Open Access Research article

Genome-wide association study identified three major QTL for carcass weight including the PLAG1-CHCHD7 QTN for stature in Japanese Black cattle

Shota Nishimura1, Toshio Watanabe15, Kazunori Mizoshita2, Ken Tatsuda3, Tatsuo Fujita4, Naoto Watanabe4, Yoshikazu Sugimoto1 and Akiko Takasuga15*

Author Affiliations

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

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

3 Hyogo Prefectural Institute of Agriculture, Forestry & Fisheries, Befu, Kasai, Hyogo, 679-0198, Japan

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

5 National Livestock Breeding Center, Odakura, Nishigo, Fukushima, 961-8511, Japan

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BMC Genetics 2012, 13:40  doi:10.1186/1471-2156-13-40

Published: 20 May 2012

Additional files

Additional file 1:

Distribution of carcass weight of the animals used for the GWAS. This figure shows the distributions of carcass weight in the collected (blue bars) and the GWAS samples (red bars), respectively.

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Additional file 2:

Quantile-quantile (Q-Q) plots of GWAS. The figures show Q-Q plots before (red) and after conditioned analyses (blue).

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Additional file 3:

SNP associated with carcass weight. The table shows genome-wide significant SNP.

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Additional file 4:

F-statistic profiles for carcass weight on BTA 8. This file shows F-statistic profiles for carcass weight on BTA 8 obtained in two QTL analyses. The QTL analyses were performed as described previously [1]. The two sires are father (Sire I) and son (Sire II), and the Q haplotype was inherited by the son from the father (data not shown). Marker locations were obtained from the Shirakawa-USDA linkage map [27]. Boxes on the x-axis indicate the 95% confidence interval of the QTL. Horizontal lines indicate the thresholds for chromosome-wise 0.1% (− − −), 1% (− −), and 5% (—–) significance levels.

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Additional file 5:

Microsatellite markers and haplotypes of the animals used for targeted resequencing. This table shows marker information, such as primer sequences and physical positions, as well as haplotypes of the animals used for targeted resequencing.

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Additional file 6:

Candidate QTN examined for an association with carcass weight. This table shows the information on sequence variations such as genomic positions, primer sequences, and Q and q alleles in the Japanese Black sires segregating CW-1.

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Additional file 7:

Haplotypes of Japanese Black sires. This table shows Q and q alleles in Japanese Black sires around the causative variations for bovine stature.

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Open Data