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Genome-Wide Association Study Uncovers Loci and Candidate Genes Underlying Phytosterol Variation in Sesame (Sesamum indicum L.)

Sesame is one of the most important oilseed crops grown worldwide. It provides diverse nutraceuticals—including lignans, unsaturated fatty acids (UFA), phytosterols, etc.—to humans. Among sesame’s nutraceuticals, phytosterols have received less attention from sesame breeders, although their biological and pharmacological functions have been recorded. Therefore, in the present study, we evaluated the variation of phytosterol contents in 402 sesame accessions grown in two environments and revealed their associated loci and candidate genes. Gas chromatography (GC) analysis unveiled that sesame mainly contains four phytosterols: campesterol, stigmasterol, β-sitosterol, and Δ5-avenasterol. β-sitosterol (1.6–4.656 mg/g) was the major phytosterol, followed by campesterol (0–2.847 mg/g), stigmasterol (0.356–1.826 mg/g), and Δ5-avenasterol (0–1.307 mg/g). The total phytosterol content varied from 2.694 to 8.388 mg/g. Genome-wide association study identified 33 significant associated single nucleotide polymorphism (SNP) loci for the four traits, of which Ch6-39270 and Ch11-142842 were environmentally stable and simultaneously linked with campesterol and stigmasterol content variation. Candidate genes screening indicated that SINPZ1100015 encoding a NAC domain-containing protein 43 is likely the major candidate effect gene of phytosterol variation in sesame. The results of this study extend knowledge of phytosterol variation in sesame and provide important resources for markers-assisted breeding of high-phytosterol content varieties.