MARKER-ASSISTED BREEDING FOR SIMPLE INHERITED TRAITS CONFERRING STRESS RESISTANCE IN CROP PLANTS

1

KEYWORDS

Prof. P. C. Mishra Felicitation Volume

Paper presented in

National Seminar on Ecology Environment &Development

25 - 27 January, 2013

organised by

Deptt. of Environmental Sciences,

Sambalpur University, Sambalpur

ISSN: 0974 - 0376

NSave Nature to Survive

: Special issue, Vol. III:

www.theecoscan.inAN INTERNATIONAL QUARTERLY JOURNAL OF ENVIRONMENTAL SCIENCES

Jogeswar Panigrahi et al.

DNA Marker

Oligogenic

Stress Resistance

Crop

23 - 26

MARKER-ASSISTED BREEDING FOR SIMPLE INHERITED TRAITS

CONFERRING STRESS RESISTANCE IN CROP PLANTS

2

JOGESWAR PANIGRAHI*, RAMYA RANJAN MISHRA, ALOK RANJAN SAHU,

SOBHA CHANDRA RATH, SEN SETH AND SATYENDRA PRASAD MISHRA

Plant Biotechnology Laboratory, School of Life Sciences,

Sambalpur University, Jyoti Vihar, Sambalpur - 768 019, Odisha, INDIA

E-mail: [email protected]

INTRODUCTION

Crop plants are constantly exposed to pathogens, insects and the harshenvironment; hence one of the major objectives of crop breeding has alwaysbeen adaptation of crop plants. The strategies of breeding through directed crossesand selection for the desired recombinants led to steady increase in cropproductivity and quality during last century. These progress of conventionalbreeding is based entirly on the availability of genetic variation and its uttilizationfor selection of host resistance against the pathogens/insects and host toleranceto harsh environment. Even though this process has proven to be very effectiveand ecofriendly means of reducing losses due to stresses, the effect of environmentin many cases masks the effect of genotype. Therefore, the phenotype-basedselection does not reflect the true genetic potential of a crop genotype. Hence, ithas been realized that a selection procedure indirectly at the genotype levelwould augment the efficiency of breeding efforts (Dekkers and Hospital, 2002).Development of DNA (or molecular) markers in the 1980s laid the foundation forthe utility of indirect selection strategies in plant breeding. Although DNA markershave manifold uses in crop breeding, the most promising one for cultivardevelopment is the use of DNA markers that are tightly linked to the target loci asa substitute for or to assist phenotypic screening during the processes of breedingfor the development of cultivars conferring resistance to biotic and abiotic stressesand other attributes required by the plant breeders for the genetic augmentationof crop species, which is considered as marker assisted breeding (MAB).

Basic Concept of Marker-Assisted Breeding (MAB)

Molecular crop breeding use the DNA based markers as handle for the miningand tagging of novel alleles. MAB aims at the introgression those alleles, whichcontrol the trait to be improved, into the desired cultivars by assuming theirgenotypes (associated DNA markers) which can be recognized easily,unambiguously and at an appropriate time without impeding the breedingprogramme. The prerequisites for this MAB are -

Development of suitable molecular markers and their characterization,

Establishment of marker to gene(s) linkage through molecular maps and

Establishment marker-trait association and validation of molecular markers acrossthe population.

Several types of DNA markers including restriction fragment length polymorphism(RFLP), random amplified polymorphic DNA (RAPD), amplified fragment lengthpolymorphism (AFLP), inter simple sequence repeat (ISSR), microsatellites or simplesequence repeat (SSR), expressed sequence tag (EST), cleaved amplifiedpolymorphic sequence (CAPS), diversity arrays technology (DArT), and singlenucleotide polymorphism (SNP) have been used in several crops (Doveri et al.,2008). Each marker system has its own advantages and disadvantages, and thevarious factors to be considered in selecting one or more of these marker systemshave been described (Semagn et al., 2006; Panigrahi, 2011). There are five main

NSave Nature to Survive QUARTERLY

DNA based polymorphism, commonly

known as DNA markers, have extensively been

used for tagging and mapping of simple

inherited trait loci (SITLs) and quantitative trait

loci (QTLs) conferring resistance to biotic and

abiotic stresses in various crop plants. These

tools have also been used for screening of

germplasms, fingerprinting, and marker-

assisted breeding (MAB) in crop systems. This

chapter presents an overview on the basic

concepts of marker-assisted breeding of simple

inherited traits, and its most widely used

applications in crop improvement

programmes, viz. marker-assisted backcross

breeding, gene introgression, gene pyramiding

and marker-assisted selection at an early

generation, with emphasis on biotic stress

resistance in several crop plants. In the post-

genomic era, the integration the molecular

data with metabolic processes, development

of cost-effective genotypic assay and efficient

breeding strategies will pave the way for the

greater adoption MAB on crop breeding

programmes.

ABSTRACT

*Corresponding author

3

PHARMACOLOGICAL EFFICACY OF MEDICINAL PLANTS

considerations for the use of DNA markers in marker-assistedbreeding: Level of polymorphism, reliability andreproducibility; quantity and quality of DNA required;technical procedure for marker assay (genotyping), and costof marker development (Mackill and Ni, 2000; Mohler andSingrun, 2004; Collard and Mackill, 2008). The most widelyused markers in major crops including cereals and legumesare SSRs or microsatellites (Gupta et al., 1999; Gupta andVarshney, 2000; Kole and Gupta, 2004; Li et al., 2008; Kumaret al., 2011), whereas in oilseed brassicas are RFLPs (Panigrahiet al., 2009). Both SSR and RFLP are highly reproducible, co-dominant in inheritance, relatively simple and cheap to useand generally highly polymorphic. The only disadvantagesof SSRs are that they typically give information only about asingle locus per assay. This problem has been overcome inmany cases by multiplexing several SSR markers in a singlereaction (Kalia et al., 2011). Sequence tagged site (STS) andsequence characterized amplified region (SCAR) that arederived from specific DNA markers (e.g., RFLPs, RAPDs, etc.)that are linked to a gene or QTL are also extremely useful forMAB (Shan et al., 1999; Sanchez et al., 2000; Sharp et al.,

2001; Collard and Mackill, 2008; Kumar et al., 2011).A genetic linkage map based on DNA markers provides usefulfirst-hand information about the nature of genomeorganization and reorganization (Kole and Gupta, 2004).These maps indicate the position and relative genetic distancesbetween markers and concerned traits along chromosomes,which is analogous to landmarks along a highway. Themolecular marker systems along with genetic linkage analysisled to the development high-density DNA marker maps (i.e.

