Genomic analyses provide insights into the history of tomato breeding (original) (raw)

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Acknowledgements

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.

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Author notes

  1. Tao Lin, Guangtao Zhu, Junhong Zhang, Xiangyang Xu, Qinghui Yu and Zheng Zheng: These authors contributed equally to this work.

Authors and Affiliations

  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
    Tao Lin, Guangtao Zhu, Zheng Zheng, Zhonghua Zhang, Yaoyao Lun, Shuai Li, Xiaoxuan Wang, Zejun Huang, Junming Li, Chunzhi Zhang, Yongchen Du & Sanwen Huang
  2. Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
    Tao Lin, Guosheng Xiong & Sanwen Huang
  3. Key Laboratory of Horticultural Plant Biology, Huazhong Agricultural University, Wuhan, China
    Junhong Zhang, Taotao Wang, Yuyang Zhang & Zhibiao Ye
  4. College of Horticulture, Northeast Agricultural University, Harbin, China
    Xiangyang Xu, Aoxue Wang & Jingfu Li
  5. Institute of Horticulture, Xinjiang Academy of Agricultural Sciences, Urumqi, China
    Qinghui Yu
  6. College of Life Sciences, Beijing Normal University, Beijing, China
    Yancong Zhang & Kui Lin
  7. State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences and National Plant Gene Research Centre, Beijing, China
    Chuanyou Li & Guosheng Xiong
  8. 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
    Yongbiao Xue
  9. Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
    Yongbiao Xue
  10. Department of Agriculture, Forests, Nature and Energy (DAFNE), University of Tuscia, Viterbo, Italy
    Andrea Mazzucato
  11. Institut National de la Recherche Agronomique (INRA), Unité de Génétique et Amélioration des Fruits et Légumes, Domaine Saint-Maurice, Montfavet, France
    Mathilde Causse
  12. US Department of Agriculture (USDA) Robert W. Holley Center for Agriculture and Health, Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York, USA
    Zhangjun Fei & James J Giovannoni
  13. Department of Plant Sciences, C.M. Rick Tomato Genetics Resource Center, University of California, Davis, Davis, California, USA.,
    Roger T Chetelat
  14. Robert H. Smith Institute of Plant Sciences and Genetics, Faculty of Agriculture, Hebrew University of Jerusalem, Rehovot, Israel
    Dani Zamir
  15. Plant Ecological Genetics, Institute of Integrative Biology, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
    Thomas Städler

Authors

  1. Tao Lin
  2. Guangtao Zhu
  3. Junhong Zhang
  4. Xiangyang Xu
  5. Qinghui Yu
  6. Zheng Zheng
  7. Zhonghua Zhang
  8. Yaoyao Lun
  9. Shuai Li
  10. Xiaoxuan Wang
  11. Zejun Huang
  12. Junming Li
  13. Chunzhi Zhang
  14. Taotao Wang
  15. Yuyang Zhang
  16. Aoxue Wang
  17. Yancong Zhang
  18. Kui Lin
  19. Chuanyou Li
  20. Guosheng Xiong
  21. Yongbiao Xue
  22. Andrea Mazzucato
  23. Mathilde Causse
  24. Zhangjun Fei
  25. James J Giovannoni
  26. Roger T Chetelat
  27. Dani Zamir
  28. Thomas Städler
  29. Jingfu Li
  30. Zhibiao Ye
  31. Yongchen Du
  32. Sanwen Huang

Contributions

S.H., Y.D., Z.Y. and Jingfu Li conceived and designed the research. T.L., G.Z., J.Z., X.X., Q.Y., Z. Zheng, Y.L., S.L., T.W. and Yuyang Zhang performed DNA sequencing and biological experiments. T.L., G.Z., Z. Zhang, K.L., Yancong Zhang, C.L., Y.X., X.W., Z.H., D.Z., Junming Li, G.X., C.Z., A.M., M.C., Z.F., J.J.G., R.T.C., A.W. and T.S. performed the data analysis. S.H., G.Z., T.L., J.Z., X.X., Q.Y. and Z. Zhang wrote the manuscript. Y.D., Z.Y., Jingfu Li, Z. Zhang, C.L., Y.X., A.M., M.C., Z.F., J.J.G., R.T.C., D.Z. and T.S. revised the manuscript.

Corresponding authors

Correspondence toJingfu Li, Zhibiao Ye, Yongchen Du or Sanwen Huang.

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Competing interests

The authors declare no competing financial interests.

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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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