Tian, L. Zhu, N. Gill, T. Joshi, M. Libault, A. Sethuraman, X.C. Zhang, K. Shinozaki, H.T. Nguyen, R.A. Wing, P. Cregan, J. Specht, J. Grimwood, D. Rokhsar, G. Stacey, R.C. Shoemaker, and S.A. Jackson. 2010. Genome sequence of the palaeopolyploid soybean. Nature 463:178–183.

Severin, A.J., S.B. Cannon, M.M. Graham, D. Grant, and R.C. Shoemaker. 2011. Changes in twelve homoeologous genomic regions in soybean following three rounds of polyploidy. Plant Cell 23:3129–3136.

Shaner, D.L., R.B. Lindenmeyer, and M.H. Ostlie. 2012. What have the mechanisms of resistance to glyphosate taught us? Pest Manag. Sci. 68:3–9.

Shin, J.H., K. Van, D.H. Kim, K.D. Kim, Y.E. Jang, B.S. Choi, M.Y. Kim, and S.H. Lee. 2008. The lipoxygenase gene family: A genomic fossil of shared polyploidy between Glycine max and Medicago truncatula. BMC Plant Biol. 8:133. doi:10.1186/1471-2229-8-133.

Wang, Y., X. Wang, H. Tang, X. Tan, S.P. Ficklin, F.A. Feltus, and A.H. Paterson. 2011. Modes of gene duplication contribute differently to genetic novelty and redundancy, but show parallels across divergent angiosperms. PLoS One 6(12):e28150. doi:10.1371/-journal.pone.0028150.

Wang, Y., X. Wang, and A.H. Paterson. 2012. Genome and gene duplications and gene expression divergence: A view from plants. Ann. N.Y. Acad. Sci. 1256:1–14.

Wang, Y., X. Tan, and A.H. Paterson. 2013. Different patterns of gene structure divergence following gene duplication in Arabidopsis. BMC Genomics 14:652. doi: 10.1186/1471-2164-14-652.

Widholm, J.M., A.R. Chinnala, J.H. Ryu, H.S. Song, T. Eggett, and J.E. Brotherton. 2001. Glyphosate selection of gene amplification in suspension cultures of 3 plant species. Physiol. Plant 112(4):540–545.

Winning, H., N. Viereck, B. Wollenweber, F.H. Larsen, S. Jacobsen, I. Sondergaard, and S.B. Engelsen. 2009. Exploring abiotic stress on asynchronous protein metabolism in single kernels of wheat studied by NMR spectroscopy and chemometrics. J. Exp. Bot. 60(1):291–300.

Xu, J.H. and J. Messing. 2009. Amplification of prolamin storage protein genes in different subfamilies of the Poacea. Theor. Appl. Genet. 119(8):1397−1412.

Zhang, J. 2003. Evolution by gene duplication: An update. Trends Ecol. Evolut. 18(6):292–298.

Zeng, Q.Y., C.Y. Yang, Q.B. Ma, X.P. Li, W.W. Dong, and H. Nian. 2012. Identification of wild soybean miRNA and their target genes responsive to aluminum stress. BMC Plant Biol. 12:182. doi:10.1186/1471-2229-12-182.

Zhou, D., J. Zhou, L. Meng, Q. Wang, H. Xie, Y. Guan, Z. Ma, Y. Zhong, F. Chen, and J. Liu. 2009. Duplication and adaptive evolution of the COR15 genes within the highly cold-tolerant Draba lineage (Brassicaceae). Gene 441(1–2):36–44.

Zhu, H.Y., S.M. Yang, F. Tang, M.Q. Gao, and H.B. Krishnan. 2010. R gene-controlled host specificity in the legume-rhizobia symbiosis. Proc. Natl. Acad. Sci. USA 107(43):18735–18740.

Ziolkowski, P.A., M. Kaczmarek, D. Babula-Skowronska, and J. Sadowski. 2012. Brassica genome evolution: Dynamic and plasticity. In: D. Edwards, J. Batley, I. Parkin, and C. Kole, editors, Genetics, genomics, and breeding of oilseed of brassicas. Science Publishers/CRC Press, Boca Raton, FL, USA.

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Analisis Molekuler dan Uji Daya Hasil Galur-galur BC2F8 Padi Pup1

J. AgroBiogen Juni 2016, vol. 12 no. 1, hlm. 1–10

Perbaikan varietas padi untuk daerah yang memiliki masalah ketersediaan fosfor (P) sangat penting dilakukan. Lokus Pup1 sebagai lokus yang berisi gen-gen yang ber-peran dalam penangkapan P telah dipetakan dengan baik dan marka untuk seleksinya telah dibuat. Berdasarkan pe-nelitian sebelumnya, telah diperoleh galur BC2F8 persilang-an Dodokan × Kasalath (DK), Dodokan × NIL-C443 (DN), Situ Bagendit × Kasalath (SK), Situ Bagendit × NIL-C443 (SN), Batur × Kasalath (BK), dan Batur × NIL-C443 (BN). Penelitian ini bertujuan menganalisis galur-galur BC2F8 se-cara molekuler dan mengevaluasi potensi hasil galur-galur tersebut pada kondisi lapang yang berbeda. Penelitian ber-langsung mulai bulan November 2013 s.d. Juni 2014. Pene-litian molekuler dilakukan di BB Biogen, Indonesia dan IRRI, Filipina, sedangkan penelitian lapang dilakukan di KP Taman Bogo, Lampung dan lahan petani di Sukabumi, Jawa Barat. Berdasarkan analisis molekuler, diperoleh hasil seluruh galur BC2F8 mengandung lokus Pup1, namun ada tiga galur (B5-SK5, B9-SN2, dan C9-BN2) yang mengandung lokus Pup1 dalam kondisi heterozigot. Susunan genom se-bagian besar galur Pup1 masih mengikuti susunan genom tetuanya, kecuali B7-SK7, C10-BN3, dan C11-BN4. Galur B1-SK1, B2-SK2, B3-SK3, B4-SK4, B6-SK6, B9-SN2, C4-BK4, C7-BK7, dan C12-BN5 memiliki bobot ubinan lebih banyak dibanding dengan tetua pemulihnya (Situ Bagendit atau Batur) pada kondisi P kurang atau cukup tersedia. Galur B6-SK6 dan C12-BN5 memiliki bobot ubinan lebih banyak dibanding dengan tetua pemulihnya dan varietas cek (Inpago 7 atau Inpago 8) pada kondisi P kurang tersedia. Galur-galur tersebut dapat digunakan untuk uji multilokasi.

(Penulis)

Kata kunci: Padi, Pup1, analisis molekuler, potensi hasil

Siti Yuriyah1, Siti Nurani2, Dwinita W. Utami1, dan Tiur S. Silitonga1 (1Balai Besar Penelitian dan Pengembangan Bioteknologi dan Sumber Daya Genetik Pertanian, 2Universitas Sultan Ageng Tirtayasa)

Evaluasi dan Identifikasi Marka Penanda Gen Ketahanan Penyakit Hawar Daun Bakteri pada Padi Lokal Sulawesi Selatan


Salah satu faktor pembatas produksi padi, di Sulawesi Selatan khususnya, adalah serangan penyakit hawar daun bakteri (HDB) yang disebabkan oleh Xanthomonas oryzae pv. oryzae (Xoo). Upaya yang dipandang efektif untuk mengendalikan penyakit HDB adalah penanaman varietas tahan. Perakitan varietas padi dengan menggunakan gen-gen tahan dari berbagai kultivar berpeluang menghasilkan varietas tahan HDB. Kultivar lokal berperan sebagai salah satu sumber keragaman genetik untuk beberapa sifat ketahanan penyakit. Penelitian ini bertujuan mengevaluasi dan mengidentifikasi marka penanda gen ketahanan penyakit hawar daun bakteri pada padi lokal Sulawesi Selatan berdasarkan sistem standar diferensial dan analisis molekuler. Analisis uji ketahanan fenotipe dilakukan meng-gunakan tiga ras HDB (ras III, IV, dan VIII) dan galur diferensial (galur IRBB). Analisis genotipe dilakukan meng-gunakan marka molekuler terkait ketahanan terhadap HDB yang ditampilkan sebagai dendrogram keragaman. Analisis asosiasi dilakukan dengan analisis gabungan (U-joint) menggunakan generalized linear model (GLM). Hasil peng-ujian ketahanan menunjukkan galur isogenik dengan gen tunggal (IRBB 5, IRBB 7, dan IRBB 21), galur isogenik dengan multipel gen (IRBB 50, IRBB 52, IRBB 53, IRBB 54, IRBB 56, IRBB 58, IRBB 64, dan IRBB 66), dan aksesi Ase Andele bersifat tahan terhadap ketiga ras uji. Dari uji asosiasi, diperoleh satu marka signifikan yang berasosiasi dengan ketahanan terhadap ras III (Xa26-STS2), empat marka signifikan berasosiasi dengan ketahanan terhadap ras IV (Xa1-STS15, Xa4-STS44, xa13-STS51, dan Xa21-STS6), dan dua marka signifikan berasosiasi dengan ketahanan terhadap ras VIII (Xa7-STS57 dan RM 20589).

(Penulis)

Kata kunci: Gen ketahanan, hawar daun bakteri, plasma nutfah

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JURNAL AGROBIOGEN VOL. 12 NO. 2, DESEMBER 2016 132–0

Ma’sumah, Tri J. Santoso, dan Kurniawan R. Trijatmiko (Balai Besar Penelitian dan Pengembangan Bioteknologi dan Sumber Daya Genetik Pertanian)

Evaluasi Sifat Daya Tembus Akar dan Identifikasi Mutan Stabil pada Populasi Penanda Aktivasi


Cekaman kekeringan merupakan salah satu faktor pem-batas penting dalam peningkatan produksi padi di Indonesia. Perakitan varietas unggul padi toleran kekering-an diperlukan untuk menjawab tantangan tersebut. Bebe-rapa galur padi Nipponbare transgenik yang membawa penanda aktivasi telah dihasilkan pada penelitian sebelum-nya. Tujuan penelitian ini adalah mengevaluasi daya tem-bus akar dan stabilitas elemen Ds pada galur-galur pe-nanda aktivasi generasi T1. Bahan yang digunakan dalam penelitian ini adalah benih T1 47 galur transgenik, varietas cek toleran kekeringan (Cabacu dan IRAT112), dan varietas cek peka (IR64 dan Nipponbare tipe liar). Benih T1 ditapis terlebih dahulu dengan perkecambahan pada larutan herbisida Basta untuk mengeliminasi individu yang tidak membawa elemen penanda aktivasi. Daya tembus akar dievaluasi menggunakan lapisan lilin sebagai tiruan lapisan tanah yang padat dan keras (hardpans). Keberadaan gen bar dan ketiadaan gen hpt yang dideteksi dengan PCR digunakan untuk mengidentifikasi mutan-mutan stabil. Dari 47 galur yang diuji, 38 galur menunjukkan daya tembus akar yang lebih baik daripada Nipponbare non transforman. Analisis PCR mengidentifikasi empat mutan stabil, yaitu M-Nip-12.12, M-Nip-19.8, M-Nip-19.9, dan M-Nip-20.13. Satu mutan stabil, M-Nip-20.13, menunjukkan daya tembus akar yang lebih baik daripada varietas cek toleran. Mutan ini menjadi kandidat yang baik untuk isolasi gen toleran kekeringan.