with many markers of known location, interspersed at shortintervals throughout the genome) in several crop species,which is the prerequisite for various applications of MAB.Demonstrated linkages between target traits/genes andmolecular markers are traditionally based on genetic mappingexperiments, and this is important to confirm that theseassociations are consistent across the mapping populationsand breeding lines. For efficient MAB, marker(s) should eitherco-segregate or be closely linked with the target trait, with adistance of 2 cM or less (Xu, 2003). Markers associated withmajor genes or QTL in one population may be used directlyfor MAB and MAS (marker assisted selection) in other breedingmaterials. For genes with relatively minor contributions, thecross-population comparison of genes, alleles, and gene effectsare required because of multilocus and multiallelic featuresthat characterize most quantitative traits. In addition, there areseveral factors including genetic background and alleledistribution around the target locus that is related to thedetection of marker-trait associations determines the efficiencyof MAB (Xu, 2003). Hence, the following four stages shouldbe followed carefully during MAB programmes aiming at theintrogression of stress resistance:

Stage-I: Identification of marker trait Association for stress

resistance using the concept of linkage mapping

Stage-II: Validation of marker trait association in different

genetic background using cross breeding population

Stage-III: Test the usefulness of marker in characterization

core germplasm

Separate the germplasm into lines that will serve as donor orrecipient of the stress resistance

↓↓↓↓↓Is the marker able to differentiate between donor and recipientgermplasm?

↓↓↓↓↓

Marker suitable for use

Yes

↓↓↓↓↓No

↓↓↓↓↓< <

Stage-IV: Implementation of the validated marker in the

breeding programmeme

Prepare simple genotyping protocol (marker assay) for themarker detection and its allele size

↓↓↓↓↓Provide the marker data along with allelic information to themolecular breeders for the MAB for stress resistance

MAB of Simple Inherited Trait loci (SITLs) Conferring Stress

Resistance

MAB for SITLs including monogenic traits and oligogenic traits,which follows simple Mendelian inheritance, is quite straightforward approach. It involves:

i. Identification of suitable DNA marker that either co-segregate with stress resistance gene/locus or a pair offlanking markers around the locus conferring resistance,and validation by testing its applicability and reliability inpredicting the stress resistance in the related populations.

ii. Deployment of identified marker(s) in various breedingprogrammes, such as marker-assisted backcross breeding(MABC), marker-assisted gene pyramiding (MAGP) andmarker-assisted selection (MAS) at early generations.

Molecular mapping of SITLs conferring stress resistance

Molecular mapping of loci controlling biotic stress resistance,most often under the control of oligogenes, is considered asgene mapping or SITL mapping. The strategy of gene mappingis quite simple. The phenotypic expression of the biotic stressresistance is recorded on the individuals of a mappingpopulation; they are converted to genotypes depending uponwhich parent they resemble, followed by linkage analysis withthe marker data already available. In some cases the phenotypicexpression may be recorded using metric data or scores. Formapping of the trait loci, these quantified phenotypic data areconverted to discrete forms resembling the parents, followedby routine linkage analysis.

The alternative strategy is using near-isogenic lines (NILs) thatare available from conventional breeding programmes forvarious major genes conferring stress resistance. Theconstruction of NILs for a specific gene is carried out by

Identify alternative marker lociclosely flanked the trait locus

↓↓↓↓↓Screen the marker against thegermplasm

↓↓↓↓↓Identify markers able to detectpolymorphism between donorand recipient and segregatinglines at par

4

JOGESWAR PANIGRAHI et al.,

repeated backcrossing of a donor parent (DP) to a recurrentparent (RP). Backcrossing accompanied by selection for thegene of interest and recovery of the recurrent parent iscontinued until the newly developed line is nearly isogenicwith the RP; except for the chromosome segment that has thetarget gene. The basic idea of the NIL gene mapping techniqueis to identify molecular markers located in the linkage blocksurrounding the introgressed stress resistance gene. Linkagebetween a molecular marker and the target gene can beassessed by determining the markers genotypes of the RP, itsNIL derivative and their corresponding DP. Putative evidenceof linkage is obtained whenever the NIL has the same markergenotype as its DP, but a different marker genotype than its RP.Since only a few genotypes (RP, NIL and DP) have to beassayed, the NIL gene mapping technique provides a propertool for narrowing down a large set of randomly choosenmarkers to a subset of a few markers, some of which are verytightly linked to the target gene introgressed into NIL. With thissubset of molecular markers, however, a traditional segregationanalysis would have to be performed in order to find a tightlylinked marker to the target gene.

The third strategy employed in major gene mapping is calledbulked segregant analysis (BSA, Michelmore et al., 1991),which is popularly known as molecular tagging of genes. BSAstrategy employs mostly F

2 segregating population for tagging

and mapping the major gene. In this method, the homozygotesof the constrasting phenotypes (resistance and susceptible tostress) are from the F

2 based on the F

3 segregation analysis.

The DNA from homozygotes of each phenotype are pooled toform a pool similar to resistant parent (which is refered asresistant bulk), and pool similar to susceptible parent (which isrefered as suceptible bulk). The genotypes to be assayed formarkers include resistant parent, resistant bulk, susceptibleparent and susceptible bulk. Putative markers associated withalternative phenotypes are identified, i.e. known as genetagging and subject to traditional linkage analysis to identifythe tightly linked marker to the target gene- molecular mappingof gene.

Literature reveals mapping of an array of such loci confereningbiotic stress resistance in several crop species using all theabove strategies. A list of mapped SITLs conferring stressresistance in different crop systems using various kinds of DNAmarkers is furnished in Table 1.

MAB for Major SITLs Conferring Stress Resistance

Tight linkage of a marker to a target gene conferring stressresistance can be exploited for indirect selection of monogenicand oligogenic traits in a breeding programme. Application ofthis method presupposes that the initial population ispolymorphic for the marker and the target gene, and both arein extreme linkage disequilibrium. Instead of testing thephenotypes of the target gene itself, selection in segregatinggenerations is based on determination of marker genotype.Only those individuals that carry the desired marker allele(s)are selected (Melchinger, 1990). However, use of two linkedmarkers bracketing the target gene should improve thereliability of MAB (Collard and Mackill, 2008). These flankedmolecular markers can be effectively employed backcrossbreeding, gene pyramiding, gene introgression and earlygeneration selection of superior cultivars aimimg at complete

stress resistance and higher stress tolerance.

