Genome-wide Association Study Of Branch Angle And Plant Height In Brassica Napus L.

As the major source of edible oil in China,the yield of rapeseed need grow in concert with the increase of human population.Branch angle and plant height are crucial plant-type trait of rapeseed,since adequate branch angle allows higher planting density,and proper plant height enhances the lodging resistance of plants.Accordingly,clarifying the genetics determining branch angle and plant height will be of great value for rapeseed architecture improvements.In this study,we utilized the Illumina Brassica 60 K Infinium~?SNP array to genotype a collection of 520 rapeseed accessions,and investigated branch angle and plant height of this population in multiple environments.Finally,we performed GWAS with three association models,the major results are listed below:(1)After excluding SNPs with low quality or lacking clearly defined clusters or with multiple copy in the genome with Genome Studio software,19,167 high-quality SNPs were retained for further research.The population structure of the association panel was calculated with STRUCTURE software,the 520 rapeseed accessions could be assigned to two groups.The average kinship coefficient of our population was 0.061,indicating that the majority of 520 accessions have a weak relationship with each other.(2)When r~2=0.1,the average LD decay for A,C subgenome and the whole genome was 1,046,7,882 and 6,660 kb.A total of 2,315 conserved haplotype blocks were detected with Haploview software.All haplotype blocks added up to 177.4 Mb,accounting for 20.9%of the assembled B.napus genome.The haplotype blocks in A subgenome accounted for 24.8%of the total length,much shorter than the 75.2%of C subgenome.We identified 9 blocks larger than 3 Mb in size,all but one block(A06)was located on C subgenome chromosomes.We found that 6 of 9 large blocks span across or locate near their corresponding centromeres,which exhibit higher retrotransposon density and lower genge density.(3)Extensive phenotypic variations were observed for branch angles in four environments,the maximum difference of extreme accession was 43.4°.Based on the phenotypic data of four environments,the broad-sense heritability of branch angle was as high as 78.5%.We identified 56 loci significantly associated with branch angle using three statistical models GLM,MLM and A-D test.Except for C01,these loci were unevenly distributed over all chromosomes,and explained up to 51.1%of the phenotypic variation.We further predicted 77 candidate causal genes for 53 branch angle GWAS loci,including homologs of Arabidopsis well-known branch angle genes SGR4,SGR2,SGR9,LAZY1,TIR,AFB5,TAR2 and ARF10.(4)Extensive phenotypic variation was observed for plant height in this association panel.In six environments,plant height varied from 48.33 cm to 228.39 cm.The broad-sense heritability of plant height was 85.2%.Finally,we identified 68 loci significantly associated with plant height using three statistical models GLM,MLM and A-D test.These loci collectively explained 42.3%of the total phenotypic variance.95 candidate genes for height regulation were predicted for 65 plant height loci,including functional rapeseed genes BnRGA and GA2ox8 and orthologous of documented Arabidopsis genes for height regulation,such as GA20ox1,GA20ox2,GA2ox3,GA2ox4,GAMT1,DET2,DWF5,BRI1,BAK1,CYP90C1,CYP90D1,UGT73C5,ABCB1 and PAO5.(5)We collected plant height QTLs information of 7 linkage and 2 association populations,and mapped them to the reference genome of Darmor-bzh with the primer sequences of their flanking markers.70.5%GWAS loci of our study overlapped the confidence intervals of previously reported QTLs,and 29.4%loci overlapped the common QTLs from at least 2 mapping populations.78.3%GLM and 71.4%A-D test GWAS loci were validated in previous mapping populations.(6)The 398 accessions of subpopulation 2 were divided into two groups according to the plant height:Subpop2-dwarf and Subpop2-tall.XP-CLR analysis across the genome was performed in Subpop2-dwarf using Subpop2-tall as the reference population.In total,107 merged regions were regarded as candidate targets of selection.These regions varied from 10 to 250 kb in length and occupied 5.1 Mb(0.8%)of the assembled B.napus genome.24 loci of our study overlapped with the selection regions.