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

Gaia Cortinovis, Leonardo Vincenzi, Robyn Anderson, Giovanni Marturano, Jacob Ian Marsh, Philipp Emanuel Bayer, Lorenzo Rocchetti, Giulia Frascarelli, Giovanna Lanzavecchia, Alice Pieri, Andrea Benazzo, Elisa Bellucci, Valerio Vittori, Laura Nanni, Juan José Ferreira Fernández, Marzia Rossato, Orlando Mario Aguilar, Peter Laurent Morrell, Monica Rodriguez, Tania Gioia, Kerstin Neumann, Juan Camilo Alvarez Diaz, Ariane Gratias, Christophe Klopp, Elena Bitocchi, Valérie Geffroy (), Massimo Delledonne (), David Edwards () and Roberto Papa ()
Additional contact information
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
Orlando Mario Aguilar: CCT La Plata
Peter Laurent Morrell: University of Minnesota
Monica Rodriguez: 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
David Edwards: University of Western Australia
Roberto Papa: Marche Polytechnic University

Nature Communications, 2024, vol. 15, issue 1, 1-15

Abstract: 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.

Date: 2024
References: View references in EconPapers View complete reference list from CitEc
Citations: View citations in EconPapers (1)

Downloads: (external link)
https://www.nature.com/articles/s41467-024-51032-2 Abstract (text/html)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-51032-2

Ordering information: This journal article can be ordered from
https://www.nature.com/ncomms/

DOI: 10.1038/s41467-024-51032-2

Access Statistics for this article

Nature Communications is currently edited by Nathalie Le Bot, Enda Bergin and Fiona Gillespie

More articles in Nature Communications from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().