ReviewMolecular markers and their applications in wheat breeding

Plant Breeding 007\ 258*289 "0888#Þ 0888 Blackwell Wissenschafts!Verlag\ BerlinISSN 9068!8430

Review

Molecular markers and their applications in wheat breeding

P[ K[ GUPTA\ R[ K[ VARSHNEY\ P[ C[ SHARMA and B[ RAMESH

Molecular Biology Laboratory\ Department of Agricultural Botany\ Ch[ Charan Singh University\ MeerutÐ149 993 "UP#\India

With 4 tables

Received March 08\ 0888:Accepted June 15\ 0888

Abstract

In recent years\ considerable emphasis has been placed on the devel!opment of molecular markers to be used for a variety of objectives[ Thisreview attempts to give an account of di}erent molecular markers *restriction fragment length polymorphisms "RFLPs#\ random ampli_edpolymorphic DNAs "RAPDs#\ sequence!tagged sites "STS#\ DNAampli_cation _ngerprinting "DAF#\ ampli_ed fragment length poly!morphisms "AFLPs# and microsatellites "STMS# * currently availablefor genome mapping and for tagging di}erent traits in wheat[ Othermarkers\ including microsatellite!primed polymerase chain reaction"MP!PCR#\ expressed sequence tags "ESTs# and single nucleotide poly!morphisms "SNPs# are also discussed[ Recent information on syntenyin cereal genomes\ marker!assisted selection\ marker validation andtheir relevance to cereal breeding in general and wheat breeding inparticular are also examined[

Key words] Triticum aestivum * gene tagging * genome mapp!ing * marker!assisted selection * molecular markers *synteny

In recent years\ molecular markers have become available\ inboth animal and plant systems\ for basic and applied studies[One of the most extensive uses of these molecular markers hasbeen the development of detailed genetic and physical chro!mosome maps in a variety of organisms\ including\ among theanimal systems\ humans and\ among the plant systems\ breadwheat[ Another important application of molecular markers inplant systems involves improvement in the e.ciency of con!ventional plant breeding by carrying out indirect selectionthrough molecular markers linked to the traits of interest *both simple and quantitative trait loci "QTL# * because thesemarkers are not in~uenced by the environment and can bescored at all stages of plant growth[ In addition to these twomajor applications\ DNA markers can also be used in plantsystems for germplasm characterization\ genetic diagnostics\characterization of transformants\ study of genome organiza!tion\ phylogenetic analysis\ etc[ "Rafalski et al[ 0885#[ Althougheach marker system is associated with some advantages anddisadvantages\ the choice of marker system is dictated to a largeextent by the intended application\ convenience and the costinvolved[ These molecular markers can be broadly classi_ed inthe following three groups]

0[ Hybridization!based DNA markers such as restriction frag!ment length polymorphisms "RFLPs# and oligonucleotide_ngerprinting[

U[ S[ Copyright Clearance Center Code Statement] 9068Ð8430:88:0794Ð9258 , 03[99:9

1[ PCR!based DNA markers such as random ampli_ed poly!morphic DNAs "RAPDs#\ which can also be converted intosequence characterized ampli_ed regions "SCARs#\ simplesequence repeats "SSRs# or microsatellites\ sequence!taggedsites "STS#\ ampli_ed fragment length polymorphisms"AFLPs#\ inter!simple sequence repeat ampli_cation "ISA#\cleaved ampli_ed polymorphic sequences "CAPS# andamplicon length polymorphisms "ALPs#[

2[ DNA chip and sequencing!based DNA markers such assingle nucleotide polymorphisms "SNPs#[

In addition to the above three groups of markers\ microsatellite!primed polymerase chain reaction "MP!PCR#\ arbitrarilyprimed PCR "AP!PCR#\ allele!speci_c PCR "AS!PCR# andDNA ampli_cation _ngerprinting "DAF# have also proved use!ful in the detection of polymorphism "for a review\ see Mohanet al[ 0886#[

Using molecular markers in plant systems\ extensive geneticmaps were initially prepared in tomato and maize[Subsequently\ these maps were prepared in a variety of otherplant systems\ including several cereal crops such as rice\ barleyand wheat[ Wheat is one of the major food crops of the world\supplying nearly 44) of the carbohydrates consumed world!wide and provides a model system for the study of polyploidcytogenetics because of the ease of chromosome manipulations[Cytogenetic studies have been facilitated in this crop by theavailability of extensive genetic:cytogenetic stocks along withthe useful Ph system[ It is a segmental allopolyploid containingthree distinct but genetically related "homoeologous# genomes\A\ B and D[ The haploid DNA content of bread wheat genomeis approximately 0[6 × 0909 bp "Arumuganathan and Earle0880# with an average of 709 Mb per chromosome "09mm#[ Theaverage wheat chromosome is 14!fold longer than the averagerice chromosome "Moore et al[ 0884b#[ Thus\ three wheat chro!mosomes are equal to the haploid maize genome and one!halfof an average wheat chromosome equals a haploid rice genome"Gill and Gill 0883#[ Such a large bread wheat genome hasresulted from polyploidy and extensive duplications\ such thatover 79) of the genome consists of repetitive DNA sequences[Using the cytogenetic ladder mapping "CLM# strategy\ it hasbeen shown that a majority of wheat genes are present as clus!ters and that small chromosome regions encompassing thesegene clusters are highly recombinogenic[ These chromosomeregions are suitable for molecular manipulations comparable

269 GUPTA\ VARSHNEY\ SHARMA and RAMESH

to those possible in other crops with small genomes such as riceand sorghum "Gill and Gill 0883\ Gill et al[ 0885#[

In contrast to the suitability of bread wheat for cytogeneticstudies\ as above\ there have been problems in the preparationof molecular maps and in the development of molecular mar!kers for marker!aided selection in this crop[ The main problemhas been the failure of a variety of molecular markers to detectadequate and useful polymorphism[ However\ despite theseproblems\ success has been achieved in recent years and molec!ular maps have become available for chromosomes of allhomoeologous groups in bread wheat[ Many of the molecularmarkers in wheat represent homoeoloci\ i[e[ the same markerbeing available on all the three chromosomes of a homoe!ologous group or on homoeologous segments available on non!homoeologous chromosomes[ Such homoeoloci facilitated thepreparation of synteny maps\ showing extensive translocationsthat are known to have occurred in cereal chromosomes duringthe evolution of these chromosomes[ There are other molecularmarkers which are more genome! and chromosome!speci_c\ sothat these may be present on one chromosome and absent onone or both of the other homoeologues[ In bread wheat\ aswith several other crops\ these molecular markers will be usedextensively for molecular marker!assisted selection\ geneisolation\ genetic evolutionary studies\ diagnostics\ germplasmcharacterization and varietal identi_cation\ etc[ In this review\we discuss the development and use of these di}erent types ofmolecular marker and examine the present status and futurepotential of these molecular markers in wheat breeding[

Hybridization!based molecular markers

RFLPs

Among the various molecular markers developed to date\RFLPs were developed _rst and were initially used for humangenome mapping "Botstein et al[ 0879#[ Later\ these markerswere adopted for mapping plant genomes "Helentjaris et al[0875\ Weber and Helentjaris 0878# including those of breadwheat Triticum aestivum "see Table 0# "Chao et al[ 0878\ Liu andTsunewaki 0880\ Anderson et al[ 0881\ Devos et al[ 0881\ Devosand Gale 0882a\b\ Xie et al[ 0882\ Nelson et al[ 0884a\b\c\ Mar!ino et al[ 0885# and Aegilops tauschii "syn[ Triticum tauschii\ Dgenome# "Lagudah et al[ 0880\ Gill\ K[S[ et al[ 0880\ Gill\ B[S[0882#[ The diversity available in Ae[ tauschii had to be used forthe preparation of RFLP maps for the D genome of this crop\because a low level of polymorphism was initially detected inthe D genome of bread wheat compared with its other twogenomes[

RFLP analysis\ however\ has some limitations\ since it istime!consuming and labour!intensive[ Further\ because of thelow frequency of RFLPs in wheat\ this approach has beenrelatively less useful in this crop[ This low frequency is some!times attributed to the polyploid nature\ high proportion ofrepetitive DNA\ large genome size and recent origin of wheat[Despite these di.culties\ su.cient interest in the past hasresulted in the application of RFLP technology for a variety ofpurposes in wheat\ including genome mapping\ varietal identi!_cation\ characterization of wheatÐrye recombinants andidenti_cation of homoeologous chromosome arms "Helentjariset al[ 0874\ Beckmann and Soller 0875\ Tanksley et al[ 0878#"see later for details#[ RFLP probes were also developed\ whichgave an {on!o}| type of polymorphism on dot blots\ thus cir!cumventing the need of resource!consuming Southern analysis[This is exempli_ed by a 2BL!speci_c probe developed by Har!court and Gale "0880#[

RFLP maps in bread wheat have generally been prepared inthe past using low!copy number clones as probes "Liu et al[0889#\ although there are also reports of the use of repetitiveDNA for RFLP work in this crop "Somers et al[ 0885#[ Whilepreparing RFLP maps\ each RFLP probe often allowed sim!ultaneous detection of at least three independent loci with singleSouthern hybridization[ However\ in a study on genomemapping\ only a small fraction of RFLP probes generallydetected polymorphism[ For example\ in a study using 80 single!or low!copy clones as probes\ only about 19) of the probesand only 02) of the probe!enzyme combinations revealed poly!morphism "Liu and Tsunewaki 0880#[ Despite this limitation\ a0799!cM genetic map covering 086 RFLP loci was preparedusing 55 F1 individuals derived from T[ aestivum cv[ {ChineseSpring| ×Triticum spelta var[ duhamelianum[ By nulli!tetra!somic analysis\ these loci were also assigned to individual chro!mosomes[ A genetic "RFLP# map of wheat was later alsoconstructed by Devos and Gale "0882a#^ this map had a numberof interesting features[ Certain markers\ when used as probes\detected sequences present in the same linear genetic order onall three homoeologous chromosomes\ revealing RFLP loci tobe essentially colinear within a homoeologous group of chro!mosomes[ The molecular genetic maps of bread wheat alsoshow a clustering of markers derived from the proximal:centromere regions[ For example\ in a study of 06 recombin!ants between chromosome 0D of wheat and 0R of rye with59 random RFLP and three PCR markers\ clustering of theRFLP markers near the centromere was observed\ even thoughthis could imply that the recombination between wheat andrye chromosomes is restricted to regions near the centromeres"Rogowsky et al[ 0882#[ Studies on molecular genetic and physi!cal mapping involving individual homoeologous groups arelisted in Table 0 and those involving the entire wheat genomeare listed in Table 1[

E}orts have also been made to develop RFLP markers formarker!aided selection in bread wheat involving simple traits aswell as QTL "Table 3#[ Unfortunately\ among adapted varietiesthat are used in commercial breeding programmes\ the level ofpolymorphism revealed by RFLP is very low and\ therefore\ inany particular cross\ breeders can exploit only a small pro!portion of the available markers[ The technique itself is alsostill too expensive and too slow for the rapid evaluation of thelarge number of progenies commonly used in a commercialbreeding programme "Gale et al[ 0884#[ In contrast to this dis!couraging situation in crosses involving adapted varieties ofbread wheat\ when the germplasm from wild relatives of wheatwas used for its improvement\ the RFLP technology has beenfound to be relatively more useful for the selection of chro!mosomal regions carrying useful genes derived from these wildrelatives "Koebner et al[ 0877\ Jia et al[ 0883#[ The work involv!ing these wild relatives usually involves the analysis of a rela!tively small number of plants in a research laboratory\ thusmaking the RFLP technique appropriate and very e}ectiveunder these speci_c situations "use of wild germplasm#[ The useof heterologous RFLP probes across species boundaries alsopermits analysis of genome synteny "see later for details#[Despite these few advantages and the utility of RFLPs seen inthe past under speci_c circumstances\ thanks to the superiorityof other molecular markers used later\ currently RFLPs areseldom if ever used for developing molecular markers formarker!aided selection in bread wheat "see later for moredetails#[

RFLPs have also been used for variety identi_cation[ For

260Molecular markers and their applications in wheat breeding

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Table 1] Molecular genetic maps of wheat "Triticum spp[# at the level of the whole genome

Marker Number ofS[ No[ Genome type mapped loci Mapping population Reference

0 D!genome RFLP 016 T[ tauschii "TA0580 × TA0693# Gill\ K[S[ et al[ "0880#

1 Einkorn wheat RFLP 52 T[ monococcum × Kojima et al[ "0887#RAPD 8 T[ boeoticum ssp[ boeoticumISSR 8

2 Durum wheat RFLP 133 T[ turìdum Blanco et al[ "0887#PCR 0 "Messapia × MG3232#

3 RecombinatSubstitution Line5A RSL RFLP 06 T[ turìdum var[ dicoccoides Chen et al[ "0883#

RFLP 46 disomic chromosome 5A:5B Du and Hart "0887#5B RSL RFLP 07 substitution line × T[ turìdum Chen et al[ "0883#

RFLP 39 L[ var[ durum cv[ {Langdon| Du and Hart "0887#

4 Bread wheat RFLP 086 T[ aestivum cv[ {Chinese Liu and Tsunewaki "0880#Spring| × T[ spelta vardutamelianum

5 Bread wheat RFLP 153 DH population Cadalen et al[ "0886#SSR 1 "{Chinese Spring| × {Courtot|#

6 Bread wheat SSR 168 W6873 × {Opata74| Ro�der et al[ "0887b#SSR 42 {Chinese Spring| × {Synthetic| Stephenson et al[ "0887#

