Genetic approaches to crop improvement

8/7/2019 Genetic approaches to crop improvement

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I dditi t icsig wld pplti, th ms ss f sis cc bt sfficitft glbl pdcti f fd fm cp plts14.Fist, th ilbility f bl ld is dcsig bcsf -sstibl fmig, sil si d dgd-ti2. Scd, th ilbility f wt f giclt willdcli1. Thid, glbl climt chgs will t ly si-sly ffct cp gwth bt will ls tht th c-sti f cltitd ld5,6. Dghts, stms, flds,ht ws d iss i s-ll pdictd t ccm fqtly, d sliity d th sil txicitis likly t b mch m pblmtic i sm s.I smi-id gis, dctis i yilds f pimycps, icldig miz, wht d ic, pdictd ith xt tw dcds7. Lstly, dmds f bi-fls ssbstitti gy scs will b icsd, dcigth ld ilbl f cltitig fd cps4.

T cm ths pblms, w gicltl tch-lgis will b dd t s glbl fd scity,i dditi t ffts t cs wt d lds. Ipticl, cp impmts tht cf tlct imtl stsss d sil txicity, s wll shigh yild d bimss, will b qid. T chithis gl, th lci tht iflc ths tits d tb idtifid t pid dstdig f thimlcl mchisms. M, gmplsm scscyig tit-hcig llls mst b idtifid, dthi bhi i pppit gtic bckgdsd imts dcmtd. H, w fist discssstblishd d mgig ppchs tht c b sd

t idtify th gtic cmpts ctllig dt-gs tits d th pssibility f sig ths cmp-ts f cp impmt. W th iw ctpgss th idtificti f gs lci ildi imptt qtitti tits f tw mi ctgis.Th fist f ths cs ctly idtifid gs thtctl yild. Th scd mi tht w fcs isth gtic chitct f tits ild i tlc tbitic stsss, spcilly t wt stss d sil stss.Ths stsss icld sbmgc, dght, sliityd th sil txicitis, sch s b d lmiimtxicity, ll f which xpctd t b m pblmtici th ft. W iw hw ths stdis h c-tibtd t dstdig f th dlyig bilgy,d ddss th pssibl pplicti f sch kwldgt cp impmt, icldig bdig sttgis dgtic mdificti.Th im f this riw is t p-

id citicl iw f th ppchs ilbl dtli th ppchs tht pmis t ics ftchcs f sccss.

Identifying useful genetic components

Established approaches molecular genetic approaches

and QTL mapping.Th idtificti f gs tht spsibl f imptt gicltl tits hs bmstly cdctd by tditil mlcl gtics(fwd d s gtic scs) f disct titsd byquanttatve trat lcus (QTL) mppig f cmplxtits810 (Box 1). I gl, th tditil mthds pwfl gh t l th gs tht ild

*Laboratory of Plant CellFunction, Bioscience

and Biotechnology Center,

Nagoya University, Chikusa,

Nagoya 4648601, Japan.Laboratory of Plant

Molecular Breeding,

Bioscience and Biotechnology

Center, Nagoya University,

Chikusa, Nagoya 4648601,

Japan.

emails:

[email protected];

[email protected]

d:10.1038/nr2342

Publshed nlne 13 May 2008

Quantitative trait locus

(QTL). A enetc lcus

cntrlln a cmple trat

(such as plant heht r ran

yeld), whch s typcally

affected by mre than ne

ene and als by the

envrnment.

Genetic approaches to cropimprovement: responding toenvironmental and population changesShin Takeda*and Makoto Matsuoka

Abstract | Crop production is threatened by global climate change, and recent demands

for crops to produce bio-fuels have started to affect the worldwide supply of some of

the most important foods. How can we support a growing human population in suchcircumstances? One potential solution is the improvement of crops to increase yield

from both irrigated and non-irrigated lands, and to create novel varieties that are more

tolerant to environmental stresses. Recent progress has been made in the isolation and

functional analyses of genes controlling yield and tolerance to abiotic stresses. In

addition, promising new methods are being developed for identifying additional genes

and variants of interest and putting these to practical use in crop improvement.

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444 | June 2008 | voLuMe 9 www.atur.m/rws/ts

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mailto:[email protected]:[email protected]:[email protected]:[email protected]


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Box 1 | Methods for identifying genes involved in specific traits

QTL ma

QTL mapping relies on statistical linkage analyses among quantitative

traits of interest and genetic markers, using a population that carries

genetic mosaics derived from parental varieties, such as second

generation (F2) plants or recombinant inbred lines (RILs). In part a of the

figure, parental varieties (A and B) are used for the preparation of RILsfor mapping. Segments derived from parental chromosome are

represented by two colours (light blue and red). At each genetic locus

(indicated by arrowheads), phenotypic variance for plants with the

genotypes AA or BB, is scored. At a QTL, indicated by the red arrowhead,

graphs representing phenotypic variations for AA and BB are separated,

as shown in the bottom section of part a. It should be noted thatRILs, rather than the F2 or F3 population, are needed to evaluate

genotype-by-environment interactions.

Assat ma

Association mapping, also called linkage disequilibrium (LD) mapping,

relies on correlation between a genetic marker and a phenotype among

collections of diverse germplasm. In part b of the figure, the principle ofassociation mapping is illustrated. Phenotypes are scored for plants that

have also been genotyped (SNP genotypes are represented by coloured

circles). For simplification, the plant variants shown here are homozygous

at each locus. Association scanning is performed by comparing

phenotypic scores respective to each haplotype. Data sets are analysed

using statistical methods, which have been designed to deal with the

population structure.Slt srSelection screening identifies genes that show signatures of selection.

This approach is based on the theory th at target loci of selection show

decreased nucleotide diversity and increased LD after strong selection,

such as during domestication and subsequent crop improvement.

Whereas association mapping is a trait-oriented method, selection

screening is primarily dependent on DNA sequence polymorphism.

In part of the figure, loci for monitoring polymorphisms arerepresented by circles, rectangles, and stars with different colours over

a genomic region. A selected gene locus is expected to undergo loss of

diversity after selection (arrow), whereas other loci are supposed to be

neutral and retain high nucleotide-sequence diversity in the

population.

Nucleotide diversity

Numberofplants

AA BBSelection

Phenotype

Markers

Comparison of SNP allele frequencies

a QTL mapping

Stress tolerant

Stress sensitive

SNP

Phenotyping

Nucleotide diversity

c Selection screening

b Association mapping

F1

RILs

F2

Self pollination(x 6 or more)

A B

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i pticl fcti, whs QTL mppig lsth ffcts f gtic its cmplx tits, whichicld mst gmic tits.

