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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #310852

Research Project: Genetic and Genomic Basis of Vegetable and Fruit Biology, Quality and Nutrient Content

Location: Plant, Soil and Nutrition Research

Title: A brief genomic history of tomato breeding

item LIN, TAO - Chinese Academy Of Agricultural Sciences
item ZHU, GUANGTAO - Chinese Academy Of Agricultural Sciences
item ZHANG, JUNHONG - Chinese Academy Of Agricultural Sciences
item XU, XIANGYANG - Chinese Academy Of Agricultural Sciences
item YU, QINGHUI - Chinese Academy Of Agricultural Sciences
item ZHENG, ZHENG - Chinese Academy Of Agricultural Sciences
item FEI, ZHZNGJUN - Boyce Thompson Institute
item Giovannoni, James
item YI, ZHIBIAO - Wuhan University
item HUANG, SANWEN - Chinese Academy Of Agricultural Sciences

Submitted to: Nature Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/22/2014
Publication Date: 10/12/2014
Publication URL: http://DOI: 10.1038/ng.3117
Citation: Lin, T., Zhu, G., Zhang, J., Xu, X., Yu, Q., Zheng, Z., Fei, Z., Giovannoni, J.J., Yi, Z., Huang, S. 2014. A brief genomic history of tomato breeding. Nature Genetics. 46:1220-1226.

Interpretive Summary: The histories of crop domestication and breeding are recorded in their genomes. Although tomato is a model species for plant biology and breeding, how human selection altered its genome remains largely unknown. Here we report a comprehensive analysis of tomato evolution based on the genome sequences of 360 varieties, primitive genotypes and related wild relatives. We reveal that domestication and improvement focused on two independent sets of genes making modern tomato fruit more than100 times larger, in some cases, than its ancestor. We discovered a major genomic signature of modern processing tomatoes, identified the causative variants that confer pink fruit color important in certain Asian and European cultures, and precisely visualized areas for improvement. This study outlines how historical selection shrank the amount of potential genetic variability available for tomato breeding and provides suggestions toward further improvement via targeted selection.

Technical Abstract: Here we report a brief genomic history of tomato breeding by analyzing the genomes of 360 diverse accessions collected all over the world. These included 333 accessions from the red fruited clade (S. pimpinellifolium, S. l. var. cerasiforme, and S. lycopersicum) that represent various geographical origins, consumption types, and improvement status, 10 accessions of wild tomato species that are known as donors of disease resistance genes (R genes), and 17 modern commercial hybrids (F1). Resequencing of the 360 accessions generated a total 2.6 Tb of sequence, with an average depth of 5.9 X and coverage of 93.1% of the tomato genome. We identified domestication and improvement sweeps jointly occupy 111 Mb (14.2% of the assembled genome) and also that likely hinder the exploitation of heterosis. Large introgressions are often related to linkage drag, occupying additional genome space. Despite their historical contribution to tomato breeding, these processes now become a hindrance to further improvement, and cannot be easily overcome by conventional breeding. Favorable trait genes could be separated from the surrounding sweeps and linkage drags by variome-guided selection for rare recombination. Elite lines carrying these ‘freed’ genes would accelerate and improve tomato breeding.