Polymorphisms of IFS1 and IFS2 gene are associated with isoflavone concentrations in soybean seeds

Soybean isoflavones are associated with many health benefits of soy consumption, and isoflavone levels are one of the most important output traits of soybean. Isoflavones are synthesized from the phenylpropanoid pathway. Isoflavone synthase (IFS) acts as the key metabolic entry point for the formation of all kinds of isoflavones. We have cloned, sequenced, and analyzed the IFS1 and IFS2 genomic regions from 33 Chinese soybean accessions including 16 Glycine soja and 17 Glycine max. The isoflavone levels in these accessions vary greatly, ranging from 536.6 μg/g to 5509.1 μg/g dry seed weight. High nucleotide diversity and low extent of linkage disequilibrium (LD) in these two genes provided sufficient genetic resolution for association analysis of polymorphisms in these genes and soybean seed isoflavone levels. As a result, three single nucleotide polymorphisms (SNPs) in IFS1 gene and two SNPs in IFS2 gene were found closely associated (P < 0.05) with all individual and total isoflavone levels in seeds, regardless of population structure. These results indicated that IFS1 and IFS2 gene both contributed to the levels of isoflavones in seeds. These polymorphisms may serve as important molecular markers for breeding.