(Penulis)

Kata kunci: Padi, mutagenesis transposon, penanda aktivasi, toleransi kekeringan

Slamet dan Ahmad Warsun (Balai Besar Penelitian dan Pengembangan Bioteknologi dan Sumber Daya Genetik Pertanian)

Pola Segregasi Ketahanan Populasi F2 Padi Ciherang/ Swarnalata terhadap Wereng Batang Cokelat


Wereng batang cokelat (WBC, Nilaparvata lugens Stål) me-rupakan hama yang menurunkan produktivitas padi secara signifikan di Indonesia. Penanaman varietas tahan merupa-kan cara yang mudah, murah, efektif, ramah lingkungan, dan sesuai dengan konsep pengendalian hama terpadu se-hingga pemulia berupaya mengembangkan varietas tahan WBC. Penelitian bertujuan menguji ketahanan varietas padi untuk pemilihan calon tetua persilangan, menguji me-tode evaluasi ketahanan terhadap WBC pada individu tanaman untuk melengkapi metode yang telah ada, dan mempelajari segregasi populasi persilangan dari tetua ter-

pilih. Penapisan ketahanan dua belas varietas padi diferen-sial dan unggul menggunakan teknik skrining massal baku dalam bak benih menunjukkan bahwa Ciherang/ Swarnalata secara berurutan konsisten rentan dan tahan terhadap WBC populasi Klaten (Jawa Tengah) dan Banyu-wangi (Jawa Timur) sehingga dipilih sebagai tetua per-silangan. Metode evaluasi ketahanan tanaman yang di-tanam dan diinfestasi dengan nimfa WBC secara individual pada tiga populasi simulasi persilangan Ciherang/ Swarnalata berhasil menentukan pola segregasi ketahanan pada populasi tersebut sesuai dengan komposisi campuran benih tahan dan rentan, yaitu 3 : 1 atau 1 : 3 dengan asumsi pola pewarisan secara berurutan monohibrid dominan atau resesif pada F2 dan komposisi 1 : 1 dengan asumsi pola pewarisan dominan pada BC1F2. Evaluasi ketahanan 125 tanaman F2 hasil persilangan Ciherang/Swarnalata ter-hadap WBC populasi Klaten menggunakan teknik penguji-an secara individual menunjukkan bahwa tanaman popu-lasi tersebut bersegregasi dengan rasio 3 : 1 yang menun-jukkan bahwa ketahanan varietas Swarnalata dikendalikan oleh satu gen mayor yang bersifat dominan penuh. Tanam-an F2 yang tahan perlu dideteksi dengan marka molekuler untuk memastikan adanya introgresi gen ketahanan dari tetua donor dan diuji ketahanannya pada generasi lanjut.

(Penulis)

Kata kunci: Segregasi, padi, ketahanan, wereng batang cokelat

Imron Riyadi1,2, Darda Efendi2, Bambang S. Purwoko2, dan Djoko Santoso1 (1Pusat Penelitian Bioteknologi dan Bioindustri Indonesia, 2Departemen Agronomi dan Hortikultura, Fakultas Pertanian, Institut Pertanian Bogor)

Embriogenesis Somatik Tidak Langsung pada Tanaman Sagu (Metroxylon sagu Rottb.) Menggunakan Sistem Kultur Suspensi, Perendaman Sesaat, dan Media Padat


Metode kultur in vitro yang tepat akan meningkatkan efektivitas dan efisiensi pada proses penggandaan kalus dan induksi embriogenesis somatik. Penelitian ini bertuju-an mengevaluasi efektivitas tiga metode kultur jaringan, yaitu sistem kultur suspensi, sistem perendaman sesaat (SPS) atau temporary immersion system (TIS), dan media padat, untuk proliferasi kalus dan pembentukan embrio somatik secara tidak langsung pada tanaman sagu “Alitir” yang berasal dari Merauke, Papua. Bahan tanaman atau eksplan awal yang digunakan adalah kalus remah hasil induksi dari kultur meristem pucuk tunas anakan sagu. Kalus tersebut dikulturkan pada media Murashige dan Skoog (MS) modifikasi dengan penambahan 2,4-D 5,0–15,0 mg/l dikombinasikan dengan kinetin 0,1 mg/l mengguna-kan ketiga metode kultur sehingga terdapat dua belas kombinasi perlakuan. Hasil penelitian menunjukkan bobot segar kalus tertinggi sebesar 12,0 g/bejana dicapai pada metode kultur suspensi dengan penambahan 2,4-D 15,0 mg/l dikombinasikan dengan kinetin 0,1 g/l. Perolehan

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jumlah embrio somatik tertinggi dicapai pada metode kul-tur suspensi dengan penambahan 2,4-D 5,0 mg/l dikom-binasikan dengan kinetin 0,1 g/l sebesar 384,7 buah/bejana. Daya hidup kultur sagu terbaik dan tertinggi (100%) diper-oleh pada metode kultur suspensi pada semua perlakuan konsentrasi 2,4-D. Selama proses induksi embrio somatik, terjadi perubahan warna kalus dari sebagian besar ke-kuningan menjadi krem dan putih-kekuningan.

(Penulis)

Kata kunci: Induksi embrio somatik, metode kultur, Metroxylon sagu Rottb., zat pengatur tumbuh, proliferasi kalus.

Yati Supriati1, Mia Kosmiatin1, Ali Husni1, dan Karsinah2 (1Balai Besar Penelitian dan Pengembangan Bioteknologi dan Sumber Daya Genetik Pertanian, 2Balai Penelitian Tanaman Jeruk dan Buah Subtropika)

Embriogenesis Somatik Mangga Varietas Madu dengan Eksplan Nuselar


Perbanyakan bibit mangga umumnya dilakukan melalui teknik sambung pucuk agar laju pertumbuhan dan panen lebih cepat. Mangga Madu sering digunakan sebagai batang bawah karena memiliki sifat perakaran yang kuat dan daya gabung yang baik dengan varietas mangga lain. Kendala yang dihadapi adalah rendahnya ketersediaan batang bawah karena pohon induk yang ada selain sudah tua, jumlahnya sangat terbatas. Mikropropagasi tanaman me-lalui embriogenesis somatik diharapkan dapat membantu perbanyakan batang bawah secara cepat, seragam, dan dalam jumlah tak terbatas. Penelitian bertujuan mendapat-kan metode untuk mengatasi masalah oksidasi fenol (pencokelatan yang berlebih) pada eksplan dan metode pembentukan kalus embriogenik dan regenerasi embrio somatik mangga varietas Madu. Percobaan disusun ber-dasarkan Rancangan Acak Lengkap dengan enam ulangan. Hasil penelitian menunjukkan, dari empat perlakuan yang diuji, perendaman dengan Potasium nitrat 0,125% selama 1 menit, lalu ditanam pada media MS yang diberi arang aktif 0,3% merupakan perlakuan terbaik untuk membantu me-ngurangi oksidasi fenol. Induksi kalus dengan mengguna-kan eksplan nuselar (nucellar explants) menunjukkan per-sentase eksplan menjadi kalus mencapai 50% pada media ½ MS yang diberi TDZ 0,4 mg/l. Induksi kalus mulai terjadi pada 3 mst dan 6 mst. Formulasi terbaik untuk pertumbuh-an kalus adalah media ½ MS dengan kombinasi BAP 2 mg/l, 2,4-D 1 mg/l, dan AgNO3 3 mg/l, serta diberi arang aktif 0,3%. Struktur kalus lebih banyak bersifat remah dan berwarna putih. Dari perkembangan kalus, terbentuk struktur embrio somatik globular, hati, torpedo sampai kecambah.

(Penulis)

Kata kunci: Mangga Madu (Mangifera indica L.), induksi kalus, oksidasi fenol, embriogenesis somatik, eksplan nuselar

Asadi, Puji Lestari, dan Nurwita Dewi (Balai Besar Penelitian dan Pengembangan Bioteknologi dan Sumber Daya Genetik Pertanian)

Pra-pemuliaan Aneka Kacang dalam Mendukung Proses Pemuliaan untuk Perakitan Varietas Unggul Baru


Aneka kacang merupakan komoditas tanaman pangan yang menempati posisi strategis ditinjau dari aspek ekonomi, pangan, dan gizi di dunia, termasuk Indonesia. Namun, kondisi cekaman biotik dan abiotik menuntut perakitan varietas unggul dengan memanfaatkan secara optimal plasma nutfah atau sumber daya genetik (SDG) aneka kacang melalui pemuliaan. Dalam ulasan ini di-sampaikan tentang bagaimana memanfaatkan koleksi SDG aneka kacang secara optimal dan pemuliaannya dalam rangka perbaikan varietas. Pra-pemuliaan berperan dalam menjembatani koleksi SDG sebagai sumber gen dengan aktivitas pemuliaan termasuk aspek genomiknya. Untuk lebih mengoptimalkan pemanfaatan SDG, perlu dibuat koleksi inti (core collection), yaitu dengan cara mengarak-terisasi dan mengevaluasi ketahanan/toleransinya terhadap sifat-sifat penting. Untuk menghadapi tantangan perubahan iklim, pra-pemuliaan dititikberatkan untuk mencari sumber gen yang tahan/toleran terhadap cekaman abiotik dan biotik. Berbagai aksesi aneka kacang yang dikoleksi dalam bank gen telah dilaporkan toleran terhadap cekaman abiotik (kekeringan, kerendaman, keracunan aluminium, dan salinitas tinggi) dan tahan terhadap cekaman biotik. SDG dengan karakter penting yang sudah teridentifikasi akan lebih mudah diakses dan diberdayakan sebagai sumber gen dalam perakitan varietas baru, sehingga akan memperkaya karakter penting pada varietas unggul yang dilepas. Kemajuan genomika pada aneka kacang berkem-bang pesat tidak hanya di kedelai namun juga di kacang hijau, kacang merah, kacang gude, kacang, tanah, chickpea/kacang arab (Cicer arietinum), kacang buncis, dan lainnya. Marka berbasis genom dan platform genotyping SNP dengan high throughput menjadikan teknologi ini menjadi harapan dalam membantu program pemuliaan aneka kacang. Hasil kegiatan pra-pemuliaan aneka kacang di Indonesia menunjukkan kemajuan berarti yang bermanfaat mendukung program pemuliaannya. Karena itu, pra-pemuliaan merupakan kegiatan penting untuk menyambungkan pengelolaan SDG aneka kacang dengan program pemuliaannya.

