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. 2018 Apr;31(4):480-488.
doi: 10.5713/ajas.17.0356. Epub 2017 Oct 20.

Genome-wide association study reveals genetic loci and candidate genes for average daily gain in Duroc pigs

Jianping Quan  1 , Rongrong Ding  1 , Xingwang Wang  1 , Ming Yang  2 , Yang Yang  1 , Enqin Zheng  1 , Ting Gu  1 , Gengyuan Cai  2 , Zhenfang Wu  1   2 , Dewu Liu  1 , Jie Yang  1
Affiliations

Genome-wide association study reveals genetic loci and candidate genes for average daily gain in Duroc pigs

Jianping Quan et al. Asian-Australas J Anim Sci. 2018 Apr.

Abstract

Objective: Average daily gain (ADG) is an important target trait of pig breeding programs. We aimed to identify single nucleotide polymorphisms (SNPs) and genomic regions that are associated with ADG in the Duroc pig population.

Methods: We performed a genome-wide association study involving 390 Duroc boars and by using the PorcineSNP60K Beadchip and two linear models.

Results: After quality control, we detected 3,5971 SNPs, which included seven SNPs that are significantly associated with the ADG of pigs. We identified six quantitative trait loci (QTL) regions for ADG. These QTLs included four previously reported QTLs on Sus scrofa chromosome (SSC) 1, SSC5, SSC9, and SSC13, as well as two novel QTLs on SSC6 and SSC16. In addition, we selected six candidate genes (general transcription factor 3C polypeptide 5, high mobility group AT-hook 2, nicotinamide phosphoribosyltransferase, oligodendrocyte transcription factor 1, pleckstrin homology and RhoGEF domain containing G4B, and ENSSSCG00000031548) associated with ADG on the basis of their physiological roles and positional information. These candidate genes are involved in skeletal muscle cell differentiation, diet-induced obesity, and nervous system development.

Conclusion: This study contributes to the identification of the casual mutation that underlies QTLs associated with ADG and to future pig breeding programs based on marker-assisted selection. Further studies are needed to elucidate the role of the identified candidate genes in the physiological processes involved in ADG regulation.

Keywords: Average Daily Gain; Duroc Pigs; Genome-wide Association Study (GWAS); Single Nucleotide Polymorphism (SNP).

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Conflict of interest statement

CONFLICT OF INTEREST

We certify that there is no conflict of interest with any financial organization regarding the material discussed in the manuscript. Yang M, Cai G, Wu Z are employees of Guangdong Wens Foodstuffs Co., Ltd..

Figures

Figure 1
Figure 1
Quantile–quantile and Manhattan plots. (A) Quantile–quantile (Q–Q) plots showing the observed versus expected log p-values for the average daily gain (ADG) trait. The horizontal axis indicates the expected 2log10 (p-values) and the vertical axis indicates the observed 2log10 (p-values). The diagonal line represents y = x, which corresponds to the null hypothesis, and the shaded region shows 95% confidence interval based on β-distribution. (B) Manhattan plot showing the significance of association between 35,791 single nucleotide polymorphisms (SNPs) and the ADG trait. In the Manhattan plots, the negative log10 p-values of the quantified SNPs were plotted against their genomic positions. The solid and dashed lines indicate the 5% genome-wide and chromosome-wide Bonferroni-corrected thresholds, respectively.
Figure 2
Figure 2
Linkage disequilibrium blocks (LD) on Sus scrofa chromosome (SSC) 1 and SSC5. (A) Linkage disequilibrium blocks on SSC1. (B) Linkage disequilibrium blocks on SSC5. LD blocks are marked with triangles. Values in boxes are the LD (r2) between SNP pairs. The boxes are colored in accordance with the standard Haploview color scheme: LOD>2 and D′ = 1, red; LOD<2 and D′<1, white (LOD is the log of the likelihood odds ratio, a measure of confidence in the value of D′).
See this image and copyright information in PMC

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