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Identification of bovine QTL for growth and carcass traits in Japanese Black cattle by replication and identical-by-descent mapping

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Abstract

To map quantitative trait loci (QTL) for growth and carcass traits in a purebred Japanese Black cattle population, we conducted multiple QTL analyses using 15 paternal half-sib families comprising 7860 offspring. We identified 40 QTL with significant linkages at false discovery rates of less than 0.1, which included 12 for intramuscular fat deposition called marbling and 12 for cold carcass weight or body weight. The QTL each explained 2%–13% of the phenotypic variance. These QTL included many replications and shared hypothetical identical-by-descent (IBD) alleles. The QTL for CW on BTA14 was replicated in five families with significant linkages and in two families with a 1% chromosome-wise significance level. The seven sires shared a 1.1-Mb superior Q haplotype as a hypothetical IBD allele that corresponds to the critical region previously refined by linkage disequilibrium mapping. The QTL for marbling on BTA4 was replicated in two families with significant linkages. The QTL for marbling on BTA6, 7, 9, 10, 20, and 21 and the QTL for body weight on BTA6 were replicated with 1% and/or 5% chromosome-wise significance levels. There were shared IBD Q or q haplotypes in the marbling QTL on BTA4, 6, and 10. The allele substitution effect of these haplotypes ranged from 0.7 to 1.2, and an additive effect between the marbling QTL on BTA6 and 10 was observed in the family examined. The abundant and replicated QTL information will enhance the opportunities for positional cloning of causative genes for the quantitative traits and efficient breeding using marker-assisted selection.

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Acknowledgments

The authors thank the technical staff at the Shirakawa Institute of Animal Genetics and the collaborating institutes for technical assistance. The work was partly supported by the Ministry of Agriculture, Forestry, and Fishery, Japan, and by the Japan Racing and Livestock Promotion Foundation.

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Authors and Affiliations

  1. Shirakawa Institute of Animal Genetics, Japan Livestock Technology Association, Odakura, Nishigo, Fukushima, 961-8061, Japan

    Akiko Takasuga, Toshio Watanabe, Yasushi Mizoguchi, Takashi Hirano, Naoya Ihara, Atsushi Takano, Kou Yokouchi & Yoshikazu Sugimoto

  2. Hokkaido Animal Research Center, Nishi, Shintoku, Hokkaido, 081-0038, Japan

    Akira Fujikawa

  3. Miyagi Prefectural Animal Industry Experiment Station, Iwadeyama, Osaki, Miyagi, 989-6445, Japan

    Kazuyoshi Chiba

  4. Gifu Prefectural Livestock Research Institute, Kiyomi, Takayama, Gifu, 506-0101, Japan

    Naohiko Kobayashi

  5. Hyogo Prefectural Institute of Agriculture, Forestry & Fisheries, Kasai, Hyogo, 679-0103, Japan

    Ken Tatsuda

  6. Tottori Animal Husbandry Experiment Station, Kotoura, Touhaku, Tottori, 689-2503, Japan

    Toshiaki Oe

  7. Okayama Prefectural Center for Animal Husbandry & Research, Misaki, Kume, Okayama, 709-3494, Japan

    Megumi Furukawa-Kuroiwa

  8. Shimane Prefectural Animal Husbandry Experiment Station, Koshi, Izumo, Simane, 693-0031, Japan

    Atsuko Nishimura-Abe

  9. Oita Prefectural Institute of Animal Industry, Kuju, Takeda, Oita, 878-0201, Japan

    Tatsuo Fujita

  10. Miyazaki Prefectural Livestock Experiment Station, Takahara, Nishimorokata, Miyazaki, 889-4411, Japan

    Kazuya Inoue

  11. Cattle Breeding Development Institute of Kagoshima Prefecture, Osumi, So, Kagoshima, 899-8212, Japan

    Kazunori Mizoshita

  12. Livestock Improvement Association of Japan, Inc., Maebashi, Gunma, 351-0121, Japan

    Atsushi Ogino

Authors
  1. Akiko Takasuga
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  2. Toshio Watanabe
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  3. Yasushi Mizoguchi
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  4. Takashi Hirano
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  5. Naoya Ihara
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  6. Atsushi Takano
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  7. Kou Yokouchi
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  8. Akira Fujikawa
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  9. Kazuyoshi Chiba
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  10. Naohiko Kobayashi
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  11. Ken Tatsuda
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  12. Toshiaki Oe
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  13. Megumi Furukawa-Kuroiwa
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  14. Atsuko Nishimura-Abe
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  15. Tatsuo Fujita
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  16. Kazuya Inoue
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  17. Kazunori Mizoshita
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  18. Atsushi Ogino
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  19. Yoshikazu Sugimoto
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Corresponding author

Correspondence to Yoshikazu Sugimoto.

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Takasuga, A., Watanabe, T., Mizoguchi, Y. et al. Identification of bovine QTL for growth and carcass traits in Japanese Black cattle by replication and identical-by-descent mapping. Mamm Genome 18, 125–136 (2007). https://doi.org/10.1007/s00335-006-0096-5

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  • DOI: https://doi.org/10.1007/s00335-006-0096-5

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