Marker-Assisted-Backcross Breeding (MABC) for SITLs

Conferring Stress Resistance

Backcross breeding has been a widely used strategy for almosta century to incorporate major gene(s) conferring resistanceto biotic and abiotic stresses into an adapted or elite variety,which is possessed with large number of desirable agronomictraits but is susceptible to the target stress (Allard, 1999). Inrepeated crossings, the hybrids (BC1-n) is backcrossed withthe recurrent parent until most of the genes stemming fromthe donor parent are eliminated except stress resistance(Becker 1993). This conventional backcross breedingprogrammes are planned on the assumption that theproportion of the recurrent parent genome is recovered at therate of {1/(2)n+1} for each ‘n’ generation of backcrossing. Thus,after six backcrosses, we expect to recover 99% of the recurrentparent. This approach was first described in 1922 and waspracticed between the 1930s and 1960s in several crops(Stoskopf et al., 1993). DNA markers are now increasinglyused in backcross breeding to increase the efficiency ofselection at three levels, viz. foreground selection (i.e. to tracethe presence of target allele or gene), background selection(i.e. selection of reconstructed recurrent parent genome inbackcross programme), and recombinant selection (i.eidentification of BC progeny with the target gene, andrecombination events between the target locus and linkedand/or flanked markers to minimize linkage drag) (Holland,2004; Collard Mackill, 2008).

Marker-assisted foreground selection is useful for stressassociated traits that have tedious and time consumingphenotypic screening procedures. By this approach thereproductive traits can also be selected at the sapling stage,and this allows for the identification of best plants at an earlystage for backcrossing as well as phenotyping. Furthermore,both dominant and recessive alleles conferring stress resistancecan also be selected and introgressed by this approach (Fig.1and 2), which is time consuming and difficult to do usingconventional breeding.

Marker-assisted background selection was initially proposedby Young and Tanksley (1989b), and the term was coined byHospital and Charcosset (1997). The background selectionrefers to the use of closely linked flanking markers for selectionof recombinant and unlinked background markers to selectthe genetic make up of recurrent parent (RP). Backgroundmarkers are unlinked to the target trait on all otherchromosomes, and these markers can be used to selectrecurrent genome against the donor genome. Hence, thisapproach is quite useful, for accelerated reconstitution ofrecurrent genome along with the desired donor fragment. Withconventional backcrossing, it takes a minimum of six BCgenerations to reconstitute the RP, which may be possessedwith several donor chromosome fragments unlinked to thetarget gene. Using marker assisted background selectionapproach, the reconstituted RP genome can be achieved intwo to four BC generations (Visscher et al., 1996; Hospitaland Charcosset, 1997; Frisch et al., 1999a,b) even byeliminating undesired donor fragment, thus saving two to fourBC generations. Thus, use of marker-assisted background

5

PHARMACOLOGICAL EFFICACY OF MEDICINAL PLANTS

Crop Trait Gene Marker Type Marker and distance in cM LG/Chr Reference

RICE Leaf blast Resistance Pi-1 RFLP NPB181(3.5) 11 Yu 1991

Pi-2(t) RAPD RG64(2.1) 6 Hittalmani et al., 1995a,b

Pi-4(t) RFLP RG869(15.3) 12 Yu et al., 1991

Pi-ta RFLP RZ397(3.3) 12 Yu et al., 1991

Pi-5(t) RFLP RG498 (5.0), RG788 (10.0) 4 Wang et al., 1994

Pi-6(t) RFLP RG869(20) 12 Yu 1991

Pi-7(t) RFLP RG103(5.1) 11 Wang et al., 1994

Pi-10(t) RAPD RRF6, RRH18 5 Naqvi et al., 1995

Pib RFLP RZ123 2 Miyamoto et al., 1996

Pi-9 RFLP RG16, pBA 14, pBA8 6 Liu et al., 2002

Pi-38 SSLPAFLP RM 206, RM21AF-1, AF-2, AF-3 11 Gowda et al., 2006

Pi-1 (t) SSR RM224 NA Prasad et al., 2009

Bacterial blight Xa-1 RFLP Npb235 (3.3) 4 Yoshimura et al., 1992

resistance Xa-2 RFLP Npb 235(3.4), Npb197(9.4) 4 Yoshimura et al., 1992

Xa-3 RFLP Npb181(2.3), Npb 78(3.5) 11 Yoshimura et al., 1992

Xa-4 RFLP Npb181(1.7), Npb 78(1.7) 11 Yoshimura et al., 1992

Xa-5 RFLP RG556 (0-1) 5 Mc Couch et al.,, 1992

Xa-10 RAPD OPO07(5.3) 11 Yoshimura et al.,1995a

Xa-13 RFLP RZ390 (0.0), RG 136(3.8) 8 Yoshimura et al.,1995b

Xa-21 RAPD Pta818(0.0), Pta 248(1.0) 11 Ronald et al., 1992

Xa-7 RGA RNM20576, MY4 6 Zhang et al., 2009

xa34(t) SSR RM493 (4.29) and RM446 (3.05) 1 Chen et al., 2011

Bph6 SSR RM6997 and RM5742 4 Qiu et al., 2010

BPH26 SSR RM309(13.3) and MSSR2(5.1) 12 Myint et al., 2012

Gallmidge Resistance Gm-2 RFLP RG329(1.3), RG476(3.4) 4 Mohan et al., 1994

Gm4-t RAPD E20570 (0.4) from R1813 and 8 Mohan et al.,1997; Nair

1.4 from S1633b et al., 1996

Gm-7 AFLP/ SCAR SA 598 4 Sardesai et al., 2002

SSR RM22550 (0.9) and RM547 (1.9) 8 Nanda et al., 2010

Gm11t SSR RM28574 (4.4) and RM28706 (3.8 ) 12 Himabindu et al.,2010

Brown planthopper bph4 SSR RM589 (1.1) and RM586 (0.6) 6 Jairin et al., 2010

BPH12 SSR RM16459 and RM1305 (1.9) 4 Qiu et al.,2012

bph20(t) SSR RM435 (2.7) and RM540 (2.5) 6 Yang et al.,2012

BYL7 and BYL8 (2.5)

bph21(t) SSR RM222 (7.9) and RM244 (4.0) 10 Yang et al.,2012Rice Stripe Virus RSV1 SSR, SRAP RM457 (4.5) and SR1 (2.9) 11 Zhao et al., 2010

