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.

Genome-Wide Variation Analysis of Four Vegetable Soybean Cultivars Based on Re-Sequencing

“…Here, the average heterozygosity rate was 11.99% in these four cultivars. These results were consistent with the previous similar studies [ 7 , 8 , 15 ], and showed the difference between vegetable and grain soybeans at the genome level. It is speculated that the SNP heterozygosity is closely related to the parental characteristics.…”

“…In this study, 16 and 10 genes were associated with sucrose and starch metabolic processes, respectively, some of which might play a role in sucrose and starch metabolism. A number of SNPs are reportedly associated with sucrose and protein contents [ 8 , 26 , 27 ]. Once confirmed, the differences could provide an insight into breeding selection of vegetable soybean as well as the loss of function of genes that may have a key role in grain soybean.…”

“…Due to the different harvesting times, it can be divided into vegetable type (as fresh vegetable for consumption) and grain type (as raw materials for processing) [ 5 , 6 ]. Vegetable soybean, also named as “Maodou” in China, “Edamame” in Japan, and “Green vegetable soybean” in North America, is a kind of food-grade specialty soybean that could be served as a fresh vegetable, snack, or be used for cooking [ 7 , 8 ].…”

“…Vegetable soybean can either be sold fresh, as pods on the stems, stripped pods, shelled beans, or sold as a frozen or canned product [ 9 , 13 ]. Vegetable soybean has become a very popular vegetable crop worldwide because of its multiple health benefits as well as its economic importance [ 6 , 8 ].…”

Genetic and Phenotypic Characterization of Soybean Landraces Collected from the Zhejiang Province in China

“…These landraces contain rich genetic resources, which are the foundation for the promotion and development of the characteristic soybean industry in this locality. Therefore, it is a current area of concern in terms of how to transform this potential advantage into a practical advantage [9,10,14,15].…”