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Genome-wide association analysis reveals genetic loci and candidate genes for meat quality traits in Chinese Laiwu pigs

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Abstract

Meat quality traits have economically significant impacts on the pig industry, and can be improved using molecular approaches in pig breeding. Since 1994 when the first genome-wide scan for quantitative trait loci (QTLs) in pig was reported, over the past two decades, numerous QTLs have been identified for meat quality traits by family based linkage analyses. However, little is known about the genetic variants for meat quality traits in Chinese purebred or outbred populations. To unveil it, we performed a genome-wide association study for 10 meat quality traits in Chinese purebred Laiwu pigs. In total, 75 significant SNPs (P < 1.01 × 10−6) and 33 suggestive SNPs (P < 2.03 × 10−5) were identified. On SSC12, a region between 56.22 and 61.49 Mb harbored a cluster of SNPs that were associated with meat color parameters (L*, lightness; a*, redness; b*, yellowness) and moisture content of longissimus muscle (LM) and semimembranosus muscle at the genome-wide significance level. A region on SSC4 also has pleiotropic effects on moisture content and drip loss of LM. In addition, this study revealed at least five novel QTLs and several candidate genes including 4-linked MYH genes (MYH1, MYH2, MYH3, and MYH13), MAL2, LPAR1, and PRKAG3 at four significant loci. Except for the SSC12 QTL, other QTLs are likely tissue-specific. These results provide new insights into the genetic basis of meat quality traits in Chinese Laiwu pigs and some significant SNPs reported here could be incorporated into the selection programs involving this breed.

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Acknowledgments

This research was supported by the Key Project of National Nature Science Foundation of China (No. 31230069), the Development Programs for Basic Research of China (973 Programs, Nos. 2012CB722502 and 2012CB124702) and National High-Tech Research and Development Program of China (2013AA102502).

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    1. Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, 330045, China

      Xinwei Xiong, Xianxian Liu, Lisheng Zhou, Jie Yang, Bin Yang, Huanban Ma, Xianhua Xie, Yixuan Huang, Shaoming Fang, Shijun Xiao, Jun Ren, Congying Chen, Junwu Ma & Lusheng Huang

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    1. Xinwei Xiong
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    Correspondence to Congying Chen or Junwu Ma.

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    Xinwei Xiong and Xianxian Liu have contributed equally to this work.

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    Xiong, X., Liu, X., Zhou, L. et al. Genome-wide association analysis reveals genetic loci and candidate genes for meat quality traits in Chinese Laiwu pigs. Mamm Genome 26, 181–190 (2015). https://doi.org/10.1007/s00335-015-9558-y

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