Sequencing the USDA core soybean collection reveals gene loss during domestication and breeding

  Bayer, P., Hu, R., Valliyodan, B., Marsh, J., Yuan, A., Vuong, T., Patil, G., Song, Q., Batley, J., Varshney, R., Lam, H. M., Edwards, D., Nguyen, H. Sequencing the USDA core soybean collection reveals gene loss during domestication and breeding. Plant Genome. 2021 June;e20109 doi: 10.1002/tpg2.20109 Epub ahead of print. PMID: 34169673

The objective of this project was to assemble a soybean pangenome representing more than 1,000 soybean accessions derived from the USDA Soybean Germplasm Collection, including both wild and cultivated lineages, to assess genome-wide changes in gene and allele frequency during domestication and breeding. We identified 3,765 genes that are absent from the Lee reference genome assembly and assessed the presence/absence of all genes across this population. The pangenome is presented here together with the presence/absence state of each gene in this population and SNPs between individuals.

Files available for download include the variant data in VCF (variant call format) for the 1000 accessions from the USDA Soybean Germplasm Collection, presence/absence matrix for gene models present or absent from the Lee assembly, and protein sequences unique to each accession.

• Variant counts of Accessions

• GFF3 file of genes not in Lee

• Protein sequences of Lee gene transcripts and protein sequences unique to each accession

• VCF file of SNPs >= 5 MAF

• Matrix of genes present/absence in Lee

• Fasta file of sequences not present in Lee

• SoyBase genome viewer representation of gene presence/absence compared to Lee gene models

• Soybean pangenome data repository at the Univ. of Western Australia