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Adaptive and maladaptive introgression in grapevine domestication.

Hua Xiao1,2, Zhongjie Liu1, Nan Wang1

  • 1State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China.

Proceedings of the National Academy of Sciences of the United States of America
|June 5, 2023
PubMed
Summary

Wild European grapes (EU) continuously interbred with cultivated grapes for 2,000 years, improving flavor but increasing genetic load. This genomic introgression offers insights for grapevine breeding.

Keywords:
grape breedingmachine learningpopulation geneticsstructural variationviticulture

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Area of Science:

  • Genomics
  • Population Genetics
  • Plant Breeding

Background:

  • Grapevines (Vitis vinifera) were domesticated ~3,000 years ago in Europe.
  • Previous research indicated wild-to-cultivated gene flow but lacked detail on timing, mechanisms, and impacts.

Purpose of the Study:

  • Investigate the timeline, mode, genomic patterns, and biological consequences of introgression between wild and cultivated European grapes.
  • Identify genetic regions and pathways affected by introgression and selection.

Main Methods:

  • Analysis of resequencing data from 345 wild and cultivated grape samples.
  • Machine learning-based population genetic analyses.
  • Inference of demographic history and selection signatures.

Main Results:

  • Evidence for a single domestication event followed by continuous gene flow (~2,000 years) between wild European (EU) and cultivated grapes, primarily from EU to wine grapes.
  • Soft-selective sweeps dominated artificial selection signals.
  • Enrichment of aromatic compound synthesis pathways in introgressed and selected regions, indicating wild grape contribution to flavor.
  • Introgression increased deleterious genetic load, primarily in heterozygous states.

Conclusions:

  • Wild European grapes served as a vital resource for enhancing cultivated grape flavor through adaptive introgression.
  • While beneficial, introgression also introduced a significant genetic burden.
  • Understanding these beneficial and detrimental effects is crucial for future genomic breeding strategies in grapevines.