Mlcl gtic ppchs ltily stight-fwd i mdl plts sch sArabidoi thalianad ic, i which gmic sqc ifmtiis ilbl d tsfmti tchiqs wll

stblishd11,12. Miz is ls sfl f gtic stdiss pltifl scs d tls h b dlpd,icldig lg-scl cllctis f mtts (bsd chmicl mtgsis d tsps istis) fbth fwd d s gtic scs13, d sqc-ig f th ti gm hs jst b cmpltd (sblw). IA. thaliana d ic, isti lis gtd

NIL 1 NIL 2

Trait A > B Trait C > D Trait A > BC > D

MAS

F1

a

P1 P2

QTL 1 QTL 1

QTL 2QTL 2

Elite variety

1 3 4 5 6 7 8 9 10

NIL-B1

NIL-B2

NIL-D2

NIL-D1

NIL-A3

NIL-A2

NIL-A1 NIL-C2

NIL-C1

2 11 122 11 12

MAS

Backcross

Grain size

Soil stress tolerance Salt tolerance

b Grain number

QTL analysis

RILs

Figure 1 | QTL yramd. a | A nearly isogenic line (NIL), carrying a QTL responsible for an advantageous trait (QTL 1)

from parental line 1 (P1) is obtained by marker assisted selection (MAS) after backcrossing using parental line 2 (P2)

as a recurrent parent of the first generation (F1) progeny of the parental lines. The resulting NIL (NIL 1) has a

chromosome segment that includes QTL 1 but is otherwise identical to the P2 genetic background. QTL pyramiding is

achieved by hybridization to another NIL (NIL 2) carrying a different advantageous QTL (QTL 2) and by subsequent

MAS, generating a line with a combination of beneficial traits. b | Ultimate QTL pyramiding, which involves the

introduction of multiple advantageous traits from a range of different varieties into an elite variety for which

improvement is desirable. The map positions of loci involved in advantageous traits must be determined; this can be

achieved by QTL analysis using different populations of recombinant inbred lines (RILs) or second generation (F2)

variants, each of which can be derived from an elite variety crossed to another variety with the trait of interest.

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by th s f T-Dna (th mdifid, tsfbl Dnaf sm spcis f bcti) ilbl, i dditi tmtt libis ppd by chmicl mtgsis dtsps istis. M, systmtic tsgicppchs sig ms cDna cllctis hb bld ctly iA. thaliana d ic. F xm-pl, th fll-lgth cDna xpss (FoX)-htigsystm14,15 ils scig cllcti f tsgiclis i which fll-lgth cDnas xpssdt dm. Hw, tsgic ppchs f bthfwd gtic scs d s gtic stdis t yt pcticl i my cp spcis (sch s wht,bly d sghm), i which g miplti tch-lgis ifficit t ilbl. ath limit-ti is libl phtypig, which is still lbis,tim-csmig tsk; itis i this will bimptt f ft pgss.

Idtifyig xistig gtic iti by QTLmppig (Box 1; Fig. 1) is imptt bcs, likmlcl gtic ppchs, this c pid bsisf cp impmt thgh ctil bdig

ppchs810. Th fsibility f QTL mppig dpds th ilbility f gtic mks d ppltis fsggtig idiidls shwig msbl phtypic

iti, whs psitil clig f QTL gs isfcilittd by sqc ifmti d/ physiclmp f th gm. By ths citi, ic is th ld-ig spcis mg cl cps, bcs its cmpltgm sqc is ilbl16. as th gm stctis csd btw ic d th cls, sch smiz, bly, wht d sghm17, sqc ifm-ti fm th ic gm is ls sfl f cmptimppig i ths mctylds (mct) cps.owig t ct dcs i sqcig tchlgy dgig gm sqcig pjcts, th ilbilityf fdmtl ifmti f mppig d cligis big icsd f wid g f cp plts 18,19.rctly, dft sqcig f th gm f sghmd miz hs b cmpltd (s th Phytzm, uSdptmt f egy (Doe) Jit Gm Istitt(JGI), Mizsqc, d Mizgm wb sits fdtils). Hw, g idtificti by QTL mppigi cp spcis is still chllgig, spcilly f lci c-tllig bitic stss tlc. This is ptly d t dif-ficltis i ctllig gwth cditis f my cpsi th fild. F xmpl, bcs plt spss tslt d dght stss lp with spss t lw-d high-tmpt stss20,21, chgs i hmid-

ity d tmpt might sily ffct ths stssspss, csig isy bckgds f phtypiclti d slts tht t pdcibl.Ths, ptd lti f ch tit sig ibdlis, which is m lbis d tim csmig, isqid t bti cicig slts.

Emerging approaches association mapping and selec-tion screens. I dditi t ths wll stblishd mp-pig mthds, tw dditil ppchs tht bsd pplti gtics d tht mk s f gticdisity h ctly mgd: ssciti mppigd slcti scs (Box 1).

I bif, ssciti mppig lis cltibtw gtic mk d phtyp f itstmg plts tht did fm cllctis f disgmplsm9,22. Ths, lg mbs f llls c b tstd this is i ctst t QTL mppig, i which lyptl llls tstd. assciti mppig thti-clly ls llws si fi mppig th th clssiclbiptl-css ppchs, i which lg mb fsggts ft dd. This is bcs hdds thsds f gtis likly t h pssd sicth stblishmt f ssciti btw mk d likd csti lll, llwig tim f lg mbsf cmbiti ts dig misis. Sch tsbk dw ssciti btw csl it d gtic mk tht is t tightly likd t it. I ss-citi mppig, th mk dsity d xpimtldsig dtmid by likg disqilibim (LD)ptts23,24, which flct cmbiti histy ddmgphic fcts, icldig pplti histyd ibdig. usig lg mk sts, sscitimppig c pttilly b pfmd css th whl

gm, ppch tht is ctly big widly ptt s i hm gtics25(Box 1).

Th fsibility f gm-wid ssciti mp-pig iA. thaliana ws ctly tstd sig 95 ccs-sis26,27 i sch f sscitis with flwig timd pthg sistc, d kw gs with mjffcts ths tits (FRI,Rpm1, Rps2 dRps5) wsccssflly idtifid. Ths, whl-gm sscitimppig iA. thaliana is pwfl gh t gt list f cdidt QTLs, lthgh pplti stcti this spcis is imptt chllg i tms flimitig fls psiti slts27,28. amg cl cps,miz is mst sitbl f ssciti lysis bcs itis tcssig spcis xhibitig high cmbitit d pid dcy f LD (


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Nearly isogenic line

(NiL). A lne carryn an

slated hmzyus sement

that cntans a taret QTL f a

parental chrmsme; ther

than ths QTL, the lne has the

ther parental enetc

backrund.

likly t s bcm m pwfl i miz (s thPz wb sit) d i ic (s th ricHpMp wbsit). Spptig this, hpltyps t th lycoene eiloncyclae (lycE) lcs h ctly b ld t bspsibl f itis i th ctt f itmi apcss i miz gis, by ssciti stdy fth cdidt gs cmbid with QTL lysis dchmicl mtgsis33.

ath ctly dlpd mthd idtifis gsf itst by lkig f sigts f slcti3436. Thistyp f sc is bsd th thy tht lci tht hb tgts f slcti shw dcs i cltiddisity d icsd LD ft stg slcti, schs dig dmsticti d sbsqt cp imp-mt37(Box 1).Dmsticti gs c b idtifidby cmpig cltid sqc disity btw cp spcis d xtt ppltis f wild ltis s pxy f th cst spcis. F xmpl, i lg-scl slcti sc, ight gs with is fctisw idtifid s cdidts f gs tht sbjct tslcti dig dmsticti i miz35. Hw,

t s th kwldg gid fm ths scs f cpimpmt, th tits tht ffctd by th slctdg d t b stblishd, lg with dstd-ig f th dlyig bilgy d sbsqt likglysis. M, this mthd might t b sitblf ll cp spcis. F xmpl, i slcti sci sghm, cmpllig idc f slcti wsfd f 371 lci tht hd b xmid38. I dditi,it hs b sggstd tht -tl ptts f di-sity c b csd by dmgphic fcts s wll s byslcti. Ths, th sflss f this ppch might blimitd t spcific spcis ppltis f which thdmgphic histy hs b stdid d c b tkit cct, sch s miz d A. thaliana. Filly,this mthd lis slcti hig tk plc fgh i th pst f sfficit gtic chgs t hccmltd.