WHEAT Powdery mildew Pm RFLP Xwg516 2B Rong et al., 1998Resistance Pm1 RFLP WHS178(3) NA Jahoor 1998

Pm2 RFLP Xbcd1871(3.5) 5D Ma et al., 1994Pm2 RFLP Xfba393 5DS Nelson et al., 1995Pm3b RFLP Xbcd1434 (1.3) 1AS Ma et al., 1994Pm4a RFLP Xbcd1231-2A (1.5) 2AL Ma et al., 1994Pm4a RFLP Xcdo678-2A (1.6) 2AL Ma et al., 1994Pm12 RFLP Xpsr10,Xpsr106,Nor2,Xpsr141,Xpsr113 6DS Jia et al., 1996Pm12 RFLP Xpsr142, Xpsr149, Xpsr2, Xpsr605 6DL Jia et al., 1996Pm34 SSR Xbarc1775D (5.4), Xbarc1445D (2.6) 5D Miranda et al., 2006PmY39 SSR Xgwm257, Xgwm296, Xgwm319 (0) 2B Zhu et al., 2006Pm35 SSR Xcfd (10.3), Xgdm (8.6), Xcfd (11.9) 5DL Miranda et al., 2006PmTb7A.2 STS MAG2185 and MAG1759 7A Chhuneja et al., 2012PmTb7A.1 DArT and SSRwPt4553 and Xcfa2019 (4.3)Pm-M53 AFLP Apm109 (1.0) and Apm161 (3.0) 5D Li et al., 2011PmHNK54 SSR Xbarc5 (5.0) and Xgwm312 (6.0) 2AL Xu et al., 2011Pm4d STS Xgwm526 (3.4) and Xbarc122 (1.0) 2AL Schmolke et al., 2012PmAS846 EST BJ261635 and CJ840011 5BL Xue et al., 2012Pm45 SSR Xcfd80,Xmag6139 (0.7) and Xmag6140 (2.7) 6DS Ma et al., 2011

Cyst nematode Cre1 RFLP Xglk605 (7.3), Xglk588 (8.4) 2BL. Williams et al., 1994resistance Ccn-D1 RAPD OPE20 (tight) 2DS Eastwood et al., 1994High-temperature HTAP RGAP Xbarc182 and Xwgp5258 (2.3) 7BL Ren et al., 2012adult-plant stripe rust SSRresistanceHigh temperature Yrxy2 SSR Two markers flanked at (4.0) and (6.4) 2A7A Zhou et al., 2011resistance to stripe rust Yrxy1 RGAP M8 (2.3) and M9 (3.5)

SSR Xbarc49 (15.8) and Xwmc422 (26.1)

Streak mosaic virus Wsm1 STS Wg232 (tight) 4L Talbert et al., 1996

Table 1: A list of mapped Simple inherited trait loci (SITL) conferring stress resistance using various kinds of molecular markers in some major

crops

6


crops


WSSMV RFLP Xbcd1095, Xcdo373 2DL Khan et al., 2000

Hessian fly resistance H23 RFLP XksuH4 (6.9), XksuG48a (15.6) 6D Ma et al., 1993

H24 RFLP Xcnl BCD 451 (5.9), Xcnl CDO 482 (5.9), Xksu G48b (12.9) 3DL

Ma et al., 1993

Stem rust resistance Sr2 RFLP Xbcd1871 (3.5) 5B Nelson et al., 1995

Sr40 SSR Xwmc 344 (0.7) 2B Wu et al., 2009

Sr13 SSR barc37 (4.0) 6A Admassu et al., 2011

Leaf rust resistance Lr1 RFLP PSR580(13.8), PSR567 5DL Feuillet et al., 1995

Lr3 RFLP Xmwg 798 (0) 6BL Sacco et al., 1998

Lr13 RFLP Xbcd 1709(<7.9), Xpsrs 912 (9.1) 2B Seyfarth et al., 1998

Lr32 RFLP Xbcd 1278 (3.6), Xcdo 395 (6.9) 3DS Autrique et al., 1995

Lr34 SSR Xgwm1220, Xgwm295 7D Spielmeyer et al., 2005

Lr52 (W) SSR Xgwm 443 (16.5) 5B Hiebert et al., 2005

Lr34 EST-SSR SWM-10 7DS Bosolini et al., 2006

Lr22a SSR GWM-296 2DS Hiebert et al., 2007

Lr1 RGA WR-03 (0.07) 5DL Qiu et al., 2007

Lr41 SSR Xbarc 124 (<1.0) 2DS Sun et al., 2009

Stripe rust resistance Yr15 RFLP STMS Nor1 B (11)WMS533(4.5) 1B Sun et al., 1999

Fahima et al., 1997

yrH 52 RFLPSTMS Nor1 (1.4)NA (0.02-0.35) 1B Peng et al., 1999

Yr36 STS Xbarc 101 (2.0) 6B Uauy et al., 2005

YrCH42 SSR Xgwm498(1.6), Xbarc-187 (2.3) 1B Li et al., 2006

YrZH84 SSR Xcfa2040-7B(1.4), Xbarc32-7B (4.8) 7BL Li et al., 2006

Yr34 RGA Awn Inhibitor gene A-1 (12.2) 5AL Barian et al., 2006

Yr26 SSR/STS Xwe173 (1.4)/ Xbarc181(6.7) 1B Wang et al., 2008

YrZak SSR Xwgp 102, Xgwm 501 2B Sui et al., 2009

High-temperature HTAP RGAPSSR Xbarc182 and Xwgp5258 (2.3) 7BL Ren et al., 2012

adult-plant stripe rust resistance

High temperature Yrxy2 SSR Two markers flanked at (4.0) and (6.4) 2A7A Zhou et al., 2011

resistance to stripe rust Yrxy1 RGAP M8 (2.3) and M9 (3.5)

SSR Xbarc49 (15.8) and Xwmc422 (26.1)

Loose smut resistance T 10 RAPD UBC 353 (14) 2BL Procunier et al., 1997

RFLP Xcrc4.2 (14), Xcrc 153.2 (10) 2BL Procunier et al., 1997

Septoria nodorum RAPD UBC521 (15), RC37 (13) 3A Cao et al., 1998

blotch resistance

Scab resistance FHB AFLP XeageMetal (16.2) 3BS, 2AL, Anderson

ksuH16 (12.7) 6BS et al., 1998

Xbcd1331(7.3)

