The histories of crop domestication and breeding are recorded in genomes. Although tomato is a model species for plant biology and breeding, the nature of human selection that altered its genome remains largely unknown. Here we report a comprehensive analysis of tomato evolution based on the genome sequences of 360 accessions. We provide evidence that domestication and improvement focused on two independent sets of quantitative trait loci (QTLs), resulting in modern tomato fruit ∼100 times larger than its ancestor. Furthermore, we discovered a major genomic signature for modern processing tomatoes, identified the causative variants that confer pink fruit color and precisely visualized the linkage drag associated with wild introgressions. This study outlines the accomplishments as well as the costs of historical selection and provides molecular insights toward further improvement.
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We thank J. Maloof (University of California, Davis) for providing tomato RNA sequencing data and L.A. Mueller and N. Menda (Cornell University) for setting up a genome browser of SNPs. This work was supported by funding from the National Program on Key Basic Research Projects in China (973 program; 2012CB113900 and 2011CB100600), the National Science Fund for Distinguished Young Scholars (31225025 to S.H.), the National HighTech Research Development Program in China (863 Program; 2012AA100101 and 2012AA100105), the National Natural Science Foundation of China (31272160, 31230064, 31272171 and 31171962), the Chinese Ministry of Finance (1251610601001), CAAS (an Agricultural Science and Technology Innovation Program grant to S.H.), the China Agriculture Research System (CARS-25-A-09 and CARS-25-A-15), the Special Fund for Agro-Scientific Research in the Public Interest of China (201303115), the Major Special Science and Technology Project during the Twelfth Five-Year Plan Period of Xinjiang (201230116-3) and the US National Science Foundation Plant Genome Program (IOS-0923312). This work was also supported by the Shenzhen municipal and Dapeng district governments.
The authors declare no competing financial interests.
Integrated supplementary information
ΔK analysis for a different number of clusters (K) for a tomato population consisting of 331 accessions (excluding 10 wild accessions). ΔK showed a peak at 2, suggesting two clusters as the optimal option. Source data
A total of 2,340,973 whole-genome SNPs (MAF > 10%, missing ≤ 5%) were used for PCA. Two-dimension coordinates were plotted for the 331 tomato accessions. CER (orange) and BIG (blue) accessions have a relatively concentrated distribution, whereas PIM accessions (green) are dispersed widely. Source data
Private SNPs are presented for each chromosome in PIM (green), CER (orange) and BIG (blue). Source data
LD decay is estimated by the squared correlations of allele frequency (r2) against distance between polymorphic sites in PIM (green), CER (orange) and BIG (blue). Source data
(a) Frequency distribution of fruit weight in the F2 population. The fruit weight of both parents and the F1 are shown. (b) Fruit appearances of individuals from the F2 population. The two bulks (big bulk and small bulk) are constructed by selecting the fruits shown in the first and last two rows, respectively. Source data
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Lin, T., Zhu, G., Zhang, J. et al. Genomic analyses provide insights into the history of tomato breeding. Nat Genet 46, 1220–1226 (2014). https://doi.org/10.1038/ng.3117
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