marker-assisted selection in wheat - ictsd

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