RFLP Xcdo 1387 (7.4) Xcdo 524 (5.9) 4AL6BS Anderson et al., 1998

Yellow mosaic YmYF SSR Xwmc41 (8.1), Xgwm349 (11.6) 2D Liu et al., 2005

virus resistance

BARLEY Stem rust resistance rpg 4 RAPD 7M Borokova et al., 1995

Powdery mildew MiLa RFLP WG645 (Cosegregating) 2 Saghai-Maroof et al., 1994

Resistance

Alluminium tolerance Al RFLP Xwg464 (21.6) 4H Echart et al., 2006

Crown rust resistance rpc-1 RAPD OPO-08700

(2.5) 3H Agrama et al., 2004

Leaf rust resistance Rph-5 RFLPAFLP VT-1(0.3) 3H Mamadov et al., 2003

C970 (0.5)

Rph-7 RFLP Hv3Lrk (3.20 3HS Brunner et al., 2000

CHICKPEAResistance to Foc1 SSR H3A12 (3.9) and TA110 (2.1) Gowda et al., 2009

Fusarium wilt Foc2 SSR TA96 (0.2) and H3A12 (2.7)

Foc3 SSR H1B06y (0.2) and TA194 (0.7)

Mungbean Bruchid resistance Bruchid RFLP PA882 (3.6) 8 Young et al., 1992

Br-2 RAPD, STS OPC-06 (11.0)STSbr2 (5.8) 8 Sun et al., 2008

Pigeonpea Sterlity Mosaic SMD AFLP E-CAA/M-GTG150

(5.7) NA Ganapthy et al., 2009

disease Resistance E-CAA/M-GTG60

(4.8)

E-CAG/M-GCC150

(5.2)

E-CAG/M-GCC120

(20.1)

Fusarium wilt resistance - RAPD OPM03704

and OPAC11500

NA Kotresh et al., 2006

SOYBEAN SMV resistance Rsv RFLP/SSR PA 186 (1.5), pK644a(2.1), SM176(0.5) NA Yu et al., 1994

TOMATO Fusarium wilt L2 RFLP TG105 (0.0 ±4.8) 11 Sarfatti et al., 1989

resistance

TMV resistance Tm2 RFLP TG3 (0.3), CD3 (0.9) 9 Young and Tanksley 1989


7

selection accelerates the development of NIL at par with RPcontaining desired stress resistance and has been referred toas ‘complete line conversion’ (Ribaut et al., 2002).

A case study of goreground and background selection

through MAB

Marker assisted backcross breeding strategy has provenvaluable in accelerating the backcross programmes toincorporate two major blast resistant genes Pi-2(t) and Pi-1from pyramided donor parent into the background of IR64,an elite cultivar widely grown in Asia. Simultaneously recurrentparent genome was recovered with the help of both RAPDand RFLP markers to have the introgressed line identical withthat of IR64 (Hittalmani S., personal communication). Duringeach generation of F

1, BC

1F

1 and BC

2F

2 the progenies were

screened for tracking the major resistant genes Pi-2(t) and Pi-1

using tightly linked markers (Fig. 3). The broad based Pi-2(t)

major blast resistant gene, present in chromosome 6, wasconfirmed by using the previously established co-dominantRG64 SAP marker (Hittalmani et al., 1995a). Similarly, the


Powdery Mildew Lv RAPD OP57,OP58, OP218 12 Chunwongse et al., 1994

Resistance Lv RFLP CT211, CT 219 (5.5) 12 Chunwongse et al., 1994

Ol-2 RAPD OPU31500

4 de Giovanni et al., 2004

Ol-1, Lv AFLP — 6,12 Bai et al., 2003

Salt Tolerance Isozyme Est3, Prx7, Pgdh2, pgt1 1, 3, 12 Foolad and Jones 1993

Tomato Yellow leaf Ty-2 RFLP Tg36 11 Hanson et al., 2006

curl virus resistance Ty-3 SCAR cLET31-P16, T1079, P169c 6 Ji and Scott 2006

Alternaria Stem Canker ASc RFLP YAC (11.2) 3 Mesbah et al., 1999

Vander Biezen et al., 1995

Bacterial spot Xv4 RFLP TG599, TG134 3 Astua Monge et al., 2000

Bs4 AFLP P11M6, P11M1 5 Ballvora et al., 2001

Mustard White rust resistance Ac2l RAPD WR2 (7), WR1a/3 (1.4) NA Prabhu et al., 1998

Ac2 (t) RAPD OPB061000

(5.5) NA Mukherjee et al.,2001

Rapeseed Turnip mosaic TuRBO1 RFLP pO120b (3.6) 6 Walsh et al.,1999

Virus resistance

Black leg resistance LEM1 RFLP wg2a3b (1), wg5a1a (1.9) 6 Figdore et al., 1993

LepR3 SSR SR12281a, SN2428Rb(2.9) N10 Yu et al.,,2008

White rust resistance ACA1 RFLP tg6a12 (12.9) 9 Ferreira et al., 1995a,b

Indianrape White rust resistance Aca1 RFLP wg6c1a (5.0), ec2b3a (5.5) 4 Kole et al., 2002;

Kole et al., 1996


crops

tightly linked RM-144/c481 (2 cM) rice microsatellite markerconfirmed the introgression of complimentary resistance Pi-1

gene. This resistant gene is present on chromosome number11 and is linked to c481 clone, which is a PCR-based STSmarker (Mew et al., 1994). Simultaneously, progenies from F

1,

BC1F

1 and BC

2F

1, having Pi-2(t) and Pi1 major resistance genes

were screened for the fast recovery of recurrent parent genomeusing both RAPD and SSR primers. Through backgroundscreening it was possible to recover 96% of IR64 backgroundby BC

2F

1 generation (Fig. 3).

Marker-assisted recombinant selections reduce the size of thedonor segment of the genome containing the target locus.This approach is important because the decrease of donorfragment size reduce the deleterious effect of many undesirablegenes, linked to the target gene, that negatively affect cropperformance - this is referred to as ‘minimization of linkagedrag’ (Hospital, 2005). Using conventional breeding methods,the donor segment can remain very large even with many BCgenerations (Young and Tanksley, 1989a; Ribaut andHoisington, 1998; Salina et al., 2003) because the conventionalbreeding is phenotype-biased selection. By using flanking

Figure 1: Sketch showing marker assisted back cross approach to

transfer a single dominant allele conferring stress resistance

Figure 2: Sketch showing marker assisted back cross approach to

transfer a single recessive allele associated with stress resistance

8

markers around a stress resistant gene (e.g., less than 5 cM oneither side), linkage drag can be minimized (Collard andMackgill, 2008). Further, these markers enable the breedersto detect the double recombination events occurring on bothsides of stress resistance locus, which are extremely rare, andthis recombinant selection is usually performed using at leasttwo BC generations (Frisch et al., 1999b).