(Penulis)

Kata kunci: Aneka kacang, varietas unggul baru, pra-pemuliaan, genomika

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Tasliah, Ma’sumah, dan Joko Prasetiyono (Balai Besar Penelitian dan Pengembangan Bioteknologi dan Sumber Daya Genetik Pertanian)

Eksplorasi Lokus Pup1 pada 55 Genotipe Padi Berdasarkan Analisis Marka Molekuler dan Sekuensing

J. AgroBiogen Desember 2016, vol. 12 no. 2, hlm. 63–72

Fosfor (P) merupakan unsur penting pada padi yang keter-sediaannya di bumi semakin berkurang. Eksplorasi lokus yang berperan dalam penangkapan P (Pup1) pada plasma nutfah padi bermanfaat untuk mendapatkan calon tetua yang toleran terhadap defisiensi P. Penelitian ini bertujuan mengeksplorasi lokus Pup1 pada 55 genotipe padi guna mendapatkan genotipe yang memiliki alel Kasalath dari empat marka spesifik gen-gen di dalam lokus Pup1 dan memiliki kesamaan sekuen yang tinggi dengan sekuen rujukan lokus Pup1. Hasil amplifikasi DNA genomik dari tiga genotipe padi cek, yaitu Kasalath, NIL-C443, dan Nipponbare; 36 padi gogo, 15 padi sawah, dan 1 padi amfibi, menggunakan empat marka spesifik yang berada di dalam lokus Pup1, yaitu K05−1, K20−2 + Bsp12861, K29−1, dan K46−2, menunjukkan bahwa persentase padi gogo yang memiliki lokus Pup1 hampir sama dengan padi sawah, berturut-turut 49% dan 47,3%. Tiga genotipe, yaitu Gajah Mungkur, Cabacu, dan IR36, memiliki alel Kasalath pada keempat marka yang menunjukkan bahwa genotipe ter-sebut memiliki lokus Pup1. Kasalath, NIL-C443, Gajah Mungkur, Cabacu, dan IR36 memiliki kesamaan sekuen basa yang bervariasi pada daerah marka K20−2 + Bsp12681 dan K46−2, berturut-turut 54,7−95,2% dan 94,6−97,5%, dibanding dengan sekuen rujukan Pup1. Gajah Mungkur, Cabacu, dan IR36 pada daerah tersebut memiliki kesamaan sekuen basa yang tinggi dibanding dengan sekuen rujukan Pup1 (berturut-turut 87,3−92,4% dan 94,6−96%) sehingga ketiga genotipe memiliki potensi sebagai sumber lokus Pup1 yang baru menggantikan Kasalath.

(Penulis)

Kata kunci: Padi, defisiensi P, Pup1, plasma nutfah, analisis sekuen

Aqwin Polosoro dan Wening Enggarini (Balai Besar Penelitian dan Pengembangan Bioteknologi dan Sumber Daya Genetik Pertanian)

Keragaman Jumlah Salinan Transgen Galur T0 Padi Kultivar Nipponbare Berdasarkan Analisis qPCR dengan Penanda Gen hptII


Perakitan tanaman transgenik dengan bantuan Agrobacterium tumefaciens menghasilkan penyisipan transgen yang berbeda, baik dalam jumlah salinan maupun letak transgen dalam genom tanaman. Penelitian ini bertu-juan mendeteksi keberadaan kimera berdasarkan analisis jumlah salinan transgen pada tiap anakan dalam satu rum-pun dan beberapa rumpun padi Nipponbare transforman

T0 yang berasal dari kalus yang sama. Gen CsNitr1–L dan hptII sebagai penanda pada plasmid biner pCAMBIA1300 ditranformasikan ke dalam genom tanaman padi kultivar Nipponbare dengan bantuan A. tumefaciens strain LBA 4404. Analisis molekuler dilakukan terhadap tiga anakan masing-masing dari empat rumpun tanaman Nipponbare transgenik generasi T0 (event 1, 2, 3, dan 4) dan empat ke-lompok rumpun tanaman T0 yang berasal dari kalus yang sama. Dari setiap kelompok tersebut diambil tiga rumpun T0. Hasil analisis qPCR menunjukkan bahwa anakan yang berasal dari rumpun tanaman T0 yang sama memiliki jumlah salinan transgen yang seragam. Selain itu, hasil analisis qPCR juga menunjukkan bahwa tidak semua tanaman yang berasal dari kalus yang sama memiliki jumlah salinan transgen yang seragam. Implikasi hasil pe-nelitian ini adalah setiap rumpun padi T0 yang tumbuh dari kalus hasil transformasi perlu dipisahkan saat aklimatisasi agar benih T1 yang dihasilkan seragam.

(Penulis)

Kata kunci: Jumlah salinan, qPCR, Agrobacterium tumefaciens, Nipponbare

Wage R. Rohaeni, Untung Susanto, Nani Yunani, N. Usyati, dan Satoto (Balai Besar Penelitian Tanaman Padi)

Kekerabatan Beberapa Aksesi Padi Lokal Tahan Hama Penyakit Berdasarkan Analisis Polimorfisme Marka SSR


Tingkat kekerabatan antarpadi lokal dengan keunggulan tahan terhadap hama dan penyakit tanaman (HPT) perlu dipelajari untuk mengetahui seberapa jauh kekerabatan-nya, sehingga informasi yang diperoleh dapat digunakan untuk kebutuhan pemilihan tetua persilangan. Marka simple sequence repeat (SSR) dapat dijadikan salah satu alat bantu untuk mengetahui tingkat kekerabatan antarge-notipe. Penelitian ini bertujuan mengetahui tingkat keke-rabatan dan jarak genetik beberapa aksesi padi lokal unggul tahan HPT berdasarkan analisis polimorfisme marka SSR. Materi genetik yang digunakan adalah lima belas padi lokal tahan HPT dan varietas Ciherang. Analisis molekuler dilakukan menggunakan delapan belas marka SSR. Pola pita DNA hasil amplifikasi PCR pada elektrofo-resis gel poliakrilamida didokumentasi dengan visualisasi gel doc/UV transilluminator. Pohon kekerabatan menunjuk-kan tiga klaster yang terpisah jelas. Klaster 1 terdiri atas aksesi-aksesi subspesies indica tahan blas dan HDB, yaitu Gadis Langsat, Kebo, Bandang Si Gadis, Ciherang, Jawa Wangi Sleman, Marahmay, Takong, Ampek Panjang, Benoraja, dan Siawak. Klaster 2 terdiri atas aksesi-aksesi subspesies javanica dan japonica tahan WBC, tungro, blas, dan HDB, yaitu Ase Balucung, Ase Bukne, Pare Lottong, Pare Pulu, dan Jadul. Klaster 3 berisi aksesi subspesies japonica tahan blas, yaitu Kapas. Kekerabatan paling jauh dimiliki antara Pare Pulu dan Ampek Panjang dengan koefisien jarak genetik 0,816. Kekerabatan paling dekat dimiliki antara Pare Pulu dan Pare Lottong dengan jarak

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genetik 0,139. Data yang diperoleh dalam penelitian ini dapat digunakan sebagai referensi dalam penentuan tetua yang akan digunakan dalam program pemuliaan tanaman untuk perbaikan varietas padi lokal Indonesia.

(Penulis)

Kata kunci: Jarak genetik, padi lokal, kekerabatan, marka SSR

Farida Yulianti, Norry E. Palupi, dan Dita Agisimanto (Balai Penelitian Tanaman Jeruk dan Buah Subtropika)

Keragaman Jeruk Fungsional Indonesia Berdasarkan Karakter Morfologis dan Marka RAPD


Identifikasi variabilitas genetik tanaman jeruk diperlukan dalam pengelolaan sumber daya genetik dan proses se-leksi dalam program pemuliaan. Tujuan penelitian adalah mempelajari keragaman lima belas aksesi jeruk fungsional Indonesia berdasarkan karakter morfologis dan marka mo-lekuler. Penelitian dilaksanakan di Laboratorium Pemulia-an Tanaman, Balai Penelitian Tanaman Jeruk dan Buah Subtropika, Malang, Jawa Timur. Keragaman morfologis didasarkan pada hasil pengamatan morfologi, sedangkan keragaman molekuler didasarkan pada hasil amplifikasi marka RAPD. Keragaman morfologis dan molekuler di-analisis menggunakan program DARWin5. Hasil penelitian menunjukkan bahwa keragaman morfologis jeruk fungsio-nal Indonesia lebih tinggi dibanding dengan keragaman molekulernya. Keragaman tertinggi berdasarkan karakter morfologis terjadi antara Citrumelo dan Carrizo Citrange dengan Lemon seedless (79%), sedangkan keragaman tertinggi berdasarkan marka RAPD terjadi antara Lemo Swangi dan Lemon seedless (49%). Pita DNA spesifik di-temukan oleh marka OPH15(235,280) pada aksesi Jari Budha, Etrog Citron, dan Lemon seedless, marka OPD07(400) dan OPC17(416) pada aksesi dengan daun tipe trifoliata (Troyer Citrange, Citrumelo, dan Carrizo Citrange) dan OPH04(583) dan OPD07(330) pada aksesi Keprok Tening.

(Penulis)

Kata kunci: Keragaman morfologis, keragaman molekuler, jeruk fungsional, RAPD

Muhamad Sabda dan Nurwita Dewi (Balai Besar Penelitian dan Pengembangan Bioteknologi dan Sumber Daya Genetik Pertanian)

Multiplikasi Tunas dan Konservasi In Vitro Tanaman Belitung (Xanthosoma sagittifolium [L.] Schott) dengan Metode Pertumbuhan Minimal


Belitung merupakan salah satu tanaman potensial yang memiliki berbagai manfaat. Koleksi plasma nutfah belitung yang dikonservasi di lapang kadangkala hilang atau rusak

akibat pengaruh cekaman biotik dan abiotik. Oleh karena itu, konservasi secara in vitro sangat penting dilakukan untuk memperkecil kehilangan koleksi. Tujuan penelitian ini adalah mempelajari pengaruh benzil amino purin (BAP) terhadap multiplikasi tunas belitung secara in vitro, pengaruh pengenceran media dan pengurangan konsen-trasi sukrosa, serta pengaruh osmotikum (manitol) dan retardan (paklobutrazol/PBZ) terhadap pertumbuhan be-litung dalam konservasi in vitro. Rancangan percobaan yang digunakan adalah Rancangan Acak Lengkap dengan tiga ulangan. Tunas umbi digunakan sebagai eksplan. Perlakuan multiplikasi tunas terdiri atas media MS + BAP (0, 1, 2, 3 mg/l). Perlakuan konservasi terdiri atas media MS + 30 g/l sukrosa, ½ MS + 30 g/l sukrosa, MS + 15 g/l sukrosa, MS + manitol (20, 40, 60 g/l), dan MS + PBZ (1, 2, 3 mg/l). Hasil penelitian menunjukkan bahwa penambahan BAP meningkatan jumlah tunas yang terbentuk. Jumlah tunas terbanyak (7,6 tunas) dihasilkan pada media dengan konsentrasi BAP 3 mg/l. Penggunaan media MS ditambah manitol (20 g/l dan 40 g/l) dan PBZ (1, 2, 3 mg/l) dapat me-nekan laju pertumbuhan belitung yang dikonservasi. Media MS + PBZ 2 mg/l merupakan media terbaik untuk konser-vasi belitung. Pada media ini, belitung dapat disimpan sampai dengan 8 bulan tanpa disubkultur.

