Assembly, comparative analysis, and utilization of a single haplotype reference genome for soybean

Authors: ESPINA, MARY JANE - University Of Minnesota; LOVELL, JOHN - Hudsonalpha Institute For Biotechnology; SREEDAYSYAM, AVINASH - Hudsonalpha Institute For Biotechnology; JENKINS, JERRY - Hudsonalpha Institute For Biotechnology; GRIMWOOD, JANE - Hudsonalpha Institute For Biotechnology; Jordan, Brandon; Cannon, Steven; LORENZ, AARON - University Of Minnesota; SCHMUTZ, JEREMY - Hudsonalpha Institute For Biotechnology; STUPAR, ROBERT - University Of Minnesota

Submitted to: The Plant Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/30/2024
Publication Date: 9/14/2024
Citation: Espina, M.C., Lovell, J., Sreedaysyam, A., Jenkins, J., Grimwood, J., Jordan, B.D., Cannon, S.B., Lorenz, A.J., Schmutz, J., Stupar, R.M. 2024. Assembly, comparative analysis, and utilization of a single haplotype reference genome for soybean. The Plant Journal. https://doi.org/10.1111/tpj.17026.
DOI: https://doi.org/10.1111/tpj.17026

Interpretive Summary: Plant breeders and researchers working on crop improvement rely on maps of important features in the chromosomes of the species that they work with. The most detailed maps of this type are genome assemblies and associated addresses or locations of predicted genes. The work described here reports the near-complete genome assembly of one of the predominant soybean varieties used in research and breeding in the U.S. This genome assembly of the Williams 82 variety improves on several previous assembly versions of this variety. Additionally, the paper reports a new genome assembly of another cultivar, Fiskeby III, which is an important source of disease resistance and early maturation in soybean breeding programs. This latest genome assembly of the Williams 82 cultivar -- the sixth published version of this variety in the last 15 years, is based on a "pure-line selection" from Williams 82, and offers improved accuracy and precision in regions that are especially important for disease resistance. This sixth assembly is entirely complete for eight of the 20 chromosomes and near-complete on the remaining chromosomes. In total, the genome assembly spans more than 1.01 billion DNA letters. There are additional improvements in predictions of genes. The genome assemblies reported here provide important resources for improving soybean through plant breeding and research work. Accurate maps of the genome sequence and gene locations will aid breeding efforts, ultimately benefitting both growers and consumers through new varieties that are higher-yielding and more nutritious and stress- and disease-resistant.

Technical Abstract: Cultivar ‘Williams 82’ (Wm82) has served as the reference genome for the soybean research community since 2008, but is known to have areas of genomic heterogeneity among different sub-lines. This work provides an updated assembly (version Wm82.a6) derived from a specific sub-line known as ‘Wm82-ISU-01’ (seeds available under USDA accession number PI 704477). The genome was assembled using Pacific BioSciences HiFi reads and integrated into chromosomes using HiC. The 20 soybean chromosomes assembled into a genome of 1.01Gb, consisting of 36 contigs. The genome annotation identified 48,387 gene models, named in accordance with previous assembly versions Wm82.a2 and Wm82.a4. Comparisons of Wm82.a6 with other near-gapless assemblies of ‘Williams 82’ reveal large regions of genomic heterogeneity, including regions of differential introgression from the genotype ‘Kingwa’ within approximately 30 Mb and 25 Mb segments on chromosomes 03 and 07, respectively. Additionally, our analysis revealed a previously unknown large (~20 Mb) heterogeneous region in the pericentromeric region of chromosome 12, where Wm82.a6 matches the ‘Williams’ haplotype while the other two completed assemblies do not match the haplotype of either parent of ‘Williams 82’. In addition to the Wm82.a6 assembly, we also assembled the genome of soybean line ‘Fiskeby III,’ a rich resource for abiotic stress resistance genes. A genome comparison of Wm82.a6 with ‘Fiskeby III’ revealed the nucleotide and structural polymorphisms between the two genomes within a QTL region for iron deficiency chlorosis resistance. The Wm82.a6 and ‘Fiskeby III’ genomes described here will enhance comparative and functional genomics capacities and applications in the soybean community.