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Bayesian QTL mapping using genome-wide SSR markers and segregating population derived from a cross of two commercial F1 hybrids of tomato

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Using newly developed euchromatin-derived genomic SSR markers and a flexible Bayesian mapping method, 13 significant agricultural QTLs were identified in a segregating population derived from a four-way cross of tomato.

Abstract

So far, many QTL mapping studies in tomato have been performed for progeny obtained from crosses between two genetically distant parents, e.g., domesticated tomatoes and wild relatives. However, QTL information of quantitative traits related to yield (e.g., flower or fruit number, and total or average weight of fruits) in such intercross populations would be of limited use for breeding commercial tomato cultivars because individuals in the populations have specific genetic backgrounds underlying extremely different phenotypes between the parents such as large fruit in domesticated tomatoes and small fruit in wild relatives, which may not be reflective of the genetic variation in tomato breeding populations. In this study, we constructed F2 population derived from a cross between two commercial F1 cultivars in tomato to extract QTL information practical for tomato breeding. This cross corresponded to a four-way cross, because the four parental lines of the two F1 cultivars were considered to be the founders. We developed 2510 new expressed sequence tag (EST)-based (euchromatin-derived) genomic SSR markers and selected 262 markers from these new SSR markers and publicly available SSR markers to construct a linkage map. QTL analysis for ten agricultural traits of tomato was performed based on the phenotypes and marker genotypes of F2 plants using a flexible Bayesian method. As results, 13 QTL regions were detected for six traits by the Bayesian method developed in this study.

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Acknowledgements

We thank N. Fukushima of NIVFS for her technical assistance. This work was supported by grants from the Ministry of Agriculture, Forestry and Fisheries of Japan (Genomics for Agricultural Innovation, DD-4020; Development of DNA markers for Horticultural Crop Breeding, SGE1002; Genomics-based Technology for Agricultural Improvement, NGB2005 and NGB2010), and by Cabinet Office, Government of Japan, Cross-ministerial Strategic Innovation Promotion Program (SIP), “Technologies for creating next-generation agriculture, forestry and fisheries” (funding agency: Bio-oriented Technology Research Advancement Institution, NARO).

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  1. Hiroyuki Fukuoka

    Present address: Takii & Company, Limited, 1360 Hari, Konan, Shiga, 520-3231, Japan

  2. Akio Ohyama and Kenta Shirasawa contributed equally to this work.

Authors and Affiliations

  1. National Agriculture and Food Research Organization (NARO), Institute of Vegetable and Floriculture Science (NIVFS), 3-1-1 Kannondai, Tsukuba, Ibaraki, 305-8519, Japan

    Akio Ohyama

  2. NARO, NIVFS, 360 Kusawa, Ano, Tsu, Mie, 514-2392, Japan

    Akio Ohyama, Hiroshi Matsunaga, Satomi Negoro, Koji Miyatake, Hirotaka Yamaguchi & Tsukasa Nunome

  3. Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba, 292-0818, Japan

    Kenta Shirasawa

  4. Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan

    Hiroyoshi Iwata

  5. NARO, Institute of Vegetable and Tea Science (NIVTS), 360 Kusawa, Ano, Tsu, Mie, 514-2392, Japan

    Hiroyuki Fukuoka

  6. NARO, Institute of Crop Science (NICS), 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan

    Takeshi Hayashi

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  1. Akio Ohyama
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  2. Kenta Shirasawa
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  3. Hiroshi Matsunaga
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Correspondence to Akio Ohyama or Takeshi Hayashi.

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Communicated by Emilio A Carbonell.

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Ohyama, A., Shirasawa, K., Matsunaga, H. et al. Bayesian QTL mapping using genome-wide SSR markers and segregating population derived from a cross of two commercial F1 hybrids of tomato. Theor Appl Genet 130, 1601–1616 (2017). https://doi.org/10.1007/s00122-017-2913-5

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