Prof Hon-Ming Lam from The Chinese University of Hong Kong teamed with BGI Genomics and other experts to complete the first reference-grade wild soybean genome, published in Nature Communications
Soybean is an economically important crop first domesticated in China. Wild soybeans contain genes that could be used to improve agronomic traits of cultivated soybean, including stress tolerance, seed protein and secondary metabolite contents, etc. Until recently, genomic research of soybean relied solely on the reference genome of the cultivated soybean Williams 82, thus hindering the discovery of genetic information that are specific to wild soybeans. Prof Hon-Ming Lam from The Chinese University of Hong Kong has led a team of experts from BGI Genomics, UK, USA, Japan and Korea to build and decode the first high-quality wild soybean reference genome, providing an important tool to facilitate the mining of gene resources from wild soybeans. The findings were published as a research article entitled “A reference-grade wild soybean genome” in Nature Communications. BGI Genomics provided the sequencing service and participated in the assembly of this new genome.
The team adopted a combination of high-end technologies, including PacBio sequencing, Bionano Genomics optical mapping (OM), and Hi-C sequencing, to assemble the wild soybean W05 genome at chromosome scale. The assembled genome is 1,013.2 Mb in size with contig N50 3.3 Mb. Compared with the existing Williams 82 reference genome, the contig N50 shows a 17 times improvement. Based on the ample amount of RNA-seq data and PacBio Isoseq data, a total of 55,539 protein-coding genes were annotated.
Making use of this newly assembled genome, researchers were able to identify the structural differences between wild and cultivated soybean genomes. For example, a translocation between chromosome 11 and chromosome 13 was found. Such translocation may affect the breeding between wild and cultivated soybeans and QTL analyses in the affected regions, which has a strong impact on breeding strategies.
In addition, researchers discovered a large genomic inversion in the I locus which controls the seed coat color. This inversion explained the long mystery of the switching from dark seeds to yellow seeds during soybean domestication.
In combination with the OM technology, the wild soybean reference genome could have an even wider scope of application. Researchers made use of the new reference genome to assemble and analyze OM data from wild and cultivated soybeans of different origins. The translocation between chromosome 11 and chromosome 13 and the inversion in the I locus seem to be common phenomena in different accessions. Moreover, researchers also noticed a reduction in the number of genes encoding anti-nutrient proteins in cultivated soybeans, possibly as a result of human selection.
The release of this wild soybean reference formed a solid foundation for comparative genomic studies of legumes and soybean improvement programs. It expedites the investigations of genomic information and important traits of wild soybeans, facilitates the continuous improvement of soybean cultivars, and hence extends the habitats of soybean cultivation and contribute to sustainable agriculture.
Read the full study here: https://www.nature.com/articles/s41467-019-09142-9