Transferring useful traits for crop improvement

T tsf gtic ifmti cfig dtgstits t clti f pfc, bth tsgic (gticmdificti) d -tsgic ppchs c bsd. Th -tsgic ppch is bsd hybidi-zti f tw itis cyig dtgs QTLs sfl g llls, d sbsqt mk-ssistd slc-ti f ths gtic cmpts (Fig. 1). Th ltimtslcti f highly dtgs cmbitis f QTLs

is clld QTL pymidig10. This ppch ds t c-ssily qi th idtificti f th csl gs btc b cid t sig smll chmsm sgmts,ch f which cis ly QTL. Thticlly,spi llls fm sl m difft ptl

itis c b itdcd it lit ity f it-st (Fig. 1b). Disdtgs tht this mthd is lbitsi d tim csmig, d tht th tsff lt llls by hybidizti is stictd t thsm spcis.M impttly, th ffctiss f thisppch dpds th gtic chitct f th tit.This is spcilly imptt bcs, if th ttl itif tit ws bsd my gs f smll ffct, this

sttgy wld t b stightfwd, mstly bcsf cmplxitis tht is wig t gtic d/ g-typ-by-imt itctis. I sch cs, QTLsc b mppd, bt it ds t m tht ths lci dy t b sd f bdig. Th pblm is tht it isft hd t tck ths lci i sbstitti lis inearly senc lnes (nILs), pbbly bcs th ltgtic itctis lst. oly wh th ffcts fQTLs sigifict gh i nILs thy llyilbl f bdig d ls f g clig. Thsm is t wh QTL is tsfd it itywith difft gtic bckgd.

By ctst, th tsgic ppch ds t qihybidizti, bt ds qi idtificti f th gspsibl f dtgs tit. e gs fm-plt spcis c pttilly b sd. I picipl,cmbitis f sl bficil gs c b ts-fd it th sm plt. Hw, t ll cp sp-cis cltis sily tsfmd. I cl cpsth th ic, tsfmti mthds h ith tb stblishd (f xmpl, i sghm) xistigmthds h ly lw fficicy (f xmpl, i whtd bly). e i ic, sm cltis tsfmdly t lw lls. Ths, tchicl dcs i gmiplti will b qid f impmt f thsplts i th ft. ath pttil limitti is thtth fcti f hmlgs gs is ft t xctly thsm mg plt spcis (, idd, mg plt d-plt spcis), which might cs xpctdd wtd sid-ffcts. F pcticl pplicti,mk-ssistd bckcssig f tsg it cm-mcilly ibl ity is ft dd. Th is ls thiss f th pblic ccptc f gticlly mdifidcps, which is byd th scp f this riw.

Yield improvement

amg th tits ffctig cp yilds, w fcs thstht likd t gtic pgmms ctllig thsiz d mb f pdcti gs th thtits tht idictly ild i yild stbility, schs th smi-dwf tit. Hw, it shld b tdtht mdt dcti f plt hight i cl cpsis imptt t id ldgig d thby t icsyilds, s pstd by th G rlti tit.Gs ild i this fm f yild impmt iwht ic kw t cd fct tht it-fs with th sigl tsdcti pthwy f th gwthhm gibblli (Ga) with pdcti f Ga,

s iwd pisly39. I tms f dlpmtlspcts, tmil-bchig ptt d fit-sizctl sm t b th pdmit dtmits fth yild impmt f fits d gis. I ic,f xmpl, tw bsic tits lgly ffct gi yild: thmb f gis p picl d th siz f th gis.Th mb f gis mstly dpds th bchigptt f picls, whichis dtmid by th ctiityd siz f th sht mistm s wll s th timig ftsiti fm sht t flw4042, whs th sizf th gis flcts cll-diisi ctiity. Stdis thgtic ctl f iflscc stct i miz dth gsss h ctly b iwd43,44.

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a piig stdy f cp yild ws th idtific-ti f g ctllig fit siz i tmt by QTLmppig45. This g fw2.2, th fist QTL g t bpsitilly cld i plts is spsibl f 30% fth diffc i fit mss btw wild d cltdtmt.fw2.2 cds pti with ptil hmlgyt th hm raS cpti, d cts s gtiglt f cll diisi45. Sbsqt stdis shwdtht th ccmlti ffw2.2 tscipts id i tmsf timig d qtity btw th tw ccssis46, dtht xpssi lls gtily cltd t fitmss i tificil g dsg sis47.

I cl cps, my QTLs ffctig yild d thimp psitis h b listd i thGm dtbs.rctly, ic gs ctllig gi mss h bidtifid by QTL mppig.g3 ws idtifid s mjQTL f gi lgth d mi QTL f gi widthd thickss48.g3 cds ptti tsmmbpti, which might fcti s gti gltf th gwth f gis. ath QTL ctllig giwidth d wight,gw2, hs ls b idtifid49,50.gw2

cds rInG-typ biqiti e3 ligs, sggstig thtit fctis thgh dgdti f kw tgtpti by th 26S ptsm. Th cdd pti issggstd t b gti glt f cll diisi ispiklt hlls, s lss f fcti icss cll diisid thby gi mss.

I tms f bch mbs, Gn1a hs b idti-fid s mj QTL ffctig th mb f scdyd ttiy bchs i ic, d thby gi mbsp picl51. Gn1a cds cytkii xids/dhyd-gs (osCKX2), zym tht dgds cytkii,th phythm tht pmts cll diisi. a ic

ity with high gi yild, Hbtki, hs ptillss-f-fcti lll f ckx2, th g cdigosCKX2, which is xpssd t lw lls th iKshihiki, ity with lw gi yild (Box 2).Th dcd xpssi css cytkii ccmltii iflscc mistms d icss th mbf pdcti gs, cctig f th ics iyild. M, Chis ity, 5150, which hs mgis p picl th Hbtki, ws shw t h ll lll fckx2. Th lw ll xpssi fck2 i5150 is ls cltd with high lls f cytkiii th iflscc mistm. ashiki et al. chidsccssfl QTL pymidig f yild impmtby itdcig th ic G rlti g, d1,which dcs plt hight i th Kshiki gtic

bckgd, thby gtig ity cyig twbficil tits: high yild d ldgig sistc. Thisw ity is w big ltd ifth fild tilsf fd pdctii Jp.

QTL-mppig stdis f gi siz d f scd-y d ttiy bchig h ld tht ctlf th cll-diisi cycl is cmm ky gltymchism tht iflcs tw spcts f cp yild.Hw, it is still kw hw th fcts tht hb idtifid glt cll diisi i ch dlp-mtl stg. It ls mis t b lcidtd whthth sm glty mchism pts i th cpspcis, d whth th kwldg gid c thf

b pt t s i yild impmt css difftspcis. rct wks h shw tht th mbf pimy bchs i picls is pbbly d thctl f fw mj QTLs (M.M., pblishd bs-

tis), d it will b itstig t s whth thsQTLs ls ild i th cll cycl. F fth yildimpmt i ic, th itdcti f cmbitif th mj QTLs f th difft bt ltd tits sch sg3, Gn1a, d QTLs f pimy bch-ig dditil tits ffctig yild tht likly tb idtifid s52 will b pmisig ppch.Fth impmt shld ls b pssibl, if sp-i g llls cld b fd d itdcd sig lll-miig ppch (Box 2).

