High-resolution genome-wide association study reveals two genes influencing dietary fiber content in sesame (Sesamum indicum L.)

Abstract

Dietary fiber is widely recognized for its beneficial effects on human health, and sesame (Sesamum indicum L.) seeds are an important source of dietary fiber. However, efforts to improve sesame for higher fiber have been constrained by limited knowledge of the genetic factors underlying this trait. In this study, we identified a strong correlation between fiber and sugar content, both of which are significantly influenced by genetic factors. A large-scale analysis of 222 sesame germplasm resources revealed genome-wide single nucleotide polymorphism (n = 1,535,018), insertions and deletions (InDels; n = 325,371), and structure variations (SVs; n = 29,028). Linkage disequilibrium and genome-wide association studies identified an InDel quantitative trait locus targeting the SiLAC3 gene, which caused a gene frameshift mutation significantly associated with both sugar and dietary fiber traits. Furthermore, a 1201-bp deletion SV in the coding and 3′ untranslated regions of the SiXTH30 gene was associated with high fiber content. Notably, two accessions (CX150 and CX546) with pyramiding favorable alleles of these two mutated genes exhibited a significant increase in fiber content compared to accessions with only one favorable allele. We also found two candidate genes highly expressed during the early and middle stages of seed development, both of which have been previously reported to play important roles in cell wall fiber content. In conclusion, our findings highlight two key fiber-associated candidate genes, which could serve as valuable resources for molecular breeding aimed at increasing fiber content in sesame seeds.