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Genome-wide genotyping elucidates the geographical diversification and dispersal of the polyploid and clonally propagated yam (Dioscorea alata)

BACKGROUND AND AIMS: Inferring the diffusion history of many human-dispersed species is still not straightforward due to unresolved past human migrations. The centre of diversification and routes of migration of the autopolyploid and clonally propagated greater yam, Dioscorea alata, one of the oldes...

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Autores principales: Sharif, Bilal Muhammad, Burgarella, Concetta, Cormier, Fabien, Mournet, Pierre, Causse, Sandrine, Van, Kien Nguyen, Kaoh, Juliane, Rajaonah, Mamy Tiana, Lakshan, Senanayake Ravinda, Waki, Jeffrey, Bhattacharjee, Ranjana, Badara, Gueye, Pachakkil, Babil, Arnau, Gemma, Chaïr, Hana
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7596366/
https://www.ncbi.nlm.nih.gov/pubmed/32592585
http://dx.doi.org/10.1093/aob/mcaa122
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author Sharif, Bilal Muhammad
Burgarella, Concetta
Cormier, Fabien
Mournet, Pierre
Causse, Sandrine
Van, Kien Nguyen
Kaoh, Juliane
Rajaonah, Mamy Tiana
Lakshan, Senanayake Ravinda
Waki, Jeffrey
Bhattacharjee, Ranjana
Badara, Gueye
Pachakkil, Babil
Arnau, Gemma
Chaïr, Hana
author_facet Sharif, Bilal Muhammad
Burgarella, Concetta
Cormier, Fabien
Mournet, Pierre
Causse, Sandrine
Van, Kien Nguyen
Kaoh, Juliane
Rajaonah, Mamy Tiana
Lakshan, Senanayake Ravinda
Waki, Jeffrey
Bhattacharjee, Ranjana
Badara, Gueye
Pachakkil, Babil
Arnau, Gemma
Chaïr, Hana
author_sort Sharif, Bilal Muhammad
collection PubMed
description BACKGROUND AND AIMS: Inferring the diffusion history of many human-dispersed species is still not straightforward due to unresolved past human migrations. The centre of diversification and routes of migration of the autopolyploid and clonally propagated greater yam, Dioscorea alata, one of the oldest edible tubers, remain unclear. Here, we address yam demographic and dispersal history using a worldwide sample. METHODS: We characterized genome-wide patterns of genetic variation using genotyping by sequencing 643 greater yam accessions spanning four continents. First, we disentangled the polyploid and clonal components of yam diversity using allele frequency distribution and identity by descent approaches. We then addressed yam geographical origin and diffusion history with a model-based coalescent inferential approach. KEY RESULTS: Diploid genotypes were more frequent than triploids and tetraploids worldwide. Genetic diversity was generally low and clonality appeared to be a main factor of diversification. The most likely evolutionary scenario supported an early divergence of mainland Southeast Asian and Pacific gene pools with continuous migration between them. The genetic make-up of triploids and tetraploids suggests that they have originated from these two regions before westward yam migration. The Indian Peninsula gene pool gave origin to the African gene pool, which was later introduced to the Caribbean region. CONCLUSIONS: Our results are congruent with the hypothesis of independent domestication origins of the two main Asian and Pacific gene pools. The low genetic diversity and high clonality observed suggest a strong domestication bottleneck followed by thousands of years of widespread vegetative propagation and polyploidization. Both processes reduced the extent of diversity available for breeding, and this is likely to threaten future adaptation.
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spelling pubmed-75963662020-11-03 Genome-wide genotyping elucidates the geographical diversification and dispersal of the polyploid and clonally propagated yam (Dioscorea alata) Sharif, Bilal Muhammad Burgarella, Concetta Cormier, Fabien Mournet, Pierre Causse, Sandrine Van, Kien Nguyen Kaoh, Juliane Rajaonah, Mamy Tiana Lakshan, Senanayake Ravinda Waki, Jeffrey Bhattacharjee, Ranjana Badara, Gueye Pachakkil, Babil Arnau, Gemma Chaïr, Hana Ann Bot Original Articles BACKGROUND AND AIMS: Inferring the diffusion history of many human-dispersed species is still not straightforward due to unresolved past human migrations. The centre of diversification and routes of migration of the autopolyploid and clonally propagated greater yam, Dioscorea alata, one of the oldest edible tubers, remain unclear. Here, we address yam demographic and dispersal history using a worldwide sample. METHODS: We characterized genome-wide patterns of genetic variation using genotyping by sequencing 643 greater yam accessions spanning four continents. First, we disentangled the polyploid and clonal components of yam diversity using allele frequency distribution and identity by descent approaches. We then addressed yam geographical origin and diffusion history with a model-based coalescent inferential approach. KEY RESULTS: Diploid genotypes were more frequent than triploids and tetraploids worldwide. Genetic diversity was generally low and clonality appeared to be a main factor of diversification. The most likely evolutionary scenario supported an early divergence of mainland Southeast Asian and Pacific gene pools with continuous migration between them. The genetic make-up of triploids and tetraploids suggests that they have originated from these two regions before westward yam migration. The Indian Peninsula gene pool gave origin to the African gene pool, which was later introduced to the Caribbean region. CONCLUSIONS: Our results are congruent with the hypothesis of independent domestication origins of the two main Asian and Pacific gene pools. The low genetic diversity and high clonality observed suggest a strong domestication bottleneck followed by thousands of years of widespread vegetative propagation and polyploidization. Both processes reduced the extent of diversity available for breeding, and this is likely to threaten future adaptation. Oxford University Press 2020-06-27 /pmc/articles/PMC7596366/ /pubmed/32592585 http://dx.doi.org/10.1093/aob/mcaa122 Text en © The Author(s) 2020. Published by Oxford University Press on behalf of the Annals of Botany Company. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Original Articles
Sharif, Bilal Muhammad
Burgarella, Concetta
Cormier, Fabien
Mournet, Pierre
Causse, Sandrine
Van, Kien Nguyen
Kaoh, Juliane
Rajaonah, Mamy Tiana
Lakshan, Senanayake Ravinda
Waki, Jeffrey
Bhattacharjee, Ranjana
Badara, Gueye
Pachakkil, Babil
Arnau, Gemma
Chaïr, Hana
Genome-wide genotyping elucidates the geographical diversification and dispersal of the polyploid and clonally propagated yam (Dioscorea alata)
title Genome-wide genotyping elucidates the geographical diversification and dispersal of the polyploid and clonally propagated yam (Dioscorea alata)
title_full Genome-wide genotyping elucidates the geographical diversification and dispersal of the polyploid and clonally propagated yam (Dioscorea alata)
title_fullStr Genome-wide genotyping elucidates the geographical diversification and dispersal of the polyploid and clonally propagated yam (Dioscorea alata)
title_full_unstemmed Genome-wide genotyping elucidates the geographical diversification and dispersal of the polyploid and clonally propagated yam (Dioscorea alata)
title_short Genome-wide genotyping elucidates the geographical diversification and dispersal of the polyploid and clonally propagated yam (Dioscorea alata)
title_sort genome-wide genotyping elucidates the geographical diversification and dispersal of the polyploid and clonally propagated yam (dioscorea alata)
topic Original Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7596366/
https://www.ncbi.nlm.nih.gov/pubmed/32592585
http://dx.doi.org/10.1093/aob/mcaa122
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