One of the more, hah, fruitful applications of genomic data has been in crop and livestock improvement. Biologists know that domesticating plants and animals for human use has involved powerful artificial selection — usually inadvertent at first, then intensive and deliberate. Compared to their wild ancestors, domesticated populations usually have more cultivation-friendly phenology and mating systems, produce more of the whatever feature it is that humans use, and even show behavioral changes. Genome sequencing lets us find the actual changes in the genetic code that underly those selected changes.
A nice new example of this work is online as a preprint at bioRxiv, which reports analysis of population genomic samples of cultivated and wild grapes. The paper’s coauthors, led by Yongfeng Zhou, are particularly interested in the fact that domestic grapes are perennials, propagated by cloning from cuttings. Clonal propagation is far and away the easiest route to domestication, especially of a perennial plant, because it skips over multi-year or multi-decade generation times, and it lets cultivators and breeders rapidly access useful traits in individual lines of the plant. But it also means that the cultivated population can rapidly lose genetic diversity — this is the reason bananas are particularly vulnerable to disease — and ongoing clonal propagation may allow a buildup of deleterious mutations. Comparing population samples from both cultivated and wild grapes lets Zhou et al. examine that “cost of domestication”.