Genome-Wide Association Study for Certain Carcass Traits and Organ Weights in a Large White×Minzhu Intercross Porcine Population

doi:10.1016/S2095-3119(14)60787-5

Journal of Integrative Agriculture ›› 2014, Vol. 13 ›› Issue (12): 2721-2730.DOI: 10.1016/S2095-3119(14)60787-5

Genome-Wide Association Study for Certain Carcass Traits and Organ Weights in a Large White×Minzhu Intercross Porcine Population

LIU Xin, WANG Li-gang, LIANG Jing, YAN Hua, ZHAO Ke-bin, LI Na, ZHANG Long-chao, WANGLi-xian

1、Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation, Ministry of Agriculture/Institute of Animal Science, Chinese
Academy of Agricultural Sciences, Beijing 100193, P.R.China
2、Jilin Academy of Agricultural Sciences, Changchun 130033, P.R.China

收稿日期:2014-02-10 出版日期:2014-12-01 发布日期:2014-12-10
通讯作者: WANG Li-xian, Tel: +86-10-62816011, Fax: +86-10-62818771, E-mail: iaswlx@263.net; ZHANG Longchao,Tel: +86-10-62816011, E-mail: lczhang@iascaas.net.cn
作者简介:LIU Xin, E-mail: firstliuxin@163.com
基金资助:
This research was supported by the Agricultural Science and Technology Innovation Program, China (ASTIPIAS02), the National Key Technology R&D Program of China (2011BAD28B01), the National Natural Science Foundation of China (31201781), the Earmarked Fund for Modern Agroindustry Technology Research System, National Technology Program of China (2011ZX08006-003) and the Chinese Academy of Agricultural Sciences Foundation (2011cj-5, 2012ZL069 and 2014ywf-yb-8).

Genome-Wide Association Study for Certain Carcass Traits and Organ Weights in a Large White×Minzhu Intercross Porcine Population

LIU Xin, WANG Li-gang, LIANG Jing, YAN Hua, ZHAO Ke-bin, LI Na, ZHANG Long-chao, WANGLi-xian

1、Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation, Ministry of Agriculture/Institute of Animal Science, Chinese
Academy of Agricultural Sciences, Beijing 100193, P.R.China
2、Jilin Academy of Agricultural Sciences, Changchun 130033, P.R.China

Received:2014-02-10 Online:2014-12-01 Published:2014-12-10
Contact: WANG Li-xian, Tel: +86-10-62816011, Fax: +86-10-62818771, E-mail: iaswlx@263.net; ZHANG Longchao,Tel: +86-10-62816011, E-mail: lczhang@iascaas.net.cn
About author:LIU Xin, E-mail: firstliuxin@163.com
Supported by:
This research was supported by the Agricultural Science and Technology Innovation Program, China (ASTIPIAS02), the National Key Technology R&D Program of China (2011BAD28B01), the National Natural Science Foundation of China (31201781), the Earmarked Fund for Modern Agroindustry Technology Research System, National Technology Program of China (2011ZX08006-003) and the Chinese Academy of Agricultural Sciences Foundation (2011cj-5, 2012ZL069 and 2014ywf-yb-8).

摘要/Abstract

摘要： Porcine carcass traits and organ weights have important economic roles in the swine industry. A total of 576 animals from a Large White×Minzhu intercross population were genotyped using the Illumina PorcineSNP60K Beadchip and were phenotyped for 10 traits, specifically, backfat thickness (6-7 libs), carcass length, carcass weight, foot weight, head weight, heart weight, leaf fat weight, liver weight, lung weight and slaughter body weight. The genome-wide association study (GWAS) was assessed by Genome Wide Rapid Association using the mixed model and regression-genomic control approach. A total of 31 single nucleotide polymorphisms (SNPs) (with the most significant SNP being MARC0033464, P value=6.80×10-13) were located in a 9.76-Mb (31.24-41.00 Mb) region on SSC7 and were found to be significantly associated with one or more carcass traits and organ weights. High percentage of phenotypic variance explanation was observed for each trait ranging from 31.21 to 67.42%. Linkage analysis revealed one haplotype block of 495 kb, in which the most significant SNP being MARC0033464 was contained, on SSC7 at complete linkage disequilibrium. Annotation of the pig reference genome suggested 6 genes (GRM4, HMGA1, NUDT3, RPS10, SPDEF and PACSIN1) in this candidate linkage disequilibrium (LD) interval. Functional analysis indicated that the HMGA1 gene presents the prime biological candidate for carcass traits and organ weights in pig, with potential application in breeding programs.