(Penulis)

Kata kunci: Belitung (Xanthosoma sagittifolium), multipli-kasi tunas, konservasi, manitol, paklobutrazol

Ika Roostika1, Sedyo Hartono2, dan Deden Sukmadjaja1 (1Balai Besar Penelitian dan Pengembangan Bioteknologi dan Sumber Daya Genetik Pertanian, 2Jurusan Hama dan Penyakit Tumbuhan, Fakultas Pertanian, Universitas Gadjah Mada)

Organogenesis dan Krioterapi Tebu untuk Mengeliminasi Sugarcane Streak Mosaic Virus


Penggunaan bibit bebas virus menjadi salah satu cara pengendalian penyakit virus yang efektif. Beberapa macam teknik kultur jaringan dilaporkan mampu mengeliminasi virus di dalam jaringan tanaman. Tujuan penelitian adalah mengetahui respons tiga varietas tebu terhadap teknik organogenesis dan krioterapi serta untuk mengetahui kemampuan kedua teknik tersebut dalam mengeliminasi Sugarcane streak mosaic virus (SCSMV). Bahan tanaman yang digunakan adalah varietas tebu PS862 asal Cirebon, PS881 asal Jember, dan PSJK922 asal Malang yang terinfek-si SCSMV. Induksi kalus dilakukan dengan menggunakan media MS yang ditambah dengan 2,4-D 3 mg/l dan kasein hidrolisat 3 g/l. Terdapat tiga macam perlakuan subkultur (SK0, SK1, dan SK2). Regenerasi tunas dilakukan pada media MS dengan penambahan BA 0,3 mg/l, IBA 0,5 mg/l, dan PVP 100 mg/l. Teknik krioterapi yang diterapkan adalah vitrifikasi dengan tahapan prakultur menggunakan sukrosa 0,3 M selama 3 hari, loading dengan larutan LS selama 10 menit, dehidrasi dengan larutan PVS2 selama 40

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menit, krioterapi dengan nitrogen cair selama 1 jam, deloading dengan larutan RS selama 30 menit, pemulihan, dan regenerasi. Indeksing virus dilakukan secara RT-PCR menggunakan primer spesifik SCSMV. Hasil penelitian me-nunjukkan bahwa ketiga varietas mampu membentuk kalus dan tunas, baik tanpa atau melalui proses subkultur. Di antara tiga varietas yang diuji, hanya PS862 asal Cirebon yang mampu bertahan hidup pasca-perlakuan krioterapi. Teknik organogenesis hingga dua kali subkultur tidak mampu mengeliminasi SCSMV, walaupun telah dilakukan subkultur hingga dua kali. Teknik krioterapi dapat meng-eliminasi SCSMV dengan proporsi sebesar satu pertiga (33,3%).

(Penulis)

Kata kunci: Saccharum officinarum L., kalus embriogenik, vitrifikasi, nitrogen cair, eliminasi virus

Puji Lestari1, Suk-Ha Lee2, I Made Tasma1, dan Asadi1 (1Balai Besar Penelitian dan Pengembangan Bioteknologi dan Sumber Daya Genetik Pertanian, 2Department of Plant Science, College of Agriculture and Life Sciences, Seoul National University)

Duplikasi Gen Mengungkap Petunjuk Adaptasi Tanaman terhadap Cekaman Lingkungan: Studi Kasus Gen NBS-LRR pada Kedelai


Gen responsif terhadap cekaman lingkungan yang ber-tahan setelah mengalami duplikasi genom skala kecil me-rupakan bagian dari duplikasi genom. Namun demikian, informasi duplikasi gen yang berpengaruh terhadap sifat adaptif tanaman terhadap perubahan lingkungan masih

terbatas. Ulasan ini menyajikan gambaran peristiwa dupli-kasi dalam genom tanaman yang berdampak terhadap duplikasi gen yang berkaitan dengan perubahan lingkung-an, informasi duplikasi gen yang merupakan bagian dari mekanisme adaptasi, kasus duplikasi gen nucleotide-binding site-leucine-rich repeat (NBS-LRR) pada kedelai, dan implementasi informasi duplikasi gen terhadap pe-muliaan kedelai di Indonesia. Peristiwa duplikasi genom menghasilkan duplikasi gen dan berperan terhadap evolusi adaptasi pada perubahan lingkungan. Informasi umum ten-tang tanaman yang beradaptasi dengan cekaman lingkung-an memungkinkan untuk meningkatkan pemahaman kita tentang duplikasi gen sebagai mekanisme adaptasi. Gen-gen NBS-LRR yang terduplikasi diketahui berasosiasi dengan QTL terkait ketahanan penyakit dan ekspresi di-ferensialnya membuktikan kontribusi gen tersebut pada ke-tahanan kedelai terhadap cekaman biotik. Model yang di-usulkan dari proses gen duplikasi NBS-LRR dapat mem-bantu dalam memahami respons gen tersebut terhadap perubahan lingkungan. Duplikasi gen ketahanan terhadap hama/penyakit, NBS-LRR khususnya, memberikan infor-masi penting dalam pemilihan tetua pemuliaan dan pe-ngembangan marka molekuler terkait ketahanan penyakit untuk memperbaiki kedelai di Indonesia secara genetik. Karena itu, sangat mungkin untuk meningkatkan program pemuliaan yang menargetkan gen ketahanan terhadap cekaman biotik/abiotik dan memberikan dasar molekuler sebagai strategi perlindungan tanaman terhadap cekaman dan pengembangan kultivar kedelai khusus untuk lingkungan ekstrim.

(Penulis)

Kata kunci: Cekaman lingkungan, duplikasi gen, hama/ penyakit, kedelai, NBS-LRR

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2016 Indeks Abstrak Bahasa Inggris

137–0

Jurnal AgroBiogen

ISSN 1907–1094 Volume 12, 2016

The desciption given are free terms. This abstract sheets be reproduced without permission of change

Joko Prasetiyono, Tasliah, Ma’sumah, Nurul Hidayatun, Tintin Suhartini, and Ida H. Soemantri (Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development)

Molecular Analysis and Yield Trials of BC2F8 Pup1 Rice Lines

J. AgroBiogen Juni 2016, vol. 12 no. 1, p. 1–10

Improved rice varieties at areas that have problems with the availability of phosphorus (P) is very important. Pup1 locus, the locus containing genes that play a role in the P uptake, has been well mapped and some markers for selection have been developed. Based on previous studies, BC2F8 lines have been obtained from crosses of Dodokan × Kasalath (DK), Dodokan × NIL-C443 (DN), Situ Bagendit × Kasalath (SK), Situ Bagendit × NIL-C443 (SN), Batur × Kasalath (BK), and Batur × NIL-C443 (BN). This study aimed to evaluate the BC2F8 lines at molecular level as well as their yield potential. The molecular research was conducted from November 2013 to June 2014 at ICABIOGRAD, Indonesia and IRRI, Philippines, whereas the field trials were conducted at Taman Bogo Field Station, Lampung and a farmer’s land at Sukabumi, West Java. Molecular analysis demonstrated that all of the BC2F8-Pup1 lines contained Pup1 locus. However, three lines (B5-SK5, B9-SN2, and C9-BN2) containing the Pup1 locus were found in heterozygotes condition. All of the Pup1 lines still retained the genome composition of the parent, except for B7-SK7, C10-BN3, and C11-BN4. B1-SK1, B2-SK2, B3-SK3, B4-SK4, B6-SK6, B9-SN2, C4-BK4, C7-BK7, and C12-BN5 Pup1 lines have yield more than their recurrent parents (Situ Bagendit or Batur) in areas with either low or enough available P conditions. B6-SK6 and C12-BN5 Pup1 lines have yield more than their recurrent parents and check varieties (Inpago 7 and Inpago 8) in area with low available P condition. These lines could be used for multilocation trial.

(Author)

Keywords: Rice, Pup1, molecular analysis, yield potency

Siti Yuriyah1, Siti Nurani2, Dwinita W. Utami1, and Tiur S. Silitonga1 (1Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development, 2Sultan Ageng Tirtayasa University)

Evaluation and Identification of Bacterial Leaf Blight Disease Resistance Gene Marker on South Sulawesi Local Rice


One of the limiting factors on rice production, especially in South Sulawesi, is the bacterial leaf blight (BLB) disease infection caused by Xanthomonas oryzae pv. oryzae (Xoo). The use of resistant variety is considered as the most effective method to control Xoo. Local cultivar could serve as resistance source for Xoo resistance. The objectives of this research were to evaluate and identify markers for Xoo resistance in rice local cultivars from South Sulawesi based on comparison with the resistance response of the differential varieties and association analysis between resistance phenotype and genotype of molecular markers. Three Xoo races (race III, IV, and VIII) were tested on IRBB differential lines and local cultivars. The genotype analysis was done by using the molecular marker linked to Xoo resistance. Meanwhile, the association analysis was done by combination analysis (U-joint) using generalized linear model (GLM). The resistance test result showed that single gene isogenic lines (IRBB 5, IRBB 7, and IRBB 21), multiple genes isogenic lines (IRBB 50, IRBB 52, IRBB 53, IRBB 54, IRBB 56, IRBB 58, IRBB 64, and IRBB 66), and Ase Andele accession were resistant to the three Xoo races. Association test obtained one significant marker that associated with the resistance to race III (marker Xa26-STS2), four markers significantly associated with the resistance to race IV (Xa1-STS15, Xa4-STS44, xa13-STS51, and Xa21-STS6), and two markers significantly associated with the resistance to race VIII (Xa7-STS57 and RM 20589).

