Researchers at the Chinese Academy of Agricultural Sciences, China, have applied machine learning to genetic sequence data from wild and domestic European grapes.
In the study published in PNASthe researchers investigated the history of genetic hybridization between domesticated grapes and their European wild relatives, tracing the origin back to a single domestication event in the wine grape.
According to the study’s authors, domesticated grapevines spread to Europe about 3,000 years ago. Archaeological evidence indicates that the first domestication of grapevines dates back to around 5900 BC, with sylvestris species widespread in the southern Caucasus, northern Fertile Crescent, and the Levant.
After their domestication, grapes spread throughout the Mediterranean world, diversifying into many local varieties. Within the last 3,000 years, vineyards were established in Europe, where imported varieties came into contact with genetically distinct wild sylvestris populations.
Certain wine grape gene regions relevant to aromatic compound synthesis were enriched with wild versions, suggesting that European wild grapes were an essential resource for improving the flavor of wine grapes.
The team collected current sequencing data from 305 samples and sequenced 40 samples from the USDA Grape Germplasm Collections in Davis, California using the Illumina HiSeq 4000 platform. The combined collection covered a broad distribution of global wild and cultivated grapes.
Machine learning-based population genetic analysis revealed evidence of a single grapevine domestication event, followed by continuous genetic flow between European wild grapes (EU) and cultivated grapes over the past 2000 years.
Through outcrossing events and intentional breeding improvements, genetic fragments with a higher deleterious burden were introduced, with most of the deleterious single nucleotide polymorphisms (SNPs) and hidden structural variants in the heterozygous state.
The authors suggest that the beneficial effects of crossbreeding carry a potential cost because certain regions have elevated numbers of known deleterious variants. Identification of beneficial and detrimental variants can be important factors for a more genome-based strategy for breeding grapevines.
The harmful burden suggestion is based on segments of DNA that are not specifically beneficial, usually non-coding and something that would normally be eliminated in wild plants by natural selection.
It should be noted that a harmful burden can be found in any type of domesticated plant: potatoes, tomatoes, rice, soybeans, and maize contain a lot of additional genomic components that natural selection has not removed due to human reproduction. While it may be possible to engineer plant genomes to have lower deleterious burdens, it is unclear if this would have any positive effect on the resulting plant since these regions are usually inactive.
The presence of regions that are not critical to the function of any organism can be an advantage. If a random mutation occurs in a critical gene, the downstream effect will be detrimental to the organism. If the same random mutation occurs in the harmful burden gene, the result will be less harmful to the organism. About 98% of the human genome is non-coding, and while not all “junk DNA” is completely useless, it is a convenient barrier against the truly harmful effects of random mutations that alter coding genes.
Table grapes were also considered in the study. These cultivars were found to have 100 times fewer hybridization events, indicating that while wine grapes have undergone an intense process of crop improvement, table grapes have been perfect all along.
Hua Xiao et al, Adaptive and non-adaptive introductions into grape domestication, Proceedings of the National Academy of Sciences (2023). DOI: 10.1073/pnas.2222041120
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