Resequencing of 410 Sesame Accessions Identifies SINST1 as the Major Underlying Gene for Lignans Variation

Abstract

Sesame is a promising oilseed crop that produces specific lignans of clinical importance. Hence, a molecular description of the regulatory mechanisms of lignan biosynthesis is essential for crop improvement. Here, we resequence 410 sesame accessions and identify 5.38 and 1.16 million SNPs (single nucleotide polymorphisms) and InDels, respectively. Population genomic analyses reveal that sesame has evolved a geographic pattern categorized into northern (NC), middle (MC), and southern (SC) groups, with potential origin in the southern region and subsequent introduction to the other regions. Selective sweeps analysis uncovers 120 and 75 significant selected genomic regions in MC and NC groups, respectively. By screening these genomic regions, we unveiled 184 common genes positively selected in these subpopulations for exploitation in sesame improvement. Genome-wide association study identifies 17 and 72 SNP loci for sesamin and sesamolin variation, respectively, and 11 candidate causative genes. The major pleiotropic SNPC/A locus for lignans variation is located in the exon of the gene SiNST1. Further analyses revealed that this locus was positively selected in higher lignan content sesame accessions, and the “C” allele is favorable for a higher accumulation of lignans. Overexpression of SiNST1C in sesame hairy roots significantly up-regulated the expression of SiMYB58, SiMYB209, SiMYB134, SiMYB276, and most of the monolignol biosynthetic genes. Consequently, the lignans content was significantly increased, and the lignin content was slightly increased. Our findings provide insights into lignans and lignin regulation in sesame and will facilitate molecular breeding of elite varieties and marker-traits association studies.

Identification of QTLs and allelic effect controlling lignan content in sesame (Sesamum indicum L.) using QTL-seq approach

“…Furthermore, lignans in sesame have been shown to be functional components with antioxidant, anti-dementia, and antihypertensive activities, and the genetic mechanisms required for lignan synthesis have been reported using QTL, GWAS, and transcriptomics in several studies ( Harada et al, 2020 ; Xu et al, 2021 ; Dossou et al, 2023 ). CYP92B14, an enzyme that converts sesamin to sesamolin and sesaminol, which was elucidated through functional characterization ( Harada et al, 2020 ), and the SiSNT1 gene located on chromosome 11, inferred through genetic mapping ( Xu et al, 2021 ; Dossou et al, 2023 ), may explain the genetic mechanisms of lignan synthesis in sesame. However, these are still poorly understood compared to other major crops.…”

Current Progress, Applications and Challenges of Multi-Omics Approaches in Sesame Genetic Improvement

“…Then, the SiTPS1 gene was found to be a key regulatory gene for fatty acid biosynthesis and triacylglycerol metabolism in sesame [ 55 ]. Dossou et al identified 5.38 and 1.16 million SNPs and InDels from 410 sesame accessions, and found 17 and 72 SNP loci for the sesamin and sesamolin variation, respectively [ 56 ]. Therefore, the application of WGS in plants, along with the quick development of sequencing technology, can provide high-quality SNPs for phylogenetic and population analysis, and those results could contribute to subsequent molecular breeding, functional and evolutionary research.…”

Molecular Genetics Enhances Plant Breeding

“…The authors managed to retrieve 4 QTLs and 41 genes, 25 of which were validated via qRT-PCR. Similarly, Dossou et al [ 14 ] characterized 410 sesame ( S. indicum ) accessions using WGR, and performed GWAS for lignan–lignin biosynthesis. The team found that SiNST1 is a major target gene for the molecular breeding of lignan content.…”