marker-assisted selection in wheat - ictsd

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Chapter 5 – Marker-assisted selection for improving quantitative traits of forage crops 61IntroductionMost agronomical characteristics of foragecrops have a quantitative, polygenic andmostly complex nature. For these reasons,genetic improvement of such traits islaborious and time consuming. Improvingnitrogen use efficiency (NUE) in perennialryegrass (Lolium perenne, 2n = 14), themajor grass species in northern Europe, isin this respect a good example. The highinput of nitrogen needed to attain highforage yields for animal husbandry hascaused severe water pollution (van Loo etal., 2003), and therefore lowering nitrogeninputs through improving nitrogen use bybreeding is of utmost importance.Selection for NUE, however, is not easilyimplemented in conventional grass breedingbased on field evaluations. Adequatetesting requires separate and long-term trialswith good control of the N stress, andsuch experiments tend to be rather inaccurate.To circumvent the disadvantagesof field testing, a hydroponics system wasused in this study in which the crop situationis simulated with growth-dependentN application (van Loo et al., 1992), theaim being to grow plants having an equalsuboptimal N content. The set-up has acapacity to test about 1 600 plants in paralleland enables all plants to experience moreor less the same N strain. Criteria used tomeasure NUE are several plant growthcharacteristics, such as tillering, and shootand root growth. Each test usually requiresfour to five cuts. The trait is vigour-relatedand complex, and is extremely important inrelation to regrowth after cutting. Together,all these aspects make NUE a very attractivetrait for MAS.Analysis of genetic variationThe genetic variation for NUE presentin an F 1 plant originating from a crossbetween two contrasting genotypes forNUE was first analysed by crossing theF 1 with a doubled haploid. The resultingtest cross progeny was then used to producea molecular marker map and analysethe variation. This approach was chosento avoid inbreeding effects and to be ableto use dominant molecular markers. Theperformance of the mapping population forNUE-related traits was studied on hydroponicswith the system set at a moderatelylow nitrogen deficiency (3.6 percent N ofleaf dry weight). The outcome of the mappingstudy was a genetic map with sevenlinkage groups.Putative genes (quantitative trait loci[QTL]) for the components of NUE werefound on four linkage groups. The locationof the selection markers for QTL is depictedin Figure 1. The map shows five genomicsites with 1-5 QTL. In total, 13 QTL forseven NUE related traits were found. Threesites contain more than one QTL.The findings of the current study aretypical for genetic analyses of quantitativetraits in forage crops and also indicativeof the problems associated with exploitationof QTL information through markerassistedbreeding. These included uncertaintieswith respect to effect and locationof QTL, the fairly large number of QTLoften found in genetic analyses, the cosegregationof QTL and the weighing ofthe different component traits of NUE andNUE-QTL. Below is a description of howthese breeding problems were solved orcircumvented in a divergent marker selectionstudy to validate the QTL found in themapping study.Divergent marker selectionThe plant materials used in the validationstudy were an F 2 generation obtained byselfing of the heterozygous F 1 genotype
62Marker-assisted selection – Current status and future perspectives in crops, livestock, forestry and fishFigure 1Map position of the selection markers (in blue) for QTL for seven components ofnitrogen use efficiencyLG1LG3LG4LG6E32M49-164E37M49-4030 K10F08-1415 K10F08-14410 E32M52-02R15 E32M49-21920 E32M54-05R25 E38M48-04R30 E38M48-13035E32M52-352E32M48-3034045 E41M48-23950 E32M52-01R55E36M48-220E41M47-42560E32M52-04R65E41M61-362707580859095100105110115120125130135140145150155160165170E36M48-180E36M50-094Uni-001-147K07H08-165E40M47-380E38M51-285E38M49-223LW1 E36M49-213LAE3 E37M49-343E37M49-118E35M48-252E38M49-309E41M48-479E38M51-429K14F12-113K14F12-123E32M54-03RE38M49-305E35M48-339E38M51-01RE33M49-233E32M51-313E37M49-201E37M48-265E41M48-205E38M49-242TN1DWS1LAE1DWT1LWR1Rye35-117K04D01-157K04D01-239E35M48-328E41M48-268E37M48-347E36M50-233E38M48-11RADH-1000Rye12-148Rye26-147E32M51-303E36M49-133E38M48-416E32M51-328E41M48-296E38M51-247E33M49-277E36M49-217E38M48-08RE37M48-331E38M51-14RE41M48-299E32M51-212E38M47-334E38M47-255E38M47-348E35M47-135E41M48-208E38M48-093E38M51-291E38M51-04RE32M51-304E33M51-03RE38M52-262E38M52-260E38M51-12RE38M51-267Meth300-250E36M48-108E37M47-441KXX104-108TN2DWS2LAE2DWT2DWR1Rye14-221Rye14-223E38M52-289E36M49-297E36M50-173E32M52-169E38M51-13RE38M48-10RE38M48-05RE38M48-06RE32M52-08RE38M48-110E38M51-264E32M52-126E32M52-06RE36M48-163E35M48-141E38M47-116E32M54-06RE37M47-327E32M52-137E32M52-07RE35M47-278LWR2TN: Tiller numberLAE: Leaf area expansionLW: Leaf widthLWR: Leaf weight ratioDWR: Dry weight rootsDWS: Dry weight shootsDWT: Total dry weightused to generate the mapping populationmentioned above (van Loo et al., 2003). Intotal, about 200 genotypes were genotypedfor five amplified fragment length polymorphism(AFLP) selection markers usingthe fluorescent AFLP technique developedby Applied BioSystems (Figure 1). Themarkers were co-dominantly scored usingthe heights of the fluorescence peaks relativeto those of homozygous fragments asa criterion.The genotyping data were used subsequentlyas a basis for a divergent massselection programme. The selection strategyis outlined in Figure 2. The selectioncriterion was a genotype-specific selectionindex, being the summation of allpositive QTL alleles (or chromosome segments)over the five QTL sites considered(Figures 1 and 2).Application of marker selectionThe AFLP technique is usually not themarker technology of choice for selectionpurposes because of its dominant nature andhigh costs per selection marker. However,co-dominant scoring of the five selectionmarkers was quite adequate. The trimodalfrequency distributions allowed properclassification of plants, although some misclassificationcannot be fully excluded. Theadvantages of co-dominant AFLP scoringfrom a selection point of view are so largethat a small number of genotyping errorsare acceptable.The decision to use a summation indexas the criterion for selection was made primarilybecause of the difficulty of weightingthe individual NUE related traits and theco-localization of QTL. The designationof the positive QTL alleles (chromosome
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iiiContentsAcknowledgementsForeword
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Section v - marker-assisted selecti
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viiForewordSince almost the beginni
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ixAbbreviations and acronymsAATFAB-
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xiFIVIMSFNPFSCFSILGABIGASGCAGCPGDPG
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xiiiOBMOECDOIEOPVPAGEPBRsPCRPGRFAPI
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xvContributorsAmalia BaroneProfesso
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xviiElcio Perpétuo GuimarãesSenio
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xixAndrea SonninoSenior Agricultura
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Chapter 1Marker-assisted selection
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Chapter 1 - An overview of the issu
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Section VMarker-assisted selectioni
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Chapter 19Technical, economic and p
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This book provides a comprehensive
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