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Genomic analyses provide insights into the history of tomato breeding

Tao Lin 1, 2 Guangtao Zhu 1 Junhong Zhang 3 Xiangyang Xu 4 Qinghui Yu 5 Zheng Zheng 1 Zhonghua Zhang 1 Yaoyao Lun 1 Shuai Li 1 Xiaoxuan Wang 1 Zejun Huang 1 Junming Li 1 Chunzhi Zhang 1 Taotao Wang 3 Yuyang Zhang 3 Aoxue Wang 4 Yancong Zhang 6 Kui Lin 6 Chuanyou Li 7 Guosheng Xiong 7, 2 Yongbiao Xue 8, 9, 10 Andrea Mazzucato 11 Mathilde Causse 12 Zhangjun Fei 13 James J. Giovannoni 13 Roger T. Chetelat 14 Dani Zamir 15 Thomas Staedler 16 Jingfu Li 4 Zhibiao Ye 3 Yongchen Du 1 Sanwen Huang 1, 2
Abstract : 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 similar to 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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https://hal.inrae.fr/hal-02639866
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Submitted on : Thursday, May 28, 2020 - 1:01:34 PM
Last modification on : Thursday, December 3, 2020 - 4:46:03 PM

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Tao Lin, Guangtao Zhu, Junhong Zhang, Xiangyang Xu, Qinghui Yu, et al.. Genomic analyses provide insights into the history of tomato breeding. Nature Genetics, Nature Publishing Group, 2014, 46 (11), pp.1220 - 1226. ⟨10.1038/ng.3117⟩. ⟨hal-02639866⟩

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