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Although seed weight(SW)and silique length(SL)are important determinants of yield potential in rapeseed(Brassica napus L.),their genetic basis have been poorly understood.To dissect the genetic basis of SW and SL in rapeseed,we conducted the preliminary mapping of quantitative trait loci(QTLs)by linkage analysis and the fine-mapping of the target major QTL by regional association analysis.A total of thirteen and nine consensus QTLs were identified,which explained 0.7-67.1%and 2.1-54.4%of the phenotypic variance for SW and SL,respectively.Three pairs of SW and SL QTLs were co-localized and integrated into three unique QTLs.The significance-level and genetic effect of the three pairs of co-localized SW/SL QTLs showed great decline after the conditional QTL analysis.Moreover,the allelic effects of the three QTLs for SW were highly accordant with those for SL.Two co-localized major QTLs,uq.A09-1(mean R2 = 20.1%and 19.0%for SW and SL,respectively)and uq.A09-2(mean R2 = 13.5%and 13.2%for SW and SL,respectively),were detected in all four environments and showed the opposite additive-effect direction.These QTLs were validated and fine-mapped(their confidence intervals were narrowed down from 5.3 to 1 cM for uq.A09-1 and 13.2 to 2.5 cM for uq.A09-2)by regional association analysis with a panel of 576 inbred lines.Therefore,all of the meta-,conditional and allelic effect analyses supported that pleiotropy,rather than tight linkage,was the genetic basis of the co-localization of SW/SL QTLs.Our results strongly suggested that regional association analysis was an effective and highly efficient strategy for the direct fine-mapping of target major QTL identified by preliminary linkage mapping.