关键词: genome-wide association study (GWAS) , carcass trait , HMGA1 gene , organ weight , pig

Abstract: Porcine carcass traits and organ weights have important economic roles in the swine industry. A total of 576 animals from a Large White×Minzhu intercross population were genotyped using the Illumina PorcineSNP60K Beadchip and were phenotyped for 10 traits, specifically, backfat thickness (6-7 libs), carcass length, carcass weight, foot weight, head weight, heart weight, leaf fat weight, liver weight, lung weight and slaughter body weight. The genome-wide association study (GWAS) was assessed by Genome Wide Rapid Association using the mixed model and regression-genomic control approach. A total of 31 single nucleotide polymorphisms (SNPs) (with the most significant SNP being MARC0033464, P value=6.80×10-13) were located in a 9.76-Mb (31.24-41.00 Mb) region on SSC7 and were found to be significantly associated with one or more carcass traits and organ weights. High percentage of phenotypic variance explanation was observed for each trait ranging from 31.21 to 67.42%. Linkage analysis revealed one haplotype block of 495 kb, in which the most significant SNP being MARC0033464 was contained, on SSC7 at complete linkage disequilibrium. Annotation of the pig reference genome suggested 6 genes (GRM4, HMGA1, NUDT3, RPS10, SPDEF and PACSIN1) in this candidate linkage disequilibrium (LD) interval. Functional analysis indicated that the HMGA1 gene presents the prime biological candidate for carcass traits and organ weights in pig, with potential application in breeding programs.

Key words: genome-wide association study (GWAS) , carcass trait , HMGA1 gene , organ weight , pig

LIU Xin, WANG Li-gang, LIANG Jing, YAN Hua, ZHAO Ke-bin, LI Na, ZHANG Long-chao, WANGLi-xian. Genome-Wide Association Study for Certain Carcass Traits and Organ Weights in a Large White×Minzhu Intercross Porcine Population[J]. Journal of Integrative Agriculture, 2014, 13(12): 2721-2730.

LIU Xin, WANG Li-gang, LIANG Jing, YAN Hua, ZHAO Ke-bin, LI Na, ZHANG Long-chao, WANGLi-xian . Genome-Wide Association Study for Certain Carcass Traits and Organ Weights in a Large White×Minzhu Intercross Porcine Population[J]. Journal of Integrative Agriculture, 2014, 13(12): 2721-2730.

参考文献

Anderson L, Georges M. 2004. Domestic-animal genomics:deciphering the genetics of complex traits. Nature Reviews Genetics, 5, 202-212

Amin N, van Duijin 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. Genomewiderapid association using mixed model and regression: Afast and simple method for genome-wide pedigree-basedquantitative trait loci association analysis. Genetics, 177,577-585

Barrett J C, Fry B, Maller J, Daly M J. 2005. HAPLOVIEW:analysis and visualization of LD and haplotype maps.Bioinformatics, 21, 263-265

Berndt S I, Gustafsson S, Mägi R, Ganna A, Wheeler E, FeitosaM F, Justice A E, Monda K L, Croteau-Chonka D C, DayF R, Esko T, Fall T, Ferreira T, Gentilini D, Jackson A U,Luan J, Randall J C, Vedantam S, Willer C J, Winkler TW, et al. 2013. Genome-wide meta-analysis identifies 11new loci for anthropometric traits and provides insightsinto genetic architecture. Nature Genetics, 45, 501-512

Bolormaa S, Hayes B J, Savin K, Hawken R, Barendse W,Arthur P F, Herd R M, Goddard M E. 2011. Genome-wideassociation studies for feedlot and growth traits in cattle.Journal of Animal Science, 89, 1684-1697

Chiappetta G, Avantaggiato V, Visconti R, Fedele M, BattistaS, Trapasso F, Merciai B M, Fidanza V, Giancotti V,Santoro M, Simeone A, Fusco A. 1996. High levelexpression of the HMGI(Y) gene during embryonicdevelopment. Oncogene, 13, 2439-2446

Cleynen I, van de Ven W J. 2008. The HMGA proteins: Amyriad of functions (Review). International Journal ofOncology, 32, 289-305

Fan B, Onteru S K, Du Z Q, Garrick D J, Stalder K J, RothschildM F. 2011. Genome-wide association study identifies locifor body composition and structural soundness traits inpigs. PLoS One, 6, e14726.