Improving stress tolerance

Drought tolerance. Dght, tgth with sil sliity, is f th stsss tht tht wldwid cp pdc-tiity mst sly. I tms f physilgy, bth dghtd slt stsss, s wll s ht cld stss, pdclppig spss i plts, icldig ccml-

ti f smptctts d ht shck ptis, smf which mditd by th ctis f th phyth-m bscisic cid (aBa)20,21,5356. extsi stdis itth sigl tsdcti d tsciptil gltiild i ths spss, mily iA. thaliana, hb iwd ctly21,55,56, d ths t dscibdh. ehcmt f ths spss by g mip-lti ft slts i impd tlc t biticstss, bt th sigificc f my f th gs idti-fid by ths stdis hs t yt b ifid i cpplts i tms f ilbility f bdig. a xcp-ti is nFYB2, tscipti fct f miz, whichcfs dght tlc, ldig t yild impmtd wt-limitd cditis i fild fficcy tils57.This fct ws idtifid s big thlgs t thA. thaliana tscipti fctnFYB1, which ws igi-lly isltd by systmtic tsgic ppch i sc f m th 1,500 tscipti fcts tht wxpssd cstittily iA. thaliana.

amg cp spcis, sghm hs b stdid s mdl f dght sistc bcs f its dptti tht d dy imts. a pticlly lt titcfig dght tlc twds impmt fsghm is th sty g tit. This is chctizdby dlyd lf sscc dig gi ipig dwt-limitd cditis, which ss btt gifillig d is ft sscitd with sistc t chcl

t d ldgig58. Physilgiclly, this tit hs bsggstd t clt with sg ctt f stms dwith lls f cytkiis58. Csistt with this, dghttlc is hcd by dlyig lf sscc wh isptyltsfs g f cytkii sythsis isxpssd d th ctl f stss- d mtti-idcd pmt59. Sl QTL-mppig stdis fsty g idtifid f mj QTLs, dsigtd stg1,stg2, stg3, d stg4, which cct f ppximtly20%, 30%, 16% d 10% f th phtypic ic,spctily60. althgh th gs spsibl f thsmj QTLs h t yt b idtifid, it is xpctdtht ct pgss i th sghm gm sqc

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http://www.gramene.org/http://www.gramene.org/http://www.gramene.org/db/qtl/qtl_display?qtl_id=3386http://www.gramene.org/db/qtl/qtl_display?qtl_id=3919http://www.gramene.org/db/qtl/qtl_display?qtl_id=3919http://www.gramene.org/db/qtl/qtl_display?qtl_id=10693http://www.gramene.org/db/protein/protein_search?gene_product_id=156175http://www.gramene.org/db/genes/search_gene?acc=GR:0020051http://www.gramene.org/db/genes/search_gene?acc=GR:0060842http://www.expasy.org/uniprot/Q9SLG0http://www.expasy.org/uniprot/Q9SLG0http://www.expasy.org/uniprot/Q9SLG0http://www.gramene.org/db/genes/search_gene?acc=GR:0060842http://www.gramene.org/db/genes/search_gene?acc=GR:0020051http://www.gramene.org/db/protein/protein_search?gene_product_id=156175http://www.gramene.org/db/qtl/qtl_display?qtl_id=10693http://www.gramene.org/db/qtl/qtl_display?qtl_id=3919http://www.gramene.org/db/qtl/qtl_display?qtl_id=3386http://www.gramene.org/


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pjct (s th Phytzm wb sit) will fcilitt fimppig f QTLs d sbsqt g idtificti.

I miz, mj QTL dsigtd root-ABA1 isild i t chitct, aBa cctti dth tits ccdig t wt ilbility61. This QTLccts f 32% f th phtypic iti i aBacctti i th lf. oth QTL stdis i slcps f dght tlc dght-ltd tits hb smmizd i ct iws58,62. M ctly,mj QTLs with lg ffcts (cctig f 3233%f th gtic iti) f gi yild d dght

stss cditis i pld d lwld ic h bptd63,64. Hw, th gs spsibl h tyt b idtifid i y f ths stdis. Whthth gs dlyig ths QTLs p t b l idticl t pisly idtifid gs, thy pm-isig pptitis f impig dght tlc i

is cps.

Submergence tolerance. Sbmgc stss wig tflsh fldig is mj cstit t ic pdctii sth d sthst asi. It css dcd xyg

Box 2 | Allele mining of natural variation and the design of artificial variants

After identification of genes

that are responsible for

quantitative traits, allele

mining can be performed.

This compares the level of

function of a particular gene,

and its availability for

breeding, in two parentalvarieties.

For example, in the case of

ckx2 alleles, which encode

a cytokinin oxidase/

dehydrogenase (part A in thefigure) the variety with higher

grain yield, Habataki, has

lower levels of expression

than one of the standard

varieties, Koshihikari,

although both alleles encode

functional cytokinin oxidase/

dehydrogenase. In Habataki,

the lower expression results in lower levels of cytokinin-degrading enzymes in the inflorescence meristem, leading to

an increase in the number of grains. Hence, a partial loss-of-function allele of ckx2 in Habataki has been selected in theprocess of breeding, whereas Koshihikari contains a gain-of-function allele. The expected direction for finding a

superior allele leading to better yield is mining of a gene allele with less function. The predicted direction of suitability

(indicated by the arrow at the bottom of the graph) was verified by the finding that a high-yielding variety, 5150, with

much higher grain yield than Habataki carries a null allele of ckx2, this being the most suitable allele for high yield.

In general in contrast to the simple case as described above to find the most suitable function among gene

alleles, other gene variants with different levels of gene function should be tested in terms of availability for breeding.

Possible situations in which conflicts between gene function and availability for breeding affect the overall suitability of

an allele are illustrated in part B of the figure, which is based on the effects of two initial gene alleles. In the case ofpattern a, in which two additional gene variants with increased function exist among naturally occurring variation(indicated by brown circles), one has a more advantageous effect on availability for breeding, but a second additional

allele with an even greater gain-of-function causes detrimental side-effects with respect to this attribute. Consequently,

the former is the most suitable allele, as any artificially designed alleles with increased function are also likely to have

negative effects on suitability for breeding (dashed brown line). By contrast, in patterns b and , increased gene functionamong variants that occur within naturally existing variation (alleles represented as yellow and blue circles) does not

have a negative effect on availability for breeding. In such cases, artificial design of new variants (indicated bytriangles) and introduction of these variants by transgenic approaches should be useful for finding the most suitable

alleles, which might lie beyond the limits of natural variation. In pattern b, optimal gene function is found amongartificially designed alleles. In the case of pattern , the generation of additional gain-of-function alleles is required foroptimization (dashed blue line).