(Author)

Keywords: Resistance gene, bacterial leaf blight, germplasm

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JURNAL AGROBIOGEN VOL. 12 NO. 2, DESEMBER 2016 138–

Ma’sumah, Tri J. Santoso, and Kurniawan R. Trijatmiko (Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development)

Evaluation of Root Penetration Ability and Identification of Stable Mutants in an Activation Tag Rice Population


Drought stress is one of the important limiting factors in increasing rice production in Indonesia. Development of rice varieties with increased tolerance to drought is needed to meet the rice production challenge. Some transgenic Nipponbare rice lines that carry activation tag have been generated from the previous study. The purpose of this study was to evaluate the root penetration ability and the stability of Ds element in the T1 generation of activation tag rice lines. Materials used in the study were T1 seeds of 47 transgenic lines, drought tolerant check varieties (Cabacu and IRAT112), and sensitive check varieties (IR64 and wild type Nipponbare). T1 seeds were prescreened by germination in Basta herbicide solution to eliminate T1 individuals that did not carry activation tag element. Root penetration ability was evaluated using wax-petrolatum layers as a proxy for compacted soil layers. The presence of bar gene and the absence of hpt gene as detected by PCR were used to identify T1 stable mutants. Out of 47 transgenic lines tested, 38 lines showed better root penetration ability than non transformed Nipponbare. PCR analysis identified four stable mutants, namely M-Nip-12.12, M-Nip-19.8, M-Nip-19.9, and M-Nip-20.13. One stable mutant, M-Nip-20.13, showed better root penetration ability than tolerant check varieties. This mutant is a good candidate for isolation of drought tolerance gene.

(Author)

Keywords: Rice, transposon mutagenesis, activation tagging, drought tolerance

Slamet and Ahmad Warsun (Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development)

Resistance Segregation Pattern of F2 Population of a Cross Between Ciherang and Swarnalata to Rice Brown Planthopper


Brown planthopper (BPH, Nilaparvata lugens Stål) is a serious pest of rice that significantly decreasesrice yield in Indonesia. Planting resistant varieties is an easy, inexpensive, effective, environmentally friendly, and in accordance with the concept of integrated pest management, and hence breeders continuously attempt todevelop resistant varieties to this pest. The objective of this study was to determine the resistance segregation of F2 plants derived from Ciherang/Swarnalata cross. The study was preceded by selection of candidate parents and followed by an evaluation of test method developed for individually potted and infested seedlings on artificial

segregating populations. Standard seedbox mass screening technique of twelve differential and improved rice varieties consistently identified Ciherang and Swarnalata as susceptible and resistant to BPH populations originated from Klaten (Central Java) and Banyuwangi (East Java), respectively. Resistance evaluation of artifical F2 and BC1F2

progenies of Ciherang/Swarnalata crossusing individually potted and infested seedlings method could demonstrated that the segregation patterns of artificial progenies were in accordance with the mixture ratios of resistant and susceptible varieties, i.e. 3 : 1 or 1 : 3 and 1 : 1 assuming inheritance pattern of monohybrid dominant or recessive in F2 and monoybrid dominant BC1F2 populations, respectively. Resistance test of 125 F2 plants derived from Ciherang/ Swarnalata cross using the developed test method showed that the plants segregated into 3 : 1 ratio for resistance and susceptible, indicating that BPH resistance in the donor parent was controlled by a single major dominant gene. The resistant F2 plants needs to be confirmed by molecular markers to ascertain the introgression of the resistance gene and tested for their resistance in advanced generation.

(Author)

Keywords: Segregation, rice, resistance, brown planthopper

Imron Riyadi1,2, Darda Efendi2, Bambang S. Purwoko2, and Djoko Santoso1 (1Indonesian Research Institute for Biotechnology and Bioindustry, 2Department of Agronomy and Horticulture, Bogor Agricultural University)

Indirect Somatic Embryogenesis on Sago Palm [Metroxylon sagu Rottb.] Using Suspension Culture and Temporary Immersion Solid Media System


The accurate method of in vitro culture will increase the effectiveness and efficiency of sago palm callus proliferation and somatic embryogenesis induction. The research was conducted to evaluate the effectiveness of three methods for tissue culture, i.e. suspension, temporary immersion system (TIS), and solid media culture, for indirect somatic embryogenesis of sago palm “Alitir” derived from Merauke, Papua. A clump of friable calli derived from sucker’s tip meristem culture was used as starting material. The calli were cultured on a modified Murashige and Skoog medium with 5.0–15.0 mg/l 2,4-D combined with 0.1 mg/l kinetin using three culture methods. There were twelve treatment combinations. The results showed that the highest fresh weight of calli was 12.0 g/flask achieved by suspension culture method supplemented with 15 mg/l 2.4-D combined with 0.1 mg/l kinetin. The highest number of somatic embryo was 384.7 pcs/flask achieved by suspension culture method with supplemented 5 mg/l 2.4-D combined with 0.1 mg/l kinetin. The best survival rate (100%) was obtained by suspension culture method for all treatments with 2.4-D concentration. During the somatic embryo induction of sago palm, the

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color of calli has changed from mostly yellowish to light yellow and yellowish-white.

(Author)

Keywords: Calli proliferation, culture method, Metroxylon sagu Rottb., plant growth regulator, somatic embryo induction

Yati Supriati1, Mia Kosmiatin1, Ali Husni1, and Karsinah2 (1Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development, 2Indonesian Citrus and Subtropical Fruits Research Institute)

Somatic Embriogenesis of Mango Var. Madu through Nucellar Explant


In order to obtain a good growth rate and to fasten the harvest time, farmer usually use mango seedlings of shoot grafting. Therefore, a lots of mango rootstock was needed. Mango var. Madu is one of very populars rootstock due to its strong rooting system and has a good compatibility with other manggo varieties. In vitro culture through somatic embriogenesis is one alternative technique which is possible for seedlings production in uniform size, fast, and in a large quantity. The main objective of this research was to obtain the best method for embriogenic callus production. The research consist of two experiments are decreasing of phenol oxidation shoot of Madu mango explants and induction of embriogenic callus from nucellar. The experiments one were arranged in Complete Randomized Design with six replications. The results showed that between of four treatment, explants submertion at 0.125% Potasium nitrat in 3 second, then planted in MS medium suplemented with active charcoal of 0.3% is the best treatment of decreasing phenol oxidation. The best formula for callus induction of mango nucellar explants was ½ MS media with 3.0 mg of TDZ with callus percentage of 50%, which was occur at 3 weeks and 6 weeks after planting. To optimalize callus proliferation, 300 mg/l charcoal active was added in a half strong basal media, which is completted with 2 mg/l BA, 1 mg/l 2,4-D, and 3 mg/l AgNO3. This formula producing callus with white color, crumb, with globular and torpedo form, indicated as embryogenic callus.

(Author)

Keywords: Mango var. Madu (Mangifera indica L.), callus induction, phenol oxidation, somatic embriogenesis, nucellar explants

Asadi, Puji Lestari, and Nurwita Dewi (Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development)

Pre-breeding of Legumes to Support Breeding Process for Developing Newly Improved Variety


Legumes are considered as food crops with a strategic position in the aspects of economic, food, and nutrition in the world, including Indonesia. However, biotic and abiotic stresses conditions demand the development of newly improved varieties by utilizing plant genetic resources (PGR) through breeding. This review described how to optimally use legume germplasm collection and their breeding to improve varieties. In addition, how pre-breeding could bridge between the PGR and the breeding including genomics approach was explained. To further optimize the utilization of the germplasm, a core collection should be established by characterization and evaluation of the resistance/tolerance to desired important traits. To cope with the climate change challenges, pre-breeding should emphasize on the improvement of characters related to resistance to abiotic and biotic stresses. Various accessions in the gene bank have been identified to possess resistance/tolerance to abiotic (drought, submerge, and salinity) and biotic stresses. The PGR with well identified important characters will be more accessible and utilized easily as genes sources/donors for improving varieties, enriching the existing important characters in the released varieties. Significant progress have been made on legumes genomics, not only in soybean but also in the mungbean, red bean, pigeon pea, groundnut, chickpea, common bean and others. Genome-based markers and SNP genotyping platform with high throughput expectedly support breeding program of legume. Therefore, pre-breeding is a promising alternative to link the legume PGR and the breeding program.

(Author)

Keywords: Legumes, newly improved variety, pre-breeding, genomics

Tasliah, Ma’sumah, and Joko Prasetiyono (Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development)

Exploration of the Pup1 Locus on 55 Rice Genotypes Based on Molecular Marker and Sequencing Analysis

J. AgroBiogen December 2016, vol. 12 no. 2, p. 63–72

Phosphorus (P) is an essential nutrient for rice growth. The scarcity of rock phosphate, the main source of P fertilizer, has prompted breeders to seek rice genotypes tolerant to P deficiency by exploring Pup1 locus, which plays a role in the P uptake, among the rice genotypes. This study was aimed at exploring Pup1 locus among 55 rice genotypes to identify genotypes possesing Kasalath alleles at four specific markers of genes in the Pup1 locus and high similarity of nucleotide sequence of the markers compared

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to Pup1 locus reference sequence. Amplification of genomic DNA of three check genotypes, i.e. Kasalath, NIL-C443, and Nipponbare; 36 upland, 15 lowland, and 1 amphibian rice, with K05−1, K20−2 + Bsp12861, K29−1, and K46−2 markers, showed that the number of upland rice containing Pup1 locus was comparable to lowland rice (49% and 47.3%, respectively). Three genotypes, i.e. Gajah Mungkur, Cabacu, and IR36, contained Kasalath alleles on the four markers, indicating that they have Pup1 locus. Kasalath, NIL-C443, Gajah Mungkur, Cabacu, and IR36 had varying levels of nucleotide sequence similarity based on K20−2 + Bsp12681 and K46−2 marker regions, ranged from 54.7−95.2% and 94.6−97.5%, respectively, compared to the Pup1 reference sequence. Based on Kasalath allelic pattterns and high nucleotide sequence similarity to the Pup1 reference sequence (87.3−92.4% and 94.6−96%, respectively), Gajah Mungkur, Cabacu, and IR35 were identified as new sources of Pup1 locus to replace Kasalath.

(Author)

Keywords: Rice, P deficiency, Pup1, germplasm, sequence analysis

Aqwin Polosoro and Wening Enggarini (Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development)

Diversity of Transgene Copy Number on T0 Rice Lines of Nipponbare Based on qPCR Analysis Using hptII Gene Marker


The development of transgenic crop using Agrobacterium tumefaciens produces different inserted transgenes, whether copy numbers or location in the plant genome. The research was performed to detect chimeric phenomena based on the transgene quantity analysis in tillers of a clump and of some clumps which were derived from the same calli. CsNitr1–L gene and hptII gene as a marker on a binary plasmid pCAMBIA1300 was transformed into the Nipponbare rice genome using A. tumefaciens strain LBA 4404. Molecular analysis was carried out on three tillers of each four clumps of Nipponbare transgenic T0 generation (events number 1, 2, 3, and 4) and four groups of T0 clump derived from one callus. Three T0 clump samples were collected from each of the four groups of T0 clumps. The results of qPCR analysis showed that the transgene copy numbers of tillers which were derived from one T0 clump were the same. qPCR analysis also discovered that not all plants from one callus demonstrated the same transgene copy numbers. This implies that each T0 rice clump which grows from the transformed calli was needed to be split in the acclimatization step so that the uniform T1 seeds would be obtained.

