Local DNA switches drive most gene differences between wild and cultivated tomatoes

A gene that is more active in a wild tomato than in a cultivated one has two possible explanations. The cause may sit in the DNA right next to the gene, a cis effect that sets how strongly that one gene turns on, or somewhere else in the genome, a trans effect that often moves many genes at once ^[7]. Compared across two separate plants, the two look the same ^[7]. Inside a hybrid they come apart. "The hybrid gives us a natural controlled experiment," said Zhangjun Fei, a BTI professor who co-led the work, published in Genome Biology, with senior research associate Carmen Catala ^[2]. "Both versions of each gene sit in the same cells and receive the same regulatory signals. If one version is more active than the other, we know the difference is written into the DNA right next to that gene." ^[4]

Cis changes dominated in every species, tissue and developmental stage ^[6]. At their peak they touched about five times as large a share of active genes as trans changes did at theirs ^[1]. Both figures are maxima across all the comparisons, so the gap is between two ceilings that may come from different tissues or stages ^[6].

Many of the switches were also narrow, working in only one tissue at one moment of fruit development ^[9]. Bitterness runs on a developmental switch, with trans regulation helping to keep bitter compounds high early in fruit development ^[12].

Domestication and breeding removed much of tomato's genetic diversity, and flavor has proved hard to breed back in ^[14]. Catala described the bind. "Wild tomatoes are an enormous reservoir of diversity for flavor, nutrition and resilience, but bringing those traits into modern varieties can come at the expense of other traits that breeders have spent decades improving, like yield, fruit size or shelf life. This can be countered with precise information on how the genes responsible for such traits are controlled," she said ^[13].

I think the cis result is good news for that problem, on two conditions. A switch that behaves one way in a hybrid has to behave the same way in a plant that is otherwise fully cultivated. The gene it tunes also has to change what a person tastes. Gene activity alone cannot show that. The published account reports which genes change, in which tissue and when; it does not describe a variety bred from these targets ^[1].