This advanced allele mining strategy, which is extended by the artificial design of genes, is potentially powerful for

crop improvement. Using this strategy, the limitations of plant species for allele mining by crossing using traditional

breeding approaches could also be overcome, for example, by introducing a corresponding gene with a more relevant

function from other species, such as a transgene. Such a new allele might be found, for example, by carrying out an

in vitro assay of the activity of the encoded proteins so that the effects of artificial mutations could be examined more

efficiently. Alternatively, advantageous gene variants might be found in wild relatives or other species, the habitats of

which feature stressful environments. Once such a superior gene allele is found, homologous recombination might also

be useful to introduce small mutations at the specific loci107. Thus, a combination of QTL mapping and the transgenic

approach is likely to become increasingly important in the near future.

Function ofckx2

Yield

Availabilityforbreed

ing

Function of gene

c

b

a

QTLQTL

?

A B

Suitability Suitability

Natural variation Natural variation Artificial design

5150Null allele

Allele 1

Allele 2

Habataki

Partial loss-of-function allele

KoshihikariGain-of-function allele

Most suitablefunction

Most suitablefunction

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Ethylene response factor

(ERF). Refers t members

f a subfamly f the AP2

transcrptn factr famly,whch s unque t the plant

lneae. ERF subfamly

prtens carry a dman

that s cnserved n ethylene-

respnsve element-bndn

prtens.

Major intrinsic proteins

(MiPs). A lare prten famly,

the members f whch act as

channels n membranes t

facltate passve transprt f

small plar mlecules such

as water, lycerl and urea

acrss the membrane.

spply d thby ihibiti f spiti. ric, whichhs itcctd gs spcs clld chym, is th f th fw cps spcis tht hs bility t g-mit d gw i wtlggd sils. Hw, dcmplt sbmgc cditis mst ic cltisct si f m th wk, bt fw clti-

s, sch s Fr13a f th indica clti, c sip t tw wks. a mj QTL, subergence1 (sub1),is likd t th sbmgc tlc f Fr13a65. Thislcs ctis clst f th gs (sub1A, sub1B,d sub1C) thtcd ptti ethylene respnse fac-trs (erFs)66. Th spsibl g f sbmgctlc hs b idtifid s sub1A67. amg sub1lcs hpltyps i 17 indica d 4jaonica itis, thtlc is cltd withth spcific lll sub1A-1,with SnP btw this d th itlt lll. ectpicxpssi fsub1A-1 i itlt ity icsssil dig sbmgc. M, itgssif th sub1 gs it th widly gw Idi itySw, which lcks sub1A, cfs stg sbmgctlc witht ffctig yild, plt hight, hst

idx, gi qlity idictd by myls ctt.Dlpmt f sbmgc-tlt itis sigth sm bdig pcd is t dcd stgf sth asi ctis, d hs ls b ptdi Thild68.

I tms f mchism, th t f sbmgctlc mis cl. SuB1a hs b ppsdt sppss cbhydt csmpti d thbycmpmis gy dficit d sbmgc by ihi-biti f cti f SuB1C, thyl d Ga69. Hw,th hs t b s mch pgss sbmgctlc by gtic lyss th th sub1 stdis.M, difft mchisms might ctl sbm-gc tlc i cps th th ic. Csidigtht my cps ssiti t sil dmpss, fthistigti is dd t dstd th mchismsf sbmgc tlc i ths spcis.

Aluminium tolerance.I highly cidic sils, whichcstitt p t hlf f th wlds bl lds, l-miim (al) txicity css sigifict dcti icp pdcti70. at lw pH lls (


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t-t-sht tspt f b by xylm ldig.Bor1 hs t ptti tsmmb dmis, is sim-il t iml bicbt tspts d its xps-si i yst slts i dcsd b ccttis,idictig tht Bor1 is fflx-typ t spt.Bor1 is spcificlly lclizd i th picycl f ts iA. thaliana, d mdits b xpt fm picyclclls it th t stl pplsm gist cct-ti gdit. ud b-limitig cditis, -xpssi f Bor1 icss bth b tslctit th sht px d its t-t-sht tslcti82.ud cditis f high b cctti, Bor1is tsfd fm th plsm mmb i thdsms t th cl d th dgdd83. This is mchism t id ccmlti f txic lls fb i shts.rctly, th ic thlg f Bor1hs b shw t h l i b ptk dxylm pldig84. It will b itstig t dtmiwhth th gtic miplti f tspts icp spcis will pid pcticl ms f ptctifm b dficicy.

By ctst, i stdis f plt sistc t btxicity, b-tlt clti f bly Sh ccmltd lw lls f b ccmlti ibth sht d t85. It ws sggstd tht this wsmditd by cti fflx pmpig fm t clls.Csistt with this, high xpssi lls fBOR2, bly hmlg fBOR1 lctd t chmsm4H, cltd with dcti i b cct-ti i ts wh sig lis tht w gtd bybckcssig Sh with b-ssiti clti,Slp86. QTLs spsibl f tlc t b tx-icity hd ls b idtifid i css f Sh dth ssiti ity, Clipp87. Th mj lcs

ffcts b ccmlti d lf symptms db-txic cditis88. By high-slti mppigf this lcs, Bot1, BOR1 thlg cdig fctil b fflx tspt, ws idtifid sth g spsibl f th b-txicity tlc88.Cmpd with Clipp, Sh ctis f timsm Bot1 cpis, d 160-fld d 18-fld high llsfBot1 tscipts i ts d lf blds, spctily.Th imptc f Bor1-ltd fflx tsptsws fth dmsttd by fctil lyss fA. thaliana Bor4 (REF. 89). I ctst t Bor1, Bor4is t dgdd bt is ccmltd t icsd lls ihigh-b cditis. M, B or4 is lclizdi th plsm mmb f th distl sits f pidmlclls i th lgti z f ts, pbbly -blig th dictil xpt f b t th sil (Fig. 2).Fthm, xpssi f Bor4 css stgtlc t txic ccttis f b, ccmittwith lw lls f b ccmlti i ts dshts cmpd with wild-typ plts.

Bth th QTL stdis i mct cps d th

mlcl lyss iA. thaliana sggst tht imp-mt f cp pdctiity i b-txic sils shldb chibl by th itdcti f b fflx ts-pt gs with hcd xpssi. Ths sltsls sggst tht cll typ-spcific glti f ts-pt gs is imptt f ffcti b tspt.Csidig tht th mchism cfig b tl-c is s csd css spcis, it might b pssibl tmiplt BOR gs i my difft cp spcist chi th sm ffct, phps sig th smtsg i difft spcis, if di by sitbl p-mts. This hypthsis will qi cfl xmitid fild cditis.

Salt tolerance.Th h b ms mlclgtic d physilgicl stdis slt tlc,mstly iA. thaliana20,53,54,90(Fig. 3a). Bcs high c-cttis f cytslic n+ txic, it is impttt limit n+ fm th cytsl by tspts. Thn+H+ xchg SoS1 fcilitts fflx f n+ cssth plsm mmb, whs th cl n +H+tiptnHX1 tspts cytslic n+ it c-ls20,53,54,90. oxpssi f SoS1, nHX1 d thihmlgs cfs hcd slt tlc i myplt spcis, icldig ic d miz54. Th sm ist f avP1, H+-pyphsphts; itstigly,xpssi f AVp1 lll tht cis gi-f-

fcti mtti slts i t ly hcd tlct slt d dght, bt ls icsd t bimssd phsphs titi9193.

at whl-plt lls, it is thght tht th blcf n+ d K+ is (th clll n+/K+ ti) is lsimptt f slt tlc, spcilly i clcps94,95. Spptig this thy, th Kna1 lcs wsidtifid s ctibtig t lw n+/K+ ti d thigh slt tlc i bd wht94 d, i wild l-tis f bly with stg slt tlc, ccmltif n+ i lf blds fllwig slt stss w t stik-igly lw lls cmpd with th cltitd bly96.I ic, sl sch gps h dissctd th QTLs

CoEp En Pc Xy

Root

B

Cs

B

B

BOR4BOR1 NIP5-1

B

Figure 2 | Br trasrtrs. Transport of boric acid (B)

across membranes inArabidopsis thaliana is facilitated by

a plasma membrane-located channel protein, NIP5-1, and

by cell-type specific efflux transporters (BOR1 and BOR4).