7 Bread wheat SSR 31 DH population Penner et al[ "0887#AFLP 519 "{Garnet| × {Saunders|#

Table 2] RAPD polymorphism in wheat

Total primers PRP0 Positive primers1 Reference

39 15 0 "OPA06# Joshi and Nguyen "0882#159 2 1 "OPE19\ OPF01# Eastwood et al[ "0883#349 1 1 "OPA98\ OPA06# Dweikat et al[ "0883#284 19 2 "OPA!96\ OPJ!02\ OPR!04# Schachermayr et al[ "0883#185 None * Autrique et al[ "0884#289 22 1 "UBC079\ OPC19# Penner et al[ "0884#259 00 0 "OPJ!8# Schachermayr et al[ "0884#014 0 "OPH4# Dedryver et al[ "0885#854 69 7 "OPB7\ OPD05\ OPF4\ OPF4\ OPF03\ OPH06\ OPJ09\ OPM8# Demeke et al[ "0885#079 7 * Qi et al[ "0885#099 07 0 "J04# Talbert et al[ "0885#29 1[2) * Procunier et al[ "0886#239 39 0 "OPB02# Sun et al[ "0886#399 29Ð39) 2 "OPG94\ OPI05\ OPR92# William et al[ "0886#239 7 1 "UBC410\ RC26# Cao et al[ "0887#059 31 Ð Gupta V[ et al[ "0887#0099 01 0 "UBC757# Lintott et al[ "0887#299 3 "OPB09\ OPM8\ OPN0\ OP900# Myburg et al[ "0887#79 3 0 "OPJ90# Naik et al[ "0887#327 16 Peil et al[ "0887#79 14 * Rao et al[ "0887#

0 Primers giving reproducible polymorphism[1 showed linkage with any trait "the relevant traits are listed in Table 3#[

example\ RFLP analysis has been conducted in considerabledetail for mapping di}erent storage protein loci "for details seeGupta\ P[K[ et al[ 0887#\ so that the polymorphic RFLP probesspeci_c for HMW!glutenins "e[g[ K8# and g!gliadins "K21#could be used for the identi_cation of 43 common wheat culti!vars\ mostly Italian types "Vaccino et al[ 0882#[

Oligonucleotide _ngerprinting

Oligonucleotide _ngerprinting involves the use of synthetic oli!gonucleotide probes complementary to microsatellites or simple

sequence repeats "SSRs# for in!gel or Southern hybridizationwith genomic DNA digested with individual restriction enzymesand electrophoresed on agarose gel[ The technique of in!gelhybridization o}ers several advantages over Southern blottingand has been increasingly used to reveal hypervariable targetregions in a variety of plant materials "see Weising et al[ 0884\Gupta and Varshney\ unpublished data#[ The quality\ intensityand number of fragments that hybridize with synthetic oli!gonucleotides vary considerably from probe to probe and fromspecies to species[ Since SSRs "microsatellites# are abundant


Table 3] Tagging and molecular mapping of some major genes and QTL in wheat using molecular markers

MappingMarker population:

S[ Gene: type Designation and Linkage: MolecularNo[ Trait QTL "number# chromosomal location contribution mapping Reference

0 Grain protein QTL STMS "0# Xwmc30 "1DL# 07[6) 099 RILs "F7# Prasad et al[ "0888a#content RFLP "05# Gail0 "3BS# 16[6)J

Xpsr511 "3BS# 19[1)G

Xmgb232 "3BS# 09[8)G

Xpsb26 "3BS# 00[7)G

Xpsr801 "4AL# 5[8)G

Xpsr800 "4AL# 6[2)G

Xpsr056 "5AS# 02[0)G

XksuG7 "5AS# 02[5)f 54 RILs "F6# Blanco et al[ "0885#Xpsr516 "5AL# 8[1)F

Xmgb45 "5AL# 5[7)G

Gli!B1 "5BS# 6[8)G

Xpsr389 "6BS# 8[3)G

Pc "6BS# 8[2)G

Xpsr092 "6BL# 7[0)G

Xpsr041 "6BL# 8[7)G

Xpsr292 "6BL# 5[7)j

1 Preharvest QTL RFLP "09# Xcnl[bcd0323 "0AS# 09[1)J

sprouting tolerance Xcnl[cdo320 "0AS# 7[5)G

Xcnl[cdo684 "<# 6[0)f 67 RILs "F4# Anderson et al[ "0882#Xcnl[cdo53 "1S# 7[2)F

Xcnl[wg885a "1L# 4[8)G

Xcnl[bcd019a "1L# 7[7)j

Xcnl[bcd349 "4DL# 7[0)J

Xcnl[bcd0315 "5BL# 09[6)f 027 RILs "F4#Xcnl[cdo434 "3AL# 7[1)F

Xcnl[cdo371 "2BL# 6[9)j

Major gene STMS "0# Xwmc093 "5BS# * _ 099 RILs "F4# Roy et al[ "0888#STS "0# Xmst090 "6DL# * ~

2 Vernalization Vrn0 RFLP "0# Xpsar315 "4A# * Galiba et al[ "0884#response RFLP "0# Xrz284 "4AL# 79 cM from Molecular mapping Nelson et al[ "0884a#

centromereRFLP "0# Xwg33 "4AL# 6[4 cM_ 003 F1 lines Korzun et al[ "0886b#STMS "0# Xgwm075 "4AL# 12[5 cM~

Vrn!Am0 RFLP "1# Xwg897 "4AmL# _ Flanking Molecular mapping Dubcovsky et al[Xabg691 "4AmL#~ markers "0887#

Vrn!Am1 RFLP "1# Xwg088 "4AmL# 014 cM from Molecular mapping DubcovskyJ

centromere et al[ "0887#h

Xbcd391 "4AmL# * j

Vrn!D0 STMS "1# Xgwm101 "4D# 2[2 cM_ * Snape et al[ "0887#Xgwm181 "4D# 3[0 cM~

3 Cadmium uptake Cdu0 RAPD "1# OPC!19 3[5 cM_ 69 RILs "F7# Penner et al[ "0884#UBC!079 10[1 cM~

4 Aluminium Alt1 RFLP "2# Xpsr803 3[9 cMJ Disomic substi! Luo and Dvoraktolerance Xpsr0940 * h tution lines "0885#

Xmwg1079 * j

AltBH RFLP "1# Xbcd0129 "3DL# 0[0 cM_ 090 RILs "F4# Riede and AndersonXcdo0284 "3DL# 00[2 cM~ "0885#

5 Kernel hardness ha RFLP "0# Xfbb127 "4DS# 22) * Nelson et al[ "0884a#RFLP "4# Xmta8 "4DS# 52[1)J

XksuF00 "1AL# 4[6)G

Xbcd019 "1DL# 3[9)h 003 RILs "F6# Sourdille et al[ "0885#XksuA0 "4BL# 4[2)G

XksuG37 "5DS# 3[7)j

6 Bread!making quality Glu!D0 PCR "1# Allele speci_c PCR * * D|Ovidio and"0Dx4# Anderson "0883#

7 Dwar_ng genes Rht01 STMS "2# Xgwm180 "4AL# 4[3 cMJ

Xgwm309 "4AL# 00[9 cMh 003 F1 lines Korzun et al[ "0886b#Xgwm068 "4AL# * j

RFLP "3# Xpsr0190 "4AL# 04[0 cMJ

Xwg003 "4AL# * f 003 F1 lines Korzun et al[ "0886b#Xpsr053 "4AL# * F

Xmwg505 "4AL# * j

Table continued


Table 3] Continued

Marker Mapping population:Gene: type Designation and Linkage: Molecular

S[ No[ Trait QTL "number# chromosomal location contribution mapping Reference

Rht7 STMS "0# WMS150 "1DS# Tight linkage 30 single Korzun et al[ "0887#9[5 cM chromosome

substitution linesRht!B0 RFLP "0# Xpsr033!3B "3BS# 02[1 cM 005 F1 lines Sourdille et al[ "0887#

RFLP "0# Xfba0!3B "3BS# 4) 164 DH lines Cadalen et al[ "0887#Rht!D0 RFLP "0# Xglk467!3D "3DS# 1[7 cM 004 F1 lines Sourdille et al[ "0887#

RFLP "0# Xfba100!3D "3BS# 19) 164 DH lines Cadalen et al[ "0887#

8 ABA production RFLP "2# Xpsr315 "4A#_ Flanking J 10 chromosomeand response Xpsr464 "4A#~ markers h substitution lines Quarrie et al[ "0883#

Xpsr315 7[9 cM and DH linesj

RFLP "0# Xbs017 "1A\ 1B\ 1D# 09 cM from Molecular mapping Nelson et al[ "0884b#centromere

09 Fertility restoration Rf3 RFLP "0# Xksu37 "5BS# 02[0)J

Rf2 RFLP "1# Xbcd138 "0BS# 15[8)f BC0F0 lines MaandSorrells "0884#Xcdo331 "0BS# 08[2)F

4DRf RFLP "0# Xcdo675 "4D# 7[7)j

00 Red grain colour R2 RFLP "0# Xabc063 "2BL# ×14)_ Molecular mapping Nelson et al[ "0884a#R0 RFLP "0# XksuH04 "2DL# ×14)~

01 Flour colour RFLP "1# + "Group 5# 24) 049 F3 lines Parker et al[ "0886#AFLP "6#

02 Amylose content Wx!B0 RFLP "1# Xbcd0627: 5[1 cM_ 87 single Araki et al[ "0888#Xcdo0276 "3A# * ~ chromosome

substitution lines

03 Coleoptile Rc0 RFLP "1# Xcdo06 "6AS# 33)_ Molecular mapping Nelson et al[ "0884a#pigmentation Xbcd237 "1AS# 8)~

04 Milling yield RFLP "3# * 09)_ 049 F3 lines Parker et al[ "0886#STMS "0# * 6)~

05 Eyespot Pch1 RFLP "0# Xpsr010 "6D# 2[7 cM Chromosome de la Pena et al[ "0885#recombinationsubstitution lines

RFLP "1# Xcdo236 "6AL# 00[9 cM "distal#J 091 chromosome de la Pena et al[ "0886#Xwg279 "6AL# 07[7 cM recombinationh

"proximal# substitution linesj

06 Tan spot RFLP "6# Xgli0 "0AS#\ 1DL# 24) J

Xfba100 "3AL# 09[6)G

Xfbb0 "3AS# 02[6)G

Xpsr892 "2BL# 7[5)f 024 RILs Faris et al[ "0886#Xcdo235 "0BL# 6[5)F

Xbcd019 "1DL# * G

Xgli0[Xbcd019 00[4)G

"0AS:1DL# j

07 Tolerance to salt Kna0 protein poly! "0[1 cM on * True breeding Gao et al[ "0887#stress morphism 3D:3B map# * 3B:3D recombinant

lines

08 Na¦:K¦ RFLP "0# "3D# * * Allen et al[ "0884#discrimination

19 Powdery mildew Pm RFLP "0# Xwg405 "1B# 38[3 cM apart Recombinant Rong et al[ "0887#resistance from Xcdo345 substitution lines

and 19[9 cM "RSLs#distal to Xrez333

Pm0 RFLP "0# Xcdo236!6A "6AL# * 64 F1 lines Ma et al[ "0883#RFLP "0# WHS067 2[9 cM NILs Jahoor "0887#

Pm1 RFLP "0# Xbcd0760!4D 2[4 cM * Ma etal[ "0883#RFLP "0# WHS184 "4D# 2[5 cM * Hartl et al[ "0884#RFLP "0# WHS249 "4D# 2[7 cM * Mohler and Jahoor

"0885#RFLP "0# Xfba282 "4DS# Molecular mapping Nelson et al[ "0884a#

Pm2b RFLP "0# Xbcd0323!0A "0AS# 0[2 cMJ

Pm3a RFLP "1# Xbcd0120!1A "1AL# 0[4 cMh Ma et al[ "0883#Xcdo567!1A "1AL# 0[5 cMj

RFLP "1# Xbcd0120 "1BL#_ ×29 cM apart Moleular mapping Nelson et al[ "0884b#Xcdo567 "1BL# ~ on 1BL

Table Continued


Table 3] Continued



Pm3b AFLP "5# S05M01:204JS05M04:048GS04M12:199f Coverage DH lines Hartl et al[ "0887#S10M12:212F ³02 cMS08M12:212GS06M19:022j

Pm3a + STS "0# Xbac0120 Tight linkage 54 F1 lines Liu\ D[J[ et al[ "0887#Pm3b

Pm5 RFLP "2# Xbcd024 0[420[3 cM J

Xbcd296 3[621[4 cM hNILs Liu\ D[J[ et al[ "0887#Xbcd155 3[421[3 cM j

Pm01 RFLP "00# Xpsr09\ Xpsr095\ Nor1 J

Xpsr030\ Xpsr002 "all on G

5DS#^ Xpsr031\ Xpsr038\ Tight linkage 019 F1 lines Jia et al[ "0885#h

Xpsr1\ Xpsr594\ Xpsr043\GXpsr435 "all on 5DL# j

Pm10 RAPD "0# * * Qi et al[ "0885#

10 Adult plant APR STMS "1# Xwms293 06[8)J

resistance to Xwms183 01[2)f 079 F2 lines Liu\ S[ et al[ "0887#powdery mildew RFLP "1# Xwg885 8[1)F

