Identification of Sequence Variants in Candidate Genes for Oil Content Using Whole Genome Re-Sequencing of Soybean Germplasm

Soybean is an important crop contributing about one third of edible oil requirement world-wide. Mature soybean seeds typically contain 40% protein, 25% carbohydrate, and only 18-20% oil. Genetic improvement for seed oil content is one of the challenges in soybean due to its narrow genetic pool.  Whole genome re-sequencing strategies provide an opportunity to explore the allelic diversity for seed oil accumulation in soybean. In the present study, candidate genes for seed oil content were identified in the soybean genome by integrating functional annotation, expression profiling, and quantitative trait loci (QTL) information. In order to identify DNA sequence variants (SNPs), candidate genes were selected from 8 Meta-QTLs reported by other groups and 5 QTLs from Nguyen lab studies. In addition, genes and transcription factors related to fatty acid biosynthesis/metabolism were also included. We have identified ~50 candidate genes from 8 meta-QTL regions and 7 from 5-QTL region associated with oil metabolism. Sequence variants present in these candidate genes were identified using whole genome re-sequencing of germplasm and the functional and structural effects of each variant were estimated. The information about allelic diversity for key candidate genes generated in the present study will be helpful to understand evolution, molecular mechanisms, and genetic potential related to seed oil content in soybean.