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Frontiers of Agricultural Science and Engineering

Front. Agr. Sci. Eng.    2014, Vol. 1 Issue (2) : 137-143     https://doi.org/10.15302/J-FASE-2014014
RESEARCH ARTICLE |
A genome-wide association study of five meat quality traits in Yorkshire pigs
Qian DONG,Huiying LIU,Xinyun LI,Wei WEI,Shuhong ZHAO,Jianhua CAO()
Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education of China, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
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Abstract

Meat quality is an important trait in the pig industry. To identify genomic regions and haplotype blocks responsible for meat quality traits in pigs, a genome-wide association study was conducted for five traits including intramuscular fat content, pH at 45 min and 24 h, drip loss within 24 h and water-holding capacity in 231 Yorkshire barrows using illumina porcine 60k SNP chips. The results showed that a total of 344 single nucleotide polymorphisms (SNP) were significantly associated with five meat quality traits (P<1×10-4). Moreover, 323 SNPs were within the reported QTL regions, of which 21 were novel. Also, 158 SNPs fell into the proximal region of meat quality related genes. In addition, 25 haplotype blocks based on 116 SNPs were revealed with SNP combination patterns for five traits. Our study added new SNP information for identification of meat quality traits in pigs and will help elucidate the mechanisms of meat quality in pigs.

Keywords Pig      GWAS      meat quality trait      SNP     
Corresponding Authors: Jianhua CAO   
Online First Date: 22 September 2014    Issue Date: 10 October 2014
 Cite this article:   
Qian DONG,Huiying LIU,Xinyun LI, et al. A genome-wide association study of five meat quality traits in Yorkshire pigs[J]. Front. Agr. Sci. Eng. , 2014, 1(2): 137-143.
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http://journal.hep.com.cn/fase/EN/10.15302/J-FASE-2014014
http://journal.hep.com.cn/fase/EN/Y2014/V1/I2/137
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Qian DONG
Huiying LIU
Xinyun LI
Wei WEI
Shuhong ZHAO
Jianhua CAO
TraitDLIMFpH24hpH45mWHC
DL210.151.97×10-31.40×10-23.40×10-4
IMF20.1010.760.300.75
pH24h0.220.0212.42×10-41.51×10-5
pH45m0.17-0.070.2410.93
WHC20.260.020.296.06×10-31
Tab.1  The correlation matrix of five traits important for pig meat quality1
SNPChr.PositionGeneDistance/bpP-value
DL
ALGA00903321638074310Intergenic4.89×10-5
MARC00174941639223780Intergenic4.89×10-5
MARC00242581639271097Intergenic4.89×10-5
MARC00242581639333524Intergenic4.89×10-5
ASGA00731791642352377Intergenic6.92×10-5
IMF
DRGA00104051030401943ERCC6L2Intron5.00×10-6
ALGA00791061484221823Intergenic5.00×10-6
ASGA009431313186196852Intergenic7.00×10-6
MARC00560511115872871ENSSSCG00000009374Intron1.10×10-5
ALGA00766351430356957ENSSSCG00000009761Intron1.40×10-5
pH24h
H3GA000047617211765PARK2Intron1.00×10-6
ALGA00052081109000000Intergenic1.00×10-6
MARC0056864283903786FCHO2Intron1.00×10-6
ALGA0014045283953431FCHO2Intron1.00×10-6
MARC00721281108000000ENSSSCG0000000450812242.00×10-6
pH45m
ASGA0028877686912890Intergenic2.00×10-6
ASGA0103250669632278ARHGEF1917103.00×10-6
MARC00543941111385436Intergenic3.00×10-6
MARC0114889687000361Intergenic4.00×10-6
ALGA00608231111412132Intergenic4.00×10-6
WHC
ALGA00105411301699159ENSSSCG0000000560920356.74×10-5
ALGA00652251214679312PECAM1Intron5.13×10-5
ASGA00533791214874907Intergenic7.54×10-5
MARC00102911852785500Intergenic1.00×10-6
Tab.2  Top five significant SNPs of five traits important in pig meat quality
Fig.1  Manhattan plots of GWAS results for five meat quality traits in pigs. The five traits, drip loss within 24 h (a), intramuscular fat content (b), pH at 24 h (c), pH at 45 min (d) and water-holding capacity (e), were assessed across porcine 19 chromosomes (no Y chromosome) based on normal distributed phenotypes. The P values were calibrated as –lg(p). The horizontal lines represented the threshold P value, blue for 1×10-4 and yellow for 1×10-5, respectively.
Fig.2  Haploview plots for the pH traits in pigs based on the LD of significant SNPs. A total of 109 SNPs composed of nine haplotype blocks for pH at 24 h trait (a, b and d) and 23 SNPs forming 2 blocks for pH at 45 min trait (c) for traits a to c given in Table 1. The coefficient of LD (r2) between significant SNPs was calculated within 500 kb chromosomal distance and the complete linkage (r2 = 1) was considered to a haplotype block represented by black diamonds. The range of blocks is shown on the top left corner in the block. The recombination rates located below the blocks represent the frequencies of haplotypes in population and the connection coefficients between the blocks are shown under the frequencies.
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