(Author)

Keywords: Copy number, qPCR, Agrobacterium tumefaciens, Nipponbare

Wage R. Rohaeni, Untung Susanto, Nani Yunani, N. Usyati, and Satoto (Indonesian Center for Rice Research)

Phylogeny of Some Local Paddy Accession Tolerant to Host Pest Based on Polymorphism Analysis of SSR Markers


The level of phylogeny among local rice that has identified the resistances to plant pests and diseases needs to be studied to determine the genetic distance, so that information can be used for a recommendation parental crosses. Simple sequence repeat (SSR) markers could be used as one tool to know the degree of phylogeny and the genetic distance between genotypes. The aim of this study was to determine phylogenetic tree and the coefficient of genetic distance of several local rice resistant to host and pest based polymorphic analysis of SSR markers. Fifteen host and pest resistant local rice and one popular variety (Ciherang) were used. Molecular analysis was carried out using eighteen SSR markers. The banding patterns of DNA amplification resulted from PCR on polyacrylamide electrophoresis gel was documented by using UV Transilluminator. The phylogenetic tree showed three clearly separated clusters. Cluster 1 consisted of indica accessions resistant to blast and BLB: Gadis Langsat, Kebo, Bandang Si Gadis, Ciherang, Jawa Wangi Sleman, Marahmay, Takong, Ampek Panjang, Benoraja, and Siawak. Cluster 2 consisted of javanica and indica accessions resistant to BPH, tungro, blast, and BLB: Ase Balucung, Ase Bukne, Pare Lottong, Pare Pulu, and Jadul. Cluster 3 consisted of japonica accession resistant to blast: Kapas. The farthest genetic distance was between Pare Pulu and Ampek Panjang (DA = 0.816). The closest genetic distance was between Pare Pulu dan Pare Lottong (DA = 0.098). This research data can be used as a reference in determining the crossing parents that will be used in plant breeding program for varieties improvement of Indonesian local rice.

(Author)

Keywords: Genetic distance, local rice, kinship, SSR markers

Farida Yulianti, Norry E. Palupi, and Dita Agisimanto (Indonesian Citrus and Subtropical Fruits Research Institute)

Variability of Indonesian Functional Citrus Based on Morphological Characters and RAPD Markers


Identification of citrus genetic variability is prerequisite for effective genetic resources management and selection process in breeding program. The objective of the research was to study fifteen accessions of Indonesian functional citrus based on morphological characters and molecular marker. The research was conducted in Plant Breeding Laboratory, Indonesian Citrus and Subtropical Fruits Reserach Institute, Malang, West Java. The morphological

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variability was based on observation of morphological characters, while molecular variability was based on amplification of RAPD markers. Morphology and molecular diversities were analyzed by DARWin5 program. The results showed that morphological diversity is higher than molecular diversity. The highest morphology diversity occured between Citrumelo and Carrizo Citrange with seedless Lemon (79%), while the highest molecular diversity occured between Lemo Swangi with seedless Lemon (49%). The specific bands were found on Jari Budha, Etrog Citron, and seedless Lemon accessions using RAPD marker OPH15(235,280), on accession with trifoliate leaf (Troyer Citrange, Citrumelo, and Carrizo Citrange) using OPD07(400) and OPC17(416) and on Keprok Tening using OPH04(583) and OPD07(330.

(Author)

Keywords: Morphology diversity, molecular diversity, functional citrus, RAPD

Muhamad Sabda and Nurwita Dewi (Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development)

In Vitro Shoot Multiplication and Conservation of Belitung [Xanthosoma sagittifolium {L.} Schott] using Minimal Growth Conservation Method


Belitung is one of potential food crops, which has a lot of benefit. Collection of belitung germplasm conserved in the field is sometimes lost or damaged by biotic and abiotic stress. Therefore, in vitro conservation is very important to do to minimize loss of collection. The purpose of this research was to study the effect of benzylaminopurine (BAP) on in vitro shoot multiplication of belitung and to study the influences of osmoticum (mannitol) and retardant (paclobutrazol/PBZ) to the growth of belitung culture. Experimental design used in this research was Randomized Completely Design with three replications. Shoots from sucker were used as explant. In this study of shoot multiplication, the treatment medium was MS + BAP (0, 1, 2, 3 mg/l). In the study of conservation, the treatment medium was MS + 30 g/l sucrose, ½ MS + 30 g/l sucrose, MS + 15 g/l sucrose, MS + mannitol (20, 40, 60 g/l), and MS + PBZ (1, 2, 3 mg/l). The result showed that the addition of BAP into MS medium increased number of shoot. The best medium for micropropagation of belitung germplasm was MS + BAP 3 mg/l. The highest number of shoot (7.6 shoots) was produced by MS + BAP 3 mg/l medium. MS + mannitol (20 g/l and 40 g/l) and MS + PBZ (1, 2, 3 mg/l) medium could reduce the plant growth. MS + PBZ 2 mg/l was the best medium for belitung conservation. This media could reduce plant growth during 8 months conservation period and prolong subculture interval.

(Author)

Keywords: Belitung (Xanthosoma sagittifolium), shoot multiplication, conservation, mannitol, paclobutrazol

Ika Roostika1, Sedyo Hartono2, and Deden Sukmadjaja1 (1Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development, 2Faculty of Agriculture, Gadjah Mada University)

Organogenesis and Cryotherapy Techniques of Sugarcane to Eliminate Sugarcane Streak Mosaic Virus


The use of virus-free seedlings is an effective option to control viral disease. It was reported that several tissue culture methods could eliminate virus infection from plant tissues. The objective of the study was to know the in vitro responses of three sugarcane varieties to the organogenesis and cryotherapy techniques and to know the potential rate of both techniques in eliminating Sugarcane streak mosaic virus (SCSMV). The plant materials were virus-infected sugarcane of three varieties of sugarcane (PS862 from Cirebon, PS881 from Jember, and PSJK922 from Malang). Callus induction was conducted on MS medium with addition of 3 mg/l 2,4-D and 3 g/l casein hydrolysate. There were three treatments of subculture (SK0, SK1, and SK2). Regeneration of shoots was conducted on MS medium with addition of 0.3 mg/l BA, 0.5 mg/l IBA, and 100 mg/l PVP. Cryotheraphy was done by using vitrification technique, starting with preculture on 0.3 M sucrose-containing medium for 3 days, loading with LS solution for 10 minutes, dehydration with PVS2 solution for 40 minutes, plunging in liquid nitrogen for 1 hour, deloading with RS solution for 30 minutes, recovery, and regeneration. Virus indexing was conducted by RT-PCR assay using specific primer of SCSMV. The result showed that all varieties were able to form for calli and shoots, both with and without subculture. Within the three varieties, only PS862 from Cirebon could survive post cryotherapy treatment. Organogenesis regeneration up to twice subculture was not able to eliminate SCSMV. Cryotherapy could eliminate SCSMV virus with the proportion of one third (33.3%).

(Author)

Keywords: Saccharum officinarum L., embryogenic callus, vitrification, liquid nitrogen, virus elimination

Puji Lestari1, Suk-Ha Lee2, I Made Tasma1, and Asadi1 (1Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development, 2Department of Plant Science, College of Agriculture and Life Sciences, Seoul National University)

Gene Duplication to Reveal Adaptation Clue of Plant to Environmental Stress: A Case Study of NBS-LRR Genes in Soybean


Genes responsive to the environmental stresses which are retained after small scale duplication are part of plant genome duplication. However, information of duplicated genes that could be adaptive to environmental changes in

5


plant is limited. This review presents an overview of duplication events in plant genomes which impact to gene duplication in relation to environmental changes, gene duplication as an adaptation mechanism, a case of duplicated nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes in soybean, and the gene duplication implementation for soybean plant breeding in Indonesia. Notably, genome duplication events generate gene duplication and contribute to adaptive evolution against environmental changes. Generalization of plants adaptation to the stressful conditions also probably improves our understanding of gene duplication as a mechanism of adaptation. Several recently duplicated NBS-LRR genes in soybean retain disease resistance QTL and the differential expression convince their contribution to biotic stress

resistance in soybean. Proposed models of NBS-LRR genes duplication process may help to understand these genes response to the environmental changes. The duplication of genes resistant to pest/disease, particularly NBS-LRR, provides important information for breeding parents selection and developing molecular markers related to desease resistance to genetically improve soybean in Indonesia. Overall, it may therefore be possible to enhance breeding programs which target on genes tolerant/resistant to biotic/abiotic stresses and provide a molecular basis for crop-stress protection strategy and improve soybean cultivars specified for harsh environment.

(Author)

Keywords: Environmental stress, gene duplication, soybean, pest/disease, NBS-LRR

6

2016 Indeks Penulis/Author Index

143–1

Jurnal AgroBiogen

Indeks Penulis/Author Index

Vol. 12 No. 1, Juni 2016

Asadi “Pra-pemuliaan Aneka Kacang dalam Mendukung Proses Pemuliaan untuk Perakitan Varietas Unggul Baru” 12(1):51–62.

Dewi, N. “Pra-pemuliaan Aneka Kacang dalam Mendukung Proses Pemuliaan untuk Perakitan Varietas Unggul Baru” 12(1):51–62.

Efendi, D. “Embriogenesis Somatik Tidak Langsung pada Tanaman Sagu (Metroxylon sagu Rottb.) Menggunakan Sistem Kultur Suspensi, Perendaman Sesaat, dan Media Padat” 12(1):37–44.

Hidayatun, N. “Analisis Molekuler dan Uji Daya Hasil Galur-galur BC2F8 Padi Pup1” 12(1):1–10.

Husni, A. “Embriogenesis Somatik Mangga Varietas Madu dengan Eksplan Nuselar” 12(1):45–50.

Karsinah “Embriogenesis Somatik Mangga Varietas Madu dengan Eksplan Nuselar” 12(1):45–50.

Kosmiatin, M. “Embriogenesis Somatik Mangga Varietas Madu dengan Eksplan Nuselar” 12(1):45–50.

Lestari, P. “Pra-pemuliaan Aneka Kacang dalam Mendukung Proses Pemuliaan untuk Perakitan Varietas Unggul Baru” 12(1):51–62.

Ma’sumah “Analisis Molekuler dan Uji Daya Hasil Galur-galur BC2F8 Padi Pup1” 12(1):1–10.

Ma’sumah “Evaluasi Sifat Daya Tembus Akar dan Identifikasi Mutan Stabil pada Populasi Penanda Aktivasi” 12(1):21–28.

Nurani, S. “Evaluasi dan Identifikasi Marka Penanda Gen Ketahanan Penyakit Hawar Daun Bakteri pada Padi Lokal Sulawesi Selatan” 12(1):11–20.

