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Frontiers of Agricultural Science and Engineering

ISSN 2095-7505

ISSN 2095-977X(Online)

CN 10-1204/S

邮发代号 80-906

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Frontiers of Agricultural Science and Engineering  2014, Vol. 1 Issue (2): 137-143   https://doi.org/10.15302/J-FASE-2014014
  本期目录
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.
Key words： Pig    GWAS    meat quality trait    SNP
收稿日期: 2014-07-23      出版日期: 2014-10-10
Corresponding Author(s): Jianhua CAO   
 引用本文:   
. [J]. Frontiers of Agricultural Science and Engineering, 2014, 1(2): 137-143.
Qian DONG,Huiying LIU,Xinyun LI,Wei WEI,Shuhong ZHAO,Jianhua CAO. A genome-wide association study of five meat quality traits in Yorkshire pigs. Front. Agr. Sci. Eng. , 2014, 1(2): 137-143.
 链接本文:  
https://academic.hep.com.cn/fase/CN/10.15302/J-FASE-2014014
https://academic.hep.com.cn/fase/CN/Y2014/V1/I2/137
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  
SNPChr.PositionGeneDistance/bpP-value
DL
ALGA00903321638074310–Intergenic4.89×10-5
MARC00174941639223780–Intergenic4.89×10-5
MARC00242581639271097–Intergenic4.89×10-5
MARC00242581639333524–Intergenic4.89×10-5
ASGA00731791642352377–Intergenic6.92×10-5
IMF
DRGA00104051030401943ERCC6L2Intron5.00×10-6
ALGA00791061484221823–Intergenic5.00×10-6
ASGA009431313186196852–Intergenic7.00×10-6
MARC00560511115872871ENSSSCG00000009374Intron1.10×10-5
ALGA00766351430356957ENSSSCG00000009761Intron1.40×10-5
pH24h
H3GA000047617211765PARK2Intron1.00×10-6
ALGA00052081109000000–Intergenic1.00×10-6
MARC0056864283903786FCHO2Intron1.00×10-6
ALGA0014045283953431FCHO2Intron1.00×10-6
MARC00721281108000000ENSSSCG0000000450812242.00×10-6
pH45m
ASGA0028877686912890–Intergenic2.00×10-6
ASGA0103250669632278ARHGEF1917103.00×10-6
MARC00543941111385436–Intergenic3.00×10-6
MARC0114889687000361–Intergenic4.00×10-6
ALGA00608231111412132–Intergenic4.00×10-6
WHC
ALGA00105411301699159ENSSSCG0000000560920356.74×10-5
ALGA00652251214679312PECAM1Intron5.13×10-5
ASGA00533791214874907–Intergenic7.54×10-5
MARC00102911852785500–Intergenic1.00×10-6
Tab.2  
Fig.1  
Fig.2  
1 Hammond K, Leitch H W, Rothschild M F, Ruvinsky A. In: Rothschild M F, and Ruvinsky A, ed. The Genetics of the Pig. 1st ed. CAB International, New York Genetic resources and the global programme for their management, 1998, 405–425
2 Fan B, Lkhagvadorj S, Cai W, Young J, Smith R M, Dekkers J C, Huff-Lonergan E, Lonergan S M, Rothschild M F. Identification of genetic markers associated with residual feed intake and meat quality traits in the pig. Meat Science, 2010, 84(4): 645–650
https://doi.org/10.1016/j.meatsci.2009.10.025 pmid: 20374837
3 Franco D, Vazquez J A, Lorenzo J M. Growth performance, carcass and meat quality of the Celta pig crossbred with Duroc and Landrance genotypes. Meat Science, 2014, 96(1): 195–202
https://doi.org/10.1016/j.meatsci.2013.06.024 pmid: 23896154
4 Srikanchai T, Murani E, Wimmers K, Ponsuksili S. Four loci differentially expressed in muscle tissue depending on water-holding capacity are associated with meat quality in commercial pig herds. Molecular Biology Reports, 2010, 37(1): 595–601
https://doi.org/10.1007/s11033-009-9856-0 pmid: 19823956