A case study for removal of linkage drag using MAB

Keygene, an agrobased company, was involved in a markerassisted breeding approach for the development of a novellettuce variety resistant to the aphid, Nasonovia ribisnigri,during mid nineties (Jansen, 1996). The resistance gene to thisaphid was present in its wild relative, Lactuca virosa, whichcould be introgressed from a by repeated backcrossing.Although the backcrossing programme developed aphidresistant genotype, the new product was of extremely poorquality, bearing yellow leaves and a greatly reduced head.Marker analysis revealed that this reduced quality was causedby a negative trait closely linked to aphid resistance, so calledlinkage drag. In this case, the linkage drag was recessive, onlyappeared in the homozygous state, thereby increasing thedifficulty in phenotype based selection of recombinationevents. With the identification of DNA markers flanking theaphid resistant locus, individuals having recombination eventsin the vicinity of the gene was pre-selected for further analysis.More than 1000 F

2 plants were screened this way, leading to

the selection of some 100 individuals bearing a recombinationor even double recombination in the vicinity of the aphidresistance gene. Only those individuals needed to bephenotyped for both the resistance and the absence of thenegative characteristics at F

3 level. This approach eventually

led to the selection of an individual bearing recombinationevents very close to each side of the gene, thereby removingthe recessive linkage drag located on both sides of theresistance gene, in addition to being tightly linked. By removingthe linkage drag, the mildly sweet, crunchy iceberg lettucewith aphid resistance (Cultivar-Fortunas Rz) was developedby the seed breeding company Rijk Zwann, Berlin.

Some examples of MABC for traits conferring stress resistancein rice, wheat, barley, maize, tomato and soybean is furnishedin Table 2.

Marker-Assisted Gene Pyramiding (MAGP) for SITLs

Conferring Stress Resistance

Pyramiding stress resistance genes to develop durable resistantvariety is another strategy of MAB. Breakdown of disease orpest resistance conferred by single major gene is a commonphenomenon in several crops, due to the emergence of newpathogenic races and/or biotypes after its wide cultivation(Kiyosawa, 1982; Ou, 1985). Therefore, breeding for durableresistance would be more effective if two or more major andminor resistance genes are combined into a single geneticbackground. This will lessen the chances of biotic resistancebreakdown by continuing evolution of new races ofpathogens and biotypes of pests. Pyramiding of two or moremajor and minor biotic stress resistance genes throughconventional breeding method is possible, but it is not easy toidentify the plants containing more than one genesimultaneously due to the different genetic behavior of genes, C

rop

Agro

no

mic

Tra

its

Mark

ers

use

dEn

d p

rod

uct

Refe

ren

ce

RIC

EB

acte

rial

bli

gh

t re

sist

an

ce (

Xa21

)R

FLP

, P

CR

base

d m

ark

ers

Min

gh

ui-

63

(X

a2

1):

A h

yb

rid

rest

ore

r li

ne

Ch

en

et

al.

, 2

00

0

AFLP

IV-6

07

8 (

Xa2

1):

A h

yb

rid

rest

ore

r li

ne

Ch

en

et

al.

, 2

00

1

Bacte

rial

bli

gh

t re

sist

an

ce (

Xa5

)ST

SA

ngke-A

cu

ltiv

ar

Bu

stam

am

et

al.

, 2

00

2

Bacte

rial

bli

gh

t re

sist

an

ce (

Xa7

)ST

SC

on

de-A

cu

ltiv

ar

Bu

stam

am

et

al.

, 2

00

2

WH

EA

TLeaf

rust

resi

stan

ce

RFLP

, C

AP

SIs

ogen

ic l

ines

of

thre

e s

pri

ng c

ult

ivars

- Exp

ress

, K

ern

an

d U

C 1

03

7H

elg

uera

et

al.

, 2

00

5

Leaf

rust

resi

stan

ce (

Lr

21

)SSR

Ad

v.

Bre

ed

ing l

ines

So

mers

et

al.

, 2

00

5

Leaf

rust

resi

stan

ce (

Lr

47

)P

CR

base

d m

ark

ers

Yeco

ra r

ojo

Lr4

7-c

ult

ivar

Ch

icaiz

a e

t al.

, 2

00

6

Cere

al

Cyst

nem

ato

de

RFLP

Ad

v.

bre

ed

ing l

ines

(DH

po

pu

lati

on

base

d)

Ogb

on

naya e

t al.

, 2

00

1

Str

ipe r

ust

resi

stan

ce (

Yr-

36

)P

CR

base

d m

ark

ers

Yeco

ra r

ojo

yr3

6-G

plB

1,

UC

11

13

yr3

6-G

plB

1-

two

cu

ltiv

ars

Ch

icaiz

a e

t al.

, 2

00

6

Ste

m r

ust

resi

stan

ce (

sr-3

8)

PC

R b

ase

d m

ark

ers

An

za L

r37

/Yr1

7/

Sr3

8C

hic

aiz

a e

t al.

, 2

00

6

BA

RLEY

Resi

stan

ce t

o b

oro

n t

oxic

ity

SSR

Ad

v.

Bre

ed

lin

g l

ines

Em

eb

iri

et

al.

, 2

00

9

Resi

stan

ce t

o B

aY

MV

I-I

IIR

FLP

Mo

kkei

01

53

0-

A C

ult

ivar

Okad

a e

t al.

, 2

00

3

Resi

stan

ce t

o s

po

t n

et

blo

tch

SSR

Lin

e W

I35

86

-17

47

Egli

nto

n e

t al.

, 2

00

6

MA

IZE

Resi

stan

ce S

ou

thw

est

ern

co

rn b

ore

r (S

WC

B)

RFLP

Ad

van

ced

bre

ed

ing l

ines

Wil

lco

x e

t al.

, 2

00

2

TO

MA

TO

Resi

stan

ce t

o T

om

ato

sp

ott

ed

wil

t vir

us

CA

PS

Ad

van

ced

bre

ed

ing l

ines

Lan

gell

a e

t al.

