Interplay between large low-recombining regions and pseudo-overdominance in a plant genome

To what extent overdominance might contribute to the maintenance of genetic diversity within genomes is still an ongoing research question. Pseudo-overdominance created by the complementation of deleterious alleles in heterozygotes has recently become a subject of particular interest. Simulations and theory suggest that pseudo-overdominance may occur in low recombining regions. Here, we conduct a comprehensive investigation of large low-recombining (LLR) regions in cultivated populations of pearl millet, an outcrossing diploid African cereal. We examine seven large regions ranging from 5 to 88 Mb and six of them are pericentromeric. These LLR regions exhibit an excess of heterozygotes, a distinctive hallmark of overdominance. They display a tendency toward a higher diversity and a larger ratio of non-synonymous and deleterious variants. We conduct a more in-depth study of the largest 88 Mb region, identified on chromosome 3. Interestingly, haplotypes of this region have been introgressed from wild relatives. Using long read sequencing, we confirm their strong divergence and the presence of inversions across one of them. One of the haplotypes seems to be highly deleterious in the homozygous state. A total of 17% of the cultivated pearl millet genome exhibit a local population structure suggestive of overdominance or possibly pseudo-overdominance. Our empirical results contribute to the accumulation of knowledge, which will enhance our understanding of the potential role of overdominance or pseudo-overdominance in maintaining genetic diversity, particularly in low recombining regions.

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Publication Details

Journal
Nature Communications
Published
2025-07-12
DOI
https://doi.org/10.1038/s41467-025-61529-z
Citations
2
Primary Topic
Genetic Mapping and Diversity in Plants and Animals
Type
article
Field-Weighted Citation Impact
3.63

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article

Interplay between large low-recombining regions and pseudo-overdominance in a plant genome

Julie Orjuela, Sandrine Arribat, Miguel Navascués, Cédric Mariac et al.
2 citations
Nature Communications
Genetic Mapping and Diversity in Plants and Animals
3.63
article

Interplay between large low-recombining regions and pseudo-overdominance in a plant genome

Julie Orjuela, Sandrine Arribat, Miguel Navascués, Cédric Mariac, Stella Huynh, Anne‐Céline Thuillet, Adéline Barnaud, Nathalie Rodde, Adama Faye, Marine Salson, Maud Duranton, Leïla Zekraoui, Philippe Cubry, Cécile Berthouly‐Salazar, Marie Couderc, Ndjido Ardo Kane, Yves Vigouroux, Christine Tranchant‐Dubreuil, Concetta Burgarella
article en
2 citations

Abstract

To what extent overdominance might contribute to the maintenance of genetic diversity within genomes is still an ongoing research question. Pseudo-overdominance created by the complementation of deleterious alleles in heterozygotes has recently become a subject of particular interest. Simulations and theory suggest that pseudo-overdominance may occur in low recombining regions. Here, we conduct a comprehensive investigation of large low-recombining (LLR) regions in cultivated populations of pearl millet, an outcrossing diploid African cereal. We examine seven large regions ranging from 5 to 88 Mb and six of them are pericentromeric. These LLR regions exhibit an excess of heterozygotes, a distinctive hallmark of overdominance. They display a tendency toward a higher diversity and a larger ratio of non-synonymous and deleterious variants. We conduct a more in-depth study of the largest 88 Mb region, identified on chromosome 3. Interestingly, haplotypes of this region have been introgressed from wild relatives. Using long read sequencing, we confirm their strong divergence and the presence of inversions across one of them. One of the haplotypes seems to be highly deleterious in the homozygous state. A total of 17% of the cultivated pearl millet genome exhibit a local population structure suggestive of overdominance or possibly pseudo-overdominance. Our empirical results contribute to the accumulation of knowledge, which will enhance our understanding of the potential role of overdominance or pseudo-overdominance in maintaining genetic diversity, particularly in low recombining regions.

Nature CommunicationsVol. 16(1)
Uppsala University (SE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (FR), Université de Montpellier (FR), Institut Agro Montpellier (FR), Centre d'Etude Regional pour l'Amelioration de l'Adaptation a la Secheresse (SN), Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (FR), Diversité, adaptation et développement des plantes (FR), Amélioration Génétique et Adaptation des Plantes méditerranéennes et tropicales (FR), Institut Agro Montpelier (FR), Génétique Physiologie et Systèmes d'Elevage (FR), LMI Adaptation des Plantes et Microorganismes Associés aux Stress Environnementaux (SN), Institut de Recherche pour le Développement (FR)
European Commission, Agence Nationale de la Recherche
Zero hunger
Openalex Percentile: Top 7%
Genetic Mapping and Diversity in Plants and Animals
3.63
DOIOpen Access PDFOpenAlex
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