Xksu D11 6[6)j

11 Cereal cyst Cre0 RFLP "1# Xglk594 "1BL# 6[2 cM J Williams et al[ "0883#nematode resistance Xglk477 "1BL# 7[3 cM h

"total 42)# j

RFLP "0# CD1[1 Tight linkage Ogbonnaya et al["0887#

Ccn!D0 RAPD "0# OPE19 "1DS#_ Tight linkage F1 lines Eastwood et al[ "0883#RFLP "0# cSE19!1 "1DS#~

12 Wheat streak mosaic Wsm0 STS "0# Wg121 "3L# Tight linkage _ 80 NILs "F2ÐF3# Talbert et al[ "0885#virus resistance RAPD "0# J04 * ~

13 Hessian ~y H2 RAPD "0# 2Ð0 J

resistance H4 RAPD "1# 4Ð0\ 4Ð1 G

H5 RAPD "2# 5Ð0\ 5Ð1\ 5Ð2 G

H8 RAPD "1# 8Ð0\ 8Ð1 G

H09 RAPD "1# 09Ð0\ 09Ð1 G

H00 RAPD "1# 00Ð0\ 00Ð1 h * NILs Dweikat et al[ "0886#H01 RAPD "1# 01Ð0\ 01Ð1 G

H02 RAPD "0# 02Ð0 G

H03 RAPD "0# 03Ð0 G

H05 RAPD "0# 05Ð0 G

H06 RAPD "0# 06Ð0 j

H8 RAPD "0# OPA98:OPA06 Tight linkage NILs Dweikat et al[ "0883#H10 RAPD "0# OPE02 "1RL# Seo et al[ "0886#H12 RFLP "1# XksuH3 "5D# 5[8 cM_ F1 lines Ma etal[ "0882#

XksuG37a "5D# 04[5 cM~

H13 RFLP "2# XcnlBCD340 "2DL# 4[8 cMJ F1 lines Ma et al[ "0882#XcnlCDO371 "2DL# 4[8 cMh

XksuG37b "2DL# 01[8 cMj

14 Common bunt Bt!09 RAPD "0# UBC!085 5[1 cM F1 lines Demeke et al[ "0885#resistance Bt!00 RAPD "0# UBC!757 * F3ÐF4 Lintott et al[ "0887#

15 Karnal bunt KB RFLP "5# XATPase!Xcdo0053 06Ð13) J

resistance "2BS# f 003 RILs Nelson et al[ "0887#Xmwg1001!Xcdo "4AL# 01Ð05) F

Xabg280!Xfba240 "4AL# 01Ð054 j

16 Durable stem rust Sr1 RFLP "0# Xbcd0760 "4B# 2[4 cM Molecular mapping Nelson et al[ "0884a#resistance STS "0# XksuG42!2B "2B# Cosegregate 59 advanced breeding Bariana et al[ "0887#

linesRFLP "1# XksuG42 "2BS# 2[8 cM_ 030 RILs "F8# Johnston et al[ "0887#

Xglk572 "5DS# 1[6 cM~

Sr11 RFLP "1# Xpsr097 "6AS# * _ NILs and BC4F1 lines Paull et al[ "0883#Xpsr018 "6AL# * ~

17 Leaf rust resistance Lr0 RFLP "2# PSR479 "4DL# 02[7 cM J

PSR456 "4DL# Tight linkage h 078 F1 lines Feuillet et al[ "0884#pTAG510 "4DL# Tight linkage j

"converted to STS also#Lr2 RFLP "0# Xmwg687 "5BL# Cosegregate 50 F1 lines Sacco et al[ "0887#

Table Continued


Table 3] Tagging and molecular mapping of some major genes and QTL in wheat using molecular markers



Lr8 RFLP "0# XksuD16 "5BL# * * Autrique et al[ "0884#RFLP "1# cMWG573 Tight linkage J

PSR435 7[921[3 cM NILs Schachermayr et al[G

RAPD "2# J02 Tight linkage h "0883#OPR!04849 Tight linkage G

OPR!60499 Tight linkage j

Lr09 STS "0# "0AS# * * Schachermayr et al["0886#

Kinase gene wpk45 "0AS# 017 F1 lines Feuillet et al[ "0886#RFLP "0# Xcdo315 "0AS# Molecular mapping Nelson et al[ "0886#

Lr02 RFLP "3# Xbcd0698 "1B# ³6[8 cMJ

Xcdo277 "1B# * G

XpTAG54 "1B# * G

Xpsr801 "1B# 8[0 cMh F1 Seyfarth et al[ "0887#STMS "2# Xgwm019 "1B# * G

Xgwm208 "1B# * G

Xgwm277 "1B# * j

Lr07 N!band "0# Speci_c terminal band Yamamori "0883#"4BL#

Lr08 RFLP "7# XksuG28 "6DL# *J

Xcdo42 "6DL# *G

Xwg575 "6DL# *G

Xwg355 "6DL# *f NILs Autrique et al[ "0884#Xbcd827 "6DL# *F

Xcdo236 "6DL# *G

Xwg279 "6DL# *G

Xcdo664 "6DL# *j

Lr12 RFLP "1# Xtam61"1BS# * Nelson et al[ "0886#Xbs017 "1BS# *

Lr13 RFLP "7# Xcdo371 "2DL# *J Autrique et al[ "0884#Xbcd020 "2DL# *G

XksuE03 "2DL# *G

XksuG51 "2DL# *G

Xbg020 "2DL# *h NILsXbcd036 "2DL# *G

Xbcd261 "2DL# *G

Xwg009 "2DL# *j

RAPD "0# OP!H4 *_ 027 F1 lines Dedryver et al[ "0885#SCAR "0# SC!H4699 *~

RAPD "0# OP!J8 "developed into STS Schachermayr et al[also# * * "0884#

Lr16 RFLP "1# XksuG42 "2BS# *_ * Nelson et al[ "0886#Xcdo359 "2BS# *~

Lr17 RAPD "0# OPJ!90 converted to F2 lines Naik et al[ "0887#STS "SCAR#

Lr18 RAPD "0# "6DS# * * Procunier et al[ "0884#Lr20 RFLP "1# XksuG09 "3BL# * *_ Nelson et al[ "0886#

Xcdo19 "3BL# * *~

Lr21 RFLP "1# Xbcd0167 "2DS# 2[521[5 cM_ Autrique et al[ "0884#Xcdo284 "2DS# 5[822[5 cM~

Lr23 RFLP "0# Xwg723 "6DS# 11)\ 29 cM Molecular mapping Nelson et al[ "0884a#distal to Rc2

RFLP "0# Xbcd0327 "6DS# * Molecular mapping Nelson et al[ "0886#RAPD OPG!94 07Ð18)J

"RFLP# "2# "XcmtgO4!499# "6BL# * G

OPI!05 11Ð23)f 66 RILs "F7# William etal[ "0886#"Xcmti05!0499# "6BL# * F

OPR!92 6Ð09)G

"Xcmtr92!499# "0DS# j

Lr24 PCR "0# PSR801 "1B# STS being F1 lines Seyfarth et al[ "0887#developed

18 Stripe rust resistance Yr04 RFLP "0# Nor0B "0B# 00 cM_ NILs Sun et al[ "0886#RAPD "0# OPB020319 16 cM~

STMS "0# WMS422 3[4 cM NILs Fahima et al[ "0886#YrH41 STMS "8# 9[91Ð9[24 cM F1 lines Peng et al[ "0888#_

RFLP "0# Nor0 "0B# 0[3 cM ~

29 Loose smut T09 RAPD "0# UBC!242 "1BL# 03 cMJ

resistance RFLP "1# Xcrc3[1 "1BL# 03 cMh RILs "F5# Procunier et al[ "0886#Xcrc042[1 "1BL# 09 cMj

Table Continued


Table 3] Continued



T08 Monoclonal Mab129 "5AS# * * Knox and Howesantibody "0883#

20 Septoria nodorum RAPD "1# UBC410 "2A# 04 cM_ RILs "F4# Cao et al[ "0887#blotch resistance RC26 "2A# 02 cM~

21 Septoria tritici blotch AFLP "0# em42[0 09 cM 095 RILs "F5# Goodwin et al[ "0887#resistance

22 Fusarium head blight FHB AFLP "0# XEagcMcta[0 "2BS# 05[1)J

resistance "scab RFLP "3# XksuH05 "1AL# 01[6)f 001 F1 lines Anderson et al[ "0887#resistance# Xbcd0220 "5BS# 6[2)F

Xcdo0276 "3AL# 6[3)j

Xcdo413 "5BS# 5[8) 32 F1 linesAFLP "8# *"EcoRI:MseI#

GCTG:CGAC0 42)J

ACT:TGC6 49)G

GTG:CAGT09 34)G

AGT:CAGT7 32)G14[8 cMAAC:CGAC2 39)h"total 022 RILs "F8# Bai et al[ "0887#CTCG:AGC0 41)Gcoverage#CTCG:CTC8 28)G

ACT:CAT2 20)G

AAG:AGC09 39)j

23 Russian wheat aphid Dn RAPD "3# OPB09779c 2[2 cMJ

resistance OPB80599r 2[2 cMf F1 plants Myburg et al[ "0887#OPN0779c 2[2 cMF

OPO00899c 3[3 cMj

SCAR "1# SCAR!N0399r

SCAR!B09779c

Dn1 RFLP "0# KsuA0 "6DL# 8[7 cM_ F1 plants Ma etal[ "0887#Dn3 RFLP "0# ABC045 "0DS# 00[5 cM~

24 Haploid formation QTL AFLP "1# "3B and 0 unassigned# 11) *_ Torp et al[ "0887#16) *~

25 Green plant QTL AFLP "4# "1A\ 1B\ 2A\ 4B and 8Ð21) DH lines Torp et al[ "0887#formation 0− unassigned#

and uniformly distributed in the genomes\ a large number ofhybridized fragments\ di}ering in size\ are generally obtained[Therefore\ they may be used as multilocus probes for the fol!lowing purposes] "0# identi_cation and characterization of var!ieties\ cultivars and breeding lines^ "1# introgression ofindividual genes by backcross breeding^ "2# linkage analysis"including gene tagging# and gene isolation^ and "3# estimationof genetic relatedness[ Consequently\ oligonucleotide _nger!printing has been carried out in a number of plant species for avariety of purposes "for references see Weising et al[ 0884\Gupta and Varshney\ unpublished data#[ Multilocus probeshave the advantage of revealing polymorphism at many locisimultaneously\ so that a small collection of di}erent probes isenough to cover a representative part of the genome[ However\a disadvantage is that linkage detected by repetitive multilocusprobes cannot be used directly for isolation of the gene tagged^this would require isolation of corresponding DNA fragmentfrom the gel\ its cloning\ and sequencing followed by designingthe PCR primers that can be used as single!locus probes "Zis!chler et al[ 0880#[ Further\ the technique of in!gel hybridizationdoes not allow detection of small segments representing uniquesequences carrying microsatellites[

In some cases\ oligonucleotide _ngerprinting gave only afew bands "Vosman et al[ 0881\ Arens et al[ 0884\ Schmidt and

Heslop!Harrison 0885#\ thus limiting its utility[ For example\in our own work involving in!gel hybridization in bread wheatusing 031 probeÐenzyme combinations using nine diverse geno!types\ very little polymorphism was detected^ only very fewfragments hybridized\ and they represented long stretches ofrepetitive DNA "Varshney et al[ 0887#[ Even the use of as manyas 12 SSR probes in combination with 03 restriction enzymesdid not produce multilocus _ngerprints\ shown earlier to becharacteristic of a majority of plant genomes[ More frequently\the hybridized fragments were more than 12 kb long\ whichrepresented repetitive DNA\ with infrequent restriction sites forthe enzymes used[ It has also been shown that sometimes\ morethan one type of SSRs are also available within the same restric!tion fragment[ Thus\ oligonucleotide _ngerprinting was notfound suitable in bread wheat for detection of DNA poly!morphisms for a variety of purposes\ although in other crops\it may prove useful for developing molecular markers and forgene introgression[

PCR!based molecular markers

RAPDs

The molecular markers based on PCR o}er the potential toreduce the time\ e}ort and expense required for molecular map!


ping[ In particular\ RAPDs involving the use of a single DNAprimer to direct ampli_cation of discrete random sequences"Williams et al[ 0889# have shown promise in many crops\including cereals "D|Ovidio et al[ 0889\ Weining and Langridge0880\ Devos and Gale 0881#[ RAPDs have been used for avariety of purposes including the construction of genetic linkagemaps "Reiter et al[ 0881#\ gene tagging\ identi_cation of cul!tivars "Nybom 0883#\ assessment of genetic variation in popu!lations "Chalmers et al[ 0881# and species "Nesbitt et al[ 0884#\study of phylogenetic relationships among species\ subspeciesand cultivars "Landry et al[ 0883#\ and for many other purposesin a large number of plant species including wheat[ These appli!cations have also led to the development of species!speci_c"Chen et al[ 0887#\ genome!speci_c and chromosome!speci_cmarkers "Wang et al[ 0884# and\ more importantly\ to the devel!opment of molecular markers for identi_cation and selectionof the desired genotypes "for a variety of traits of economicimportance# in segregating populations during breeding pro!grammes[

