The Soybean High Density ‘Forrest’ by ‘Williams 82’ SNP-Based Genetic Linkage Map Identifies QTL and Candidate Genes for Seed Isoflavone Content

Isoflavones are secondary metabolites that are abundant in soybean and other legume seeds providing health and nutrition benefits for both humans and animals. The objectives of this study were to construct a single nucleotide polymorphism (SNP)-based genetic linkage map using the ‘Forrest’ by ‘Williams 82’ (F×W82) recombinant inbred line (RIL) population (n = 306); map quantitative trait loci (QTL) for seed daidzein, genistein, glycitein, and total isoflavone contents in two environments over two years (NC-2018 and IL-2020); identify candidate genes for seed isoflavone. The FXW82 SNP-based map was composed of 2075 SNPs and covered 4029.9 cM. A total of 27 QTL that control various seed isoflavone traits have been identified and mapped on chromosomes (Chrs.) 2, 4, 5, 6, 10, 12, 15, 19, and 20 in both NC-2018 (13 QTL) and IL-2020 (14 QTL). The six QTL regions on Chrs. 2, 4, 5, 12, 15, and 19 are novel regions while the other 21 QTL have been identified by other studies using different biparental mapping populations or genome-wide association studies (GWAS). A total of 130 candidate genes involved in isoflavone biosynthetic pathways have been identified on all 20 Chrs. and among them 16 have been identified and located within or close to the QTL identified in this study. Moreover, transcripts from four genes (Glyma.10G058200, Glyma.06G143000, Glyma.06G137100, and Glyma.06G137300) were highly abundant in Forrest and Williams 82 seeds. The identified QTL and four candidate genes will be useful in breeding programs to develop soybean cultivars with high beneficial isoflavone contents.

Variation in Protein and Isoflavone Contents of Collected Domestic and Foreign Soybean (Glycine max (L.) Merrill) Germplasms in Korea

This study was carried out to investigate the variations in protein and isoflavone contents of 300 soybean germplasms introduced from domestic and foreign countries and to compare their contents in terms of size, colour and country of origin. The protein content ranged from 28.7 g 100 g−1 to 44.5 g 100 g−1, with an average of 39.0 g 100 g−1. In a comparison of protein according to country of origin, the highest content was seen in soybeans from Korea (39.7 g 100 g−1), followed by North Korea (39.2 g 100 g−1), China (39.0 g 100 g−1), Japan (38.8 g 100 g−1), the USA (38.0 g 100 g−1) and Russia (37.2 g 100 g−1). The total isoflavone content ranged from 207.0 µg g−1 to 3561.8 µg g−1, with an average of 888.8 µg g−1. In the comparison of isoflavone content according to country, the highest average content was shown in soybeans from Japan (951.3 µg g−1), followed by the USA (918.7 µg g−1), Korea (902.2 µg g−1), North Korea (870.0 µg g−1) and Russia (710.6 µg g−1). Daidzein, glycitein and genistein isoflavone contents were positively correlated, while total isoflavone and protein showed a low negative correlation.

Differential Gene Expression Associated with Altered Isoflavone and Fatty Acid Contents in Soybean Mutant Diversity Pool

Soybean seeds are consumed worldwide owing to their nutritional value and health benefits. In this study we investigated the metabolic properties of 208 soybean mutant diversity pool (MDP) lines by measuring the isoflavone and fatty acid contents of the seed. The total isoflavone content (TIC) ranged from 0.88 mg/g to 7.12 mg/g and averaged 3.08 mg/g. The proportion of oleic acid among total fatty acids (TFA) ranged from 0.38% to 24.66% and averaged 11.02%. Based on the TIC and TFA among the 208 MDP lines, we selected six lines with altered isoflavone content and six lines with altered oleic acid content compared with those of the corresponding wild-types for measuring gene expression. Each of twelve genes from the isoflavone and fatty acid biosynthesis pathways were analyzed at three different seed developmental stages. Isoflavone biosynthetic genes, including CHI1A, IFS1, and IFS2, showed differences in stages and expression patterns among individuals and wild-types, whereas MaT7 showed consistently higher expression levels in three mutants with increased isoflavone content at stage 1. Expression patterns of the 12 fatty acid biosynthetic genes were classifiable into two groups that reflected the developmental stages of the seeds. The results will be useful for functional analysis of the regulatory genes involved in the isoflavone and fatty acid biosynthetic pathways in soybean.

Resequencing 250 soybean accessions: new insights into genes associated with agronomic traits and genetic networks

Limited knowledge on genomic diversity and the functional genes associated with soybean variety traits has resulted in slow breeding progress. We sequenced the genome of 250 soybean landraces and cultivars from China, America and Europe, and investigated their population structure, genetic diversity and architecture and selective sweep regions of accessions. We identified five novel agronomically important genes and studied the effects of functional mutations in respective genes. We found candidate genes GSTT1, GL3 and GSTL3 associated with isoflavone content, CKX3 associated with yield traits, and CYP85A2 associated with both architecture and yield traits. Our phenotype-gene network analysis revealed that hub nodes play a role in complex phenotypic associations. In this work, we describe novel agronomic trait associated genes and a complex genetic network, providing a valuable resource for future soybean molecular breeding.

Effect of different planting times on the quantitative variation of total seed isoflavone content and composition in Korean soybean cultivars (Glycine max (L.) Merr.)

There is great interest in the enhancement of isoflavones as one of the functional ingredients in soybean. This study aimed to investigate the effects of changes in the ecological environment over different planting times on isoflavone content. A total of 28 Korean soybean cultivars were grown at different planting times in late May, mid-June, and early July and their isoflavone content was measured over 2 years (2017 and 2018). Analyses of variance revealed significant effects of genotypes, planting times, years, and their interactions on isoflavone content. The average content of total isoflavone, as well as its component groups of malonylglucoside and aglycon, increased significantly as the seed planting time was delayed from late May to early July. The accumulation of each isoflavone component varied with changes in the planting time. The isoflavone content of the soybean cultivars for soy-sprout and soy-paste and tofu were higher for plantings in early July than for those in late May and/or mid-June, except for the black soybean cultivars. Despite significant correlations of the isoflavone content of the 28 cultivars among the three planting times, the responses of individual cultivars varied in isoflavone content by planting time. When planting was delayed, the time to flowering and maturity was also delayed and the number of days of growth from planting or flowering to maturity decreased; however, this was not related to isoflavone content. When planting was delayed, the temperature during the ripening period from flowering to maturity was lower, which was inversely related to the isoflavone content.