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Phylogeny and disparate selection signatures suggest two genetically independent domestication events in pea (Pisum L.)

Domestication is considered a model of adaptation that can be used to draw conclusions about the modus operandi of selection in natural systems. Investigating domestication may give insights into how plants react to different intensities of human manipulation, which has direct implication for the co...

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Autores principales: Hellwig, Timo, Abbo, Shahal, Ophir, Ron
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley and Sons Inc. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9303476/
https://www.ncbi.nlm.nih.gov/pubmed/35061306
http://dx.doi.org/10.1111/tpj.15678
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author Hellwig, Timo
Abbo, Shahal
Ophir, Ron
author_facet Hellwig, Timo
Abbo, Shahal
Ophir, Ron
author_sort Hellwig, Timo
collection PubMed
description Domestication is considered a model of adaptation that can be used to draw conclusions about the modus operandi of selection in natural systems. Investigating domestication may give insights into how plants react to different intensities of human manipulation, which has direct implication for the continuing efforts of crop improvement. Therefore, scientists of various disciplines study domestication‐related questions to understand the biological and cultural bases of the domestication process. We employed restriction site‐associated DNA sequencing (RAD‐seq) of 494 Pisum sativum (pea) samples from all wild and domesticated groups to analyze the genetic structure of the collection. Patterns of ancient admixture were investigated by analysis of admixture graphs. We used two complementary approaches, one diversity based and one based on differentiation, to detect the selection signatures putatively associated with domestication. An analysis of the subpopulation structure of wild P. sativum revealed five distinct groups with a notable geographic pattern. Pisum abyssinicum clustered unequivocally within the P. sativum complex, without any indication of hybrid origin. We detected 32 genomic regions putatively subjected to selection: 29 in P. sativum ssp. sativum and three in P. abyssinicum. The two domesticated groups did not share regions under selection and did not display similar haplotype patterns within those regions. Wild P. sativum is structured into well‐diverged subgroups. Although Pisum sativum ssp. humile is not supported as a taxonomic entity, the so‐called 'southern humile' is a genuine wild group. Introgression did not shape the variation observed within the sampled germplasm. The two domesticated pea groups display distinct genetic bases of domestication, suggesting two genetically independent domestication events.
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spelling pubmed-93034762022-07-28 Phylogeny and disparate selection signatures suggest two genetically independent domestication events in pea (Pisum L.) Hellwig, Timo Abbo, Shahal Ophir, Ron Plant J Original Articles Domestication is considered a model of adaptation that can be used to draw conclusions about the modus operandi of selection in natural systems. Investigating domestication may give insights into how plants react to different intensities of human manipulation, which has direct implication for the continuing efforts of crop improvement. Therefore, scientists of various disciplines study domestication‐related questions to understand the biological and cultural bases of the domestication process. We employed restriction site‐associated DNA sequencing (RAD‐seq) of 494 Pisum sativum (pea) samples from all wild and domesticated groups to analyze the genetic structure of the collection. Patterns of ancient admixture were investigated by analysis of admixture graphs. We used two complementary approaches, one diversity based and one based on differentiation, to detect the selection signatures putatively associated with domestication. An analysis of the subpopulation structure of wild P. sativum revealed five distinct groups with a notable geographic pattern. Pisum abyssinicum clustered unequivocally within the P. sativum complex, without any indication of hybrid origin. We detected 32 genomic regions putatively subjected to selection: 29 in P. sativum ssp. sativum and three in P. abyssinicum. The two domesticated groups did not share regions under selection and did not display similar haplotype patterns within those regions. Wild P. sativum is structured into well‐diverged subgroups. Although Pisum sativum ssp. humile is not supported as a taxonomic entity, the so‐called 'southern humile' is a genuine wild group. Introgression did not shape the variation observed within the sampled germplasm. The two domesticated pea groups display distinct genetic bases of domestication, suggesting two genetically independent domestication events. John Wiley and Sons Inc. 2022-02-24 2022-04 /pmc/articles/PMC9303476/ /pubmed/35061306 http://dx.doi.org/10.1111/tpj.15678 Text en © 2022 The Authors. The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd. https://creativecommons.org/licenses/by-nc/4.0/This is an open access article under the terms of the http://creativecommons.org/licenses/by-nc/4.0/ (https://creativecommons.org/licenses/by-nc/4.0/) License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.
spellingShingle Original Articles
Hellwig, Timo
Abbo, Shahal
Ophir, Ron
Phylogeny and disparate selection signatures suggest two genetically independent domestication events in pea (Pisum L.)
title Phylogeny and disparate selection signatures suggest two genetically independent domestication events in pea (Pisum L.)
title_full Phylogeny and disparate selection signatures suggest two genetically independent domestication events in pea (Pisum L.)
title_fullStr Phylogeny and disparate selection signatures suggest two genetically independent domestication events in pea (Pisum L.)
title_full_unstemmed Phylogeny and disparate selection signatures suggest two genetically independent domestication events in pea (Pisum L.)
title_short Phylogeny and disparate selection signatures suggest two genetically independent domestication events in pea (Pisum L.)
title_sort phylogeny and disparate selection signatures suggest two genetically independent domestication events in pea (pisum l.)
topic Original Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9303476/
https://www.ncbi.nlm.nih.gov/pubmed/35061306
http://dx.doi.org/10.1111/tpj.15678
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