Genome-wide association study to identification of candidate genes influencing key seed traits in Perilla frutescens

Perilla frutescens is a widely cultivated annual crop in East Asia, valued for its oil-rich seeds and edible leaves. The seeds are abundant in functional compounds such as unsaturated fatty acids, polyphenols, and flavonoids, and oil-extraction by-products are used as protein-rich animal feed and organic fertilizer. Despite its economic and nutritional significance, the genetic basis underlying major seed traits in Perilla remains poorly understood.

To investigate the genetic architecture of key seed traits, a genome-wide association study (GWAS) was conducted using 61,539 high-quality SNPs derived from genotyping-by-sequencing (GBS) of 237 Perilla germplasms. Nine phenotypes were evaluated, including eight continuous traits (e.g., capsule length, seed height, thousand-grain weight) and one categorical trait (seed coat color). GWAS identified six significant SNPs distributed across five chromosomes, with two lead SNPs-one each on chromosomes 16 and 10-associated with thousand-grain weight and seed coat color, respectively. Haplotype analysis confirmed that these SNPs caused phenotypic differences among genotype groups. Importantly, two SNPs were located in the exons of candidate genes C2S51_032383 and C2S51_020378, both resulting in non-synonymous amino acid substitutions. Protein-protein interaction network analysis revealed associations with amino acid ligase family and cell wall organization pathways. Phylogenetic analysis further demonstrated that both genes are conserved among dicot species such as Arabidopsis thaliana and Glycine max.

Our findings provide novel insights into the genetic determinants of seed-related traits in Perilla frutescens, especially seed weight and pigmentation. The trait-associated SNPs and candidate genes identified in this study offer promising targets for marker-assisted selection and molecular breeding aimed at improving seed quality and yield in Perilla.