Identification of the long InDels through whole genome resequencing to fine map of qIF05-1 controlling seed isoflavone content in soybean (Glycine max L. Merr.)

Soybean seed isoflavone can provide health and nutrition benefits for human which is a kind of secondary metabolite. In our previous study, a stable quantitative trait loci (QTL) qIF05-1 controlling seed isoflavone content in soybean had been detected on chromosome (Chr.) 05 in a recombinant inbred line (RIL) population from a cross from Huachun 2×Wayao. In this study, the parental lines were re-sequenced using the Illumina Solexa System with deep-coverage, a total of 63099 polymorphic long Insertions and Deletions (InDels) (≥15 bp) were identified between the parents Huachun 2 and Wayao, which were unevenly distributed on 20 chromosomes of soybean, varying from 1826 in Chr12 to 4544 in Chr18. 10002 long InDels (15.85% of total) were located in genic regions, including 1139 large-effect long InDels which resulted in truncated or elongated protein sequences. In the qIF05-1 region, there was 68 long InDels being detected between the two parents. Using progeny recombination experiment and genotype analysis, the qIF05- 1 locus was mapped into a 102.2-kb genomic region, 12 genes are located in this region contained 12 genes. By RNA-seq data analysis, genome sequence comparison and functional validation through ectopic expression into Arabidopsis, Glyma.05G208300 (described as GmEGL3), a basic helix-loop-helix (bHLH) transcription factor in plants, might be the likely confirmed gene in qIF05-1. These long InDels are a kind of complementary genetic method for QTL fine mapping and can facilitate genetic studies and molecular assisted selection breeding in soybean.