Prasetiyono, J. “Analisis Molekuler dan Uji Daya Hasil Galur-galur BC2F8 Padi Pup1” 12(1):1–10.

Purwoko, B.S. “Embriogenesis Somatik Tidak Langsung pada Tanaman Sagu (Metroxylon sagu Rottb.) Menggunakan Sistem Kultur Suspensi, Perendaman Sesaat, dan Media Padat” 12(1):37–44.

Riyadi, I. “Embriogenesis Somatik Tidak Langsung pada Tanaman Sagu (Metroxylon sagu Rottb.) Menggunakan

Sistem Kultur Suspensi, Perendaman Sesaat, dan Media Padat” 12(1):37–44.

Santoso, D. “Embriogenesis Somatik Tidak Langsung pada Tanaman Sagu (Metroxylon sagu Rottb.) Menggunakan Sistem Kultur Suspensi, Perendaman Sesaat, dan Media Padat” 12(1):37–44.

Santoso, T.J. “Evaluasi Sifat Daya Tembus Akar dan Identifikasi Mutan Stabil pada Populasi Penanda Aktivasi” 12(1):21–28.

Silitonga, T.S. “Evaluasi dan Identifikasi Marka Penanda Gen Ketahanan Penyakit Hawar Daun Bakteri pada Padi Lokal Sulawesi Selatan” 12(1):11–20.

Slamet “Pola Segregasi Ketahanan Populasi F2 Padi Ciherang/Swarnalata terhadap Wereng Batang Cokelat” 12(1):29–36.

Soemantri, I.H. “Analisis Molekuler dan Uji Daya Hasil Galur-galur BC2F8 Padi Pup1” 12(1):1–10.

Suhartini, T. “Analisis Molekuler dan Uji Daya Hasil Galur-galur BC2F8 Padi Pup1” 12(1):1–10.

Supriati, Y. “Embriogenesis Somatik Mangga Varietas Madu dengan Eksplan Nuselar” 12(1):45–50.

Tasliah “Analisis Molekuler dan Uji Daya Hasil Galur-galur BC2F8 Padi Pup1” 12(1):1–10.

Trijatmiko, K.R. “Evaluasi Sifat Daya Tembus Akar dan Identifikasi Mutan Stabil pada Populasi Penanda Aktivasi” 12(1):21–28.

Utami, D.W. “Evaluasi dan Identifikasi Marka Penanda Gen Ketahanan Penyakit Hawar Daun Bakteri pada Padi Lokal Sulawesi Selatan” 12(1):11–20.

Warsun, A. “Pola Segregasi Ketahanan Populasi F2 Padi Ciherang/Swarnalata terhadap Wereng Batang Cokelat” 12(1):29–36.

Yuriyah, S. “Evaluasi dan Identifikasi Marka Penanda Gen Ketahanan Penyakit Hawar Daun Bakteri pada Padi Lokal Sulawesi Selatan” 12(1):11–20.

Vol. 12 No. 2, Desember 2016

Agisimanto, D. “Keragaman Jeruk Fungsional Indonesia Berdasarkan Karakter Morfologis dan Marka RAPD” 12(2):91–100.

Asadi “Gene Duplication to Reveal Adaptation Clue of Plant to Environmental Stress: A Case Study of NBS-LRR Genes in Soybean” 12(2):118–130.

Dewi, N. “Multiplikasi Tunas dan Konservasi In Vitro Tanaman Belitung (Xanthosoma sagittifolium [L.] Schott) dengan Metode Pertumbuhan Minimal” 12(2):101–108.

Enggarini, W. “Keragaman Jumlah Salinan Transgen Galur T0 Padi Kultivar Nipponbare Berdasarkan Analisis qPCR dengan Penanda Gen hptII” 12(2):73–80.

Hartono, S. “Organogenesis dan Krioterapi Tebu untuk Mengeliminasi Sugarcane Streak Mosaic Virus” 12(2):109–118.

Lee, S-H. “Gene Duplication to Reveal Adaptation Clue of Plant to Environmental Stress: A Case Study of NBS-LRR Genes in Soybean” 12(2):118–130.

Lestari, P. “Gene Duplication to Reveal Adaptation Clue of Plant to Environmental Stress: A Case Study of NBS-LRR Genes in Soybean” 12(2):118–130.

Ma’sumah “Eksplorasi Lokus Pup1 pada 55 Genotipe Padi Berdasarkan Analisis Marka Molekuler dan Sekuensing” 12(2):63–72.


Palupi, N.E. “Keragaman Jeruk Fungsional Indonesia Berdasarkan Karakter Morfologis dan Marka RAPD” 12(2):91–100.

Polosoro, A. “Keragaman Jumlah Salinan Transgen Galur T0 Padi Kultivar Nipponbare Berdasarkan Analisis qPCR dengan Penanda Gen hptII” 12(2):73–80.

Prasetiyono, J. “Eksplorasi Lokus Pup1 pada 55 Genotipe Padi Berdasarkan Analisis Marka Molekuler dan Sekuensing” 12(2):63–72.

Rohaeni, W.R. “Kekerabatan Beberapa Aksesi Padi Lokal Tahan Hama Penyakit Berdasarkan Analisis Polimorfisme Marka SSR” 12(2):81–90.

Roostika, I. “Organogenesis dan Krioterapi Tebu untuk Mengeliminasi Sugarcane Streak Mosaic Virus” 12(2):109–118.

Sabda, M. “Multiplikasi Tunas dan Konservasi In Vitro Tanaman Belitung (Xanthosoma sagittifolium [L.] Schott) dengan Metode Pertumbuhan Minimal” 12(2):101–108.

Satoto “Kekerabatan Beberapa Aksesi Padi Lokal Tahan Hama Penyakit Berdasarkan Analisis Polimorfisme Marka SSR” 12(2):81–90.

Sukmadjaja, D. “Organogenesis dan Krioterapi Tebu untuk Mengeliminasi Sugarcane Streak Mosaic Virus” 12(2):109–118.

Susanto, U. “Kekerabatan Beberapa Aksesi Padi Lokal Tahan Hama Penyakit Berdasarkan Analisis Polimorfisme Marka SSR” 12(2):81–90.

Tasliah “Eksplorasi Lokus Pup1 pada 55 Genotipe Padi Berdasarkan Analisis Marka Molekuler dan Sekuensing” 12(2):63–72.

Tasma, I M. “Gene Duplication to Reveal Adaptation Clue of Plant to Environmental Stress: A Case Study of NBS-LRR Genes in Soybean” 12(2):118–130.

Usyati, N. “Kekerabatan Beberapa Aksesi Padi Lokal Tahan Hama Penyakit Berdasarkan Analisis Polimorfisme Marka SSR” 12(2):81–90.

Yulianti, Y. “Keragaman Jeruk Fungsional Indonesia Berdasarkan Karakter Morfologis dan Marka RAPD” 12(2):91–100.

Yunani, N. “Kekerabatan Beberapa Aksesi Padi Lokal Tahan Hama Penyakit Berdasarkan Analisis Polimorfisme Marka SSR” 12(2):81–90.

2016 Indeks Subjek Volume 12, 2016

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Jurnal AgroBiogen

Indeks Subjek Volume 12, 2016

Agrobacterium tumefaciens 73 Analisis molekuler 1 Analisis sekuen 63 Aneka kacang 51 Defisiensi P 63 Disease 119 Eksplan nuselar 45 Eliminasi virus 109 Embriogenesis somatik 45 Environmental stress 119 Gen ketahanan 11 Gene duplication 119 Genomika 51 Hawar daun bakteri 11 Induksi embrio somatic 37 Induksi kalus 45 Jarak genetik 81 Jeruk fungsional 91 Jumlah salinan 73

Kalus embriogenik 109 Kekerabatan 81 Keragaman molekuler 91 Keragaman morfologis 91 Ketahanan 29 Konservasi 101 Mangga Madu 45 Manitol 101 Marka SSR 81 Metode kultur 37 Metroxylon sagu Rottb. 37 Multiplikasi tunas 101 Mutagenesis transposon 21 NBS-LRR 119 Nipponbare 73 Nitrogen cair 109 Oksidasi fenol 45 Padi 1, 21, 29, 63 Padi lokal 81

Paklobutrazol 101 Penanda aktivasi 21 Pest 119 Plasma nutfah 11, 63 Potensi hasil 1 Pra-pemuliaan 51 Proliferasi kalus 37 Pup1 1, 63 qPCR 73 RAPD 91 Saccharum officinarum L. 109 Segregasi 29 Soybean 119 Toleransi kekeringan 21 Varietas unggul baru 51 Vitrifikasi 109 Wereng batang cokelat 29 Xanthosoma sagittifolium 101 Zat pengatur tumbuh 37

PEDOMAN BAGI PENULIS

JURNAL AGROBIOGEN semula bernama Buletin AgroBio yang diterbitkan pada tahun 1996 hingga 2004. Sejak tahun 2005, Buletin AgroBio berubah menjadi Jurnal AgroBiogen seiring dengan perubahan Balitbio menjadi Balitbiogen dan BB Biogen. Jurnal ini memuat artikel primer dan tinjauan hasil penelitian bioteknologi dan sumber daya genetika tanaman, serangga, dan mikroba pertanian. Naskah yang diterima berupa hasil penelitian lengkap atau tinjauan yang belum pernah dipublikasi. Terbit dua kali setahun pada bulan Juni dan Desember oleh Balai Besar Penelitian dan Pengembangan Bioteknologi dan Sumber Daya Genetik Pertanian. Jurnal ini telah mendapat akreditasi ulang ketiga pada tanggal 15 April 2015.

BAHASA Jurnal memuat karangan berbahasa Indonesia atau berbahasa Inggris. Pemakaian istilah mengikuti Pedoman Pusat Pembinaan dan Pengembangan Bahasa (http://badanbahasa.kemdikbud.go.id/lamanbahasa/ sites/default/files/pedoman_umum-ejaan_yang_disempurnakan.pdf).

BENTUK NASKAH Naskah diketik pada Microsoft Office Word, dua spasi, tipe huruf Times New Roman 12, dan dicetak satu muka pada kertas berukuran A4. Batas pinggir kertas 3 cm (dari atas, bawah, dan kanan) dan 4 cm (dari kiri). Panjang naskah tidak melebihi 20 halaman, termasuk tabel dan gambar. Naskah primer disusun dalam urutan: judul, nama penulis, nama dan alamat instansi, abstrak, pendahuluan, bahan dan metode, hasil dan pembahasan, kesimpulan, ucapan terima kasih, serta daftar pustaka. Naskah tinjauan disusun seperti naskah primer tanpa bahan dan metode serta hasil dan pembahasan.

