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A GWA study reveals genetic loci for body conformation traits in Chinese Laiwu pigs and its implications for human BMI

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Abstract

Pigs share numerous physiological and phenotypic similarities with human and thus have been considered as a good model in nonrodent mammals for the study of genetic basis of human obesity. Researches on candidate genes for obesity traits have successfully identified some common genes between humans and pigs. However, few studies have assessed how many similarities exist between the genetic architecture of obesity in pigs and humans by large-scale comparative genomics. Here, we performed a genome-wide association study (GWAS) using the porcine 60 K SNP Beadchip for BMI and other four conformation traits at three different ages in a Chinese Laiwu pig population, which shows a large variability in fat deposition. In total, 35 SNPs were found to be significant at Bonferroni-corrected 5 % chromosome-wise level (P = 2.13 × 10−5) and 88 SNPs had suggestive (P < 10−4) association with the conformation traits. Some SNPs showed age-dependent association. Intriguingly, out of 32 regions associated with BMI in pigs, 18 were homologous with the loci for BMI in humans. Furthermore, five closest genes to GWAS peaks including HIF1AN, SMYD3, COX10, SLMAP, and GBE1 have been already associated with BMI in humans, which makes them very promising candidates for these QTLs. The result of GO analysis provided strong support to the fact that mitochondria and synapse play important roles in obesity susceptibility, which is consistent with previous findings on human obesity, and it also implicated new gene sets related to chromatin modification and Ig-like C2-type 5 domain. Therefore, these results not only provide new insights into the genetic architecture of BMI in pigs but also highlight that humans and pigs share the significant overlap of obesity-related genes.

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Acknowledgments

The study was supported by the Development Programs for Basic Research of China (973 Programs, No. 2014CB160311) and the Key Project of National Nature Science Foundation of China (No. 31230069).

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    Authors and Affiliations

    1. National Key Laboratory for Swine Genetics, Breeding and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China

      Lisheng Zhou, Jiuxiu Ji, Song Peng, Zhen Zhang, Shaoming Fang, Lin Li, Yaling Zhu, Lusheng Huang, Congying Chen & Junwu Ma

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    1. Lisheng Zhou
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    2. Jiuxiu Ji
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    3. Song Peng
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    Correspondence to Congying Chen or Junwu Ma.

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    Lisheng Zhou and Jiuxiu Ji have contributed equally to this work.

    Electronic supplementary material

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    335_2016_9657_MOESM1_ESM.docx

    Supplementary material 1 (DOCX 17 kb) Table S1: Correlations of the several relative weight indices with body length and fatness

    335_2016_9657_MOESM2_ESM.docx

    Supplementary material 2 (DOCX 42 kb) Table S2: Description of SNPs suggestively associated with body conformation traits

    Supplementary material 3 (TIFF 2033 kb) Figure S1: Q–Q plots for assessing the influence of population stratification

    335_2016_9657_MOESM4_ESM.tif

    Supplementary material 4 (TIFF 4420 kb) Figure S2: Manhattans plots of GWAS for BW_210, BL_210 and CC_210. Description: Chromosomes 1-18 and 19 (X) are shown in different colors. The solid lines indicate the Bonferroni-corrected thresholds of chromosome-wide significance and the dashed lines indicate the thresholds of suggestive significance

    335_2016_9657_MOESM5_ESM.tif

    Supplementary material 5 (TIFF 5376 kb) Figure S3: Manhattans plots of GWAS for body conformation traits. Description: Chromosomes 1-18 and 19 (X) are shown in different colors. The solid lines indicate the Bonferroni-corrected thresholds of chromosome-wide significance and the dashed lines indicate the thresholds of suggestive significance

    335_2016_9657_MOESM6_ESM.tif

    Supplementary material 6 (TIFF 111 kb) Figure S4: Extent of LD (predicted r2) as a function of inter-SNP distance in Laiwu pigs

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    Zhou, L., Ji, J., Peng, S. et al. A GWA study reveals genetic loci for body conformation traits in Chinese Laiwu pigs and its implications for human BMI. Mamm Genome 27, 610–621 (2016). https://doi.org/10.1007/s00335-016-9657-4

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