Abstract
BackgroundSeed weight (SW) and silique length (SL) are important determinants of the yield potential in rapeseed (Brassica napus L.). However, the genetic basis of both traits is poorly understood. The main objectives of this study were to dissect the genetic basis of SW and SL in rapeseed through the preliminary mapping of quantitative trait locus (QTL) by linkage analysis and fine mapping of the target major QTL by regional association analysis.ResultsPreliminary linkage mapping identified thirteen and nine consensus QTLs for SW and SL, respectively. These QTLs explained 0.7-67.1% and 2.1-54.4% of the phenotypic variance for SW and SL, respectively. Of these QTLs, three pairs of SW and SL QTLs were co-localized and integrated into three unique QTLs. In addition, the significance level and genetic effect of the three co-localized QTLs for both SW and SL showed great variation before and after the conditional analysis. Moreover, the allelic effects of the three QTLs for SW were highly consistent with those for SL. Two of the three co-localized QTLs, uq.A09-1 (mean R2 = 20.1% and 19.0% for SW and SL, respectively) and uq.A09-3 (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 cM to 1 cM for uq.A09-1 and 13.2 cM to 2.5 cM for uq.A09-3) by regional association analysis with a panel of 576 inbred lines, which has a relatively rapid linkage disequilibrium decay (0.3 Mb) in the target QTL region.ConclusionsA few QTLs with major effects and several QTLs with moderate effects might contribute to the natural variation of SW and SL in rapeseed. The meta-, conditional and allelic effect analyses suggested that pleiotropy, rather than tight linkage, was the genetic basis of the three pairs of co-localized of SW and SL QTLs. Regional association analysis was an effective and highly efficient strategy for the direct fine mapping of target major QTL identified by preliminary linkage mapping.
Highlights
Seed weight (SW) and silique length (SL) are important determinants of the yield potential in rapeseed (Brassica napus L.)
Main raceme thousand seed weight (SWm) was higher than Raceme branch thousand seed weight (SWb) by approximately 10% for both the parents and all of the populations in all environments, which was in agreement with a previous report [32]
When SW was conditioned by SL (SWm|SL), none of the three loci remained significant for SW in all experiments; when SL was conditioned by SW (SL|SWm), these loci were not significant for SL in half of the experiments. These results strongly suggested that pleiotropy, rather than tight linkage was likely to be the genetic cause of the three unique quantitative trait locus (QTL) for both SW and SL, and that SW was possibly contributed by SL for these loci
Summary
Seed weight (SW) and silique length (SL) are important determinants of the yield potential in rapeseed (Brassica napus L.). The main objectives of this study were to dissect the genetic basis of SW and SL in rapeseed through the preliminary mapping of quantitative trait locus (QTL) by linkage analysis and fine mapping of the target major QTL by regional association analysis. MAGIC (Multi-parent advanced generation inter-crosses) [14] and NAM (nested association mapping) [15] Both the seed weight (SW) and silique length (SL) are important determinants of yield potential in rapeseed and are good targets for selection in breeding [16,17] due to their high heritability [18]. An increase in silique length may lead to an increase in the source of matter [22], which results in larger seeds Both SW and SL are quantitatively inherited, which are controlled by multiple QTLs, mainly with additive effects [20,21,23]. Linkage analysis has been used for mapping QTLs of SW and SL in rapeseed [20,21,24,25,26,27,28,29], and no association analysis studies have been reported until now
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