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| Genome-wide association study for rib eye muscle area in a Large White×Minzhu F2 pig resource population |
| GUO Yun-yan, ZHANG Long-chao, WANG Li-xian, LIU Wen-zhong |
1、College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, P.R.China
2、Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R.China |
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摘要 Rib eye muscle area (REMA) is an economically important trait and one of the main selection criteria for breeding in the swine industry. In the genome-wide association study (GWAS), the Illumina PorcineSNP60 BeadChip containing 62 163 single nucleotide polymorphisms (SNPs) was used to genotype 557 pigs from a porcine Large White×Minzhu intercross population. The REMA (at the 5th–6th, 10th–11th and the last ribs) was measured after slaughtered at the age of (240±7) d for each animal. Association tests between REMA trait and SNPs were performed via the Genome-Wide Rapid Association using the Mixed Model and Regression-Genomic Control (GRAMMAR-GC) approach. From the Ensembl porcine database, SNP annotation was implemented using Sus scrofa Build 10.2. Thirty-three SNPs on SSC12 and 3 SNPs on SSC2 showed significant association with REMA at the last rib at the chromosome-wide significance level. None of the SNPs of REMA at the 5th–6th rib and only a few numbers of the SNPs of REMA at the 10th–11th ribs were found in this study. The Haploview V3.31 program and the Haplo.Stats R package were used to detect and visualize haplotype blocks and to analyze the association of the detected haplotype blocks with REMA at the last rib. A linkage analysis revealed that 4 haplotype blocks contained 4, 4, 2, and 4 SNPs, respectively. Annotations from pig reference genome suggested 2 genes (NOS2, NLK) in block 1 (266 kb), one gene (TMIGD1) in block 2 (348 kb), and one gene (MAP2K4) in block 3 (453 kb). A functional analysis indicated that MYH3 and MYH13 genes are the potential genes controlling REMA at the last rib. We screened several candidate intervals and genes based on the SNPs location and the gene function, and inferred that NOS2 and NLK genes maybe the main genes of REMA at the last ribs.
Abstract Rib eye muscle area (REMA) is an economically important trait and one of the main selection criteria for breeding in the swine industry. In the genome-wide association study (GWAS), the Illumina PorcineSNP60 BeadChip containing 62 163 single nucleotide polymorphisms (SNPs) was used to genotype 557 pigs from a porcine Large White×Minzhu intercross population. The REMA (at the 5th–6th, 10th–11th and the last ribs) was measured after slaughtered at the age of (240±7) d for each animal. Association tests between REMA trait and SNPs were performed via the Genome-Wide Rapid Association using the Mixed Model and Regression-Genomic Control (GRAMMAR-GC) approach. From the Ensembl porcine database, SNP annotation was implemented using Sus scrofa Build 10.2. Thirty-three SNPs on SSC12 and 3 SNPs on SSC2 showed significant association with REMA at the last rib at the chromosome-wide significance level. None of the SNPs of REMA at the 5th–6th rib and only a few numbers of the SNPs of REMA at the 10th–11th ribs were found in this study. The Haploview V3.31 program and the Haplo.Stats R package were used to detect and visualize haplotype blocks and to analyze the association of the detected haplotype blocks with REMA at the last rib. A linkage analysis revealed that 4 haplotype blocks contained 4, 4, 2, and 4 SNPs, respectively. Annotations from pig reference genome suggested 2 genes (NOS2, NLK) in block 1 (266 kb), one gene (TMIGD1) in block 2 (348 kb), and one gene (MAP2K4) in block 3 (453 kb). A functional analysis indicated that MYH3 and MYH13 genes are the potential genes controlling REMA at the last rib. We screened several candidate intervals and genes based on the SNPs location and the gene function, and inferred that NOS2 and NLK genes maybe the main genes of REMA at the last ribs.
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Received: 31 December 2014
Accepted:
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| Fund: This research was supported by the Agricultural Science and Technology Innovation Program, China (ASTIP-IAS02), the National Key Technology R&D Program of China (2011BAD28B01), the National Natural Science Foundationand Development Program of China (2011ZX08006- 003), the Earmarked Fund for Modern Agro-industry Technology Research System of China, and Chinese Academy of Agricultural Sciences Foundation (2011cj-5). |
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Corresponding Authors:
WANG Li-xian, E-mail: iaswlx@263.net;LIU Wen-zhong, E-mail: tglwzyc@163.com
E-mail: tglwzyc@163.com
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| About author: GUO Yun-yan, E-mail: xmsyxbg@163.com; |
Cite this article:
GUO Yun-yan, ZHANG Long-chao, WANG Li-xian, LIU Wen-zhong.