, 2

00

4

Tab

le 2

: M

ark

er

ass

iste

d b

ack c

ross

bre

ed

ing o

f so

me S

ITLs

co

nfe

rrin

g s

tress

resi

stan

ce f

or

the d

evelo

pm

en

t o

f cu

ltiv

ars

an

d a

dvan

ce b

reed

ing lin

es

in s

evera

l cro

p s

yst

em

s


9

the mode of gene action inter se, the appearance of samephenotype and destructive bioassay, etc. Since DNA markerassays are non-destructive and markers for multiple specificgenes can be tested simultaneously using a single DNA samplewithout phenotyping (Hittalmani et al., 1995b; Yoshimura et

al., 1995; Huang et al., 1997; Hittalmani et al., 2000; Werneret al., 2005; Saghaimaroof et al., 2008), the MAGPsubstantially enhance the selection process in crop breeding.

A schematic approach for acumulating six genes into a singlegenotype was demonstrated (Fig.4) by Servin et al. (2004).Accordingly the gene pyramiding scheme consists of two steps,viz. Pedigree step and Fixation step. The pedigree step aims at C

rop

Agro

no

mic

tra

itP

yra

mid

ed

gen

e(s

)R

efe

ren

ce

RIC

EB

last

resi

stan

ce

Pi1

, P

iz5

and

Pit

aH

itta

lman

i et

al.

, 2

00

0

Bacte

rial

Bli

gh

t R

esi

stan

ce

Xa4

, Xa5

, Xa13

an

d X

a 2

1H

uan

g e

tal.

19

97

Xa7

an

d X

a 2

1Z

han

g e

t al.

,2006

Xa5

, Xa13

an

d X

a 2

1K

ott

ap

all

i et

al.

, 2

01

0

Xa3

and

Xa 2

6Li

et

al.

, 2

01

2

Bacte

rial

Bli

gh

t, Y

ell

ow

ste

m b

ore

r an

d s

heath

bli

gh

tXa21

, cry

1A

b,

RC

7 C

hit

inase

an

d c

ry1

Ac

Datt

a e

t al.

, 2

00

2

Bacte

rial

Bli

gh

t, Y

ell

ow

ste

m b

ore

rXa21

, cry

1A

b a

nd

cry

1A

cJi

an

g e

t al.

, 2

00

4

Bro

wn

pla

nt

ho

pp

er

Bph1

an

d B

ph2

Sh

arm

a e

t al.

, 2

00

4

Gall

mid

ge R

esi

stan

ce

Gm

1 a

nd

Gm

4K

um

ara

vad

ivel

et

al.

, 2

00

6

Gm

2 a

nd

Gm

6(t

)K

att

iyar

et

al.

, 2

00

1

WH

EA

TP

ow

dery

Mil

dew

Pm

2 a

nd

Pm

4a

Liu

et

al.

, 2

00

0

Leaf

rust

resi

stan

ce

Lr41

, Lr

42

an

d L

r43

Co

x e

t al.

, 1

99

4

Gre

en

bu

g r

esi

stan

ce

Gb2

, G

b3

an

d G

b6

Po

rter

et

al.

, 2

00

0

Cyst

nem

ato

de r

esi

stan

ce

Cre

X a

nd

Cre

YB

arl

oy e

t al.

, 2

00

7

BA

RLEY

Yell

ow

mo

saic

vir

us

resi

stan

ce

rym

1 a

nd

rym

5O

kad

a e

t al.

, 2

00

4

Rym

4,

rym

9,

rym

11

Wern

er

et

al.

, 2

00

5

PEA

RL M

ILLET

Do

wn

ey M

ild

ew

Resi

stan

ce

P7

-3 a

nd

P7

-4H

ash

et

al.

, 2

00

6

SO

YB

EA

NSo

yb

ean

mo

saic

Vir

us

Resi

stan

ce

Rsv

1,

Rsv

3 a

nd

Rsv

4Sh

i et

al.

, 2

00

9Sagh

aim

aro

of

et

al.

, 2

00

8

GR

AP

E V

INE

Po

wd

ery

mil

dew

an

d D

ow

ney M

ild

ew

Resi

stan

ce

Ru

n1

an

d R

pv1

Eib

ach

et

al.

, 2

00

7

Tab

le 3

: M

ark

er

Ass

iste

d G

en

e P

yra

mid

ing o

f SIT

Ls

co

nfe

rrin

g r

esi

stan

ce t

o b

ioti

c a

nd

ab

ioti

c s

tress

in

so

me m

ajo

r cro

ps

Figure 3: Schematic sketch of marker assisted backcross breeding for

introgression of two major blast resistance genes, Pi-1 and Pi-2(t), in

rice

BC 3 F 1

Selection for major genes Pi -1 and Pi -2(t) using closelylinked PCR markers RM144 and RG64(SAP).

Selected F 1 plants backcrossed with recurrent parents .

Selection for major genes Pi -1 and Pi -2 (t)using close ly linked PCR markers.Background screening using both RAPD and

rice microsatellite primers.

As in BC 1 F 1

(Recurrent parent)(Donor parent)

Pheno typic evaluation of disease resistance with parentsand checks in blast hot spots (Ponnampet). Selection of blast

resistant plants having high RPG.

Pi -1 & P i-2 (t) isogenic line X IR64

BC 1 F 1 X IR64

BC 2 F 1 X IR64

M L Y T

Evaluation of resistant plants for yield and diseaseresistance in replicated trail under different

environments (Multi - location yield Trail) .

BC 3 F 2

Selfing of plants based ongenotypic & phen otypic

confirmation.

Release/Stabilization of variety

F 1 X IR64

Figure 4: Gene pyramiding strategy in plants (Redrawn from Servin

et al., 2004)

10

acumulating of all target genes in a single genotype called theroot genotype, and the fixation step aims at fixing the all targetgenes into a homozygous state i.e. to derive the ideal genotype(ideotype). Although the pedigree step may be common,several different procedures can be used to undergo fixationin gene pyramiding.

The marker-assisted gene pyramiding involves following steps

in general

• Fine-map the donor genes conferring stress resistance anddevelop tightly linked flanking markers for each resistantgene.

• The plant with known tagged gene (X-1) is crossed with thesecond plant carrying another target gene (X-2), andsimilarly with the others genes.

• The F1 plants of the above crosses are screened for the

presence of both the resistance genes (X-1 and X-2) byassaying for the presence both pair of flanking markers.

• F2 individual plants are screened for the presence of all

combination of genes using markers and plants carryingall gene combination are forwarded to next generation.

• Homozygous plants carrying all the desired combinationof target genes identified and further tested for their traits.

