Evaluation of genetic diversity and association mapping for seed weight and size in vegetable soybean germplasm

Abstract Edamame is a vegetable‐typesoybean [ Glycine max (L.) Merr.] with large seed size, typically twice that of commodity soybean. Understanding the genetic diversity among large‐seeded germplasm as well as the genetic variation for seed size in the germplasm pool is important for edamame breeding. The objectives of this study were to analyze the genetic diversity of 343 edamame soybean accessions and 36 breeding lines, and to identify quantitative trait loci (QTLs) associated with seed weight (SW), seed volume (VOL), seed length (SL), seed breadth (SB), and seed height (SH) through genome‐wide association studies. We observed two main genetic groups among the 343 accessions and found that the breeding lines were genetically dissimilar to germplasm accessions. Through single‐ and multi‐locus models, a total of two, two, seven, one, and four SNPs were reported to be associated with SW, VOL, SL, SB, and SH located across two, two, five, one, and four chromosomes, respectively. There were three SNPs associated with SL, SB, and/or SH that were not found to be within a previously reported SL, SB, or SH QTL. The SNP ss715587475, positioned at the 24.9‐Mb position on chromosome 4, was located within the gene Glyma04g21680 which was associated with SW in Arabidopsis and may be a candidate gene for SW in edamame soybean. There were four additional SNPs positioned within genes that encode proteins that may relate to plant growth and development in soybean. Identifying and pyramiding favorable alleles for seed size and weight will enhance edamame breeding efforts.