Large-Scale Next-Generation Resequencing of Soybean Germplasm for Trait Discovery

With the advances in next-generation sequencing (NGS) technology and significant reduction in sequencing costs it is now possible to sequence large sets of crop germplasm and generate whole genome scale structural variations and genotypic data. In-depth informatics analysis of the genotypic data can provide better understanding of the links with the observed phenotypic changes. This approach can be used to further understand and study different traits for the improvement of crops by design.

We have conducted resequencing of 500+ soybean germplasm lines from selected for major traits including oil, protein, soybean cyst nematode resistance (SCN), abiotic stress resistance(drought, heat and salt) and root system architecture. We have done bioinformatics analysis and identified SNPs and insertion, deletion using GATK3.0 software. We have also conducted copy number variations (CNV) analysis with cn.MOPS and SNP annotations with SnpEff. We also have performed linkage disequilibrium and haplotype analysis using LDExplorer.  The analysis identified major SNPs associated with the phenotypic changes between these lines. Approximately 2.3 million SNPs and indels are identified per line. Around 40% of them have intergenic effects and more than 20,000 are high-impact SNPs. We detected thousands of CNV regions and more than 20,000 haplotype blocks per line.

Analysis was conducted using XSEDE as the computing infrastructure, iPlant as the data and cloud infrastructure, and the Pegasus workflow systems to control and coordinate the data management and computational tasks. All data including GWAS, SNP annotations can be accessed through Soybean Knowledge Base (SoyKB) at http://soykb.org.