Genetic Variation and Association Mapping of Seed-Related Traits in Cultivated Peanut (Arachis hypogaea L.) Using Single-Locus Simple Sequence Repeat Markers

Cultivated peanut (Arachis hypogaea L.) is an allotetraploid (AABB, 2n = 4x = 40), valued for its edible oil and digestible protein. Seed size and weight are important agronomical traits significantly influence the yield and nutritional composition of peanut. However, the genetic basis of seed-related traits remains ambiguous. Association mapping is a powerful approach for quickly and efficiently exploring the genetic basis of important traits in plants. In this study, a total of 104 peanut accessions were used to identify molecular markers associated with seed-related traits using 554 single-locus simple sequence repeat (SSR) markers. Most of the accessions had no or weak relationship in the peanut panel. The linkage disequilibrium (LD) decayed with the genetic distance of 1cM at the genome level and the LD of B subgenome decayed faster than that of the A subgenome. Large phenotypic variation was observed for four seed-related traits in the association panel. Using mixed linear model with population structure and kinship, a total of 30 significant SSR markers were detected to be associated with four seed-related traits (P < 1.81 × 10-3) in different environments, which explained 11.22–32.30% of the phenotypic variation for each trait. The marker AHGA44686 was simultaneously and repeatedly associated with seed length and hundred-seed weight in multiple environments with large phenotypic variance (26.23 ∼ 32.30%). The favorable alleles of associated markers for each seed-related trait and the optimal combination of favorable alleles of associated markers were identified to significantly enhance trait performance, revealing a potential of utilization of these associated markers in peanut breeding program.