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Adaptive and maladaptive introgression in grapevine domestication

文献类型： 外文期刊

作者： Xiao, Hua 1 ; Liu, Zhongjie 1 ; Wang, Nan 1 ; Long, Qiming 1 ; Cao, Shuo 1 ; Huang, Guizhou 1 ; Liu, Wenwen 1 ; Peng, Yanling 1 ; Riaz, Summaira 3 ; Walker, Andrew M. 3 ; Gaut, Brandon S. 4 ; Zhou, Yongfeng 1 ;

作者机构： 1.Chinese Acad Agr Sci, Agr Genom Inst Shenzhen, Guangdong Lab Lingnan Modern Agr, Minist Agr & Rural Affairs,Key Lab Synthet Biol,St, Shenzhen 518000, Peoples R China

2.Xinjiang Acad Agr Sci, Inst Hort Crops, State Key Lab Genet Improvement & Germplasm Innova, Key Lab Genome Res & Genet Improvement Xinjiang Ch, Urumqi 830091, Peoples R China

3.Univ Calif Davis, Dept Viticulture & Enol, Davis, CA 95616 USA

4.Univ Calif Irvine, Dept Ecol & Evolutionary Biol, Irvine, CA 92697 USA

5.Trop Crops Genet Resources Inst, Chinese Acad Trop Agr Sci, State Key Lab Trop Crop Breeding, Haikou 571101, Peoples R China

关键词： population genetics; grape breeding; machine learning; viticulture; structural variation

期刊名称：PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA （ 影响因子：11.1； 五年影响因子：12.0 ）

ISSN： 0027-8424

年卷期： 2023 年 120 卷 24 期

页码：

收录情况： SCI

摘要： 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 similar to 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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