Genome-wide association analysis of sucrose and alanine contents in edamame beans

Abstract

The sucrose and Alanine (Ala) content in edamame beans significantly impacts the sweetness flavor of edamame-derived products as an important attribute to consumers’ acceptance. Unlike grain-type soybeans, edamame beans are harvested as fresh beans at the R6 to R7 growth stages when beans are filled 80-90% of the pod capacity. The genetic basis of sucrose and Ala contents in fresh edamame beans may differ from those in dry seeds. To date, there is no report on the genetic basis of sucrose and Ala contents in the edamame beans. In this study, a genome-wide association study was conducted to identify single nucleotide polymorphisms (SNPs) related to sucrose and Ala levels in edamame beans using an association mapping panel of 189 edamame accessions genotyped with a SoySNP50K BeadChip. A total of 43 and 25 SNPs was associated with sucrose content and Ala content in the edamame beans, respectively. Four genes (Glyma.10g270800, Glyma.08g137500, Glyma.10g268500, and Glyma.18g193600) with known effects on the process of sucrose biosynthesis and 37 novel sucrose-related genes were characterized. Three genes (Gm17g070500, Glyma.14g201100 and Glyma.18g269600) with likely relevant effects in regulating Ala content and 22 novel Ala-related genes were identified. In addition, by summarizing the phenotypic data of edamame beans from three locations in two years, three PI accessions (PI 532469, PI 243551, and PI 407748) were selected as the high sucrose and high Ala parental lines for the perspective breeding of sweet edamame varieties. Thus, the beneficial alleles, candidate genes, and selected PI accessions identified in this study will be fundamental to develop edamame varieties with improved consumers’ acceptance, and eventually promote edamame production as a specialty crop in the United States.

Determining Genetic Markers and Seed Compositions Related to High Test Weight in Glycine max

“…All accessions were planted similarly to Singer et al 2022 and Wang et al 2022 [ 23 , 24 ]. Briefly, a total of 390 soybean accessions from a total of 17 countries from the Southern Core Collection that has been maintained at Virginia Tech were grown in Blacksburg (BB) and Warsaw (W), Virginia, for three years from 2019 to 2021.…”

Soybean genetics, genomics, and breeding for improving nutritional value and reducing antinutritional traits in food and feed

“…The sweetness flavor of edamame beans is a crucial factor for consumer acceptance, and it is influenced by the content of sucrose and alanine (Ala). Wang et al (2023) conducted a GWAS of fresh edamame beans of 189 accessions and identified 43 and 25 genetic markers associated with sucrose and Ala content, respectively. Four genes that affect sucrose biosynthesis and 37 novel genes related to sucrose content were identified, along with three genes with likely relevant effects on Ala content and 22 novel Ala-related genes.…”

“…Because the ME of sucrose (3900 kcal•kg −1 ) is significantly greater than that of starch (2918-3396 kcal•kg −1 ), animal producers are interested in feed formulation with higher sucrose concentration (John, 2008;Ostezan et al, 2023). Additionally, higher sucrose concentration is positively correlated with the sweetness of soy-based products, including natto, tofu, edamame, and soymilk (Rosset et al, 2012;Sui et al, 2020;Wang et al, 2023). Thus, improving sucrose content has become more common in soybean breeding programs due to its higher ME efficiency for animal feed and the natural sweetness in soymeal for human consumption (Ficht et al, 2022;Sui et al, 2020).…”

Novel genetic resources associated with sucrose and stachyose content through genome-wide association study in soybean (Glycine max (L.) Merr.)

“…Since the largest soybean meal consumers are non-ruminant animals, developing new soybean cultivars with high sucrose and low RFOs is crucial to improve digestibility and feed efficiency. In addition, increased sucrose content in soybean seeds is also essential to improve the sweet flavor of soy-based products, such as tofu, edamame, and soymilk (Rosset et al, 2012;Sui et al, 2020;Wang et al, 2023).…”