Genome-Wide Association Studies of 39 Seed Yield-Related Traits in Sesame (Sesamum indicum L.)

Abstract

Sesame is poised to become a major oilseed crop owing to its high oil quality and adaptation to various ecological areas. However, the seed yield of sesame is very low and the underlying genetic basis is still elusive. Here, we performed genome-wide association studies of 39 seed yield-related traits categorized into five major trait groups, in three different environments, using 705 diverse lines. Extensive variation was observed for the traits with capsule size, capsule number and seed size-related traits, found to be highly correlated with seed yield indexes. In total, 646 loci were significantly associated with the 39 traits (p < 10^-7) and resolved to 547 quantitative trait loci QTLs. We identified six multi-environment QTLs and 76 pleiotropic QTLs associated with two to five different traits. By analyzing the candidate genes for the assayed traits, we retrieved 48 potential genes containing significant functional loci. Several homologs of these candidate genes in Arabidopsis are described to be involved in seed or biomass formation. However, we also identified novel candidate genes, such as SiLPT3 and SiACS8, which may control capsule length and capsule number traits. Altogether, we provided the highly-anticipated basis for research on genetics and functional genomics towards seed yield improvement in sesame.

Keywords: QTL; candidate gene; genome-wide association study; sesame; yield.

Figure 1

Boxplots displaying variation of six traits across three different environments (SY = Sanya, NN = Nanning and WH = Wuhan). Definition of the labels can be found at the end of this article.

Figure 2

Correlation between all the seed yield-related traits in sesame. Blue color depicts positive correlation while red color means negative correlation. A, B and C correspond to the clusters of traits. Definition of the labels can be found at the end of this article.

Figure 3

Genomic location of the 547 QTLs identified for seed yield-related traits in sesame. QTLs were named as follow: ENVIRONMENT-TRAIT-LINKAGEGROUP_POSITION. Bars represent the linkage groups of sesame genome. Red portions of the bars represent the previous QTLs detected by Wu et al. [10]. Red stars represent loci previously detected by Wei et al. [16]. Definition of the labels can be found at the end of this article.

Figure 4

Venn diagram depicting the shared and common QTLs between five groups of seed yield-related traits analyzed in this study.

Figure 5

Genome-wide association mapping of effective capsule number in main stem (CNM) in sesame from three different environments (SY = Sanya, NN = Nanning and WH = Wuhan).

Figure 6

Genome-wide association mapping of length of medial capsule in main stem (LMM) in sesame from three different environments (SY = Sanya, NN = Nanning and WH = Wuhan).

Figure 7

Functional analysis of 48 candidate gene-containing significant SNPs. (a) Biological function of the SNP-containing genes. (b) Identification of the favorable allele for the gene SiACS8. 262 genotypes harboring the C allele and 420 harboring the T allele were used. Different letters above bars represent significant difference (p < 0.05) between genotypes. The error bar indicates the standard error of the mean. Definition of the labels can be found at the end of this article.

Figure 8

Expression analysis of the candidate gene for LMM trait between two contrasting accessions. (a) Phenotypes of G330 and G346 displaying long and short capsule length, respectively, at 3, 6, 9, 12 and 21 days after pollination. (b) Identification of the favorable allele at the locus 15,219,964 bp on the LG11. A total of 427 genotypes harboring the A allele and 175 harboring the G allele were used. (c) qRT-PCR relative expression level of the gene SIN_1010995 between G330 and G346 at different days after pollination. Different letters above bars represent significant difference (p < 0.05) between genotypes. The error bar indicates the standard error of the mean. The sesame Actin gene (SIN_1006268) was used as the internal reference and 3 biological replicates and 3 technical replicates were used.