NIP5-1 and BOR1 are involved in boron uptake under

boron-deficient conditions, whereas the boron-exclusion

activity of BOR4 confers tolerance to toxic concentrations

of boron. Boron that is taken up into root cells from the

soil is moved through a symplastic pathway by

plasmodesmata (dashed arrows), whereas apoplastic

movement is hindered by the casparian strip (Cs). Co,cortex; En, endodermis; Ep, epidermis; Pc, pericycle;

Xy, xylem. This figure is modified, with permission, from

REF. 84 (2007) American Society of Plant Biologists.

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http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=100127239&ordinalpos=3&itool=EntrezSystem2.PEntrez.Gene.Gene_ResultsPanel.Gene_RVDocSumhttp://www.expasy.org/uniprot/Q9LKW9http://www.expasy.org/uniprot/Q68KI4http://www.expasy.org/uniprot/P31414http://www.expasy.org/uniprot/P31414http://www.expasy.org/uniprot/Q68KI4http://www.expasy.org/uniprot/Q9LKW9http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=100127239&ordinalpos=3&itool=EntrezSystem2.PEntrez.Gene.Gene_ResultsPanel.Gene_RVDocSum


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Vacuole

SOS1 NHX1 AVP1

PPi 2Pi

Osmoprotectants CoEp Ex Sc En St

Root

Shoot

Cs Cs

?

H+

H+

H+

H+ H+

ATP

ADP

ATP

ADP

Plasma membrane

HSPs

NSCC

Xp

?

Xp

Cytosol

?

Na+

Na+Na+

Na

+ Na+ Na+

Na+

Na+

Na+

Na+

Xylemvessel

SKC1

HKT1

NSCC

a b

spsibl f itis i n+ d K+ ctt97. usigth slt tlt indica ic ity n Bk d thslt ssitijaonica ity Kshihiki, Li et al.mppd mj QTL f sht K+ ctt i sdligs,skc1, which ws ld t cd HKT-typ ts-pt, SKC1 (ls kw s HKT8 d lt dsigtds HKT1;5)98100. SKC1is th slcti tspt fn+, which is lclizd t th plsm mmb d ispftilly xpssd i th pchym clls s-dig th xylm ssls (Fig. 3b). Th ly isgicli NIL(sKC1), which ctis th slt-tlt sKC1lll f n Bk withi th gtic bckgd fslt-ssiti Kshihiki, ws dmsttd t cfslt tlc t th sdlig stg. ud slt stss,NIL(sKC1) xhibits high K+ ctt d lw n+

ctt i th sht th th Kshihiki ity. Its, bth n+ d K+ ctt th sm i thtw lis d bth ml d stss cditis,lthgh xpssi fsKC1 is pgltd by sltstss i ts bt t i shts. I xylm sps btt phlm sps, NIL(sKC1) hs m K+ d lss

n+ th i Kshihiki d slt stss, lthgh diffc ws bsd d ml cditis.

Bsd ths slts, it is sggstd tht SKC1 c-tibts t n+ d K+ tslcti btw ts dshts, pssibly by n+ ldig fm xylm, thbyffctig th n+/K+ ti i th shts. Th sbsttil diffcs i th xpssi ptt btwNIL(sKC1) d Kshihiki. Hw, wh xpssdi thXenou laevi cyts, SKC1 fm n Bkxhibits high sdim-tsptig ctiity th SKC1fm Kshihiki. Ths, th f-mi-cid diffcbtw th cdd SKC1 ptis, which is lctd ith lps btw th ptti tsmmb dmis,is likly t b spsibl f th fctil diffcbtw th tw itis.

I dm wht, th QTL Nax1 hs b stdid s gtic cmpt tht cfs lw n+ d high K+ccttis i th lf bld101. usig nILs, Nax1 wsshw t h l cfig slt tlc thghhigh lls f n+ xclsi fm th xylm i th tsd lf shth, thby dcig n+ cctti

Figure 3 | Mast mdls salt tlra. a | Cellular responses to Na+ toxicity. It is thought that Na+ is

passively transported into the cytosol by non-selective cation channels (NSCCs)108.To decrease cytosolic Na+

concentration, two mechanisms operate. One is to exclude Na+ across the plasma membrane. SOS1, a Na+H+

exchanger located at the plasma membrane, is the only transporter identified in plants that carries out this function.

Another mechanism is to compartmentalize Na+ into vacuoles, where Na+ is less toxic. This is performed by the

vacuolar Na+H+ antiporter, NHX1. Both transporter activities require an H+ gradient across the membranes, which is

generated either by a plasma membrane H+-ATPase or by a vacuolar H+-ATPase (yellow ovals), and by vacuolar H+-

pyrophosphatase (AVP1). Accumulation of osmoprotectants (for example, betaine, proline and sugar alcohols) and

heat shock proteins (HSPs) are also induced by salt stress. Overexpression of SOS1, NHX1, and AVP1, as well as HSPs

or proteins for the biosynthesis of osmoprotectants, has been reported to enhance salt tolerance in several plant

species. For more details, see REFS 53,54 for reviews. b | Transport of sodium ions in rice. Na+, which is taken up intoroot cells from soils, presumably by NSCCs, is moved by the symplastic pathway through plasmodesmata, whereas

apoplastic movement of Na+ is hindered by the casparian strip (Cs). For long-distance movement through xylem vessels

in an apoplastic manner, Na+ is uploaded from root xylem parenchyma cells (Xp) and unloaded by leaf xylem

parenchyma cells. SKC1, a rice HKT transporter (also known as OsHKT1;5 and previously named OsHKT8), is proposed

to take up Na+ from xylem vessels into xylem parenchyma. The role of this HKT transporter is also supported by recent

studies of anArabidopsis thaliana homologue, HKT1;1. Another HKT-type transporter, HKT1 (also known as

OsHKT2;1)109 is involved in Na+ uptake in the epidermis (Ep) and cortex (Co) in roots only in soil conditions with low

concentrations of K+ and Na+. This uptake is downregulated in the presence of K+ and Na+, thus it is negligible in stress

conditions involving salinity. Export of Na+ from epidermal cells and xylem parenchyma is mediated by SOS1 in

A. thaliana, and possibly by the SOS1 homologue in rice. For more detailed information, see REF. 90 for a review.

Ex, exodermis; Sc; sclerenchyma cells; En, endodermis; St, stele. Dashed line, breakage of cortex cells generating

aerenchyma. Part a is modified, with permission, from REF. 54 (2005) Cell Press. Part b is modified, with permission,

from NatureGeneticsREF. 110 (2005) Macmillan Publishers Ltd.

