Dissecting Structural Variation of the Soybean Genomes Through Resequencing of Germplasm Collections

Genetic diversity in the US soybean germplasm pool is much lower than in other crops. The lowered diversity is due to inherently low genetic variation and bottlenecks soybean underwent in its evolutionary history, including domestication from G. soja to produce landraces in Asia, introduction to North America, as well as modern breeding activities. The narrow genetic basis of soybean poses challenges for continuous improvement of soybean yield and quality. There is a real need for deep sequencing and assembly of additional reference genomes for soybean genetics and breeding research. The advances in sequencing and genotyping technologies allow genome-wide association studies (GWAS) and also help bridging knowledge gap between genotype and phenotype in soybean. In order to achieve these objectives we have initiated an effort to sequence soybean germplasm lines under three major phases with a first tier target of a total of 4,000 germplasm lines, accounting for ~20% of USDA soybean germplasm collection, and produce 10 cultivated soybean (Glycine max) reference genomes and 5 wild soybean (G. soja) reference genomes. Genome-wide characterization of genetic diversity in the USDA germplasm collection will provide a knowledge base and technological platform for future genetic improvement of soybean. Currently, sequencing of selected batches of germplasm is in progress. In a pilot project (as part of the first phase with 300 lines), we sequenced six soybean accessions at an average of 12.8 X clean sequence. Consensus sequences of these accessions were assembled using a Bayesian model. These consensus sequences, together with a RIL population that was sequenced at a low coverage (0.2 X), enabled us to pinpoint the gene underlying a major QTL for root knot nematode resistance without a laborious and time-consuming fine-mapping process. These data suggest that whole genome re-sequencing of germplasm may greatly accelerate soybean genetic and breeding research. Also, comparisons between genome sequences of G. max and G. soja show significant differences between the genomic compositions of the two. The differences also highlight the phenotypic differences between the two in terms of seed development, oil and protein traits.