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Genome-Wide Admixture Mapping Identifies Wild Ancestry-of-Origin Segments in Cultivated Robusta Coffee

Humans have had a major influence on the dissemination of crops beyond their native range, thereby offering new hybridization opportunities. Characterizing admixed genomes with mosaic origins generates valuable insight into the adaptive history of crops and the impact on current varietal diversity....

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Detalles Bibliográficos
Autores principales: Vi, Tram, Vigouroux, Yves, Cubry, Philippe, Marraccini, Pierre, Phan, Ha Viet, Khong, Giang Ngan, Poncet, Valerie
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10159586/
https://www.ncbi.nlm.nih.gov/pubmed/37079743
http://dx.doi.org/10.1093/gbe/evad065
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author Vi, Tram
Vigouroux, Yves
Cubry, Philippe
Marraccini, Pierre
Phan, Ha Viet
Khong, Giang Ngan
Poncet, Valerie
author_facet Vi, Tram
Vigouroux, Yves
Cubry, Philippe
Marraccini, Pierre
Phan, Ha Viet
Khong, Giang Ngan
Poncet, Valerie
author_sort Vi, Tram
collection PubMed
description Humans have had a major influence on the dissemination of crops beyond their native range, thereby offering new hybridization opportunities. Characterizing admixed genomes with mosaic origins generates valuable insight into the adaptive history of crops and the impact on current varietal diversity. We applied the ELAI tool—an efficient local ancestry inference method based on a two-layer hidden Markov model to track segments of wild origin in cultivated accessions in the case of multiway admixtures. Source populations—which may actually be limited and partially admixed—must be generally specified when using such inference models. We thus developed a framework to identify local ancestry with admixed source populations. Using sequencing data for wild and cultivated Coffea canephora (commonly called Robusta), our approach was found to be highly efficient and accurate on simulated hybrids. Application of the method to assess elite Robusta varieties from Vietnam led to the identification of an accession derived from a likely backcross between two genetic groups from the Congo Basin and the western coastal region of Central Africa. Admixtures resulting from crop hybridization and diffusion could thus lead to the generation of elite high-yielding varieties. Our methods should be widely applicable to gain insight into the role of hybridization during plant and animal evolutionary history.
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spelling pubmed-101595862023-05-05 Genome-Wide Admixture Mapping Identifies Wild Ancestry-of-Origin Segments in Cultivated Robusta Coffee Vi, Tram Vigouroux, Yves Cubry, Philippe Marraccini, Pierre Phan, Ha Viet Khong, Giang Ngan Poncet, Valerie Genome Biol Evol Article Humans have had a major influence on the dissemination of crops beyond their native range, thereby offering new hybridization opportunities. Characterizing admixed genomes with mosaic origins generates valuable insight into the adaptive history of crops and the impact on current varietal diversity. We applied the ELAI tool—an efficient local ancestry inference method based on a two-layer hidden Markov model to track segments of wild origin in cultivated accessions in the case of multiway admixtures. Source populations—which may actually be limited and partially admixed—must be generally specified when using such inference models. We thus developed a framework to identify local ancestry with admixed source populations. Using sequencing data for wild and cultivated Coffea canephora (commonly called Robusta), our approach was found to be highly efficient and accurate on simulated hybrids. Application of the method to assess elite Robusta varieties from Vietnam led to the identification of an accession derived from a likely backcross between two genetic groups from the Congo Basin and the western coastal region of Central Africa. Admixtures resulting from crop hybridization and diffusion could thus lead to the generation of elite high-yielding varieties. Our methods should be widely applicable to gain insight into the role of hybridization during plant and animal evolutionary history. Oxford University Press 2023-04-20 /pmc/articles/PMC10159586/ /pubmed/37079743 http://dx.doi.org/10.1093/gbe/evad065 Text en © The Author(s) 2023. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution. https://creativecommons.org/licenses/by-nc/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Article
Vi, Tram
Vigouroux, Yves
Cubry, Philippe
Marraccini, Pierre
Phan, Ha Viet
Khong, Giang Ngan
Poncet, Valerie
Genome-Wide Admixture Mapping Identifies Wild Ancestry-of-Origin Segments in Cultivated Robusta Coffee
title Genome-Wide Admixture Mapping Identifies Wild Ancestry-of-Origin Segments in Cultivated Robusta Coffee
title_full Genome-Wide Admixture Mapping Identifies Wild Ancestry-of-Origin Segments in Cultivated Robusta Coffee
title_fullStr Genome-Wide Admixture Mapping Identifies Wild Ancestry-of-Origin Segments in Cultivated Robusta Coffee
title_full_unstemmed Genome-Wide Admixture Mapping Identifies Wild Ancestry-of-Origin Segments in Cultivated Robusta Coffee
title_short Genome-Wide Admixture Mapping Identifies Wild Ancestry-of-Origin Segments in Cultivated Robusta Coffee
title_sort genome-wide admixture mapping identifies wild ancestry-of-origin segments in cultivated robusta coffee
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10159586/
https://www.ncbi.nlm.nih.gov/pubmed/37079743
http://dx.doi.org/10.1093/gbe/evad065
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