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http://www.expasy.org/uniprot/Q0JNB6http://www.nature.com/ng/index.htmlhttp://www.nature.com/ng/index.htmlhttp://www.nature.com/ng/index.htmlhttp://www.nature.com/ng/index.htmlhttp://www.expasy.org/uniprot/Q0JNB6


11/14

Recombinant inbred line

(RiL). A preny lne carryn

dspersed hmzyus

sements f a parental

chrmsme, frmed after

several selfed eneratns

f an F2lne.

i th lf blds102. By cmpti mppig f whtd ic chmsms, HKT7-A2, cdig sdimtspt, ws sggstd t b stg cdidtg f Nax1 (REF. 103). HKT7-A2 is xpssd ibth ts d lf shths, bt t i lf blds, fslt-tlt wht li 149 d Triticu onococcuC68-101, whs tscipts dtctd i th slt-ssiti Tmi it. This pssibly ccts f thdcsd lls f n+ i lf blds i th tlt lis,by mchism simil t tht ppsd fm th stdyf SKC1 i ic.

It is still mbigs, hw, t wht xtt SKC1-ltd tspts cct f slt tlc i gl,gi tht th mj QTLs th th sKC1 ctibtt sdlig sibility d slt stss i ic98. echf ths QTLs ccts f 14% t 18% f th ttl ph-typic ic. Ths, idtificti f th gs fsch QTLs d m gtic stdis i mct cpsshld b imptt f btt dstdig f thslt-tlc mchism t th sdlig stg.

as i th cs f b fflx tspts, mip-lti f th n+ tspt g i cll typ-spcificm shld b ffcti t cf slt tlc imy cps. Sch fi glti wld ls b bfi-

cil t miimiz pttil sid-ffcts. usig stss-idcd pmt is ltti wy t chi thispps, s xmplifid pisly104. T tsf thbtid kwldg t m pcticl pplicti,it is imptt t csid gtic itctis dgtyp-by-imt itctis. It will b ss-til t dictly cmp th bility f is gs tcf slt tlc, sig th cltis gildmds thgh ith itgssi f th mjQTLs thgh miplti f gs. Cmbitilitdcti f bficil gs by bdig d ts-gic ppchs shld ls b ltd t s thipttil bilitis m ffctily.

Table 1 | Genes responsible for abiotic stress tolerance and yield improvement in crops identified by QTL analysis

Trat cr g (adrrt ara xlad)

edd rt Dr btwt artal arts

natur alllsutabl r us mrmt

Rs

Fruit size Tomato fw2.2 (30%) RAS-related protein Expression level Low expression 4547

Grain size (weight) Rice gs3 (20%) Transmembrane protein Nonsense mutation Loss of function 48

Grain size (length) Rice gs3 (55%) Transmembrane protein Nonsense mutation Loss of function 48Grain size (width) Rice gw2 (58%) RING-type ubiquitin E3

ligase3Premature stop Loss of function 49, 50

Grain number Rice Gn1a (44%) Cytokinin oxidase/dehydrogenase

Expression level Loss of function 51

Submergence tolerance Rice Sub1A (70%) ERF-related factor Presence or absence Gain of function 65, 67

Aluminium tolerance Wheat ALMT1 (80%) Malate efflux transporter Expression level High expression 72

Aluminium tolerance Sorghum MATE (80%) Citrate efflux transporter Expression level High expression 74

Boron toxicity tolerance Barley Bot1 (34%) Boron efflux transporter Expression level High expression 8688

Salt tolerance (shoot K+concentration)

Rice SKC1 (40%) HKT-type Na+ transporter Amino-acid substitution Gain of function 98, 99

Salt tolerance (low Na+in leaves)

Wheat Nax1 (38%) HKT-type Na+ transporter Expression level High expression 103

Conclusions and future directions

Tditil mlcl gtic stdis h ctibtdt dstdig f th dlyig bilgy ildi bitic stss tlc d yild ctl, whsQTL stdis h ld gtic cmpts tht ilbl f thi impmt i xistig itis.Th hs b gd pgss i g idtificti byQTL mppig f tits, icldig yild d tlc tsil stsss (TABLE 1), sm f which pid dditilcls f impmt f spcific tits i giclt.assciti mppig d slcti scs pt-tilly sfl ppchs f ft mppig stdis, bth s f b pfmd ly i miz dA. thal-iana. T s ths mthds, d QTL mppig, mffctily, it will b imptt t dlp pplicblscs, icldig lg-scl cllctis f cltis,ldcs gmplsm lis s wll s ibd lisdid fm thm, with xtsi ifmti btSnPs d th gtic mks. als, btt kwl-dg f pplti stcts is imptt f bttdsig f ssciti stdis d f dt itptti.Stdis tht cmbi QTL mppig d sscitilysis might p m sccssfl th ithsttgy l. a gig fft t bl sch std-

is is th dlpmt f lg-scl miz-mppigpplti, cmpisig 5,000recmbnant nbred lnesdid fm cssig ch f 25 dis ibd lis t stdd li, B73, i cjcti with lid-ti f thsds f SnPs (f dtils, s th Pzwb sit)22. assciti stdis f cdidt gs,th fctis f which ld by QTL mppigd/ th ppchs, will b spcilly sfl flll miig.

Sm iitil isights h b pidd it thchitct f tits lt t cp impmt,which gis imptt ifmti f sttgis t sth gtic cmpts tht idtifid. F xmpl,

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f gi yild i ic, sl mj QTLs cct flg ptis f th phtypic iti. Th it-dcti f sch mj QTLs pids fficitsttgy f cp impmt, d itdcig cm-bitis f difft bficil lci by QTL pymid-ig is pmisig ppch. Sch sttgy is mchlss pwfl if tit is ctlld by my QTLs withsmll ffcts. Impttly, thf, th sccss f thQTL-bsd ppch lgly dpds th chic fptl itis t th sttig pit. a ity c-yig mkd impmt i dtgs titis mst dsibl t b sd i cmbiti with stdd ity tht hs b slctd by tditilbdig pgmms. Hw, s f, QTL stdish ft b sttd with itis tht chs th bsis f th ilbility f gtic mks, thth th dtgsss f tits, ldig t dcdchc f fidig mj QTLs with lg ffcts. This isi pt bcs f th limitti f ilbl sqcifmti , m spcificlly, mk ifmti.rct d ft dcs i sqc tchlgis

d plymphism dtcti will ld t imp-mts i this d will fcilitt m tit-itdstdis.

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spdig t imtl iti pticllyth iti sscitd with climt chg.

Stdis cid t s f h ls pidd isightsit th xtt t which gs implictd i dt-gs tits likly t b sfl css difft cpspcis. F impig tlc t sil stsss, it-dcti f spcific i tspts is likly t b ffcti sttgy. Bcs ths tspts highlycsd, miplti f th sm g cld ls bsd css spcis. This is i ctst t th g f glt pti ild i sbmgc tlci ic, which sms t b ffcti ly i spcis-spcific m. Fth impmt sig tspt-s shld b chid if spi g llls cldb fd i tl itis d i idcd gtic

itis (f xmpl, by chmicl mtgsis), by tificil dsig.

