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. 2015 Sep 29;10(9):e0139207.
doi: 10.1371/journal.pone.0139207. eCollection 2015.

Genome Wide Association Analysis Reveals New Production Trait Genes in a Male Duroc Population

Kejun Wang  1 , Dewu Liu  2 , Jules Hernandez-Sanchez  3 , Jie Chen  1 , Chengkun Liu  1 , Zhenfang Wu  2 , Meiying Fang  1 , Ning Li  4
Affiliations

Genome Wide Association Analysis Reveals New Production Trait Genes in a Male Duroc Population

Kejun Wang et al. PLoS One. .

Abstract

In this study, 796 male Duroc pigs were used to identify genomic regions controlling growth traits. Three production traits were studied: food conversion ratio, days to 100 KG, and average daily gain, using a panel of 39,436 single nucleotide polymorphisms. In total, we detected 11 genome-wide and 162 chromosome-wide single nucleotide polymorphism trait associations. The Gene ontology analysis identified 14 candidate genes close to significant single nucleotide polymorphisms, with growth-related functions: six for days to 100 KG (WT1, FBXO3, DOCK7, PPP3CA, AGPAT9, and NKX6-1), seven for food conversion ratio (MAP2, TBX15, IVL, ARL15, CPS1, VWC2L, and VAV3), and one for average daily gain (COL27A1). Gene ontology analysis indicated that most of the candidate genes are involved in muscle, fat, bone or nervous system development, nutrient absorption, and metabolism, which are all either directly or indirectly related to growth traits in pigs. Additionally, we found four haplotype blocks composed of suggestive single nucleotide polymorphisms located in the growth trait-related quantitative trait loci and further narrowed down the ranges, the largest of which decreased by ~60 Mb. Hence, our results could be used to improve pig production traits by increasing the frequency of favorable alleles via artificial selection.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Manhattan plots of genome-wide association studies for three production traits in male Duroc pigs.
The inserted quantile–quantile (Q–Q) plots show the observed versus expected log p-values.
Fig 2
Fig 2. Principle component analysis (PCA) plot of population structure with the top two principle components.
PC1: Principle component 1; PC2: Principle component 2.
Fig 3
Fig 3. IBS similarity matrix.
Fig 4
Fig 4. Distribution of haplotype length along the genome.
*denotes mean length.
Fig 5
Fig 5. Distribution of the number of SNPs in each haplotype block along the genome.
*denotes mean number of SNPs.
Fig 6
Fig 6. Haplotype blocks for significant SNPs.
The black line indicated the identified blocks. 6A: A haplotype block composed of suggestive D100 SNPs located in SSC8; 6B: A haplotype block composed of suggestive FCR SNPs located in SSC15; 6C: A haplotype block composed of suggestive FCR SNPs located in SSC16; 6D: A haplotype block composed of suggestive ADG SNPs located in SSC10.
See this image and copyright information in PMC

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