Genome-wide Association Study Of Main Agronomic Traits In Sesame

Sesame（Sesamum indicum L.,2n=26）,a member of the Pedaliaceae family,is one of the most important oil crops in China.Sesame seed not only contains high oil content and high quality protein,but also is rich in vitamins and minerals.It is widely used in food processing and human healthcare.In this study,366 elite germplasm accessions were selected from the primary core collection.Genetic structure,diversity and linkage disequilibrium of 366 sesame accessions were evaluated by using 89,924 single nucleotide polymorphisms（SNPs）,which were identified by specific-length amplified fragment sequencing（SLAF-seq）.A total of 44,109 SNPs were selected for 363 accessions to perform genome-wide association analyses.The main results are as follows:1.A set of 366 sesame germplasm accessions were genotyped by using 89,924 SNPs and analysed for genetic variation.The number of SNPs on each chromosome was consistent with the physical length of the respectively chromosome,and the average marker density was approximately 2.67 kb/SNP.The genetic structure analysis revealed that these sesame germplasm accessions were divided into 3 subgroups.Principal components analysis（PCA）and neighbor-joining phylogenetic tree showed that these accessions were structured primarily along the basis of their geographic collection,and that an extensive admixture occurred in the panel.The genetic diversity analysis showed that the average nucleotide diversity of the panel was 1.1×10-3,with averages of 1.0×10-4,2.7×10-4,and 3.6×10-4 obtained,respectively for three identified subgroups of the panel:Pop 1,Pop 2,and the Mixed.The genome-wide linkage disequilibrium（LD）analysis showed that an average LD extended up to-99 kb.2.Phenotypic variations were analyzed and genome-wide association analyses were performed for yield-related traits.Yield-related traits of 363 sesame accessions were complicated quantitative traits.Extensive phenotypic variations were observed for all traits,and the broad sense herntability（hB2）of yield-related traits were 49.04%（harvest index）～87.65%（first capsule height）.One hundred and seventy-three association SNPs were identified by GWAS.Sixteen SNPs were identified for yield per plant and phenotypic variances were explained from 4.14%to 13.73%.Twenty-five association SNPs were identified for capsule number per plant and phenotypic variances were explained from 3.36%to 16.52%.Twenty-four SNPs were identified for first capsule height and phenotypic variances were explained from 3.83%to 12.64%.Thirty SNPs were identified for plant height and phenotypic variances were explained from 3.30%to 16.44%.Thirty SNPs were identified for seed number per capsule and phenotypic variances were explained from 3.52%to 12.92%.Thirty-two SNPs were identified for thousand seed weight and phenotypic variances were explained from 4.02%to 20.32%.Sixteen SNPs were identified for harvest index and phenotypic variances were explained from 4.80%to 11.61%.Finally,136 SNPs were identified after the same loci were merged.Sixteen association SNPs were identified across more than 2 envirenments,and 642 candidate genes were identified in the candidate region of 198kb.Of these 642 candidate genes,3 were important candidate genes for yield-related traits.SIN₁006340 encoding bHLH93 was involved in the gibberellin catabolic process and regulation of gibberellin biosynthetic process.SIN₁006338（SiACS）was probably the causative gene for capsule number per axil.SIN₁014512 was involved in auxin-activated signaling pathway.3.Genome-wide association analyses were performed for quality traits of 363 sesame accessions.A total of 79 association SNPs were identified.Twenty-four association SNPs were identified for seed coat color and phenotypic variances were explained from 3.73%to 16.93%.Twenty-eight association SNPs were identified for oil content and phenotypic variances were explained from 2.81%to 11.04%.Twenty-seven association SNPs were identified for protein content and phenotypic variances were explained from 5.34%to 18.09%.The SNPs,which were identified in more than 2 envirenments or explained phenotypic variances more than 10%,were selected to search the candidate regions.Four hundrend and eighty candidate genes were identified in the candidate regions.Of these candidate genes,6 were important candidate genes for quality traits.SIN₁006022 belonged to the cytochrome P450,and SIN₁016759 was annotated as polyphenol oxidase.SIN₁010859 was annotated as monoglyceride lipase,which was involved in the pathway of triacylglycerol degradation.SIN₁010914 was annotated as 4-coumarate-CoA ligase,SIN₁003867 was annotated as acetyl-coenzyme A carboxylase carboxyl transferase subunit alpha-carboxyltransferase subunits,which was component of the acetyl coenzyme A carboxylase（ACC）complex and involved in step one of the subpathway that synthesizes malonyl-CoA from acetyl-CoA.SIN 1005755 was annotated as NAC domain-containing protein 43,which involved in biosynthesis of secondary walls.5.Three hundred and sixty-three sesame accessions were tested by artificial waterlogging stress at flowering stage and used to performe GWAS.Phenotypic datas of each line were obtained,including wilting rate and mortality of plants.The degree of wilting was divided into 5 ranks,which were used to calculate waterlogging index.Three hundred and sixty-three sesame accessions were evaluated by waterlogging index.There were 2 accessions with extreme tolerance to waterlogging and 43 accessions with tolerance to waterlogging.Genome-wide association analyses were performed for 363 sesame accessions in 3 years and a total of 18 association SNPs were identified for waterlogging index,which could explain phenotypic variances from 2.18 to 14.47%.Searching the flanking regions of 13 associated SNPs,125 candidate genes were identified in the range of 198kb.According to gene ontology（GO）analysis,SIN₀09471,SIN₁014016,SIN₁024041 and SIN₁008036 were ethylene-responsive transcription factor genes.SIN₁005731 was was annotated as transcription factor bHLH13.