Gao X, Starmer J, Martin E R. 2008. A multiple testingcorrection method for genetic association studies usingcorrelated single nucleotide polymorphisms. GeneticEpidemiology, 32, 361-369

Gilbert H, LE Roy P, Milan D, Bidanel J P. 2007. Linked andpleiotropic QTLs influencing carcass composition traitsdetected on porcine chromosome 7. Genetical Research,89, 65-72

Goddard M E, Hayes B J. 2009. Mapping genes for complextraits in domestic animals and their use in breedingprogrammes. Nature Reviews Genetics, 10, 381-391

Hirschhorn J N, Daly M J. 2005. Genome-wide associationstudies for common diseases and complex traits. NatureReviews Genetics, 6, 95-108

Hristov A, Cope L, Di Cello F, Reyes M D, Singh M, Hillion JA, Belton A, Joseph B, Schuldenfrei A, Iacobuzio-DonahueC A, Maitra A, Resar L M. 2010. HMGA1 correlates withadvanced tumor grade and decreased survival in pancreaticductal adenocarcinoma. Modern Pathology, 23, 98-104

Iiritano S, Chiefari E, Ventura V, Arcidiacono B, PossidenteK, Nocera A, Nevolo M T, Fedele M, Greco A, GrecoM, Brunetti G, Fusco A, Foti D, Brunetti A. 2012. TheHMGA1-IGF-I/IGFBP system: a novel pathway formodulating glucose uptake. Molecular Endocrinology,26, 1578-1589

Jiang L, Liu J, Sun D, Ma P, Ding X, Yu Y, Zhang Q. 2010.Genome wide association studies for milk production traitsin Chinese Holstein population. PLoS One, 5, e13661.

Kim K S, Lee J J, Shin H Y, Choi B H, Lee C K, Kim J J, Cho BW, Kim T H. 2006. Association of melanocortin 4 receptor(MC4R) and high mobility group A T-hook 1 (HMGA1)polymorphisms with pig growth and fat deposition traits.Animal Genetics, 37, 419-421

Kim K S, Thomsen H, Bastiaansen J, Nguyen N T, DekkersJ C, Plastow G S, Rothschild M F. 2004. Investigationof obesity candidate genes on porcine fat depositionquantitative trait loci regions. Obesity Research, 12,1981-1994

van Laere A S, Nguyen M, Braunschweiq M, Nezer C, ColletteC, Moreau L, Archibald A L, Haley C S, Buys N, Tally M,Andersson G, Georges M, Andersson L. 2003. A regulatorymutation in IGF2 causes a major QTL effect on musclegrowth in the pig. Nature, 425, 832-836

Liu R, Sun Y, Zhao G, Wang F, Wu D, Zheng M, Chen J, ZhangL, Hu Y, Wen J. 2013. Genome-wide association studyidentifies loci and candidate genes for body compositionand meat quality traits in Beijing-You chickens. PLOSONE, 8, e61172.

Luo W, Chen S, Cheng D, Wang L, Li Y, Ma X, Song X,Liu X, Li W, Liang J, Yan H, Zhao K, Wang C, Wang L,Zhang. 2012. Genome-wide association study of porcinehematological parameters in a Large White×Minzhu F2resource population. International Journal of BiologicalSciences, 8, 870-881

Ma J, Ren J, Guo Y, Duan Y, Ding N, Zhou L, Li L, YanX, Yang K, Huang L, Song Y, Xie J, Milan D, Huang L.2009. Genome-wide identification of quantitative trait locifor carcass composition and meat quality in a large-scaleWhite Duroc×Chinese Erhualian resource population.Animal Genetics, 40, 637-647

Ma J, Yang J, Zhou L, Zhang Z, Ma H, Xie X, Zhang F, XiongX, Cui L, Yang H, Liu X, Duan Y, Xiao S, Ai H, Ren J,Huang L. 2013. Genome-wide association study of meatquality traits in a white duroc×Erhualian F2 intercross andchinese sutai pigs. PLOS ONE, 8, e64047.

