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Adaptive and maladaptive introgression in grapevine domestication

Domesticated grapevines spread to Europe around 3,000 years ago. Previous studies have revealed genomic signals of introgression from wild to cultivated grapes in Europe, but the time, mode, genomic pattern, and biological effects of these introgression events have not been investigated. Here, we st...

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Autores principales: Xiao, Hua, Liu, Zhongjie, Wang, Nan, Long, Qiming, Cao, Shuo, Huang, Guizhou, Liu, Wenwen, Peng, Yanling, Riaz, Summaira, Walker, Andrew M., Gaut, Brandon S., Zhou, Yongfeng
Formato: Online Artículo Texto
Lenguaje:English
Publicado: National Academy of Sciences 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10268302/
https://www.ncbi.nlm.nih.gov/pubmed/37276420
http://dx.doi.org/10.1073/pnas.2222041120
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author Xiao, Hua
Liu, Zhongjie
Wang, Nan
Long, Qiming
Cao, Shuo
Huang, Guizhou
Liu, Wenwen
Peng, Yanling
Riaz, Summaira
Walker, Andrew M.
Gaut, Brandon S.
Zhou, Yongfeng
author_facet Xiao, Hua
Liu, Zhongjie
Wang, Nan
Long, Qiming
Cao, Shuo
Huang, Guizhou
Liu, Wenwen
Peng, Yanling
Riaz, Summaira
Walker, Andrew M.
Gaut, Brandon S.
Zhou, Yongfeng
author_sort Xiao, Hua
collection PubMed
description Domesticated grapevines spread to Europe around 3,000 years ago. Previous studies have revealed genomic signals of introgression from wild to cultivated grapes in Europe, but the time, mode, genomic pattern, and biological effects of these introgression events have not been investigated. Here, we studied resequencing data from 345 samples spanning the distributional range of wild (Vitis vinifera ssp. sylvestris) and cultivated (V. vinifera ssp. vinifera) grapes. Based on machine learning–based population genetic analyses, we detected evidence for a single domestication of grapevine, followed by continuous gene flow between European wild grapes (EU) and cultivated grapes over the past ~2,000 y, especially from EU to wine grapes. We also inferred that soft-selective sweeps were the dominant signals of artificial selection. Gene pathways associated with the synthesis of aromatic compounds were enriched in regions that were both selected and introgressed, suggesting EU wild grapes were an important resource for improving the flavor of cultivated grapes. Despite the potential benefits of introgression in grape improvement, the introgressed fragments introduced a higher deleterious burden, with most deleterious SNPs and structural variants hidden in a heterozygous state. Cultivated wine grapes have benefited from adaptive introgression with wild grapes, but introgression has also increased the genetic load. In general, our study of beneficial and harmful effects of introgression is critical for genomic breeding of grapevine to take advantage of wild resources.
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spelling pubmed-102683022023-06-15 Adaptive and maladaptive introgression in grapevine domestication Xiao, Hua Liu, Zhongjie Wang, Nan Long, Qiming Cao, Shuo Huang, Guizhou Liu, Wenwen Peng, Yanling Riaz, Summaira Walker, Andrew M. Gaut, Brandon S. Zhou, Yongfeng Proc Natl Acad Sci U S A Biological Sciences Domesticated grapevines spread to Europe around 3,000 years ago. Previous studies have revealed genomic signals of introgression from wild to cultivated grapes in Europe, but the time, mode, genomic pattern, and biological effects of these introgression events have not been investigated. Here, we studied resequencing data from 345 samples spanning the distributional range of wild (Vitis vinifera ssp. sylvestris) and cultivated (V. vinifera ssp. vinifera) grapes. Based on machine learning–based population genetic analyses, we detected evidence for a single domestication of grapevine, followed by continuous gene flow between European wild grapes (EU) and cultivated grapes over the past ~2,000 y, especially from EU to wine grapes. We also inferred that soft-selective sweeps were the dominant signals of artificial selection. Gene pathways associated with the synthesis of aromatic compounds were enriched in regions that were both selected and introgressed, suggesting EU wild grapes were an important resource for improving the flavor of cultivated grapes. Despite the potential benefits of introgression in grape improvement, the introgressed fragments introduced a higher deleterious burden, with most deleterious SNPs and structural variants hidden in a heterozygous state. Cultivated wine grapes have benefited from adaptive introgression with wild grapes, but introgression has also increased the genetic load. In general, our study of beneficial and harmful effects of introgression is critical for genomic breeding of grapevine to take advantage of wild resources. National Academy of Sciences 2023-06-05 2023-06-13 /pmc/articles/PMC10268302/ /pubmed/37276420 http://dx.doi.org/10.1073/pnas.2222041120 Text en Copyright © 2023 the Author(s). Published by PNAS. https://creativecommons.org/licenses/by/4.0/This open access article is distributed under Creative Commons Attribution License 4.0 (CC BY) (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Biological Sciences
Xiao, Hua
Liu, Zhongjie
Wang, Nan
Long, Qiming
Cao, Shuo
Huang, Guizhou
Liu, Wenwen
Peng, Yanling
Riaz, Summaira
Walker, Andrew M.
Gaut, Brandon S.
Zhou, Yongfeng
Adaptive and maladaptive introgression in grapevine domestication
title Adaptive and maladaptive introgression in grapevine domestication
title_full Adaptive and maladaptive introgression in grapevine domestication
title_fullStr Adaptive and maladaptive introgression in grapevine domestication
title_full_unstemmed Adaptive and maladaptive introgression in grapevine domestication
title_short Adaptive and maladaptive introgression in grapevine domestication
title_sort adaptive and maladaptive introgression in grapevine domestication
topic Biological Sciences
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10268302/
https://www.ncbi.nlm.nih.gov/pubmed/37276420
http://dx.doi.org/10.1073/pnas.2222041120
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