Development of a versatile resource for post-genomic research through consolidating and characterizing 1500 diverse wild and cultivated soybean genomes

Authors: ZHANG, HENGYOU - Danforth Plant Science Center; JIANG, HELEN - Danforth Plant Science Center; HU, ZHENBIN - Danforth Plant Science Center; Song, Qijian; An, Yong-Qiang - Charles

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/20/2022
Publication Date: 3/31/2022
Citation: Zhang, H., Jiang, H., Hu, Z., Song, Q., An, Y. 2022. Development of a versatile resource for post-genomic research through consolidating and characterizing 1500 diverse wild and cultivated soybean genomes. BMC Genomics. 23. Article 250. https://doi.org/10.1186/s12864-022-08326-w.
DOI: https://doi.org/10.1186/s12864-022-08326-w

Interpretive Summary: With the advance of high throughput technologies, world-wide soybean scientists have generated a massive amount of biological data. The amount of biological data is continuing to increase exponentially, which provides unprecedented and revolutionary opportunities for agricultural research. However, the biological data is under-utilized mostly because most laboratories are lack of the abilities to analyze the massive amount of data. It is critical to develop a big-data technology and resources to facilitate soybean research community to translate the data into new biological discovery and product development to increase US competitiveness. Here the report describes our consolidating, characterizing and analyzing genome sequencing data of 1,500 diverse soybean accessions available in the public, identifying and extensively annotate 32 million single nucleotide polymorphisms, further developing them into a user-friendly and expandable data resource for soybean community, and demonstrating their versatile uses in soybean genetics, breeding and molecular biology research. We make the resource available at SoyBase (https://soybase.org) and Ag Data Commons (https://data.nal.usda.gov/) for soybean research community to access.

Technical Abstract: Background With advances in next-generation sequencing technologies, an unprecedented amount of soybean accessions has been sequenced by many individual studies and made available as raw sequencing reads for post-genomic research. Results To develop a consolidated and user-friendly genomic resource for post-genomic research, we consolidated the raw resequencing data of 1465 soybean genomes available in the public and 91 highly diverse wild soybean genomes newly sequenced. These altogether provided a collection of 1556 sequenced genomes of 1501 diverse accessions (1.5'K). The collection comprises of wild, landraces and elite cultivars of soybean that were grown in East Asia or major soybean cultivating areas around the world. Our extensive sequence analysis discovered 32 million single nucleotide polymorphisms (32mSNPs) and revealed a SNP density of 30 SNPs/kb and 12 non-synonymous SNPs/gene reflecting a high structural and functional genomic diversity of the new collection. Each SNP was annotated with 30 categories of structural and/or functional information. We further identified paired accessions between the 1.5'K and 20,087 (20'K) accessions in US collection as genomic “equivalent” accessions sharing the highest genomic identity for minimizing the barriers in soybean germplasm exchange between countries. We also exemplified the utility of 32mSNPs in enhancing post-genomics research through in-silico genotyping, high-resolution GWAS, discovering and/or characterizing genes and alleles/mutations, identifying germplasms containing beneficial alleles that are potentially experiencing artificial selection. Conclusion The comprehensive analysis of publicly available large-scale genome sequencing data of diverse cultivated accessions and the newly in-house sequenced wild accessions greatly increased the soybean genome-wide variation resolution. This could facilitate a variety of genetic and molecular-level analyses in soybean. The 32mSNPs and 1.5'K accessions with their comprehensive annotation have been made available at the SoyBase and Ag Data Commons. The dataset could further serve as a versatile and expandable core resource for exploring the exponentially increasing genome sequencing data for a variety of post-genomic research.