ArticleNature communications2024
Adaptive gene loss in the common bean pan-genome during range expansion and domestication.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- Unlocking the future of crop improvement with crop wild relatives.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Review
- Integrating genomics, multi-omics, CRISPR and speed breeding for stress-resilient vegetable legume improvement.Functional & integrative genomics · 2026Review
- The I gene defines a dynamic NLR cluster conferring broad potyvirus resistance in common bean.Nature communications · 2026Article
- Physiological and Biochemical Responses of Two Major Legume Crops to Seed Priming-A Systematic Review.Plants (Basel, Switzerland) · 2026Review
- Visible-Near-Infrared Hyperspectral Imaging Enables Nondestructive Identification of Bean Accessions via 1D Spectral Reflectance Analysis.ACS omega · 2026Article
- GWAS identifies regulators of seed and leaf morphology in common bean, revealing OFP5 as a major seed size determinant.The Plant journal : for cell and molecular biology · 2026Article
- Functional insights into dispensable genes using genome-wide loss-of-function burden tests in Arabidopsis.The Plant cell · 2026Article
- From structural pangenomes to functional panomics in plants.Molecular biology and evolution · 2026Review
- Domestication and genome evolution iniScience · 2026Review
- VIS-NIR-SWIR Hyperspectral Imaging and Advanced Machine and Deep Learning Algorithms for a Controlled Benchmark of Bean Seed Identification and Classification.Plants (Basel, Switzerland) · 2026Article
- Cross-domain cooperation drives nutrient acquisition and metabolism in the bark beetle holobiont.The ISME journal · 2026Article
- Graph pan-genome advances genetic discoveries and the improvement of eggplant.Horticulture research · 2026Article
- Establishment and phenotypic characterization of genetically diverse core collections of Lupinus albus.BMC plant biology · 2025Article
- Elucidating the interplay between metabolites and microorganisms in the spermosphere of common bean (mSystems · 2025Article
- Integration of crop modeling and sensing into molecular breeding for nutritional quality and stress tolerance.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Review
- A panomics-driven framework for the improvement of major food legume crops: advances, challenges, and future prospects.Horticulture research · 2025Article
- Genome-wide analysis of the ammonium transporters gene family in Phaseolus vulgaris and its roles in response to drought and salinity stress.Scientific reports · 2025Article
- Functional Genomics: From Soybean to Legume.International journal of molecular sciences · 2025Review
- Genetic control of seed iron and zinc concentration in Rwandan common bean population revealed by the Genome Wide Association Study (GWAS).Breeding science · 2025Article
- The unexplored diversity of rough-seeded lupins provides rich genomic resources and insights into lupin evolution.Nature communications · 2025Article
Corrections and comments
- Erratum issued
Authors and funding
29 authors.
Funding
Abstract
The common bean (Phaseolus vulgaris L.) is a crucial legume crop and an ideal evolutionary model to study adaptive diversity in wild and domesticated populations. Here, we present a common bean pan-genome based on five high-quality genomes and whole-genome reads representing 339 genotypes. It reveals ~234 Mb of additional sequences containing 6,905 protein-coding genes missing from the reference, constituting 49% of all presence/absence variants (PAVs). More non-synonymous mutations are found in PAVs than core genes, probably reflecting the lower effective population size of PAVs and fitness advantages due to the purging effect of gene loss. Our results suggest pan-genome shrinkage occurred during wild range expansion. Selection signatures provide evidence that partial or complete gene loss was a key adaptive genetic change in common bean populations with major implications for plant adaptation. The pan-genome is a valuable resource for food legume research and breeding for climate change mitigation and sustainable agriculture.
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