5 Fan B, Glenn K L, Geiger B, Mileham A, Rothschild M F. Investigation of QTL regions on Chromosome 17 for genes associated with meat color in the pig. Journal of Animal Breeding and Genetics, 2008, 125(4): 240–247
https://doi.org/10.1111/j.1439-0388.2008.00749.x pmid: 18717966
6 Zhang M, Wang D, Geng Z, Bian H, Liu F, Zhu Y, Xu W. The level of heat shock protein 90 in pig Longissimus dorsi muscle and its relationship with meat pH and quality. Food Chemistry, 2014, 165: 337–341
https://doi.org/10.1016/j.foodchem.2014.05.111 pmid: 25038684
7 Ma J, Yang J, Zhou L, Zhang Z, Ma H, Xie X, Zhang F, Xiong X, Cui L, Yang H, Liu X, Duan Y, Xiao S, Ai H, Ren J, Huang L. Genome-wide association study of meat quality traits in a White Duroc×Erhualian F2 intercross and Chinese Sutai pigs. PLoS ONE, 2013, 8(5): e64047
https://doi.org/10.1371/journal.pone.0064047 pmid: 23724019
8 Luo W, Cheng D, Chen S, Wang L, Li Y, Ma X, Song X, Liu X, Li W, Liang J, Yan H, Zhao K, Wang C, Wang L, Zhang L. Genome-wide association analysis of meat quality traits in a porcine Large White × Minzhu intercross population. International Journal of Biological Sciences, 2012, 8(4): 580–595
https://doi.org/10.7150/ijbs.3614 pmid: 22532790
9 Milan D, Jeon J T, Looft C, Amarger V, Robic A, Thelander M, Rogel-Gaillard C, Paul S, Iannuccelli N, Rask L, Ronne H, Lundstr?m K, Reinsch N, Gellin J, Kalm E, Roy P L, Chardon P, Andersson L. A mutation in PRKAG3 associated with excess glycogen content in pig skeletal muscle. Science, 2000, 288(5469): 1248–1251
https://doi.org/10.1126/science.288.5469.1248 pmid: 10818001
10 Lopez-Buesa P, Burgos C, Galve A, Varona L. Joint analysis of additive, dominant and first-order epistatic effects of four genes (IGF2, MC4R, PRKAG3 and LEPR) with known effects on fat content and fat distribution in pigs. Animal Genetics, 2014, 45(1): 133–137
pmid: 24111741
11 Ramos A M, Crooijmans R P M A, Affara N A, Amaral A J, Archibald A L, Beever J E, Bendixen C, Churcher C, Clark R, Dehais P, Hansen M S, Hedegaard J, Hu Z L, Kerstens H H, Law A S, Megens H J, Milan D, Nonneman D J, Rohrer G A, Rothschild M F, Smith T P, Schnabel R D, Van Tassell C P, Taylor J F, Wiedmann R T, Schook L B, Groenen M A. Design of a high density SNP genotyping assay in the pig using SNPs identified and characterized by next generation sequencing technology. PLoS ONE, 2009, 4(8): e6524
https://doi.org/10.1371/journal.pone.0006524 pmid: 19654876
12 Wierbicki E, Deatherage F E. Water content of meats, determination of water-holding capacity of fresh meats. Journal of Agricultural and Food Chemistry, 1958, 6(5): 387–392
https://doi.org/10.1021/jf60087a011
13 Corrêa C C, Forato L A, Colnago L A. High-throughput non-destructive nuclear magnetic resonance method to measure intramuscular fat content in beef. Analytical and Bioanalytical Chemistry, 2009, 393(4): 1357–1360
https://doi.org/10.1007/s00216-008-2526-6 pmid: 19043697
14 Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira M A, Bender D, Maller J, Sklar P, de Bakker P I, Daly M J, Sham P C. PLINK: a tool set for whole-genome association and population-based linkage analyses. American Journal of Human Genetics, 2007, 81(3): 559–575
https://doi.org/10.1086/519795 pmid: 17701901
