Tomato breeding history revealed by Chinese scientists

Recently, an international tomato variome research team led by Huang Sanwen, a researcher at the Institute of Vegetables and Flowers of the Chinese Academy of Agricultural Sciences and deputy director of the Agricultural Genomics Institute at Shenzhen, constructed a complete tomato genetic variation map by resequencing and analyzing 360 tomato germplasm accessions from around the world, laying the foundation for revealing the evolutionary history of tomato, gene mining and molecular breeding. The latest research results were published online in the October 13 issue of Nature Genetics.

According to the introduction, the large-fruited cultivated tomato that people eat was domesticated from wild tomato, and during the long domestication process, wild tomato fruits underwent significant changes in weight, color, shape and other aspects. Wild tomato fruits are very small, weighing only 1-2 grams, while the fruit weight of modern cultivated tomato is more than 100 times that of its ancestor. However, the process of tomato artificial domestication had never been comprehensively studied. Through population genetics analysis, this research team successfully revealed that the enlargement of tomato fruit underwent two evolutionary processes, from Solanum pimpinellifolium to cherry tomato and then to large-fruited cultivated tomato, during which 5 and 13 fruit weight genes were respectively subject to directional selection by humans.

At the same time, by comparing genomic differences among different tomato populations, the research team found that chromosome 5 is the main genomic region determining the difference between fresh-market tomato and processing tomato. This region contains multiple genes controlling soluble solids and fruit firmness in tomato, and these genes give processing tomato its distinctive characteristics. Through genome-wide association analysis, the research team found the key variant site determining the peel color of pink tomato. The variation at this site leads to a deletion in the promoter region of the SIMYB12 gene, thereby affecting the expression of this gene, so that flavonoids cannot accumulate in the peel of ripe pink tomato. This discovery provides an effective molecular breeding tool for breeding pink tomato varieties.

In addition, in response to the problem that wild germplasm resources are widely used in modern tomato breeding, the team accurately defined the positions and lengths of wild tomato genomic segments in the cultivated tomato genome through comparative genomics, thus making it possible to further expand the space for tomato breeding. In response to the problem that the quality of tomato has declined in commercial breeding due to the pursuit of high yield and storage and transportation tolerance, on the basis of big data from the tomato variome, Huang Sanwen's team is working closely with the tomato quality breeding team led by Professor Harry Klee, a member of the U.S. National Academy of Sciences, to elucidate the metabolism and accumulation mechanisms of more than 20 volatile compounds affecting tomato flavor, providing new tools for breeding more delicious tomatoes.