2015.
Genome-wide association study for rib eye muscle area in a Large White×Minzhu F2 pig resource population. Journal of Integrative Agriculture, 14(12): 2590-2597.
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| Ai H, Xiao S, Zhang Z, Yang B, Li L, Guo Y, Lin G, Ren J, HuangL. 2014. Three novel quantitative trait loci for skin thicknessin swine identified by linkage and genome-wide associationstudies. Animal Genetics, 45, 524-533Amin N, van Duijn C M, Aulchenko Y S. 2007. A genomicbackground based method for association analysis inrelated individuals. PLoS ONE, 2, e1274.Aulchenko Y S, de Koning D J, Haley C. 2007. Genome-widerapid association using mixed model and regression: Afast and simple method for genome-wide pedigree-basedquantitative trait loci association analysis. Genetics, 177,577-585Barrett J C, Fry B, Maller J, Daly M J. 2005. Haploview:Aanalysis and visualization of LD and haplotype maps.Bioinformatics, 21, 263-265Davoli R, Fontanesi L, Zambonelli P, Bigi D, Gellin J, YerleM, Milc J, Braglia S, Cenci V, Cagnazzo M, Russo V.2002. Isolation of porcine expressed sequence tags for theconstruction of a first genomic transcript map of the skeletalmuscle in pig. Animal Genetics, 33, 3-18De R, Bush W S, Moore J H. 2014. Bioinformatics challengesin genome-wide association studies (GWAS). Methods inMolecular Biology, 1168, 63-81Fan B, Du Z Q, Danielle M, Rothschild M F. 2010. Developmentand application of high-density SNP arrays in genomicstudies of domestic animal. Asian-Australasian Journal ofAnimal Sciences, 23, 833-847Fan B, Onteru S K, Nikkila M T, Stalder K J, Rothschild M F.2009. The COL9A1 gene is associated with longissimusdorsimuscle area in the pig. Animal Genetics, 40, 788.Guo J F, Wang C, Lin H C, Liu C, Zhang Y, Wu Y. 2011. Studyon correlation of carcass performance, meat quality andweight of finishing pigs. Acta Ecologiae Animalis Domastici,32, 34-38 (in Chinese)Hill E W, McGivney B A, Gu J, Whiston R, Machugh D E. 2010. Agenome-wide SNP-association study confirms a sequencevariant (g.66493737C>T) in the equine myostatin (MSTN)gene as the most powerful predictor of optimum racingdistance for thoroughbred racehorses. BMC Genomics,11, 552-561Kemper K E, Emery D L, Bishop S C, Oddy H, Hayes BJ, Dominik S, Henshall J M, Goddard M E. 2011. Thedistribution of SNP marker effects for faecal worm eggcount in sheep, and the feasibility of using these markersto predict genetic merit for resistance to worm infections. Genetics Research, 93, 203-219King C R, Nicolae D L. 2014. GWAS to sequencing: Divergencein study design and analysis. Genes (Basel), 28, 460-476Li X P, Kim S W, Do K T, Ha Y K, Lee Y M, Yoon S H, Kim HB, Kim J J, Choi B H, Kim K S. 2011. Analyses of porcinepublic SNPs in coding-gene regions by re-sequencing andphenotypic association studies. Molecular Biology Reports,38, 3805-3820Liu X, Wang L G, Luo W Z, Li Y, Liang J, Yan H, Zhao K B,Wang L X, Zhang L C. 2014. A genome -wideSNP scan in a porcine Large White×Minzhu intercrosspopulation reveals a locus influencing muscle mass onchromosome 2. Journal of Animal Science, 85, 969-975Lo L L, McLaren D G, McKeith F K, Fernando R L, NovakofskiJ. 1992. Genetic analysis of growth, real-time ultrasound,carcass, and pork quality traits in Duroc and Landracepigs: 11. Heritabilities and correlations. Journal of AnimalScience, 70, 2387-2396Luo 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.2012. Genome-wide association analysis of meat qualityin a porcine Large White×Minzhu intercross population.International Journal of Biological Sciences, 8, 580-595Ma J, Ren J, Guo Y, Duan Y, Ding N, Zhou L, Li L, Yan X,Yang K, Huang L, Song Y, Xie J, Milan D, Huang L. 2009.Genome-wide identification of quantitative trait loci forcarcass composition and meat quality in a large-scale WhiteDuroc×Chinese Erhualian resource population. AnimalGenetics, 40, 637-647Madsen P, Sørensen P, Su G, Damgaard L H, ThomsenH, Labouriau R. 2006. DMU - a package for analyzingmultivariate mixed models. In: 8th World Congress onGenetics Applied to Livestock Production. 