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A genome-wide association study identifies genomic loci associated with backfat thickness, carcass weight, and body weight in two commercial pig populations

  • Animal Genetics • Original Paper
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Abstract

Growth and fatness traits are economically important in the pig industry. To dissect the genetic architecture of these traits in commercial pigs, we conducted a genome-wide association study (GWAS) for carcass weight, backfat thickness, and body weight in two commercial populations: Duroc × (Landrace × Yorkshire) (DLY) and Duroc populations. To enhance the detection power, three GWAS approaches including single-trait GWAS, multi-trait GWAS and meta-analysis were used in this study. A total of 13 suggestive loci were identified on nine chromosomes. The most significant locus was detected at 272.05 Mb on SSC1, and it was associated with backfat thickness at the first rib in the DLY population. Three genes at the identified loci (TBC1D1, BAAT and PHLPP1) were highlighted as functionally plausible candidate genes for pig growth and fatness traits. Genome-wide significant locus was not evidenced in this study, indicating that large populations are required to identify QTL with minor effects on growth and fatness traits in commercial pig populations, in which intensively artificial selections have been imposed on these traits and small genetical variances usually retain in these traits.

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Acknowledgements

This study was financially supported by the National Natural Science Foundation of China (31660303, 31525023 and 31460590).

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Author notes

  1. Yuanmei Guo and Hengqing Qiu contributed equally to this work

Authors and Affiliations

  1. State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, People’s Republic of China

    Yuanmei Guo, Hengqing Qiu, Shijun Xiao, Jie Yang, Jun Ren & Lusheng Huang

  2. College of Animal Science and National Engineering Research Center for Swine Breeding Industry, South China Agricultural University, Guangzhou, Guangdong, 510642, China

    Zhenfang Wu & Jie Yang

  3. National Engineering Research Center for Swine Breeding, Guangdong Wens Foodstuff Co. Ltd., Xinxing, 527439, China

    Zhenfang Wu & Ming Yang

Authors
  1. Yuanmei Guo
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  2. Hengqing Qiu
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  3. Shijun Xiao
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  4. Zhenfang Wu
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  5. Ming Yang
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  7. Jun Ren
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Correspondence to Jun Ren.

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Additional information

Communicated by: Maciej Szydlowski

Electronic supplementary material

Tables 4, 5, and 6

ESM 1

(DOCX 45 kb)

ESM 2

Quantile–quantile plots for the recorded traits in the two populations. (GIF 118 kb)

High resolution image (TIFF 1027 kb)

ESM 3

Schematic diagram of the first two principal components based on the genomic kinships. a DLY, and b Duroc. (GIF 71 kb)

High resolution image (TIFF 917 kb)

ESM 4

Manhattan plots of meta-analyses for backfat thickness (ABF from DLY and BF100 from Duroc) and body weight (carcass weight from DLY and BW160 from Duroc). The solid and dotted horizontal lines indicate the 5% genome-wide and chromosome-wise (suggestive) significant threshold values, respectively. (GIF 117 kb)

High resolution image (TIFF 4223 kb)

ESM 5

Manhattan plots of multi-trait GWAS in DLY and Duroc populations. (GIF 95 kb)

High resolution image (TIFF 4283 kb)

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Guo, Y., Qiu, H., Xiao, S. et al. A genome-wide association study identifies genomic loci associated with backfat thickness, carcass weight, and body weight in two commercial pig populations. J Appl Genetics 58, 499–508 (2017). https://doi.org/10.1007/s13353-017-0405-6

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  • DOI: https://doi.org/10.1007/s13353-017-0405-6

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