Madsen P, Sørensen P, Su G, Damgaard L, Thomsen H. 2006.DMU-a package for analyzing multivariate mixed models.In: Proceedings of 8th World Congress on GeneticsApplied to Livestock Production. Brasil.

Malek M, Dekkers J C, Lee H K, Baas T J, Rothschild MF. 2001. A molecular genome scan analysis to identifychromosomal regions influencing economic traits inthe pig. I. Growth and body composition. MammalianGenome, 12, 630-636

Marshall T C, Slate J, Kruuk L E, Pemberton J M. 1998.Statistical confidence for likelihood-based paternityinference in natural population. Molecular Ecology, 7, 639-655

Melillo R M, Pierantoni G, Scala S, Battista S, Fedele M, StellaA, de Biasio M C, Chiappetta G, Fidanza V, Condorelli G,Santoro M, Croce C M, Viglietto G, Fusco A. 2001. Criticalrole of the HMGI(Y) proteins in adipocytic cell growthand differentiation. Molecular and Cellular Biology, 21,2485-2495

Milan D, Bidanel J P, Iannuccelli N, Riguet J, Amigues Y,Gruand J, Le Roy P, Renard C, Chevalet C. 2002. Detectionof quantitative trait loci for carcass composition traits inpigs. Genetics Selection Evolution, 34, 705-728

Okumura N, Matsumoto T, Hayashi T, Hirose K, Fukawa K,Itou T, Uenishi H, Mikawa S, Awata T. 2013. Genomicregions affecting backfat thickness and cannon bonecircumference identified by genome-wide association studyin a Duroc pig population. Animal Genetics, 44, 454-457

Onteru S K, Fan B, Du Z Q, Garrick D J, Stalder K J,Rothschild M F. 2012. A whole-genome association studyfor pig reproductive traits. Animal Genetics, 43, 18-26

Paszek A A, Wilkie P J, Flickinger G H, Miller L M, LouisC F, Rohrer G A, Alexander L J, Beattie C W, SchookL B. 2001. Interval mapping of carcass and meat qualitytraits in a divergent swine cross. Animal Biotechnology,12, 155-165

Ren J, Duan Y, Qiao R, Yao F, Zhang Z, Yang B, Guo Y, XiaoS, Wei R, Ouyang Z, Ouyang Z, Ding N, Ai H, Huang L.2011. A missense mutation in PPARD causes a major QTLeffect on ear size in pigs. PLoS Genetics, 7, e1002043.

Rothschild M F. 2004. Porcine genomics delivers new toolsand results: This little piggy did more than just go tomarket. Genetical Research, 83, 1-6

Schaid 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, 425-434

Shah S N, Cope L, Poh W, Belton A, Roy S, Talbot Jr C C,Sukumar S, Huso D L, Resar L M. 2013. HMGA1: Amaster regulator of tumor progression in triple-negativebreast cancer cells. PLOS ONE, 8, e63419.

Sutter N B, Bustamante C D, Chase K, Gray M M, Zhao K,Zhu L, Padhukasahasram B, Karlins E, Davis S, JonesP G, Quignon P, Johnson G S, Parker H G, Fretwell N,Mosher D S, Lawler D F, Satyaraj E, Nordborg M, Lark KG, Wayne R K, et al. 2007. A single IGF1 allele is a majordeterminant of small size in dogs. Science, 316, 112-115

Yue G, Strail A, Cepica S, Schroffel J, Schroffelova D,Fontanesi L, Cangnazzo M, Moser G, Bartenschlager H,Reiner G, Geldermann H. 2003. Linkage and QTL mappingfor Sus scrofa chromosome 7. Journal of Animal Breedingand Genetics, 120, 56-65.

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Genome-Wide Association Study for Certain Carcass Traits and Organ Weights in a Large White×Minzhu Intercross Porcine Population

Genome-Wide Association Study for Certain Carcass Traits and Organ Weights in a Large White×Minzhu Intercross Porcine Population

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