JUDUL NASKAH ditulis dalam bahasa Indonesia dan Inggris, hendaknya singkat (<14 kata) dan mampu menggambarkan isi pokok tulisan. Karakter pada setiap awal kata (kecuali kata depan) ditulis dengan huruf besar.

ABSTRAK ditulis dalam bahasa Indonesia dan bahasa Inggris, dua spasi, tidak lebih dari 250 kata yang dituangkan dalam satu alinea. Abstrak makalah primer merupakan intisari dari seluruh tulisan yang meliputi masalah, tujuan, bahan dan metode, hasil dan pembahasan, serta kesimpulan penelitian. Abstrak makalah tinjauan mencakup latar belakang masalah, alasan pentingnya tinjauan dibuat, tujuan, dan dampak yang diharapkan.

KATA KUNCI terdiri atas 3–5 kata atau gugus kata yang menggambarkan isi. PENDAHULUAN naskah primer mencakup latar belakang masalah, hasil penelitian terdahulu yang akan disanggah

atau dikembangkan, dan tujuan penelitian. Naskah tinjauan mencakup latar belakang masalah, alasan pentingnya tinjauan dibuat, tujuan dan dampak yang diharapkan.

BAHAN DAN METODE berisi penjelasan mengenai bahan, alat, dan metode. Metode yang sudah baku cukup merujuk pustaka acuan, sedangkan metode baru atau modifikasi dijelaskan secara rinci.

HASIL DAN PEMBAHASAN dikemukakan secara jelas, bila perlu disertai dengan tabel, ilustrasi (grafik, diagram, gambar, dan foto). Informasi yang telah dijelaskan dengan tabel dan ilustrasi tidak perlu diulang dengan uraian panjang-lebar dalam teks. Pembahasan hendaknya memuat analisis tentang hasil-hasil penelitian yang telah diperoleh, bagaimana penelitian dapat memecahkan masalah, perbedaan/persamaan dengan hasil-hasil penelitian terdahulu, serta kemungkinan pengembangannya.

KESIMPULAN berisi hal-hal penting dari hasil dan pembahasan penelitian yang selaras dengan judul dan tujuan penelitian, sedangkan untuk naskah tinjauan diakhiri dengan rangkuman isi naskah.

UCAPAN TERIMA KASIH disampaikan kepada penyandang dana dan/atau pihak-pihak yang terlibat dalam penelitian atau penyusunan naskah.

DAFTAR PUSTAKA cara penulisan mengacu pada penulisan pustaka di Agronomy Journal (https://dl.sciencesocieties.org/publications/style/), disusun secara alfabetis menurut nama penulis. Kutipan naskah menggunakan nama penulis dan tahun terbit. Secara umum, setiap pustaka terdiri atas nama penulis, tahun, judul, penerbit, dan nomor halaman. Pustaka yang dijadikan bahan kajian dibatasi pada judul yang relevan dengan topik tulisan. Jenis pustaka yang diacu mencakup 80% artikel primer 10 tahun terakhir. Jumlah pustaka untuk naskah primer dan tinjauan masing-masing minimal 10 pustaka dan 20 pustaka. Beberapa contoh penulisan sumber acuan sebagai berikut:

http://badanbahasa.kemdikbud.go.id/lamanbahasa/

https://dl.sciencesocieties.org/publications/style/)

Jurnal

Lemmon, H. 1986. Comax: An expert system for cotton crop management. Science 233:29–32. Lyle, W.M. and J.P. Bordovsky. 1995. LEPA corn irrigation with limited water supplies. Trans. ASAE 38:455–

462. Septiningsih, E.M., A.M. Pamplona, D.L. Sanchez, C.N. Neeraja, G.V. Vergara, S. Heuer, A.M. Ismail, and D.J.

Mackill. 2009. Development of submergence-tolerant rice cultivars: The Sub1 locus and beyond. Ann. Bot. 103:151–160.

Tasliah, Mahrup, dan J. Prasetiyono. 2013. Identifikasi molekuler hawar daun bakteri (Xanthomonas oryzae pv. oryzae) dan uji patogenisitasnya pada galur-galur padi isogenik. J. AgroBiogen 9(2):49–57.

Jurnal Online

Kato, C., T. Nishimura, H. Imoto, and T. Miyazaki. 2011. Predicting soil moisture and temperature of Andisols under a monsoon climate in Japan. Vadose Zone J. 10:541–551. doi:10.2136/vzj2010.0054.

Buku (termasuk warta dan laporan)

Fehr, W.R. and C.E. Caviness. 1977. Stages of soybean development. Spec. Rep. 80. Iowa Agric. Home Econ. Exp. Stn., Iowa State Univ., Ames.

Steel, R.G.D. and J.H. Torrie. 1980. Principles and procedures of statistics: A biometrical approach. 2nd ed. McGraw-Hill, New York, NY.

Tasma, I.M. 2014. Single nucleotide polymorphism (SNP) sebagai marka DNA masa depan. Warta Biogen 10(3):7–10.

Sutoro, D. Ambarwati, E. Listanto, S.G. Budiarti, Hadiatmi, M. Setyowati, Slamet, dan Sustiprijatno. 2011. Pembentukan lima galur jagung transgenik dan evaluasi 30 galur hibrida jagung efisien pupuk N produktivitas tinggi dan umur genjah <85 hari. Laporan Hasil Penelitian 2011, BB Biogen, Bogor.

Prosiding

Bahagiawati. 2009. Bioetika: Konservasi serangga dan tanaman transgenik tahan hama. Dalam: M. Machmud, B. Setiadi, dan Sutrisno, editor, Prosiding Seminar Nasional Bioetika Pertanian. Bogor, 1520 Mei 2009. Badan Penelitian dan Pengembangan Pertanian bekerjasama dengan Kedeputian Bidang Dinamika dan Masyarakat Kementerian Negara Riset dan Teknologi dan Komisi Bioetika Nasional, Jakarta. hlm. 14–25.

Golding, K.A., D.A. Davidson, and C.A. Wilson. 2010. Micromorphological evidence for the use of urban waste as a soil fertiliser in and near to historic Scottish towns. In: R.J. Gilkes and N. Prakongkep, editors, Soil solutions for a changing world. Proceedings of the 19th World Congress of Soil Science, Brisbane, Australia. Symposium 4.5.1 Brisbane, Australia: IUSS. p. 12–15. http://www.iuss.org (accessed 3 Jan. 2012).

Skripsi/Tesis/Disertasi

Prasetiyono, J. 2010. Studi efek introgresi Pup1 (P Uptake1) untuk meningkatkan toleransi padi terhadap defisiensi fosfor. Disertasi S3, Institut Pertanian Bogor, Bogor.

Informasi dari Internet

Badan Pusat Statistik. 2009. Produksi sayuran Indonesia. http://www.bps.go.id/tab_sub/view.php?tabel= 1&daftar=1&id_subjek=55&notab=15 (diakses 17 Mei 2010).

NASKAH rangkap tiga disertai file elektronik dikirim ke Redaksi Jurnal AgroBiogen (cq. Seksi Pendayagunaan Hasil Penelitian BB Biogen). Kepada setiap penulis diberikan satu eksemplar jurnal dan dua eksemplar reprint.

http://www.iuss.org

http://www.bps.go.id/tab_sub/view.php?tabel=

Ucapan Terima Kasih

Dewan Redaksi Jurnal AgroBiogen mengucapkan terima kasih atas partisipasi sebagai Mitra Bestari pada penerbitan Jurnal AgroBiogen Tahun 2016

Prof. Dr. Ika Mariska Kultur Jaringan, Forum Komunikasi Profesor Riset

Dr. Sobrizal Pemuliaan Tanaman dan Molekuler Genetik, Pusat Aplikasi Isotop dan Radiasi, Badan Tenaga Nuklir Nasional

Dr. M. Muchsin Virologi Tumbuhan, Pusat Penelitian dan Pengembangan Tanaman Pangan

Dr. Sutoro Agronomi, Balai Besar Penelitian dan Pengembangan Bioteknologi dan Sumber Daya Genetik Pertanian

Dr. Muhamad Yunus Bioteknologi Pertanian, Balai Besar Penelitian dan Pengembangan Bioteknologi dan Sumber Daya Genetik Pertanian

Dr. Agus Sutanto Pemuliaan dan Bioteknologi, Balai Penelitian Tanaman Buah Tropika

Jurnal AgroVol. No. , 20112 2 Desember 6

Daftar Isi

Eksplorasi Lokus Pup1 pada 55 Genotipe Padi Berdasarkan Analisis Marka Molekuler dan Sekuensing(Exploration of the Pup1 Locus on 55 Rice Genotypes Based on Molecular Marker and Sequencing Analysis)

Tasliah, Ma’sumah, dan Joko Prasetiyono 63–72

Keragaman Jumlah Salinan Transgen Galur T0 Padi Kultivar Nipponbare Berdasarkan Analisis qPCR dengan Penanda Gen hptII (Diversity of Transgene Copy Number on T0 Rice Lines of Nipponbare Based on qPCR Analysis Using hptII Gene Marker)

Aqwin Polosoro dan Wening Enggarini 73–80

Kekerabatan Beberapa Aksesi Padi Lokal Tahan Hama Penyakit Berdasarkan Analisis Polimorfisme Marka SSR (Phylogeny of Some Local Paddy Accession Tolerant to Host Pest Based on Polymorphism Analysis of SSR Markers)

Wage R. Rohaeni, Untung Susanto, Nani Yunani, N. Usyati, dan Satoto 81–90

Keragaman Jeruk Fungsional Indonesia Berdasarkan Karakter Morfologis dan Marka RAPD (Variability of Indonesian Functional Citrus Based on Morphological Characters and RAPD Markers)

Farida Yulianti, Norry E. Palupi, dan Dita Agisimanto 91–100

Multiplikasi Tunas dan Konservasi In Vitro Tanaman Belitung (Xanthosoma sagittifolium [L.] Schott) dengan Metode Pertumbuhan Minimal (In Vitro Shoot Multiplication and Conservation of Belitung [Xanthosoma sagittifolium {L.} Schott] using Minimal Growth Conservation Method)

Muhamad Sabda dan Nurwita Dewi 101–108

Organogenesis dan Krioterapi Tebu untuk Mengeliminasi Sugarcane treak osaic irusS M V (Organogenesis and Cryotherapy Techniques of Sugarcane to Eliminate Sugarcane treak osaic irusS M V )

Ika Roostika, Sedyo Hartono, dan Deden Sukmadjaja 109–118

Gene Duplication to Reveal Adaptation Clue of Plant to Environmental Stress: A Case Study of NBS-LRR Genes in Soybean (Duplikasi Gen Mengungkap Petunjuk Adaptasi Tanaman terhadap Cekaman Lingkungan: Studi Kasus Gen NBS-LRR pada Kedelai)

Puji Lestari, Suk-Ha Lee, I Made Tasma, and Asadi 119–130

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