Simil t QTL pymidig, th itdcti fcmbitis f difft bficil gs it lit

ity thgh th tsgic ppch is ls likly tpid imptt dicti i cp impmt

(w c cll this tsgic pymidig). Bcs stsscditis, sch s sliity d dght, y dpd-ig lcl climts d ggphicl fts, th fitig f g ctiitis will b qid f pcticlpplicti i ch . F ptimizti i spc-ti cditis, lll miig d g pymidig (byith hybidizti g miplti) will b sflt pdc sis f plts cyig difft cmbi-tis f dtgs gs t difft lls f ctiity.Slctig th ptiml cmbitis mg ths i-tis d ltig th spcific td-ffs, i tmsf bilgicl dptti, pdctiity d cmic

l, pmiss t pid sltis t p-xistigbitic stsss s wll s pspcti imtlchgs.

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AcknowledgementsWe thank M. Maeshima, T. Fujiwara, D. Saisho, M. Ashikari,

and T. Hattori for useful suggestions.

DATABASESEtrez gee:http://www.ncbi.nlm.nih.gov/entrez/query.

fcgi?db=gene

ALMT1 | Bot1|FRI|PSY1|RPM1 |RPS2|RPS5

grmee:http://www.gramene.org

ckx2|Gn1a | gs3|gw2 | HKT7A2 |OsCKX2 | sd1 | Sub1

uiPrtKb:http://ca.expasy.org/sprotAVP1|BOR1 | NFYB1 | NHX1 | NIP5-1|SKC1|SOS1

FURTHER INFORMATIONSi Tkeds mepe:

http://www.agr.nagoya-u.ac.jp/~nubs/index-e.html

DoE Jit geme Istitte (JgI):http://www.jgi.doe.gov/

sequencing/cspseqplans2006.html

Mizeseqee: http://www.maizesequence.org/index.html

Mizeeme: http://www.maizegenome.org

Pze:http://www.panzea.org

Pytzme: http://www.phytozome.net/sorghum

RiehpMp:http://www.ricehapmap.org

ALL LinkS ARe AcTive in The onLine pDf

R E V I E W Sf oc uS on g loba l c h a llE n g E S
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genehttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genehttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genehttp://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=543388&ordinalpos=1&itool=EntrezSystem2.PEntrez.Gene.Gene_ResultsPanel.Gene_RVDocSumhttp://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=100127239&ordinalpos=3&itool=EntrezSystem2.PEntrez.Gene.Gene_ResultsPanel.Gene_RVDocSumhttp://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=100127239&ordinalpos=3&itool=EntrezSystem2.PEntrez.Gene.Gene_ResultsPanel.Gene_RVDocSumhttp://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=828044&ordinalpos=1&itool=EntrezSystem2.PEntrez.Gene.Gene_ResultsPanel.Gene_RVDocSumhttp://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=828044&ordinalpos=1&itool=EntrezSystem2.PEntrez.Gene.Gene_ResultsPanel.Gene_RVDocSumhttp://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=828044&ordinalpos=1&itool=EntrezSystem2.PEntrez.Gene.Gene_ResultsPanel.Gene_RVDocSumhttp://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=100136882&ordinalpos=1&itool=EntrezSystem2.PEntrez.Gene.Gene_ResultsPanel.Gene_RVDocSumhttp://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=100136882&ordinalpos=1&itool=EntrezSystem2.PEntrez.Gene.Gene_ResultsPanel.Gene_RVDocSumhttp://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=100136882&ordinalpos=1&itool=EntrezSystem2.PEntrez.Gene.Gene_ResultsPanel.Gene_RVDocSumhttp://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=819889&ordinalpos=1&itool=EntrezSystem2.PEntrez.Gene.Gene_ResultsPanel.Gene_RVDocSumhttp://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=819889&ordinalpos=1&itool=EntrezSystem2.PEntrez.Gene.Gene_ResultsPanel.Gene_RVDocSumhttp://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=828715&ordinalpos=1&itool=EntrezSystem2.PEntrez.Gene.Gene_ResultsPanel.Gene_RVDocSumhttp://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=828715&ordinalpos=1&itool=EntrezSystem2.PEntrez.Gene.Gene_ResultsPanel.Gene_RVDocSumhttp://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=828715&ordinalpos=1&itool=EntrezSystem2.PEntrez.Gene.Gene_ResultsPanel.Gene_RVDocSumhttp://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=837775&ordinalpos=1&itool=EntrezSystem2.PEntrez.Gene.Gene_ResultsPanel.Gene_RVDocSumhttp://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=837775&ordinalpos=1&itool=EntrezSystem2.PEntrez.Gene.Gene_ResultsPanel.Gene_RVDocSumhttp://www.gramene.org/http://www.gramene.org/http://www.gramene.org/db/genes/search_gene?acc=GR:0020051http://www.gramene.org/db/genes/search_gene?acc=GR:0020051http://www.gramene.org/db/qtl/qtl_display?qtl_id=10693http://www.gramene.org/db/qtl/qtl_display?qtl_id=10693http://www.gramene.org/db/qtl/qtl_display?qtl_id=3386http://www.gramene.org/db/qtl/qtl_display?qtl_id=3386http://www.gramene.org/db/qtl/qtl_display?qtl_id=3919http://www.gramene.org/db/qtl/qtl_display?qtl_id=3919http://www.gramene.org/db/protein/protein_search?gene_product_id=185847http://www.gramene.org/db/protein/protein_search?gene_product_id=156175http://www.gramene.org/db/protein/protein_search?gene_product_id=156175http://www.gramene.org/db/genes/search_gene?acc=GR:0060842http://www.gramene.org/db/qtl/qtl_display?qtl_id=7285http://ca.expasy.org/sprothttp://www.expasy.org/uniprot/P31414http://www.expasy.org/uniprot/P31414http://www.expasy.org/uniprot/Q8VYR7http://www.expasy.org/uniprot/Q8VYR7http://www.expasy.org/uniprot/Q9SLG0http://www.expasy.org/uniprot/Q68KI4http://www.expasy.org/uniprot/Q9SV84http://www.expasy.org/uniprot/Q9SV84http://www.expasy.org/uniprot/Q0JNB6http://www.expasy.org/uniprot/Q0JNB6http://www.expasy.org/uniprot/Q0JNB6http://www.expasy.org/uniprot/Q9LKW9http://www.expasy.org/uniprot/Q9LKW9http://www.agr.nagoya-u.ac.jp/~nubs/index-e.htmlhttp://www.jgi.doe.gov/sequencing/cspseqplans2006.htmlhttp://www.jgi.doe.gov/sequencing/cspseqplans2006.htmlhttp://www.maizesequence.org/index.htmlhttp://www.maizegenome.org/http://www.maizegenome.org/http://www.panzea.org/http://www.phytozome.net/sorghumhttp://www.ricehapmap.org/http://www.ricehapmap.org/http://www.phytozome.net/sorghumhttp://www.panzea.org/http://www.maizegenome.org/http://www.maizesequence.org/index.htmlhttp://www.jgi.doe.gov/sequencing/cspseqplans2006.htmlhttp://www.jgi.doe.gov/sequencing/cspseqplans2006.htmlhttp://www.agr.nagoya-u.ac.jp/~nubs/index-e.htmlhttp://www.expasy.org/uniprot/Q9LKW9http://www.expasy.org/uniprot/Q0JNB6http://www.expasy.org/uniprot/Q9SV84http://www.expasy.org/uniprot/Q68KI4http://www.expasy.org/uniprot/Q9SLG0http://www.expasy.org/uniprot/Q8VYR7http://www.expasy.org/uniprot/P31414htt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Genetic approaches to crop improvement

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