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 M. 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)
1
Chinese Acad Agr Sci, Key Lab Biol & Genet Improvement Hort Crops, Minist Agr, Sino Dutch Joint Lab Hort Genom,Inst Vegerables F, Beijing 100193, Peoples R China
2 Chinese Acad Agr Sci, Agr Genome Inst Shenzhen, Shenzhen, Peoples R China
3 Huazhong Agr Univ, Key Lab Hort Plant Biol, Wuhan, Peoples R China
4 Northeast Agr Univ, Coll Hort, Harbin, Peoples R China
5 Xinjiang Acad Agr Sci, Inst Hort, Urumqi, Peoples R China
6 BNU - Beijing Normal University
7 Chinese Acad Sci, Inst Genet & Dev Biol, State Key Lab Plant Genom, Beijing, Peoples R China
8 Natl Plant Gene Res Ctr, Beijing, Peoples R China
9 Chinese Acad Sci, Beijing Inst Genom, Beijing, Peoples R China
10 Chinese Acad Sci, Inst Genet & Dev Biol, State Key Lab Mol Dev Biol, Beijing, Peoples R China
11 Università degli studi della Tuscia [Viterbo]
12 GAFL - Génétique et Amélioration des Fruits et Légumes
13 Cornell Univ, Boyce Thompson Inst Plant Res, USDA, Robert W Holley Ctr Agr & Hlth, Ithaca, NY 14853 USA
14 Plant - UC Davis - Department of Plant Sciences [Univ California Davis]
15 HUJ - The Hebrew University of Jerusalem
16 ETH Zürich - Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich]
2 Chinese Acad Agr Sci, Agr Genome Inst Shenzhen, Shenzhen, Peoples R China
3 Huazhong Agr Univ, Key Lab Hort Plant Biol, Wuhan, Peoples R China
4 Northeast Agr Univ, Coll Hort, Harbin, Peoples R China
5 Xinjiang Acad Agr Sci, Inst Hort, Urumqi, Peoples R China
6 BNU - Beijing Normal University
7 Chinese Acad Sci, Inst Genet & Dev Biol, State Key Lab Plant Genom, Beijing, Peoples R China
8 Natl Plant Gene Res Ctr, Beijing, Peoples R China
9 Chinese Acad Sci, Beijing Inst Genom, Beijing, Peoples R China
10 Chinese Acad Sci, Inst Genet & Dev Biol, State Key Lab Mol Dev Biol, Beijing, Peoples R China
11 Università degli studi della Tuscia [Viterbo]
12 GAFL - Génétique et Amélioration des Fruits et Légumes
13 Cornell Univ, Boyce Thompson Inst Plant Res, USDA, Robert W Holley Ctr Agr & Hlth, Ithaca, NY 14853 USA
14 Plant - UC Davis - Department of Plant Sciences [Univ California Davis]
15 HUJ - The Hebrew University of Jerusalem
16 ETH Zürich - Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich]
Mathilde M. Causse
- Fonction : Auteur
- PersonId : 737384
- IdHAL : mathilde-causse
- ORCID : 0000-0002-0407-4985
- IdRef : 078246423
Résumé
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.