Coordinate Inheritance of Seed Isoflavone and Protein in Soybean

Soybean (<i>Glycine max</i> (L.) Merr.) is an important nutritional crop, not only as a rich source of protein and oil, but also for the production of isoflavones. There is a demand to breed soybean cultivars bearing consistently high protein, oil and isoflavone yields, yet this requires a clear heritable genetic relationship among isoflavone, protein and oil production. Here, two soybean genotypes contrasting in terms of protein, oil and isoflavone contents and their 185 <i>F_8:10</i> recombinant inbred lines (RILs) were employed to characterize seed protein, oil and isoflavone contents over two years of field trials. In this population, protein, but not oil, was significantly correlated with isoflavone content. A high-density genetic linkage map containing 3943 SNP markers identified through genotyping-by-sequencing (GBS) technology was constructed for further genetic analysis, whereby a total of 25 integrated isoflavone loci were identified, including <i>qISO1</i>, <i>qISO 6.1</i>, <i>qISO 6.3</i> and <i>qISO 6.4</i>, which are newly identified QTLs. Two major QTLs identified in this study, <i>qISO5</i> and <i>qISO6.2</i>, were fine-mapped for production of daidzein and genistein derivatives, as well as for glycitein derivatives, in the sequences between nucleotide positions 41042159 and 42098680 on chromosome 5 and between 18449510 and 19395795 on chromosome 6, which, respectively, explain 9.3–20.4% and 7.8–24.8% of the phenotypic variation in these traits. Further combination of <i>qISO5</i> and <i>qISO6.2</i> resulted in additive impacts on isoflavone production. Among the 13 QTLs linked with seed protein content in this study, three also colocated with QTLs for isoflavone content, indicating that seed isoflavone and protein content may be coordinately inherited. These results contribute to understanding the relationships between isoflavone and protein or oil content in soybean seeds. This knowledge could be valuable for soybean breeding programs aiming to combine consistently high isoflavone production with high protein or oil content.