Identification of QTNs, QEIs interactions and genes for isoflavones in soybean seeds

Isoflavones are important components of soybean seeds, and the contents affect the nutritional value of soybean products. To further reveal and improve the regulation mechanism of soybean isoflavones content, it is an effective way to construct a large enough germplasm combination and explore the genetic loci related to soybean isoflavone traits. In this study, 179 local soybean germplasms mainly from China were selected to analyze the phenotypic diversity and genetic basis of isoflavone content in soybean seeds. The genome-wide association studies (GWAS) using 3VmrMLM model combined the isoflavone phenotype with 23,131 single nucleotide polymorphisms (SNPs), we identified 97 genetic loci related to isoflavone traits in single environment and 20 genetic loci related to isoflavone traits in multiple environments, after that screened 6 potential genes related to total isoflavone content, daidzein, glycitein and genistein. Glyma.09G037300 and Glyma.18G111200 related to multiple traits of soybean isoflavones are highly expressed in soybean seeds. Haplotype analysis shows that Glyma.09G037300 and Glyma.18G111200 are higher expression in the high isoflavone populations than low isoflavone populations. Transient overexpression of Glyma.18G111200 increased the content of total isoflavones in hairy roots by 30–51%. These results revealed the genetic basis of soybean isoflavones, provided a series of predictable potential genes affecting the synthesis and accumulation of soybean isoflavones, and updated the research on soybean isoflavone related genes and genetic related loci. This provide a valuable basis for the functional study of soybean isoflavones.