RAPD technology has proved useful for many crops\ asabove\ but in bread wheat\ similar to RFLPs\ it has been putto limited use\ partly owing to the low level of polymorphismdetected "as also observed for RFLPs# and sometimes alsopartly owing to lack of reproducibility of results[ For a poly!ploid crop such as bread wheat\ the level of polymorphism andits reproducibility could be enhanced by using template DNA\enriched for low!copy sequences "Eastwood et al[ 0883\ Williamet al[ 0886\ Naik et al[ 0887#[ Poor resolution of RAPD pro_leson agarose gels with only 0Ð2 major bands could also beimproved\ when RAPDs were coupled with various detectiontechniques[ These techniques included the following] "0# dena!turing gradient gel electrophoresis "DGGE#\ which could sig!ni_cantly improve the resolution of reproducible polymorphism"He et al[ 0881\ Dweikat et al[ 0883#^ and "1# temperature sweepgel electrophoresis "TSGE#\ which could resolve many more"two! to three!fold# arbitrarily primed fragments "Penner andBezte 0883#[ Using RAPDs followed by TSGE\ Penner et al["0884# later also identi_ed two RAPD markers linked to a generesponsible for cadmium uptake in durum wheat[ In this study\a total of 289 arbitrary primers were assayed on the genomicDNA extracted from two lines of durum wheat[ Joshi andNguyen "0882# also found RAPD technology satisfactory forits use in tetraploid wheats\ where 099) reproducibility wasobserved in the RAPD pro_les of wild emmer wheat[ RAPDmarkers along with inter!simple sequence repeat "ISSR# andRFLP markers were also used for mapping the einkorn wheatgenome\ where RAPD markers were found to be suitable formapping regions of the genome that were poor in RFLPs"Kojima et al[ 0887#[ In bread wheat\ however\ in several studiesconducted using RAPDs\ a very low level of polymorphism wasobserved[ Despite this\ in a recent study involving bread wheat\triticale and rye\ _ve South African cultivars and _ve Russiancultivars "as a source of aphid resistance# of bread wheat andone cultivar each of triticale and rye were _ngerprinted using18 RAPD primers[ This study resulted in the identi_cation ofcultivar!speci_c\ genome!speci_c and species!speci_c markersthrough RAPD analysis "Myburg et al[ 0886#[

RAPD markers have also been used to tag several traits inwheat "Table 3#[ In a wheat biotechnology network in India\ atthe NCL Pune centre\ some success has also been achieved intagging QTL for grain protein content and preharvest sproutingtolerance\ with the help of RAPD analysis "P[ K[ Ranjekarpers[ comm[#[ For e.cient use of the RAPD markers identi_ed

in breeding programmes there is a need to convert a RAPDmarker to a form that is suitable for PCR assay[ This strategy isespecially advantageous in reducing the unwanted backgroundsignals produced in RAPD gels by giving rise to a locus!speci_campli_cation product[ This generally involves identi_cation ofpolymorphic band"s# that were generated in RAPD assay\ clon!ing the fragment\ sequencing the clones and designing the PCRprimers[ The markers developed in such a way are SCARs\which may be dominant or codominant[ Polymorphism mayalso be detected by restriction digestions before or after ampli!_cation "CAPS#[ However\ in the literature the SCARs havesometimes been referred to as STS "Naik et al[ 0887#[ Accordingto Rafalski and Tingey "0882#\ a more suitable acronym forthese markers would be STARs "sequence!tagged ampli_edregions#[ Some RAPD markers linked with individual traits\have been converted into such markers\ making them moreuseful "Table 3#[

We have discussed some examples of the successful uses ofRAPDs in wheat genomics research[ However\ an extensive useof RAPD technology for the preparation of RAPD maps andfor the development of molecular markers for wheat!breedingprogrammes has not been possible owing to a variety of factors\including complexity of the large wheat genome\ low level ofpolymorphism revealed and lack of reproducibility[ Further!more\ a large number of primers have to be tested\ which addsto the cost and time considerably "Table 2#[ In view of this\ onemay tend to conclude that\ for marker!aided selection in wheat\as with RFLPs\ RAPD analysis is also not always suitable[ Ourown experience at Meerut "India# with RAPD markers to studythe polymorphism in wheat is no di}erent "unpubl[ data#[ Devosand Gale "0881# have evaluated the usefulness of these markersin wheat and concluded that the use of RAPDs to producegenetic markers is not worthwhile for several reasons[ First\the use of these markers across the laboratories may not bereproducible owing to inherent variation in PCR conditionsand di}erent models of thermal cyclers used[ Secondly\ if inRAPD analysis the chromosomal location of similar bands isnot con_rmed to be the same\ there will always be questionsregarding the presence of RAPD bands of similar molecularweight but di}ering in sequence[

DAF

Ampli_cation of random genomic DNA sequences can also beachieved by a single short "4Ð7 bases# oligonucleotide primer ofarbitrary sequence[ It produces a characteristic spectrum ofshort DNA products of varying complexity that are resolvedon polyacrylamide gel electrophoresis "PAGE# following silverstaining[ This strategy\ used by Caetano!Anolles et al[ "0880# todetect genetic di}erences between genotypes "particularly insoybean# was described as DNA ampli_cation _ngerprinting"DAF#[ It resembles RAPDs\ since it does not depend uponcloning or DNA sequence information[ It has been shown togenerate reliable _ngerprints from DNA of viral\ bacterial\fungal\ plant and animal origins\ in particular\ because manymore bands are resolved due to short primers[ Thus DAF tech!nology is useful for detecting polymorphism even betweenorganisms that are closely related\ such as NILs "near isogeniclines# or mutants "Caetano!Anolles et al[ 0884#[ DAF can alsobe coupled with restriction endonuclease digestion of templateDNA "Caetano!Anolles and Gressho} 0883#[ Further\ the lin!ear DAF primers can sometimes be replaced by structuredprimers containing mini!hairpin sequences at their 4?!terminus


"Caetano!Anolles and Gressho} 0883# to increase the resolvingpower for detection of polymorphism\ since a smaller coresequence "2!mer# of primer is involved in annealing\ which isprovided with greater thermostability by the hairpin loop dur!ing annealing[ When DAF was tried for the _rst time in ourlaboratory in wheat\ a handful of primers allowed detection ofa much higher level of polymorphism than was detected usingother PCR!based markers such as MP!PCR and RAPDs "Senet al[ 0886b#[ Out of 09 primers of each type\ nine linear primersand four mini!hairpin primers produced characteristic _nger!printing patterns revealing polymorphism among seven breadwheat genotypes[ Primers with relatively higher GC contentwere found to be unsuitable and\ contrary to earlier claims\neither the average number nor the proportion of polymorphicproducts suggested the superiority of mini!hairpin primers overthe linear primers "Sen et al[ 0886a#[

Unfortunately\ there are no reports of converting poly!morphic DAF bands into locus!speci_c SCARs and our owne}orts in bread wheat to develop SCARs from DAF pro_les\also met with failure "Gupta et al[ 0888a#[ However\ in pea\DAF markers close to symbiosis!ine}ective sym20 mutationhave recently been identi_ed "Men et al[ 0888#\ suggesting theutility of DAF markers for gene tagging[ It is apparent\ there!fore\ that if e}orts similar to those made with RAPDs andAFLPs are also made with DAF\ it may be possible to use DAFtechnology for gene tagging and marker!aided selection "seelater for AFLP#[

STSs

A sequence!tagged site "STS# is a short\ unique sequence thatidenti_es a speci_c locus and can be ampli_ed by PCR[ EachSTS is characterized by a pair of PCR primers\ that are designedby sequencing an RFLP probe representing a mapped low!copynumber sequence[ Talbert et al[ "0883# showed that PCR canbe used to detect polymorphism in wheat with primer sequencesderived from the a!amylase and g!gliadin genes[ Later\ the samegroup ampli_ed a set of 024 barley!speci_c markers using a setof 004 STS primer pairs developed from sequences of RFLPprobes "Blake et al[ 0885#[ This group has also designed chro!mosome!speci_c STS primer pairs from polymorphic AFLPfragments\ detected in wheat nulli!tetrasomic stocks and wheatÐbarley addition lines "Shan et al[ 0887#[ Hopefully\ these STSmarkers will help in tagging a variety of genes:QTL "includingthose derived from alien species such as barley\ rye\ etc[# forimproving the e.ciency of wheat breeding[ Recently in our ownlaboratory\ using these STS primers produced by Tom Blake"Montana State University\ USA#\ we identi_ed an STS markerthat showed strong association with preharvest sprouting tol!erance in wheat "Roy et al[ 0888#[ In another study in wheat\RFLP probe Xbcd0120\ linked with the Pm3a locus was con!verted into an STS marker "Liu\ S[ et al[ 0887#[ Conventionally\the term STS is used for the primers which are designed on thebasis of mapped low!copy RFLP loci[ The primers designed onthe basis of a RAPD\ have also sometimes been referred to asSTSs "Naik et al[ 0887#\ although they should be more appro!priately called SCARs or STARs[

AFLP

AFLP is based on selective PCR ampli_cation of restrictionfragments generated by speci_c restriction enzymes[ In thistechnique\ speci_c double!stranded DNA adapters are ligatedto the DNA restriction fragments "Vos et al[ 0884#\ so that the

sequences of adapters and the adjacent restriction sites serve asprimer!binding sites[ The primers are designed to contain thesequences that are complementary to those of adapters and therestriction sites\ along with one to three selective bases addedat their 2? ends[ The use of selective bases allows ampli_cationof only a subset of the restriction fragments\ which still generatea large number of bands facilitating the detection of poly!morphism[ A comparison of di}erent mapping techniques *RFLP\ RAPD and AFLP * for their relative e.ciency indetecting polymorphism demonstrated that AFLP is the moste.cient "Powell et al[ 0885\ Lin et al[ 0885\ Ma and Lapitan0887#[ Although the AFLP kit was initially optimized for plantsthat have small genomes "4 × 097 bp to 5 × 098 bp#\ it was lateralso used successfully in bread wheat\ despite its large genome"0[6 × 0909 bp# "Ma and Lapitan 0887#[ A single primer com!bination detected up to eight times more polymorphism than apolymorphic RFLP marker[ Thus\ AFLP detected up to 05times more loci\ assuming that in bread wheat\ as in other crops\most AFLP markers are dominant as against the codominantnature of RFLP markers "Mackill et al[ 0885\ Maughan et al[0885#[

AFLP analysis has been conducted in a number of cropplants\ including bread wheat "Barrett and Kidwell 0887\ Bar!rett et al[ 0887\ Goodwin et al[ 0887\ Koebner et al[ 0887\ Maand Lapitan 0887\ Bohn et al[ 0888\ Shan et al[ 0888#\ barley"Becker et al[ 0884\ Qi et al[ 0887\ Castigliani et al[ 0887#\ rice"Mackill et al[ 0885\ Maheswaran et al[ 0886\ Powell et al[ 0886\Virk et al[ 0887#\ Bermuda grass "Zhang et al[ 0888#\ tomato"Thomas et al[ 0884#\ potato "van Eck et al[ 0884#\ sugar beet"Hansen et al[ 0887# and soybean "Maughan et al[ 0885\ Powellet al[ 0885#[ Recently\ AFLP was also used to assess geneticdiversity among 43 spring:winter wheat cultivars adapted tothe US Paci_c North!West "Barrett and Kidwell 0887# andAFLP!based genetic diversity estimates "GDEAFLP# were alsocompared with pedigree!based diversity estimates "GDEPED#"Barrett et al[ 0887#[ A total of 000 and 007 polymorphic bandswere generated by using eight PstI:MseI "methylation sensitive#and eight EcoRI:MseI "methylation insensitive# primer pairs\respectively[ Further\ it was also shown that GDEAFLP maymore accurately re~ect the level of allelic variation among geno!types than GDEPED[ Although not many maps have yet beendeveloped using AFLP markers\ a wheat molecular map usinga total of 214 AFLP and wmc "see later# microsatellite markershas recently been constructed using a doubled!haploid popu!lation derived from the cross between two Canadian springwheat cultivars "{Garnet| × {Saunders|# "Penner et al[ 0887#[ Indurum wheat also\ 18 AFLP markers were incorporated in theexisting linkage map comprising 133 RFLP\ eight biochemicaland seven morphological markers "Lotti et al[ 0887#[

The AFLP approach is now therefore widely used fordeveloping polymorphic markers[ The high frequency of ident!i_able AFLPs coupled with high reproducibility makes thistechnology an attractive tool for detecting polymorphism andfor determining linkages by analysing individuals from a seg!regating population[ Many diagnostic molecular markers fordi}erent traits have also been identi_ed by using AFLPs inbread wheat "Goodwin et al[ 0887\ Hartl et al[ 0887^ seeTable 3#[The polymorphic bands from AFLP patterns may also be con!verted into RFLP probes or locus!speci_c PCR markers\although problems have been encountered while convertingthem into SCARs\ because of the presence of a mixture ofsequences of the same size in individual bands "R[ M[ D[ Koeb!ner pers[ comm[#[ Although in a recent study in wheat and