13-18 August,2006 Belo Horizonte, MG, Brazil. pp. 11-27Meredith B K, Kearney F J, Finlay E K, Bradley D G, Fahey A G,Berry D P, Lynn D J. 2012. Genome-wide associations formilk production and somatic cell score in Holstein-Friesiancattle in Ireland. BMC Genetics, 13, 21.Niu F, Wang L, Liu X, Wang H, Yang J, Liu Y, Chen L. 2013.Genetic diversity of MYH3 gene associated with growthand carcass traits in Chinese Qinchuan cattle. MolecularBiology Reports, 40, 5635-5643Ponsuksili S, Chomdej S, Murani E, Blaser U, SchreinREMAchersH J, Schellander K, Wimmers K. 2005. SNP detection andgenetic mapping of porcine genes encoding enzymes inhepatic metabolic pathways and evulation of linkage withcarcass traits. Animal Genetics, 36, 477-483Pringle T D, Williams S E. 2000. Fat thickness and loin eyearea effects on pork carcass quality measures. Journal ofMuscle Foods, 11, 307-318Pringle T D, Williams S E. 2001. Carcass traits, cut yields,and compositional end points in high-lean-yielding porkcarcasses: effects of 10th rib backfat and loin eye area.Journal of Animal Science, 79, 115-121Reardon W, Mullen A M, Sweeney T, Hamill R M. 2010.Association of polymorphisms in candidate genes withcolour, water-holding capacity, and composition traits inbovine M. longissimus and M. semimembranosus. MeatScience, 86, 270-275Schaid D J, Rowland C M, Tines D E, Jacobson R M, PolandG A. 2002. Score tests for association between traits andhaplotypes when linkage phase is ambiguous. AmericanJournal of Human Genetics, 70, 425-434Schurink A, Ducro B J, Bastiaansen J W, Frankena K, vanArendonk J A. 2012. Genome-wide association study ofinsect bite hypersensitivity in Dutch Shetland pony mares.Animal Genetics, 44, 44-52Shen X, Zeng H, Xie L, He J, Li J, Xie X, Luo C, Xu H, Zhou M,Nie Q, Zhang X. 2012. The GTPase activating Rap/RanGAPdomain-like 1 gene is associated with chicken reproductivetraits. PLOS ONE, 7, e33851.Sodeland M, Kent M P, Olsen H G, Opsal M A, Svendsen M,Sehested E, Hayes B J, Lien S. 2011. Quantitative traitloci for clinical mastitis on chromosomes 2, 6, 14 and 20in Norwegian Red cattle. Animal Genetics, 42, 457-465Suzuki K, Irie M, Kadowaki H, Shibata T, Kumagai M, NishidaA. 2005. Genetic parameter estimates of meat quality traitsin Duroc pigs selected for average daily gain, longissimusmuscle area, backfat thickness, and intramuscular fatcontent. Journal of Animal Science, 83, 2058-2065Suzuki K, Shibata T, Kadowaki H, Abe H, Toyoshima T. 2003.Meat quality comparison of Berkshire, Duroc and crossbredpigs sired by Berkshire and Duroc. Meat Science, 64, 35-42Wang L G, Zhang L C, Yan H, Liu X, Li N, Liang J, Pu L, ZhangY B, Shi H B, Zhao K B, Wang L X. 2014. Genome-wideassociation studies identify the loci for 5 exterior traits in aLarge White×Minzhu pig population. PLoS ONE, 8, 1-9Wolc A, Arango J, Jankowski T, Dunn I, Settar P, Fulton J E,O’Sullivan N P, Preisinger R, Fernando R L, Garrick D J,Dekkers J C. 2014. Genome-wide association study for eggproduction and quality in layer chickens. Journal of AnimalBreeding Genetics, 131, 173-182Yang Q, Cui J, Chazaro I, Cupples L A, Demissie1 S. 2005.Power and type I error rate of false discovery rateapproaches in genome-wide association studies. BMCGenetics, 6(suppl 1), S134.Zhang L, Liu J, Zhao F, Ren H, Xu L, Lu J, Zhang S, ZhangX, Wei C, Lu G, Zheng Y, Du L. 2013. Genome-wideassociation studies for growth and meat production traitsin sheep. PLOS ONE, 8, e66569. |
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