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Adaptive gene loss in the common bean pan-genome during range expansion and domestication

Author

Listed:
  • Gaia Cortinovis

    (Marche Polytechnic University)

  • Leonardo Vincenzi

    (University of Verona)

  • Robyn Anderson

    (University of Western Australia)

  • Giovanni Marturano

    (University of Verona)

  • Jacob Ian Marsh

    (University of Western Australia)

  • Philipp Emanuel Bayer

    (University of Western Australia)

  • Lorenzo Rocchetti

    (Marche Polytechnic University)

  • Giulia Frascarelli

    (Marche Polytechnic University)

  • Giovanna Lanzavecchia

    (Marche Polytechnic University)

  • Alice Pieri

    (Marche Polytechnic University)

  • Andrea Benazzo

    (University of Ferrara)

  • Elisa Bellucci

    (Marche Polytechnic University)

  • Valerio Vittori

    (Marche Polytechnic University)

  • Laura Nanni

    (Marche Polytechnic University)

  • Juan José Ferreira Fernández

    (Ctra AS-267 PK 19)

  • Marzia Rossato

    (University of Verona
    Genartis s.r.l)

  • Orlando Mario Aguilar

    (CCT La Plata)

  • Peter Laurent Morrell

    (University of Minnesota)

  • Monica Rodriguez

    (University of Sassari
    CBV—Centro per la Conservazione e Valorizzazione della Biodiversità Vegetale, University of Sassari)

  • Tania Gioia

    (University of Basilicata)

  • Kerstin Neumann

    (Leibniz Institute of Plant Genetics and Crop Plant Research (IPK))

  • Juan Camilo Alvarez Diaz

    (University Paris-Saclay)

  • Ariane Gratias

    (University Paris-Saclay)

  • Christophe Klopp

    (Sigenae, MIAT)

  • Elena Bitocchi

    (Marche Polytechnic University)

  • Valérie Geffroy

    (University Paris-Saclay)

  • Massimo Delledonne

    (University of Verona
    Genartis s.r.l)

  • David Edwards

    (University of Western Australia)

  • Roberto Papa

    (Marche Polytechnic University)

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.

Suggested Citation

  • Gaia Cortinovis & Leonardo Vincenzi & Robyn Anderson & Giovanni Marturano & Jacob Ian Marsh & Philipp Emanuel Bayer & Lorenzo Rocchetti & Giulia Frascarelli & Giovanna Lanzavecchia & Alice Pieri & And, 2024. "Adaptive gene loss in the common bean pan-genome during range expansion and domestication," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
  • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-51032-2
    DOI: 10.1038/s41467-024-51032-2
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