Table 4] Synteny among genomes of di}erent cereals:millets

Species References

Foxtail millet!rice Devos et al[ "0887#Maize\ wheat Devos et al[ "0883#Rice\ barley Saghai Maroof et al[ "0885#\ Kilian

et al[ "0884#\ Han et al[ "0887#Rice\ maize Ahn and Tanksley "0882#Rice\ barley\ wheat Dunford et al[ "0884#Rice\ maize\ wheat\ oat Van Deynze et al[ "0884a#Rice\ wheat Kurata et al[ "0883#Rice\ wheat\ maize Ahn et al[ "0880#\ Moore et al[

"0884c#Rice\ wheat\ maize\ foxtail! Moore et al[ "0884b#millet\ sugarcane\ sorghumSorghum\ maize Pereira et al[ "0883#\ Whitkus et al[

"0881#Sugarcane\ maize and sorghum Dufour et al[ "0885#Wheat\ barley\ rye Devos et al[ "0882#\ Devos and Gale

"0882a#Wheat\ rye Devos et al[ "0881#

barley 15 chromosome!speci_c AFLP fragments weresequenced to design sequence!speci_c PCR primers"SCARs:STSs#\ only six of them gave the expected chro!mosome!speci_c products\ thus con_rming that conversion ofAFLP markers into sequence!speci_c SCARs:STSs is not easy"Shan et al[ 0888#[

Microsatellites or SSRs

Microsatellites are simple sequence repeats "SSRs# of only afew base pairs "0Ð5#[ They are ubiquitous in eukaryotic genomesand their study has been greatly facilitated by recent advancesin PCR technology[ The high level of polymorphism\ relativeto RFLPs and RAPDs\ combined with a high interspersion ratemake them an abundant source of genetic markers[ The _rstreport of microsatellites in plants was made by Condit andHubbel "0880#\ suggesting their abundance in plant systems aswell "for details see Gupta et al[ 0885\ Gupta and Varshney\unpublished data#[ Later\ Akkaya et al[ "0881# reported lengthpolymorphisms of SSRs in soybean\ which opened a new sourceof PCR!based molecular markers for other plant genomes[Thereafter\ to exploit the potential of microsatellites in di}erentways\ several techniques\ described by di}erent acronyms\ havebeen used by di}erent workers "see Gupta and Varshney\unpublished data for a review#[

In wheat\ microsatellites have been studied only recently[Devos et al[ "0884# searched sequence databases and convertedtwo microsatellite sequences into PCR!based markers[ Thesemarkers were genome!speci_c and displayed a high level ofvariation[ The potential of microsatellite sequences as geneticmarkers in hexaploid wheat was also investigated by Ro�deret al[ "0884#\ who reported that in wheat\ "GA#n:"GT#n arefound every 169 kb "approximately# of DNA[ Similarly\ "AC#nmicrosatellites were found every 181 kb and "AG#n micro!satellites were found every 101 kb "Ma et al[ 0885#[ Further\the sequence data on 69 microsatellites revealed that wheatmicrosatellites representing dinucleotides are most frequent andare relatively long\ containing up to 39 repeats^ the trinucleotiderepeats were one!tenth as frequent as the dinucleotide repeatsand the tetranucleotide repeats were rare[ Plaschke et al[ "0884#have shown that the distribution of SSR loci over di}erent

chromosomes and chromosome arms in wheat was random andthe highest proportion of microsatellites occurred in B genome[

More recently\ detailed genetic map of 168 microsatellite loci"Ro�der et al[ 0887b# and another map of 42 microsatellite loci"Stephenson et al[ 0887# have been prepared in bread wheat[With international collaboration\ the Wheat MicrosatelliteConsortium "WMC# was ~oated by AGROGENE "France# andthe Institute of Arable Crops Research "IACR#!Long Ashton"UK#[ Under this consortium\ at the international level\approximately 499 markers have been developed as a result ofextensive e}orts in di}erent laboratories\ including our own atMeerut\ India[ We hope that another map using these wmcmicrosatellite loci will be available in the near future whichwould supplement and saturate the existing microsatellite maps[In these microsatellite maps of hexaploid wheat\ loci are fairlyevenly distributed along the linkage groups and no report onany signi_cant clustering of these markers is available[ Data onphysical mapping of microsatellites on group 1 chromosomesusing deletion stocks also con_rm that the microsatellites arenot physically clustered in speci_c regions of the wheat chro!mosomes "Ro�der et al[ 0887a#\ so that the microsatellite markersshould prove useful for complete coverage of the wheat genome[

The availability of extensive molecular maps of micro!satellites\ as above\ will open new avenues for tagging genes ofeconomic importance\ not only for marker!assisted selection\but also for cloning genes leading to the development of trans!genic plants for crop improvement[ In wheat\ microsatellitemarkers have been used to tag several genes or QTL\ includingthe genes Rht7 "Korzun et al[ 0887\ Worland et al[ 0887#\ Rht01and Vrn0 "Korzun et al[ 0886b#\ QGpc[ccsu[1D[0\ a QTL forgrain protein content "Prasad et al[ 0888a#\ and an anonymousgene for preharvest sprouting tolerance "Roy et al[ 0888#[ Theyhave also been used for detecting DNA polymorphism in yellowrust!resistant accessions of T[ dicoccoides "Fahima et al[ 0887#[More recently nine microsatellite markers were identi_ed to belinked to stripe!rust resistance gene YrH41 with recombinationfrequencies of 9[91Ð9[24 "Peng et al[ 0888#[ Other uses of wheatmicrosatellite markers include distinguishing intervarietal chro!mosome substitution lines "Korzun et al[ 0886a#\ conductinggenome analysis in tetraploid Elymus and studying geneticdiversity among di}erent varieties of bread wheat[ In diversitystudies\ microsatellites were shown to have a high poly!morphism information content "PIC# "Plaschke et al[ 0884\ Lel!ley and Stachel 0887\ Prasad et al[ 0888b#[

Microsatellite loci\ however\ di}er from RFLPs\ since homoe!ologous loci are not always available "Bryan et al[ 0886\ Ro�deret al[ 0887b\ Stephenson et al[ 0887#[ This restricts the appli!cation of microsatellite markers to intraspeci_c and intra!genomic analyses\ and does not allow their use for comparativeanalyses or for introgression studies involving wild speciesrelated to wheat[ Nevertheless\ the locus!speci_city and highlevel of polymorphism associated with microsatellites makethem the future markers of choice for practical wheat breeding[

MP!PCR and direct ampli_cation of minisatellite DNA by PCR

"DAMD!PCR#

Using PCR\ DNA polymorphism can be studied at loci withknown DNA repeat sequences at random sites\ representingboth microsatellites and minisatellites[ For PCR ampli_cationin this approach\ primers have been designed using di}erentstrategies[ In one such strategy\ synthetic oligonucleotides rep!resenting microsatellites have been used as single PCR primers


for the ampli_cation of ISSRs\ using genomic DNA samplesas the template[ This technique which is called microsatelliteprimed!PCR "MP!PCR# results in RAPD!like patterns afteragarose gel electrophoresis and ethidium bromide staining[PCR with an unanchored\ microsatellite complementary oli!gonucleotide as single primer was reported to produce PCR_ngerprints from genomic DNA of a wide variety of organisms\including animals\ fungi and plants "Meyer et al[ 0882\ Perringet al[ 0882\ Gupta et al[ 0883\ Sharma et al[ 0884\ Weising et al[0884#[ This MP!PCR strategy relies on the presence of twomicrosatellites having the same repeat unit in inverse orien!tation\ separated by an ampli_able distance "ISSR# within thegenome\ so that the inter!repeat sequences "ISSRs# are ampli!_ed[ The MP!PCR technique is also known to be more repro!ducible than RAPD analysis because of higher stringency[However\ the banding pattern observed after agarose gel elec!trophoresis is known to be in~uenced by all the PCRparameters\ especially the annealing temperature "Meyer et al[0882#[ Among wheats\ out of 099 ISSR primers tested in einkornwheat\ 22 gave clear polymorphic bands "Nagaoka and Ogihara0886#[ Forty!nine ISSR fragments produced from these 22 pri!mers were scored for segregation in an F1 population "Triticummonococcum × Triticum boeoticum# leading to mapping of nineISSR markers "Kojima et al[ 0887#[ In bread wheat\ however\no reports on MP!PCR are available and our own e}orts gavelittle positive results "Gupta et al[ 0888a#[

Like MP!PCR\ in another approach described as {directampli_cation of minisatellite DNA by PCR| "DAMD!PCR#\minisatellite core sequences "Je}rey|s minisatellite or M02# wereused as primers for PCR ampli_cation\ which detected poly!morphism and helped in the development of genome!speci_cprobes in bread wheat "Somers et al[ 0885#[ An annealing tem!perature of 44>C "higher than the melting temperature of mostprimers# and a higher quantity of primer "33 pmol# were usedto achieve a high level of reproducibility[ The same group laterused four minisatellite core sequences in DAMD!PCR to detectpolymorphisms in three hexaploid wheat cultivars and the cor!responding tetraploids extracted from them "Bebeli et al[ 0886#[Reproducible pro_les of the ampli_ed products revealedcharacteristic bands that were present only in hexaploid wheatbut not in their extracted tetraploids[ Some polymorphism wasalso recorded among the hexaploid cultivars[ Twenty!threeDAMD!PCR ampli_ed fragments were isolated and screenedas molecular probes on the genomic DNA of wild wheat species\hexaploid wheat and triticale cultivars[ These DAMD!PCRclones were found to reveal various degrees of polymorphismand generated individual speci_c DNA _ngerprinting patternswhich could be used for species di}erentiation and cultivaridenti_cation[ Thus\ DAMD!PCR can be used as a tool for theisolation of informative probes for DNA _ngerprinting in wheat"Bebeli et al[ 0886#[ If tried\ they should also prove useful formolecular mapping\ and for tagging of genes for economictraits[

Sequencing and DNA!chip based molecular markers

Expressed sequence tags "ESTs#

As discussed earlier\ the nonavailability of probes "or clones#among workers limits the utility of RFLPs[ Therefore\ theRFLP loci are now being regularly converted into STSs andexpressed sequence tags "ESTs#[ While STSs represent uniquesequences which may or may not be transcribed\ the ESTsrepresent only expressed genes[ An EST is simply a DNA

segment\ representing the sequence from a cDNA clone thatcorresponds to a mRNA molecule or a part of it[ It has beenshown that ESTs\ 049Ð399 bp long\ are useful in searching forsimilarity and for mapping by workers in di}erent laboratories[ESTs can also be matched with sequences available in nucle!otide sequence databases "GenBank# and protein sequence dat!abases "Protein Identi_cation Resource or PIR# and assignedto speci_c genes with the help of computer programs andsoftware[ In humans\ cDNA libraries derived from mRNA havebeen used for the generation of ESTs[ In plants also\ ESTshave been generated and mapped in a variety of species\ e[g[Arabidopsis thaliana "Hofte et al[ 0882\ Newman et al[ 0883\Cooke et al[ 0885# and Oryza sativa\ the cultivated rice "Sasakiet al[ 0883\ Liu et al[ 0884\ Yamamoto and Sasaki 0886#[ In arecent release "March 12\ 0887# of the EST database from theNational Centre for Biotechnology Information "NCBI#\ morethan 28 999 Arabidopsis ESTs are listed[ In another study\involving a report of a complete and contiguous sequence of a0[8 Mb long DNA segment from Arabidopsis chromosome 3\ itwas shown that approximately 45) of the genes expected inthis 0[8 Mb region of Arabidopsis genome matched with ESTs"Bevan et al[ 0887# suggesting that more than half the total set ofArabidopsis genes are likely to be represented in EST database"Bouchez and Hofte 0887#[ As in August 0885\ the NCBI Gen!Bank dbEST list revealed that the number of registered ESTswas far larger for human "349 163# than those for any otherorganism[ The second biggest submission was from the mouse"44 467# followed by Arabidopsis "17 996^ as shown above\ inMarch 0887\ this number was 28 999#\ the nematode Caenor!habditis "12 327# and rice "00 202#[ Among other plant species\0465 ESTs in maize and 0210 ESTs in oilseed rape have alsobeen registered in the database[ A large!scale cDNA analysisof rice has been undertaken with the aim of cataloguing all theexpressed genes of this cereal\ including tissue!speci_c\ devel!opmental\ stage!speci_c and stress!speci_c genes[ The numberof rice ESTs reported in 0886 by the Rice Genome ResearchProgramme "RGP#\ Japan was 29 999 "Sasaki 0886#^ of thesepartial sequences of at least 03 999 ESTs were available in 0886[

Several companies also possess large private EST databasesfor various crop plants "e[g[ maize and soybean#\ access towhich can be negotiated on a case!by!case basis[ EST databaseshave proven to be a tremendous resource for _nding genes andfor interspecies sequence comparisons[ They have also providedmarkers for genetic and physical mapping\ and clones forexpression analyses[ Functional genomics\ the study of the func!tions of all speci_c gene sequences and their expression in timeand space in an organism\ can also be facilitated by preparingcDNA microarrays on the basis of available EST data[ Thesemicroarrays can be used for hybridization leading to the prep!aration of expression pro_les of genes in major organs of theplants[ In one such study in Arabidopsis\ more than 0399 Ara!bidopsis EST cDNA clones were used for the preparation ofcDNA microarrays and novel expression pro_les were identi_edfor many sequences leading to the understanding of their poss!ible functions "Ruan et al[ 0887#[ Bearing in mind the import!ance of ESTs in genomics research\ a core proposal forgenerating ESTs for the wheat genome was made and approvedat 8th International Wheat Genetics Symposium held at Sas!katoon\ Canada on August 6\ 0887 "H[ S[ Balyan pers[ comm[#[In this meeting\ an International Triticeae EST Cooperative"ITEC# was ~oated at the international level[ Laboratories wereinvited to join ITEC\ with an obligation to submit 39 999 ESTsby the year 1999\ aiming towards a large EST database for this


polyploid crop[ Later\ the target number of 39 999 ESTs wasreduced to encourage small laboratories also to join ITEC tohasten progress[ To date\ approximately 1999 ESTs are knownin bread wheat from di}erent laboratories\ but in near future\we hope to have a large number of ESTs for cataloguing all theexpressed genes in this crop as well[