MAGP has been well demonstrated in several crops includingrice, wheat, pearl millet, barley, soybean, etc. (Table 3). Theexample cited in the Table 3 evidenced that the combinationof multiple resistance genes (effective against specific races ofa pathogen) can provide durable (broad spectrum) resistance.The ability of a pathogen to overcome two or more resistancegenes by mutation is considered much lower compared withthe invading of stress resistance controlled by a single gene(Kloppers and Pretorius, 1997; Shanti et al., 2001; Singh et

al., 2001). In this section, we have only cited the case of genepyramiding to improve qualitative stress related traits such asdisease and pest resistance.

Marker-Assisted Gene Introgression from Breeding Lines and

Wild Relatives

Evaluation of the exotic and adapted germplasm using DNAmarker is an integral part of MAB and it played important rolein the acquisition, storage and use of plant genetic resourcesin breeding endeavors (Bretting and Widrlechner, 1995; Xuet al., 2003). The wild allies of the domesticated crops,including its progenitors and the species in secondary andtertiary genepools, provide plant breeders with a handy sourceof desirable genes (Tanksley et al., 1989; Jena, 2010; Kole2011). The use of wild germplasm and putative progenitors incrop improvement gained importance in the 1970s and 1980s(Hajjar and Hodgkin, 2007; Dwivedi et al., 2008), and iscontinuing in several orphan crops till date (Panigrahi et al.,

2007; Varshney et al., 2010; Mishra et al., 2012). Theadvancements in genomics have considerably increased theuse of genes from exotic germplasms, in particular from thesecondary genepools, being the source agroeconomic genes.Hajjar and Hodgkin (2007) reported on the use of more than60 wild species to introgress desired genes conferring stressresistance and other agronomically important traits into 13agricultural crops during mid-1980s to 2005. The most

common use of wild relatives is as a source of pest and diseaseresistance, although other characteristics including abioticstress tolerance, yield attributes, improved quality, andcytoplasmic male sterility and fertility restoration also havebeen improved using crop wild relatives in individual cases(Fig. 5).

Figure 5: Numbers of traits introgressed into the domesticated species

from wild allies during 1990 to 2010. (Source: Partly obtained from

Hajjar and Hodgkin, 2007)

0

2

4

6

8

10

12

Rice Wheat Maize Barley Potato Tomato Lettuce

Major Crops

Nu

mb

er

of

tr

aits

Alleles for biotic stress resistance Alleles for abiotic stress resistance

The process by which beneficial traits from core collection ofgermplasm are transferred to the elite cultivars of a crop iscalled introgression. Mostly single major genes conferringstress resistance, identified in exotic or unadapted germplasm,are transferred into adapted breeding material by backcrossing(Simmonds, 1993). The use of these exotic germplasm in MABcan aid in transferring genes with minimal linkage drag, thusmaking the introgression of genes is one of the preferentialapplication of modern breeding. Introgression libraries (IL)allow for the identification of favorable alleles in exoticgermplasm, which can be exploited for improving elitebreeding material. ILs are obtained by a cross between theunadapted germplasm and an elite recurrent parent, which isfollowed by several generations of recurrent backcrossing. Aset of polymorphic markers that can distinguish betweenparental alleles is used to trace chromosome segments throughthe crosses. The backcrossing is followed by at least onegeneration of selfing, which leads to plants homozygous attargeted introgressed segments (Zamir, 2001). This systematicintrogression of individual, short, marker-defined chromosomesegments into the elite background results in a library of ILs.Each line carrying different parts of the donor genome and thelibrary can be used to screen for favorable alleles obtainedfrom the exotic unadapted germplasm. Introgression lines werefirst developed in tomato in 1994 and have since then beenadopted for several crops, including barley, maize, wheat andrye (Falke et al., 2009).

Marker-Assisted Selection (MAS) of Superior Genotypes

Having Major Genes Conferring Stress Resistance at Early

Generations

Molecular markers can be employed at any stage of a plantbreeding programme. Hence, MAS has great advantage inearly generation selections by eliminating undesirable genecombinations. Subsequently, the breeders focus on a lessernumber of high priority lines of desirable allelic or gene


Plea

se sen

d or

igin

al fi

le, i

.e. E

xcel

form

at

11

combination. MAS-based early generation selection not onlyselect suitable gene combinations but also ensure a highprobability of retaining superior breeding lines (Eathington et

al., 1997). An important prerequisite for successful early-generation selection with MAS are large populations and lowheritability of the target traits, as under individual selection,the relative efficiency of MAS is greatest for characters withlow heritability (Lande and Thompson, 1990). Results fromKuchel (2007) and Bonnett et al. (2005) showed that maximumgain can be achieved at lowest cost in marker-assisted wheatbreeding when molecular markers, closely linked to targetgenes, are utilized to enrich target loci within segregatingpopulations in early generations. When the linkage betweenthe marker and the selected trait loci conferring stress resistanceis not very close, the probability of recombination betweenthe marker and trait loci will increase, thereby increasing thenumber of gene-combination for early generation MAS. Thislead to more cost of genotyping a larger number of plants. Toavoid this disadvantage, Ribaut and Betran (1999) developeda strategy involving MAS at an early generation called singlelarge-scale MAS (SLS–MAS). This approach used flankingmarkers (less than 5 cM, on both sides of a target locus) in asingle MAS step. Alternatively, using co-dominant DNAmarkers, it is possible to fix specific alleles in their homozygousstate as early as the F

2 generation. However, this may require

large population sizes; thus, in practical terms, a small numberof loci may be fixed at each generation (Koebner and Summers,2003). Another strategy is to ‘enrich’ rather than fix alleles byselecting homozygotes and heterozygotes for a target locuswithin a population in order to reduce the size of the breedingpopulations required (Bonnett et al., 2005).

CONCLUSION

MAB for vertical (qualitative) resistance to biotic stress is aholistic approach. Till date MAB was applied in small scale forcrop breeding, but a large number of marker-trait associationhas been validated. Hence, there will be a greater level ofadoption of MAB in crop breeding endeavours within thenext decade and beyond. It is also critical that future endeavorsin MAB are based upon lessons that have been learnt frompast successes and especially failures in using MAB. Furtheroptimization of marker genotyping methods in terms of cost-effectiveness and a greater level of integration betweenmolecular and conventional breeding (especially in designingefficient and cost effective strategies) represent the criticalaspects for the greater adoption of MAB on crop breeding inthe near future.

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MARKER-ASSISTED BREEDING FOR SIMPLE INHERITED TRAITS CONFERRING STRESS RESISTANCE IN CROP PLANTS

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