title: Genomic analyses provide insights into the history of tomato breeding.
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 ∼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.
authors.affiliation: 1] Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China. [2] Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
authors.forename: Tao
authors.initials: T
authors.lastname: Lin
authors.affiliation: Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Guangtao
authors.initials: G
authors.lastname: Zhu
authors.affiliation: Key Laboratory of Horticultural Plant Biology, Huazhong Agricultural University, Wuhan, China.
authors.forename: Junhong
authors.initials: J
authors.lastname: Zhang
authors.affiliation: College of Horticulture, Northeast Agricultural University, Harbin, China.
authors.forename: Xiangyang
authors.initials: X
authors.lastname: Xu
authors.affiliation: Institute of Horticulture, Xinjiang Academy of Agricultural Sciences, Urumqi, China.
authors.forename: Qinghui
authors.initials: Q
authors.lastname: Yu
authors.affiliation: Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Zheng
authors.initials: Z
authors.lastname: Zheng
authors.affiliation: Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Zhonghua
authors.initials: Z
authors.lastname: Zhang
authors.affiliation: Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Yaoyao
authors.initials: Y
authors.lastname: Lun
authors.affiliation: Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Shuai
authors.initials: S
authors.lastname: Li
authors.affiliation: Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Xiaoxuan
authors.initials: X
authors.lastname: Wang
authors.affiliation: Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Zejun
authors.initials: Z
authors.lastname: Huang
authors.affiliation: Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Junming
authors.initials: J
authors.lastname: Li
authors.affiliation: Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Chunzhi
authors.initials: C
authors.lastname: Zhang
authors.affiliation: Key Laboratory of Horticultural Plant Biology, Huazhong Agricultural University, Wuhan, China.
authors.forename: Taotao
authors.initials: T
authors.lastname: Wang
authors.affiliation: Key Laboratory of Horticultural Plant Biology, Huazhong Agricultural University, Wuhan, China.
authors.forename: Yuyang
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: College of Horticulture, Northeast Agricultural University, Harbin, China.
authors.forename: Aoxue
authors.initials: A
authors.lastname: Wang
authors.affiliation: College of Life Sciences, Beijing Normal University, Beijing, China.
authors.forename: Yancong
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: College of Life Sciences, Beijing Normal University, Beijing, China.
authors.forename: Kui
authors.initials: K
authors.lastname: Lin
authors.affiliation: State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences and National Plant Gene Research Centre, Beijing, China.
authors.forename: Chuanyou
authors.initials: C
authors.lastname: Li
authors.affiliation: 1] Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China. [2] State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences and National Plant Gene Research Centre, Beijing, China.
authors.forename: Guosheng
authors.initials: G
authors.lastname: Xiong
authors.affiliation: 1] State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences and National Plant Gene Research Centre, Beijing, China. [2] Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
authors.forename: Yongbiao
authors.initials: Y
authors.lastname: Xue
authors.affiliation: Department of Agriculture, Forests, Nature and Energy (DAFNE), University of Tuscia, Viterbo, Italy.
authors.forename: Andrea
authors.initials: A
authors.lastname: Mazzucato
authors.affiliation: Institut National de la Recherche Agronomique (INRA), Unité de Génétique et Amélioration des Fruits et Légumes, Domaine Saint-Maurice, Montfavet, France.
authors.forename: Mathilde
authors.initials: M
authors.lastname: Causse
authors.affiliation: Boyce Thompson Institute for Plant Research, US Department of Agriculture (USDA) Robert W. Holley Center for Agriculture and Health, Cornell University, Ithaca, New York, USA.
authors.forename: Zhangjun
authors.initials: Z
authors.lastname: Fei
authors.affiliation: Boyce Thompson Institute for Plant Research, US Department of Agriculture (USDA) Robert W. Holley Center for Agriculture and Health, Cornell University, Ithaca, New York, USA.
authors.forename: James J
authors.initials: JJ
authors.lastname: Giovannoni
authors.affiliation: C.M. Rick Tomato Genetics Resource Center, Department of Plant Sciences, University of California, Davis, Davis, California, USA.
authors.forename: Roger T
authors.initials: RT
authors.lastname: Chetelat
authors.affiliation: Robert H. Smith Institute of Plant Sciences and Genetics, Faculty of Agriculture, Hebrew University of Jerusalem, Rehovot, Israel.
authors.forename: Dani
authors.initials: D
authors.lastname: Zamir
authors.affiliation: Plant Ecological Genetics, Institute of Integrative Biology, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland.
authors.forename: Thomas
authors.initials: T
authors.lastname: Städler
authors.affiliation: College of Horticulture, Northeast Agricultural University, Harbin, China.
authors.forename: Jingfu
authors.initials: J
authors.lastname: Li
authors.affiliation: Key Laboratory of Horticultural Plant Biology, Huazhong Agricultural University, Wuhan, China.
authors.forename: Zhibiao
authors.initials: Z
authors.lastname: Ye
authors.affiliation: Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Yongchen
authors.initials: Y
authors.lastname: Du
authors.affiliation: 1] Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China. [2] Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
authors.forename: Sanwen
authors.identifier: 0000000285475309
authors.initials: S
authors.lastname: Huang
mesh_terms: D001483:Base Sequence; D001947:Breeding / Q000266:history* / Q000379:methods; D002874:Chromosome Mapping; D016000:Cluster Analysis; D005828:Genetics, Population; D018745:Genome, Plant / Q000235:genetics*; D049690:History, Ancient; D016013:Likelihood Functions; D015810:Linkage Disequilibrium; D018551:Solanum lycopersicum / Q000235:genetics* / Q000266:history; D008957:Models, Genetic; D008969:Molecular Sequence Data; D010802:Phylogeny; D010858:Pigmentation / Q000235:genetics; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D040641:Quantitative Trait Loci / Q000235:genetics*; D012641:Selection, Genetic / Q000235:genetics*; D017422:Sequence Analysis, DNA