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

• Published in: International journal of molecular sciences Vol. 24; no. 2; p. 1055
• Main Authors: Dossou, Senouwa Segla Koffi, Song, Shengnan, Liu, Aili, Li, Donghua, Zhou, Rong, Berhe, Muez, Zhang, Yanxin, Sheng, Chen, Wang, Zhijian, You, Jun, Wang, Linhai
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 05-01-2023; MDPI
• Subjects: Biosynthesis; Crop improvement; Crops; Domestication; Gene expression; Genes; Genetic diversity; genome resequencing; Genome-wide association studies; Genome-Wide Association Study; Genomes; Genomic analysis; genomic signatures; GWAS; Hairy root; lignan; Lignans; Lignans - metabolism; Lignin; Metabolism; NST1; Nucleotides; Oilseed crops; Oilseeds; Phylogenetics; Seeds - metabolism; Sequence Analysis, DNA; sesame; Sesamum; Sesamum - genetics; Sesamum - metabolism; Single-nucleotide polymorphism; Subpopulations; Transcription factors; Variation; China; genomic signatures; lignan; sesame; GWAS; NST1; genome resequencing
• ISSN: 1422-0067; 1661-6596; 1422-0067
• DOI: 10.3390/ijms24021055

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 SNP
locus for lignans variation is located in the exon of the gene
. 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
in sesame hairy roots significantly up-regulated the expression of
, 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.