Identification of eQTL and Additional SSR-Based QTLs Underlying Isoflavone Contents in Soybean

Soybean (Glycine max [L.] Merr.) isoflavonoids have drawn much attention because of their contribution to human health and plant defense systems. However, due to the complexity of their accumulation, the genetic basis of soybean isoflavone synthesis is still not well understood. In this study, four key enzyme genes (PAL, CHS, IFS and F3H) in the phenylpropanoid pathway were selected as target genes (TGs) to analyze the expression level in soybean reproductive stages. Quantitative trait locus (QTL) and expression QTL (eQTL) associated with soybean isoflavone content were analyzed. Ninety-five additional SSR markers were added to the LG map of Zeng et al. (2009) in F_5:6, F _5:7 and F_5:11 populations comprised 130 RI lines from a cross between ‘Zhongdou 27’ (higher seed isoflavone content) and ‘Jiunong 20’ (lower seed isoflavone content). Twenty three new QTLs associated with individual and total seed isoflavone were found. A total of 33 eQTL underlying the expression levels of four TGs related to isoflavone synthesis were identified in fifteen chromosomes based on F_5:11 RILs population at R6 stage. These findings will be beneficial for the isolation and cloning of the genes that underlie isoflavone synthesis and accumulation, also for the selection of soybean cultivars with higher isoflavone content through MAS.