SNPs and DNA chip technology

RFLPs\ RAPDs and STMSs described earlier in this article\have been the markers of choice in the recent past\ but thesemarkers su}ered some drawbacks[ For example\ they need gel!based assays and are therefore time!consuming and expensive[Therefore\ recently SNPs\ as biallelic genetic markers\ havebeen extensively used as the marker of choice\ particularly forthe human genome[ Although\ SNPs also su}er from the dis!advantage of being biallelic\ unlike STMSs or SSLPs which arepolyallelic\ their abundance "more than 0 per 0999 bp# makesthem more attractive[ Genotyping individuals using SNPs needsonly a plus:minus assay\ permitting easier automation[ Fur!thermore\ the high density oligonucleotide arrays on DNAchips "Gupta et al[ 0888b#\ and the matrix!assisted laser desorp!tion:ionization!time of ~ight "MALDI!TOF# mass spec!trometry "Ross et al[ 0887# that recently became available\ allowgenotyping of these biallelic loci in large numbers in parallel[The approach used for this purpose relied on the capacity todistinguish a perfect match from a single base mismatch "formore details on DNA chips\ see Gupta et al[ 0888b#[

The use of SNPs\ in recent years\ o}ered great promise forrapid and highly automated genotyping\ which led to rapidadvancement in developing human genetic map[ In view of thesigni_cance that is being attached to SNPs\ the 0st InternationalMeeting on SNPs and Complex Genome Analysis was held inSweden "18 August to 0 September\ 0887#[ However\ the use ofSNPs in plant systems has yet to start\ but in the near futurethese markers will certainly be used extensively in many plantsystems\ including bread wheat[

Molecular maps and synteny

Bread wheat has always attracted the attention of cyto!geneticists\ since it is an important food crop and the availabilityof cytogenetic stocks and a well!studied Ph system allowedgenetic manipulation[ This resulted in an extensive genetic mapbased on morphological traits and molecular markers "McIn!tosh et al[ 0887#[ Several partial RFLP maps have also beenreported for wheat "Chao et al[ 0878\ Liu and Tsunewaki 0880\Devos et al[ 0882a\ Xie et al[ 0882\ van Deynze et al[ 0884a\b\c\Nelson et al[ 0884a\b\c# and local maps of small regions of thegenome have also resulted from gene tagging e}orts "Hartl et al[0882\ Ma et al[ 0882#[ The availability of a recent {grass genome|map detailing the gene and DNA sequence similarities betweengenomes of the many species of the Gramineae will enablegenetic studies in relatively small genomes\ such as rice\ to beapplied to the much larger wheat genome "Devos and Gale0886#[ This will allow identi_cation and tagging of genes foreconomic traits\ including those for tolerance to biotic andabiotic stresses\ protein content\ preharvest sprouting tolerance\grain hardness\ storage proteins\ etc[ Although synteny con!servation across genomes between potato and tomato "Bon!ierbale et al[ 0877# and between the three diploid genomes ofhexaploid wheat "Chao et al[ 0878# was reported about a decadeago\ wider comparisons between and within tribes were

reported only during the last 4 years[ The di}erent reports onsynteny among grass genomes are listed in Table 4[

The _rst consensus grass map aligning the genomes of sevendi}erent grass species was prepared by Moore et al[ "0884a#and has been extended by Gale and Devos "0887#[ This mapdescribes nine di}erent grass genomes "oat\ barley\ wheat\maize\ sorghum\ two genomes of sugarcane\ foxtail millet andrice# in terms of only 14 rice linkage blocks[ These data aremost likely to grow as more information becomes available[The consensus regions of maps can be used to construct mapsof other grass species rapidly by using a set of anchor probesand to predict from one crop species to another the locationsof key genes for adaptation[

There is also a need to continue the integration of the old{classical maps| with the newer {molecular maps|[ The recentexplosion of EST data in rice and maize and their localizationon genetic or physical maps combined with the rapidly expand!ing gene sequence databases will make a powerful gene!miningtool[ The time is rapidly approaching when the grasses\ includ!ing all the major cereals\ can be considered as a single entityand all the information available on gene structure\ gene action\metabolism\ physiology and phenotype accumulated over thepast century in the di}erent species can be pooled[ An immedi!ate practical implication is that breeders need no longer berestricted to their own species in their search for exploitablevariation[ Homoeogenes and all of their alleles in di}erent spec!ies will be available to the cereal breeder:genetic engineer of theearly 10st century "Gale and Devos 0887#[ This will be furtherfacilitated by the e}orts of genetic engineers\ who will utilizenative\ modi_ed and synthetic genes from all kinds of resourcesfor the production of transgenic crops[

Marker!assisted selection and marker validation

Molecular tags * a prerequisite for marker!assisted selection"MAS# * have been developed for many agronomic traits inseveral crop plants using di}erent kinds of molecular markers[The essential requirements for molecular marker!aided selec!tion in a plant breeding programme are] "0# marker"s# shouldcosegregate or be closely linked "0 cM or less# with the desiredtrait^ "1# an e.cient means of screening large populations forthe molecular markers should be available^ and "2# the screeningtechnique should have high reproducibility across laboratories\be economical to use and should be user friendly[ Molecularmarkers are specially advantageous for agronomic traits thatare otherwise di.cult to score[ Molecular marker studies usingNILs "Muehlbauer et al[ 0877\ Young et al[ 0877\ Martin et al[0880#\ recombinant inbred lines "RILs# "Mohan et al[ 0883#or bulked segregant analyses "Michelmore et al[ 0880# haveaccelerated the mapping of many genes in di}erent plant spec!ies\ including wheat[ Some of the major genes that are alreadytagged and mapped in wheat are listed in Table 3[

The choice of marker system to be used for the detection ofDNA polymorphism\ depends _rst on the objective of studyand the needs dictated by its speci_c application\ and secondon the facilities and skills available in a laboratory[ Therefore\a comparative study of di}erent technologies may be helpful inmaking a choice of suitable marker[ For example\ in soybeangermplasm a comparison of the utility of four important typesof molecular markers\ i[e[ RFLPs\ RAPDs\ AFLPs and SSRs"microsatellites# was conducted "Powell et al[ 0885#[ The studyincluded estimation of two parameters called average expectedheterozygosity or Hav "the probability that two di}erent alleles


were observed for each of the loci\ averaged over all loci con!sidered# and e}ective multiplex ratio "number of polymorphicloci simultaneously analysed per experiment#\ which were usedto calculate the marker index "MI � E[Hav#[ Based on thisstudy\ it was suggested that di}erent molecular markers shouldbe used for di}erent purposes and also that the choice willdepend on a variety of other factors\ including cost\ convenienceand technical feasibility[ They concluded that while SSRs andAFLPs\ despite the high cost of their development\ will becomepopular in future for their e.ciency\ the RAPDs will be popularbecause of their simplicity and low costs\ even if they are theleast e.cient[ In a separate comparative study on the utility ofRFLPs and AFLPs in bread wheat\ the AFLPs were suggestedto be more cost and resource e}ective than RFLPs in this crop"Ma and Lapitan 0887#\ although in other crops RFLPs maybe more cost e}ective than AFLPs[ In another recent study\three important types of molecular marker\ i[e[ RFLPs\ AFLPsand SSRs were also evaluated for their ability to study geneticdiversity in wheat "Bohn et al[ 0888#[ In this study\ the PIC wasnot signi_cantly di}erent for the three marker systems\ althoughrelative to AFLPs\ the marker index was low for RFLPs andSSRs so that AFLPs were recommended for _ngerprinting[

Keeping in mind the above\ we have compared the advan!tages and disadvantages associated with the use of di}erentmarker systems so that one may choose a suitable marker tech!nology\ for a speci_c purpose\ such as plant breeding\ DNA_ngerprinting\ genetic diversity analysis and comparative map!ping[ It should be recognized that di}erent marker systems maybe suitable for di}erent purposes[ For example\ it has beenshown that microsatellite markers are codominant and\ relativeto all other marker types\ have high information content "esti!mated as either the polymorphic information content or geneticdiversity index or expected heterozygosity#[ However\ the veryhigh cost of their development restricts their uses in manylaboratories[ However\ the current availability in bread wheatof approximately 0999 microsatellite primer pairs and the exten!sive molecular genetic maps based on these microsatellites over!comes this barrier and will certainly accelerate their use even insmall laboratories[ In addition\ the locus speci_city and highlevel of polymorphism associated with microsatellites makethem the marker system of choice for molecular marker!aidedselection in practical plant breeding[ For characterization ofgenomes "_ngerprinting# or to perform a study of genetic diver!sity in a population\ in our opinion\ the multiplexed methods"Rafalski et al[ 0885#\ e[g[ AFLPs\ DAFs\ ISSRs or multiplexedRAPDs are suitable since these marker systems\ relative toother markers\ have higher multiplex ratios[ For comparativemapping and the study of synteny\ RFLPs are uniquely appro!priate since they detect homoeologous loci[ Furthermore\ theRFLP marker system is codominant in nature and is easy andconvenient\ if a good collection of RFLP probes is available^the use of radioactivity can also be avoided if non radioactivedetection systems "e[g[ chemiluminescence# are used[

Before using the molecular markers in actual plant breeding\it is necessary to undertake studies on marker validation\ aprocess of examining the behaviour of markers and the associ!ated polymorphism in di}erent genetic backgrounds "Langridgeand Chalmers 0887#[ The validity of a molecular marker linkedwith any trait should be examined in other crosses\ since\ for amarker to be useful in breeding programmes\ it needs to detectthe polymorphism in di}erent crosses[ For example\ markersidenti_ed in one cross as being linked to protein content needto be tested in other crosses to determine if the alleles associated

with high and low protein contents in two genotypes involvedin the original single cross used for marker development\ arealso associated with similar phenotypes involved in othercrosses[

Marker validation involves] "0# identi_cation of potentialmarkers from available research^ "1# identi_cation of the geneticmaterial for the appropriate breeding programmes^ "2# exam!ination of the e}ectiveness of the marker:trait linkage in thebreeding material identi_ed^ "3# critical discussion of results\and suggestions from the plant breeders to decide on the vali!dation of the particular markerÐtrait combination[ However\ itmay be more di.cult to conduct marker validation for quan!titative traits where there is major genotypeÐenvironment inter!action\ so that the e}ect of a QTL in a speci_c environment isimpossible to predict\ since di}erent loci may interact di}erentlywith di}erent environments[ The di.culty may be overcome byidenti_cation of more and more QTL linked with independentmolecular markers followed by mapping of the QTL identi_edand subjecting them to interval mapping[

Conclusions

In the past\ the complexity of the wheat genome led to a delayin development and application of molecular markers in thiscrop\ so that it lags behind rice\ barley and maize in the avail!ability of markers for di}erent agronomic traits[ Despite thelow level of variability available in wheat\ extensive molecularmaps have now been prepared and as many as 25 traits havebeen tagged using di}erent molecular markers[ The utility ofmarkers in wheat for analysis of the inheritance of traits andfor understanding genome structure and organization is nowwell established[ The molecular markers have also been used tostudy synteny among di}erent grass species[ Molecular markersare now available in wheat which may either be speci_c forindividual homoeologous group or are chromosome speci_c[Thus the availability of a large number of molecular markersin wheat suggest their use in intraspeci_c analyses\ comparativeanalysis and gene introgression studies as well as in practicalwheat breeding[ However\ the application of molecular markersto practical breeding involving marker!assisted selection is stillin its infancy\ despite the availability of a large number ofmolecular markers[ Only a few reports are available on marker!assisted selection in wheat breeding[ For example\ a populationof 119 BC0F1 plants segregating for two genes Cre0 and Cre2was evaluated with three molecular markers Xglk594\ Xcdo477and CD1[1 and the markers were found to provide a reliablemeans of gene pyramiding and selecting plants carrying thegenes in wheat breeding programmes "Ogbonnaya et al[ 0887#[The close interaction between breeders and biotechnologistsmay accelerate the e}ective implementation of molecularmarker!aided selection in wheat breeding programmes[ We alsohope that the development of newer markers such as ESTs andSNPs and the availability of newer technologies such as DNAchips:microarrays and MALDI!TOF mass spectrometry willaccelerate genome mapping and tagging of genes in this poly!ploid crop for e.cient wheat breeding[

Acknowledgements

Thanks are due to the Department of Biotechnology "DBT#\ Govern!ment of India and to the Council of Scienti_c + Industrial Research"CSIR#\ New Delhi\ India\ for _nancial assistance\ which made theabove study possible[


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Blanco\ A[\ C[ De Giovanni\ B[ Laddomada\ A[ Sciancalepore\ R[