15 Hu Z L, Park C A, Wu X L, Reecy J M. Animal QTLdb: an improved database tool for livestock animal QTL/association data dissemination in the post-genome era. Nucleic Acids Research, 2013, 41(D1): D871–D879
https://doi.org/10.1093/nar/gks1150 pmid: 23180796
16 McLaren W, Pritchard B, Rios D, Chen Y, Flicek P, Cunningham F. Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor. Bioinformatics, 2010, 26(16): 2069–2070
https://doi.org/10.1093/bioinformatics/btq330 pmid: 20562413
17 Qin Z S, Niu T, Liu J S. Partition-ligation-expectation-maximization algorithm for haplotype inference with single-nucleotide polymorphisms. American Journal of Human Genetics, 2002, 71(5): 1242–1247
https://doi.org/10.1086/344207 pmid: 12452179
18 Barrett J C, Fry B, Maller J, Daly M J. Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics, 2005, 21(2): 263–265
https://doi.org/10.1093/bioinformatics/bth457 pmid: 15297300
19 Larzul C, Lefaucheur L, Ecolan P, Gogué J, Talmant A, Sellier P, Le Roy P, Monin G. Phenotypic and genetic parameters for longissimus muscle fiber characteristics in relation to growth, carcass, and meat quality traits in large white pigs. Journal of Animal Science, 1997, 75(12): 3126–3137
pmid: 9419985
20 Horák P, Stratil A, Svatonová M, Mastalková L, Patáková J, Van Poucke M, Bartenschlager H, Peelman L J, Geldermann H. Polymorphism screening and mapping of nine meat performance-related genes in the pig. Animal Genetics, 2010, 41(3): 334–335
https://doi.org/10.1111/j.1365-2052.2009.02004.x pmid: 19958346
21 Lee K T, Byun M J, Kang K S, Hwang H, Park E W, Kim J M, Kim T H, Lee S H. Single nucleotide polymorphism association study for backfat and intramuscular fat content in the region between SW2098 and SW1881 on pig chromosome 6. Journal of Animal Science, 2012, 90(4): 1081–1087
https://doi.org/10.2527/jas.2011-4228 pmid: 21984723
22 Duan Y Y, Ma J W, Yuan F, Huang L B, Yang K X, Xie J P, Wu G Z, Huang L S. Genome-wide identification of quantitative trait loci for pork temperature, pH decline, and glycolytic potential in a large-scale White Duroc × Chinese Erhualian resource population. Journal of Animal Science, 2009, 87(1): 9–16
https://doi.org/10.2527/jas.2008-1128 pmid: 18791141
23 Liu G, Jennen D G, Tholen E, Juengst H, Kleinw?chter T, H?lker M, Tesfaye D, Un G, Schreinemachers H J, Murani E, Ponsuksili S, Kim J J, Schellander K, Wimmers K. A genome scan reveals QTL for growth, fatness, leanness and meat quality in a Duroc-Pietrain resource population. Animal Genetics, 2007, 38(3): 241–252
https://doi.org/10.1111/j.1365-2052.2007.01592.x pmid: 17459017
24 Sanchez M P, Tribout T, Iannuccelli N, Bouffaud M, Servin B, Tenghe A, Dehais P, Muller N, Del Schneider M P, Mercat M J, Rogel-Gaillard C, Milan D, Bidanel J P, Gilbert H. A genome-wide association study of production traits in a commercial population of Large White pigs: evidence of haplotypes affecting meat quality. Genetics Selection Evolution, 2014, 46(1): 12
https://doi.org/10.1186/1297-9686-46-12 pmid: 24528607
25 Horii T, Morita S, Kimura M, Hatada I. Epigenetic regulation of adipocyte differentiation by a Rho guanine nucleotide exchange factor, WGEF. PLoS ONE, 2009, 4(6): e5809
https://doi.org/10.1371/journal.pone.0005809 pmid: 19503838
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