ArticleThe plant genome2022
Sequencing the USDA core soybean collection reveals gene loss during domestication and breeding.
Article in The plant genome, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 papers.
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Who cites it
65 citing papers in PubMed.
- Photosynthesis-informed breeding to enhance Soybean (Glycine max) yield potential: a framework integrating high-throughput phenomics, genomic prediction and G×E×M.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Review
- FM-3224: A potent triazolinone-based fungicide with broad-spectrum activity and computational support for putative dual-target binding.Pest management science · 2026Article
- Empowering Plant Biotechnology Research: Super-Pangenomes as a Novel Arsenal for Crop Breeding and Improvement.Molecular biotechnology · 2026Review
- Assembly of Silphium interspecific hybrid genomes opens the genus to phylogenomics, ecogenomics, and molecular breeding.Nature communications · 2026Article
- Unlocking soybean domestication history: a genomic study charting its 6,000-year journey from wild vine to global crop.Science China. Life sciences · 2026Article
- Accessing crop genetic diversity via pangenomics.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Review
- Graph-based pangenome reveals structural variation dynamics during cucumber breeding.Nature genetics · 2026Article
- Local Haplotyping Analysis for Flowering Time in Soybean Using Crosshap.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Legume Pangenome Construction Using an Iterative Mapping and Assembly Approach.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Comparative genomic analysis of QTL for resistance to Aphanomyces euteiches between pea, lentil, faba bean, and the model species Medicago truncatula.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- Molecular Network Analysis in Model and Non-Model Legumes: Challenges in Omics Data Interpretation Across Species, with a Focus onPlants (Basel, Switzerland) · 2025Review
- Using landscape genomics to infer genomic regions involved in environmental adaptation of soybean genebank accessions.BMC plant biology · 2025Article
- Domestication Reduces Plant Immune Receptor Gene Repertoires Across Lineages.Genome biology and evolution · 2025Article
- Review
- Core biological principles and tools stemming from basic Arabidopsis research.The Plant cell · 2025Review
- Landscape of rare-allele variants in cultivated and wild soybean genomes.The plant genome · 2025Article
- Genome-wide exploration of soybean domestication traits: integrating association mapping and SNP × SNP interaction analyses.Plant molecular biology · 2025Article
- The genomic landscape of gene-level structural variations in Japanese and global soybean Glycine max cultivars.Nature genetics · 2025Article
- Exploring genomic feature selection: A comparative analysis of GWAS and machine learning algorithms in a large-scale soybean dataset.The plant genome · 2025Article
- Brassica Panache: A multi-species graph pangenome representing presence absence variation across forty-one Brassica genomes.The plant genome · 2025Article
5 more citing papers are in PubMed but not listed here.
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Authors and funding
13 authors.
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Abstract
The gene content of plants varies between individuals of the same species due to gene presence/absence variation, and selection can alter the frequency of specific genes in a population. Selection during domestication and breeding will modify the genomic landscape, though the nature of these modifications is only understood for specific genes or on a more general level (e.g., by a loss of genetic diversity). Here we have assembled and analyzed a soybean (Glycine spp.) pangenome representing more than 1,000 soybean accessions derived from the USDA Soybean Germplasm Collection, including both wild and cultivated lineages, to assess genomewide 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. In addition to a loss of genetic diversity, we found a significant reduction in the average number of protein-coding genes per individual during domestication and subsequent breeding, though with some genes and allelic variants increasing in frequency associated with selection for agronomic traits. This analysis provides a genomic perspective of domestication and breeding in this important oilseed crop.
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