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Bohn\ M[\ H[ F[ Utz\ and A[ E[ Melchinger\ 0888] Genetic similaritiesamong winter wheat cultivars determined on the basis of RFLPs\AFLPs\ and SSRs and their use for predicting progeny variance[Crop Sci[ 28\ 117*126[

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Cadalen\ T[\ C[ Boeuf\ S[ Bernard\ and M[ Bernard\ 0886] An inter!varietal molecular marker map in Triticum aestivum L[ Em[ Thell[and comparison with a map from a wide cross[ Theor[ Appl[ Genet[83\ 256*266[

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Caetano!Anolles\ G[\ and P[ M[ Gressho}\ 0883] DNA ampli_cation_ngerprinting using very short arbitrary mini!hairpin oligonucleotideprimers[ Bio:Technology 01\ 508*512[

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Cao\ W[\ G[ R[ Hughes\ H[ Ma\ and Z[ Dong\ 0887] Development ofDNA based markers for resistance to Septoria nodorum blotch indurum wheat[ In] A[ E[ Slinkard "ed[#\ Proc[ 8th Int[ Wheat Genet[Symp[\ Vol[ 2\ 84*86[ Univ[ Extension Press\ Univ[ of Saskat!chewan\ Saskatoon[

Castigliani\ P[\ C[ Pozzi\ M[ Heun\ V[ Terzi\ K[ J[ Muller\ W[ Rhode\and F[ Salamini\ 0887] An AFLP!based procedure for the e.cientmapping of mutation and DNA probes in barley[ Genetics 038\

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Chen\ Z[\ M[ Devey\ N[ A[ Tuleen\ and G[ E[ Hart\ 0883] Use ofrecombinant substitution lines in the construction of RFLP!basedgenetic maps of chromosomes 5A and 5B of tetraploid wheat[ Theor[Appl[ Genet[ 78\ 692*601[

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Luo\ M[ C[\ and J[ Dvorak\ 0885] Molecular mapping of an aluminiumtolerance locus on chromosome 3D of Chinese spring wheat[ Euphy!tica 80\ 20*24[

Ma\ Z[!Q[\ and N[ L[ V[ Lapitan\ 0887] A comparison of ampli_edand restriction fragment length polymorphism in wheat[ Cereal Res[Commun[ 15\ 6*02[

* *\ and M[ E[ Sorrells\ 0884] Genetic analysis of fertility restorationin wheat using restriction fragment length polymorphisms[ Crop Sci[24\ 0026*0032[

* *\ B[ S[ Gill\ M[ E[ Sorrells\ and S[ D[ Tanksley\ 0882] RFLPmarkers linked to two Hessian ~y resistance genes in wheat "Triticumaestivum L[#\ from Triticum tauschii "Coss[# Schal[ Theor[ Appl[Genet[ 74\ 649*643[

* *\ M[ E[ Sorrells\ and S[ D[ Tanksley\ 0883] RFLP markers linkedto powdery mildew resistance genes Pm0\ Pm1\ Pm2 and Pm3 inwheat[ Genome 26\ 760*764[

* *\ M[ Ro�der\ and M[ E[ Sorrells\ 0885] Frequencies and sequencecharacteristics of di!\ tri! and tetra!nucleotide microsatellites inwheat[ Genome 28\ 012*029[

* *\ A[ Saidi\ J[ S[ Quick\ and N[ L[ V[ Lapitan\ 0887] Geneticmapping of Russian wheat aphid resistance genes Dn1 and Dn3 inwheat[ Genome 30\ 292*295[

Mackill\ D[ J[\ Z[ Zhang\ E[ D[ Redona\ and P[ M[ Colowit\ 0885] Levelof polymorphism and genetic mapping of AFLP markers in rice[Genome 28\ 858*866[

Maheswaran\ M[\ P[ K[ Subudhi\ S[ Nandi\ J[ C[ Xu\ A[ Parco\ D[C[ Yang\ and N[ Huang\ 0886] Polymorphism\ distribution\ and

segregation of AFLP markers in a doubled haploid rice population[Theor[ Appl[ Genet[ 83\ 28*34[

Marino\ C[ L[\ J[ C[ Nelson\ Y[ H[ Lu\ M[ E[ Sorrells\ P[ Leroy\ N[ A[Tuleen\ C[ R[ Lopes\ and G[ E[ Hart\ 0885] Molecular genetic mapsof the group 5 chromosomes of hexaploid wheat "Triticum aestivumL[ Em[ Thell[#[ Genome 28\ 248*255[

Martin\ G[ B[\ J[ G[ K[ Williams\ and S[ D[ Tanksley\ 0880] Rapididenti_cation of markers linked to a Pseudomonas resistance gene intomato by using random primers and near isogenic lines[ Proc[ Natl[Acad[ Sci[ USA 77\ 1225*1239[

Maughan\ P[ J[\ M[ A[ Saghai!Maroof\ G[ R[ Buss\ and G[ M[ Huestis\0885] Ampli_ed fragment length polymorphism "AFLP# in soybean]species diversity\ inheritance\ and near!isogenic analysis[ Theor[Appl[ Genet[ 82\ 281*390[

McIntosh\ R[ A[\ G[ E[ Hart\ K[ M[ Devos\ M[ D[ Gale\ and W[ J[Rogers\ 0887] Catalogue of gene symbols for wheat[ In] A[ E[ Slinkard"ed[#\ Proc[ 8th Int[ Wheat Genet[ Symp[\ Vol[ 4\ 02*61[ Univ[Extension Press\ Univ[ of Saskatchewan\ Saskatoon[

Men\ A[ E[\ A[ Y[ Borisov\ S[ M[ Rozov\ K[ V[ Ushakov\ V[ E[Tsyganov\ I[ A[ Tikhonovich\ and P[ M[ Gressho}\ 0888] Identi!_cation of DNA ampli_cation _ngerprinting "DAF# markers closeto the symbiosis!ine}ective sym20 mutation of pea[ Theor[ Appl[Genet[ 87\ 818*825[

Meyer\ W[\ T[ G[ Michell\ E[ Z[ Freedman\ and R[ Vilgalys\ 0882]Hybridization probes for conventional DNA _ngerprinting used assingle primers in the polymerase chain reaction to distinguish strainsof Cryptococcus neoformans[ J[ Clin[ Biol[ 20\ 1163*1179[

Michelmore\ R[ W[\ I[ Paran\ and R[ V[ Kesseli\ 0880] Identi_cationof markers linked to disease!resistance genes by bulked segregantanalysis] a rapid method to detect the markers in speci_c genomicregions by using segregating populations[ Proc[ Natl[ Acad[ Sci[ USA77\ 8717*8721[

Mickelson!Young\ L[\ T[ R[ Endo\ and B[ S[ Gill\ 0884] A cytogeneticladder map of the wheat homoeologous group!3 chromosomes[Theor[ Appl[ Genet[ 89\ 0996*0900[

Mohan\ M[\ S[ Nair\ J[ S[ Bentur\ U[ Prasada Rao\ and J[ Bennett\0883] RFLP and RAPD mapping of the rice Gm1 gene that confersresistance to biotype 0 of gall midge "Orseolia oryzae#[ Theor[ Appl[Genet[ 76\ 671*677[

* *\ * *\ A[ Bhagwat\ T[ G[ Krishna\ M[ Yano\ C[ R[ Bhatia\ andT[ Sasaki\ 0886] Genome mapping\ molecular markers and marker!assisted selection in crop plants[ Mol[ Breeding 2\ 76*092[

Mohler\ V[\ and A[ Jahoor\ 0885] Allele speci_c ampli_cation of poly!morphic sites for detection of powdery mildew resistance loci incereals[ Theor[ Appl[ Genet[ 82\ 0967*0971[

Moore\ G[\ K[ M[ Devos\ Z[ Wang\ and M[ D[ Gale\ 0884a] Cerealgenome evolution[ Curr[ Biol[ 4\ 626*628[

* *\ * *\ * *\ and \ 0884b] Grasses\ line up and from a circle[ Curr[Biol[ 4\ 626*628[

* *\ T[ Foote\ T[ Helentjaris\ K[ M[ Devos\ N[ Kurata\ and M[ D[Gale\ 0884c] Was there a single ancestral cereal chromosome< TrendsGenet[ 00\ 70*71[

Muehlbauer\ G[ J[\ J[ E[ Specht\ M[ A[ Thomas!Compton\ P[ E[ Stas!wick\ and R[ L[ Bernard\ 0877] Near!isogenic lines * a potentialresource in the integration of conventional and molecular markerlinkage maps[ Crop Sci[ 17\ 618*624[

Myburg\ A[ A[\ A[ M[ Botha\ B[ D[ Wing_eld\ and W[ J[ M[ Wilding\0886] Identi_cation and genetic distance analysis of wheat cultivarsusing RAPD _ngerprinting[ Cereal Res[ Commun[ 14\ 764*771[

* *\ M[ Cawood\ B[ D[ Wing_eld\ and A[ M[ Botha\ 0887] Devel!opment of RAPD and SCAR markers linked to the Russian wheataphid resistance gene Dn1 in wheat[ Theor[ Appl[ Genet[ 85\ 0051*0058[

Nagaoka\ T[\ and Y[ Ogihara\ 0886] Applicability of inter!simplesequence repeat polymorphisms in wheat for use as DNA markers incomparison to RFLP and RAPD markers[ Theor[ Appl[ Genet[ 83\

486*591[Naik\ S[\ K[ S[ Gill\ V[ S[ Prakasa Rao\ V[ S[ Gupta\ S[ A[ Tamhankar\

S[ Pujar\ B[ S[ Gill\ and P[ K[ Ranjekar\ 0887] Identi_cation of a STS


marker linked to the Aegilops speltoides!derived leaf rust resistancegene Lr17 in wheat[ Theor[ Appl[ Genet[ 86\ 424*439[

Nelson\ J[ C[\ M[ E[ Sorrells\ A[ E[ van Deynze\ Y[ H[ Lu\ M[ Atinkson\M[ Bernard\ P[ Leroy\ J[ D[ Faris\ and J[ A[ Anderson\ 0884a]Molecular mapping of wheat[ Major genes and rearrangements inhomoeologous groups 3\ 4\ and 6[ Genetics 030\ 610*620[

* *\ A[ E[ van Deynze\ E[ Autrique\ M[ E[ Sorrells\ Y[ H[ Lu\ M[Merlino\ M[ Atinkson\ and P[ Leroy\ 0884b] Molecular mapping ofwheat[ Homoeologous group 1[ Genome 27\ 405*413[

* *\ * *\ * *\ * *\ * *\ S[ Negre\ M[ Atinkson\ and P[ Leroy\0884c] Molecular mapping of wheat[ Homoeologous group 2[ Gen!ome 27\ 414*422[

* *\ R[ P[ Singh\ J[ E[ Autrique\ and M[ E[ Sorrells\ 0886] Mappinggenes conferring and suspecting leaf rust resistance in wheat[ CropSci[ 26\ 0817*0824[

* *\ J[ E[ Autrique\ G[ Fuentes!Davila\ and M[ E[ Sorrells\ 0887]Chromosomal location of genes for resistance to karnal bunt inwheat[ Crop Sci[ 27\ 120*125[

Nesbitt\ K[ A[\ B[ M[ Potts\ R[ E[ Vaillancourt\ A[ K[ West\ and J[ B[Reid\ 0884] Partioning and distribution of RAPD variation in a foresttree species\ Eucalyptus globulus "Myrtaceae#[ Heredity 63\ 517*526[

Newman\ T[ F[\ J[ deBruijin\ P[ Green\ K[ Keegstra\ H[ Kende\ L[Melentosh\ J[ Ohlrogge\ N[ Raikhel\ S[ Somerville\ M[ Thomashow\E[ Retzel\ and C[ Sommerville\ 0883] Genes galore] a summary ofmethods for accessing results from large!scale partial sequencing ofanonymous Arabidopsis cDNA clones[ Plant Physiol[ 095\ 0130*0144[

Nybom\ H[\ 0883] DNA _ngerprinting * a useful tool in fruit breeding[Euphytica 66\ 48*53[

Ogbonnaya\ F[ C[\ O[ Moullet\ R[ F[ Eastwood\ J[ Kollmorgen\ H[Eagles\ R[ Appels\ and E[ S[ Lagudah\ 0887] The use of molecularmarkers to pyramid cereal cyst nematode resistance genes in wheat[In] A[ E[ Slinkard "ed[#\ Proc[ 8th Int[ Wheat Genet[ Symp[\ Vol[ 2\027*028[ Univ[ Extension Press\ Univ[ of Saskatchewan\ Saskatoon[

Ogihara\ Y[\ K[ Hasegawa\ and H[ Tsujimoto\ 0883] High resolutioncytological mapping of the long arm of chromosome 4A in commonwheat using a series of deletion lines induced by gametocidal "Gc#genes of Aegilops speltoides[ Mol[ Gen[ Genet[ 133\ 142*148[

Parker\ G[\ C[ Ken\ R[ Anthony\ and L[ Peter\ 0886] Identi_cation ofmolecular markers linked to ~our colour and milling yield in wheat[In] 4th Int[ Congr[ Plant Mol[ Biol[\ 10Ð16 Sept[ 0886\ Singapore\Abstr[ 135[

