| Rapeseed(Brassica napus L.,2n= 38,genomes AACC)is the second-leading source of both vegetable oil and meal woldwide.The rapid growth of global human population requires significant improvement in crop yield.Yield is the most important target for the genetic improvement of most crops,including rapeseed.For rapeseed,seeds per silique(SS),seed weight(SW),and silique length(SL)are important determinant traits of seed yield potential,and are controlled by naturally occurring quantitative trait loci(QTLs).Mapping QTLs to narrow chromosomal regions provides an effective means of characterizing the genetic basis of these complex traits.Orychophragmus violaceus is a crucifer with longer siliques,more seeds per silique,and heavier seeds.A novel B.napus introgression line with more seeds per silique was previously selected from multiple crosses((B.rapa ssp.chinesis × O.violaceus)× B.napus).In the present study,in order to detect QTLs for silique-related traits,a doubled haploid(DH)population was established from a cross between the introgression line and a line with far fewer seeds per silique.By screening with a Brassica 60 K single nucleotide polymorphism(SNP)array,a high-density linkage map was constructed.Through combining the genotypes and the investigated phenotypes of DH population,we performed linkage mapping and detected major QTLs for the three traits.Using meta-analysis,consensus QTLs for the three traits have been identified,highlighting the underlying allelic variations.The candidate genes for the three traits from various Brassica species and the model crucifer Arabidopsis overlapping the consensus QTLs have also been identified.The main results are as follows:1.Phenotypic variation among DH linesThe two parents(the introgression line No.1167 and HZ396)differed significantly in SS,SW,and SL in all four environments investigated.Frequency distributions of all the traits measured in 167 DH lines were continuous and near the normal distribution in all of the environments,indicating a polygenic inheritance pattern.Regarding phenotypic variation in the entire mapping population,the traits had high coefficients of variation that ranged from 14% to 37%,indicating wide variation.Broad-sense heritability(h2)was also calculated for SS,SW,and SL.SS and SW had high(h2)values of 90.3% and 90.6%,respectively,suggesting that they were stable and insensitive to environmental effects.2.Construction of a high-resolution linkage mapThe 167 DH lines and their parents were genotyped using 52,157 SNP loci,and12,602 markers were found to be polymorphic.6,617 and 5,985 markers were mapped onto the A and C subgenomes,respectively,confirming that the A subgenome had higher genetic diversity than the C subgenome.After clustering the redundant SNPs with same genotype,finally there were 1,153 bins left for the 19 LGs,and the bin number in the A subgenome was significantly higher than that in the C subgenome(720 vs.433,p = 0.03).The lengths of the 19 LGs ranged from 70.2 c M(C06)to 220.6 c M(A09),with the sum and mean of 2,209.1 c M and 116.3 c M,respectively.The genetic distance between adjacent bins differed among LGs,and ranged from 1.1 c M to 3.7 c M,with an average interval of 1.7 c M and 2.4 c M for the A and C subgenomes,respectively.3.QTL analysis of the three silique-related traitsThe genome-wide QTL analysis was performed separately for SS,SW,and SL using the 1,153 markers coupled with corresponding phenotypic data that were obtained from the DH population in five environments(four growing environments and the BLUP values across environments),and 52 QTLs were detected for three traits.After deleting seven non-reproducible,suggestive QTLs,45 QTLs for SS,SL,and SW were detected in the five environments.The meta-analysis integrated QTLs that were located on the same LGs into consensus QTLs trait-by-trait.As a result,the 45 QTLs identified were integrated into 19 consensus QTLs.Eight,four and seven of them were detected for SS,SW,and SL,respectively.Some consensus QTLs,such as cq SS.A09 b,cq SS.C09,cq SWA05,cq SW.C09,and cq SL.C09,had major effects,whereas others exhibited minor effects.4.Alignment of present and previous QTLsIn order to facilitate the comparison and further utilization of QTLs for the Brassica researchers,we collected the results of the vast majority of QTL mapping studies conducted on B.napus.In total,221,489 and 78 QTLs for SS,SW and SL,respectively,have been reported in B.napus.QTL positions from previous studies and the present study were compared based on the reference genome of B.napus ‘Darmor-bzh’.Finally,177 QTLs for silique-related traits successfully mapped to the genome.9 previous QTLs were reproduced,and 10 QTLs were novel identified in the present study,5,2,and 3 of which were for SS,SW,and SL,respectively.As previous studies suggest that various phenological traits such as flowering time and maturity time had certain effect on grain yield and its components.We investigated the QTLs associated with the traits mentioned above.Through conducting the alignment of identified QTLs with previously published studies on flowering time and maturity time,9 and 11 QTLs overlapped with 9 and 10 consensus QTLs from this study,respectively.5.Prediction of silique-related genes in rapeseedIn order to predict candidate genes related to SS,SW,and SL,we identified B.napus genes that were homologous to Arabidopsis thaliana silique-related genes that were within the CIs of the QTLs.Based on the B.napus reference genome,27 homologous genes that controlled silique-related traits in Arabidopsis were within the CIs of nine consensus QTLs.The homologs in Arabidopsis of candidate genes we identified in this study could be divided into several functional groups,including transcription factors,enzymes,protein structure units,phytohormone response factors,and transporters. |
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