Mutant-based QTL mapping reveals key factors related to the agronomic traits and isoflavone contents of soybean (Glycine max)

Abstract

Abstract Background Soybean is a valuable source of edible protein and oil as well as secondary metabolites that can be used in food products, cosmetics, and medicines. However, because the soybean isoflavone content is a quantitative trait influenced by internal/external factors, its genetic basis remains unclear. Results This study was conducted to identify causal quantitative trait loci (QTLs). A mutant-based F2 population (190 individuals) was constructed by crossing the Korean cultivar ‘Hwangguem’ with low isoflavone contents (1,558 µg g−1) and the soybean mutant DB-088 with high isoflavone contents (6,393 µg g−1). A linkage map (3,049 cM) with an average chromosome length of 152 cM was constructed using the 180K AXIOM® SoyaSNP array. Thirteen QTLs related to agronomic traits were mapped to chromosomes 2, 3, 11, 13, 19, and 20, whereas 29 QTLs associated with isoflavone contents were mapped to chromosomes 1, 3, 8, 11, 14, 15, and 17. Notably, the Gm11_9877690–Gm11_9955924 interval on the chromosome 11 was revealed to contribute to high isoflavone contents with 11.9%–20.1% of the phenotypic variation. This interval included four candidate genes, encoding β-glucosidases 13, 14, 17-1, and 17-2. We confirmed obvious differences in the expression levels of these genes according to seed developmental stages. Whole candidate genes within causal QTLs were then assessed by enriched GO terms, KEGG pathways, and co-expression network analysis. A correlation analysis indicated certain agronomic traits (e.g., DF, DM, and PH) are positively correlated with isoflavone contents. Conclusions Alleles of soybean mutant ‘DB-088’ contributed to agronomic traits and isoflavone contents. The major interval of Gm11_9877690 – Gm11_9955924 took up 78 kb on chromosome 11, including four β-glucosidases. Thus, mutant alleles may be useful for the marker-assisted selection of soybean lines with high isoflavone contents and superior agronomic traits.