Paull\ J[ G[\ M[ A[ Pallota\ and P[ Langridge\ 0883] RFLP markersassociated with Sr11 and recombination between chromosome 6A ofbread wheat and the diploid species Triticum boeoticum[ Theor[ Appl[Genet[ 78\ 0928*0934[

Peil\ A[\ E[ Schumann\ V[ Schubert\ V[ Korzun\ and W[ E[ Weber\0887] Molecular markers for Aegilops markgra_i chromosomes[ In]A[ E[ Slinkard "ed[#\ Proc[ 8th Int[ Wheat Genet[ Symp[\ Vol[ 2\039*031[ Univ[ Extension Press\ Univ[ of Saskatchewan\ Saskatoon[

de la Pena\ R[ C[\ T[ D[ Murray\ and S[ S[ Jones\ 0885] Linkage relationsamong eyespot resistance gene Pch1\ endopeptidase EP!A0B\ andRFLP marker Xpsr010 on chromosome 6A of wheat[ Plant Breeding004\ 162*164[

* *\ * *\ and * *\ 0886] Identi_cation of an RFLP interval con!taining Pch1 on chromosome 6AL in wheat[ Genome 39\ 138*141[

Peng\ J[ H[\ T[ Fahima\ M[ S[ Ro�der\ Y[ C[ Li\ A[ Dahan\ A[ Grama\Y[ I[ Ronin\ A[ B[ Korol\ and E[ Nevo\ 0888] Microsatellite taggingof the stripe rust resistance gene YrH41 derived from wild emmerwheat\ Triticum dicoccoides\ and suggestive negative crossover inter!ference on chromosome 0B[ Theor[ Appl[ Genet[ 87\ 751*761[

Penner\ G[ A[\ and L[ Z[ Bezte\ 0883] Increased detection of poly!morphism among randomly ampli_ed wheat DNA fragments usinga modi_ed temperature sweep gel electrophoresis "TSGE# technique[Nucl[ Acids Res[ 8\ 0679*0670[

* *\ J[ Clark\ L[ Z[ Bezte\ and D[ Lisle\ 0884] Identi_cation of RAPDmarkers linked to a gene governing cadmium uptake in durum wheat[Genome 27\ 432*436[

* *\ M[ Zirino\ S[ Kruger\ and F[ Townley!Smith\ 0887] Accelerated

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Pereira\ M[ G[\ M[ Lee\ P[ Bramel!Cox\ W[ Woodman\ J[ Doebley\ andR[ Whitkus\ 0883] Construction of an RFLP map in sorghum andcomparative mapping in maize[ Genome 26\ 125*132[

Perring\ T[ M[\ A[ D[ Cooper\ R[ J[ Rodriguez\ C[ A[ Farrar\ and T[ S[Bellows\ 0882] Identi_cation of a white ~y species by genomic andbehavioural studies[ Science 148\ 63*66[

Plaschke\ J[\ M[ W[ Ganal\ and M[ S[ Ro�der\ 0884] Detection of geneticdiversity in closely related bread wheat using microsatellite markers[Theor[ Appl[ Genet[ 80\ 0990*0996[

Powell\ W[\ M[ Morgante\ C[ Andre\ M[ Hanafey\ J[ Vogel\ S[ Tingey\and A[ Rafalsky\ 0885] The comparison of RFLP\ RAPD\ AFLP andSSR "microsatellite# markers for germplasm analysis[ Mol[ Breed[ 1\

114*127[* *\ T[ B[ Thomas\ E[ Baird\ P[ Lawrence\ A[ Booth\ B[ Harrower\ J[

W[ McNicol\ and R[ Waugh\ 0886] Analysis of quantitative traitsin barley by the use of ampli_ed fragment length polymorphisms[Heredity 68\ 37*48[

Prasad\ M[\ R[ K[ Varshney\ A[ Kumar\ H[ S[ Balyan\ P[ C[ Sharma\K[ J[ Edwards\ H[ Singh\ H[ S[ Dhaliwal\ J[ K[ Roy\ and P[ K[ Gupta\0888a] A microsatellite marker associated with a QTL for grainprotein content on chromosome arm 1DL of bread wheat[ Theor[Appl[ Genet[ 88\ 230*234

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Procunier\ J[ D[\ T[ F[ Townley!Smith\ S[ Fox\ S[ Prashar\ M[ Gay\ W[K[ Kim\ E[ Czarnecki\ and P[ L[ Dyck\ 0884] PCR!basedRAPD:DGGE markers linked to lef rust resistance genes Lr18 andLr14 in wheat "Triticum aestivum L[#[ J[ Genet[ Breed[ "formerlyGenet[ Agr[# 38\ 76*81[

* *\ R[ E[ Knox\ A[ M[ Bernier\ M[ A[ Gray\ and N[ K[ Howes\ 0886]DNA markers linked to a T09 loose smut resistance gene in wheat"Triticum aestivum L[#[ Genome 39\ 065*068[

Qi\ L[ L[\ M[ S[ Cao\ P[ D[ Chen\ W[ L[ Li\ and D[ J[ Lu\ 0885]Identi_cation\ mapping\ and application of polymorphic DNAassociated with resistance gene Pm10 of wheat[ Genome 28\ 080*086[

Qi\ X[\ P[ Stan\ and P[ Lindhout\ 0887] Use of locus!speci_c AFLPmarkers to construct a high density molecular map in barley[ Theor[Appl[ Genet[ 85\ 265*273[

Quarrie\ S[ A[\ M[ Gulli\ C[ Calestani\ A[ Steed\ and N[ Marmiroli\0883] Location of a gene regulating drought!induced abcisic acidproduction on the long arm of chromosome 4A of wheat[ Theor[Appl[ Genet[ 78\ 683*799[

Rafalski\ J[ A[\ and S[ V[ Tingey\ 0882] Genetic diagnostics in plantbreeding] RAPDS\ Microsatellites and Machines[ Trends Genet[ 8\

164*179[* *\ M[ Morgante\ W[ Powell\ J[ M[ Vogel\ and S[ V[ Tingey\ 0885]

Generating and using DNA markers in plants[ In] B[ Birren\ and E[Lai "eds#\ Analysis of Non!mammalian Genomes] a Practical Guide\64*023[ Academic Press\ Boca Raton[

Rao\ V[ S[\ S[ Pujar\ S[ A[ Tamhankar\ V[ S[ Gupta\ and P[ K[ Ranjekar\0887] Assessment of diversity in Indian tetraploid wheat varietiesusing random ampli_ed polymorphic DNA markers[ In] A[ E[ Slin!kard "ed[#\ Proc[ 8th Int[ Wheat Genet[ Symp[\ Vol[ 2\ 034*036\Univ[ Extension Press\ Univ[ of Saskatchewan\ Saskatoon[

Reiter\ R[ S[\ J[ G[ K[ Williams\ K[ A[ Feldmann\ J[ A[ Rafalski\ S[ V[Tingey\ and P[ A[ Scolnik\ 0881] Global and local genome mappingin Arabidopsis thaliana by using recombinant inbred lines and randomampli_ed polymorphic DNAs[ Proc[ Natl[ Acad[ Sci[ USA 78\ 0366*0370[

Riede\ C[ R[\ and J[ A[ Anderson\ 0885] Linkage of RFLP markers toan aluminium tolerance gene in wheat[ Crop Sci[ 25\ 894*898[

Ro�der\ M[ S[\ J[ Plaschke\ S[ U[ Ko�nig\ A[ Bo�rner\ M[ E[ Sorells\ S[D[ Tanksley\ and M[ W[ Ganal\ 0884] Abundance\ variability and


chromosomal location of microsatellites in wheat[ Mol[ Gen[ Genet[135\ 216*222[

* *\ V[ Korzun\ B[ S[ Gill\ and M[ W[ Ganal\ 0887a] The physicalmapping of microsatellite markers in wheat[ Genome 30\ 167*172[

* *\ * *\ K[ Wendehake\ J[ Plaschke\ M[ H[ Tixer\ P[ Leroy\ andM[ W[ Ganal\ 0887b] A microsatellite map of wheat[ Genetics 038\

1996*1912[Rogowsky\ P[ M[\ M[ E[ Sorrells\ K[ W[ Shepherd\ and P[ Langridge\

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Rong\ J[ K[\ E[ Millet\ J[ Manisterski\ and M[ Feldman\ 0887] a powderymildew resistance gene from wild emmer transferred into commonwheat and tagged by molecular markers[ In] A[ E[ Slinkard "ed[#\Proc[ 8th Int[ Wheat Genet[ Symp[\ Vol[ 2\ 037*049\ Univ[ Exten!sion Press\ Univ[ of Saskatchewan\ Saskatoon[

Ross\ P[\ L[ Hall\ I[ Smirnov\ and L[ Ha}\ 0887] High level multiplexgenotyping by MALDI!TOF mass spectrometry[ Nature Biotech[ 05\

0236*0240[Roy\ J[ K[\ M[ Prasad\ R[ K[ Varshney\ H[ S[ Balyan\ T[ K[ Blake\ H[

S[ Dhaliwal\ H[ Singh\ K[ J[ Edwards\ and P[ K[ Gupta\ 0888]Identi_cation of a microsatellite on chromosome 5B and a STS on6D of bread wheat showing association with preharvest sproutingtolerance[ Theor[ Appl[ Genet[ 88\ 225*239[

Ruan\ Y[\ J[ Gilmore\ and T[ Conner\ 0887] Towards Arabidopsis gen!ome analysis] monitoring expression pro_les of 0399 genes usingcDNA microarrays[ Plant J[ 04\ 710*722[

Sacco\ F[\ E[ Y[ Suarez\ and T[ Naranjo\ 0887] Mapping of the leaf rustresistance gene Lr2 on chromosome 5B of Sinvalocho MA wheat[Genome 30\ 575*589[

Saghai Maroof\ M[ A[\ G[ P[ Tang\ R[ M[ Biyashev\ P[ J[ Maughan\and Q[ Zhang\ 0885] Analysis of the barley and rice genomes bycomparative RFLP linkage mapping[ Theor[ Appl[ Genet[ 81\ 430*440[

Sasaki\ T[\ 0886] 4W 0H for rice whole genome sequencing[ Rice Gen!ome 5\ 0[

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Schachermayr\ G[ M[\ H[ Siedler\ M[ D[ Gale\ H[ Winzeler\ M[Winzeler\ and B[ Keller\ 0883] Identi_cation and localization ofmolecular markers linked to the Lr8 rust gene of wheat[ Theor[ Appl[Genet[ 77\ 009*004[

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Schmidt\ T[\ and J[ S[ Heslop!Harrison\ 0885] The physical and genomicorganization of microsatellites in sugar beet[ Proc[ Natl[ Acad[ Sci[USA 82\ 7650*7654[

Sen\ A[\ H[ S[ Balyan\ P[ C[ Sharma\ B[ Ramesh\ A[ Kumar\ J[ K[Roy\ R[ K[ Varshney\ and P[ K[ Gupta\ 0886a] DNA ampli_cation_ngerprinting "DAF# as a new source of molecular markers in breadwheat[ Wheat Inf[ Serv[ 74\ 24*31[

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Seyfarth\ R[\ C[ Feuillet\ and B[ Keller\ 0887] Development and charac!terization of molecular markers for the adult leaf rust resistance genes

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678*683[* *\ P[ L[ Bruckner\ L[ Y[ Smith\ R[ Sears\ and T[ J[ Martin\ 0885]

Development of PCR markers linked to resistance to wheat streakmosaic virus in wheat[ Theor[ Appl[ Genet[ 82\ 352*356[

Tanksley\ S[ D[\ N[ D[ Young\ A[ H[ Patterson\ and M[ W[ Bonierbale\0878] RFLP mapping in plant breeding * new tools for an oldscience[ Bio:Technology 6\ 146*153[

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Vaccino\ P[\ M[ Accerbi\ and M[ Corbellini\ 0882] Cultivar identi!_cation in T[ aestivum using highly polymorphic RFLP probes[Theor[ Appl[ Genet[ 75\ 722*725[

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Virk\ P[ S[\ B[ Ford!Lloyd\ and H[ John Newbury\ 0887] MappingAFLP markers associated with subspeci_c di}erentiation of Oryzasativa "rice# and on investigation of segregation distortion[ Heredity70\ 502*519[

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Vosman\ B[\ P[ Arens\ W[ Rus!Kortekaas\ and M[ I[ M[ Smulders\0881] Identi_cation of highly polymorphic DNA regions in tomato[Theor[ Appl[ Genet[ 74\ 128*133[

Wang\ R[ R[!C[\ J[ Cheng\ and L[ R[ Joppa\ 0884] Production andidenti_cation of chromosome speci_c RAPD markers for durumwheat {Langdon| disomic substitution lines[ Crop Sci[ 24\ 775*777[

Wang\ Y[\ N[ A[ Tuleen\ and G[ E[ Hart\ 0887] Construction of aconsensus physical map of wheat homoeologous group!5 chro!mosomes and comparison with linkage maps[ In] A[ E[ Slinkard"ed[#\ Proc[ 8th Int[ Wheat Genet[ Symp[\ Vol[ 2\ 051*053\ Univ[Extension Press\ Univ[ of Saskatchewan\ Saskatoon[

Weber\ D[\ and T[ Helentjaris\ 0878] Mapping RFLP loci in maizeusing BÐA translocations[ Genetics 010\ 472*489[

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ReviewMolecular markers and their applications in wheat breeding

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Transcript of ReviewMolecular markers and their applications in wheat breeding