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Genome-wide association studies for seven production traits highlight genomic regions useful to dissect dry-cured ham quality and production traits in Duroc heavy pigs

Published online by Cambridge University Press:  30 April 2018

F. Bertolini ,
G. Schiavo ,
G. Galimberti ,
S. Bovo ,
M. D’Andrea ,
M. Gallo ,
L. Buttazzoni ,
M. F. Rothschild  and
L. Fontanesi
F. Bertolini
Affiliation:
Department of Animal Science, Iowa State University, 2255 Kildee Hall, Ames, IA 50011, USA Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale G. Fanin 46, 40127 Bologna, Italy
G. Schiavo
Affiliation:
Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale G. Fanin 46, 40127 Bologna, Italy
G. Galimberti
Affiliation:
Department of Statistical Sciences “Paolo Fortunati”, University of Bologna, Via delle Belle Arti, 40126 Bologna, Italy
S. Bovo
Affiliation:
Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale G. Fanin 46, 40127 Bologna, Italy
M. D’Andrea
Affiliation:
Department of Agricultural, Environmental and Food Sciences, University of Molise, via F. De Sanctis snc, 86100 Campobasso, Italy
M. Gallo
Affiliation:
Associazione Nazionale Allevatori Suini, Via Nizza 54, 00198 Roma, Italy
L. Buttazzoni
Affiliation:
CREA Research Centre for Animal Production and Aquaculture, Roma, Italy
M. F. Rothschild
Affiliation:
Department of Animal Science, Iowa State University, 2255 Kildee Hall, Ames, IA 50011, USA
L. Fontanesi*
Affiliation:
Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale G. Fanin 46, 40127 Bologna, Italy
*
†E-mail: [email protected]
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Abstract

Protected designation of origin dry-cured hams are obtained from heavy pigs (slaughtered at about 160 kg of live weight). A specific breeding program designed to improve meat quality for this production has included as key traits the level of intermuscular fat between the leg muscles and ham weight loss during the seasoning period together with a balance between fat and lean cuts. In this study we carried out genome-wide association studies for seven traits used in the genetic merit of Italian Duroc heavy pigs, five related to meat and carcass quality traits (visible intermuscular fat, ham weight loss at first salting, backfat thickness, ham weight and lean cuts), and two related to performance and efficiency traits (average daily gain and feed : gain ratio). A total of 573 performance-tested pigs were genotyped with the Illumina PorcineSNP60 BeadChip and genome-wide association analyses were carried out using the Bayes B approach with the 1 Mb window option of GenSel and random residuals for each of the seven traits. Detected windows were supported by independent single nucleotide polymorphism analyses with a linear mixed model (LMM) approach on the same animals for the same traits. A total of 30 windows identifying different quantitative trait loci (QTL) were detected and among those, 27 were confirmed by LMM in one of these traits. Among the confirmed windows, three QTL were reported for visible intermuscular fat, seven for ham weight loss at first salting and five and four for backfat thickness and lean cut, respectively. A total of eight QTL were detected for the other production traits. No overlapping QTL were reported except for one window on porcine chromosome 10 between lean cuts and ham weight that contained the CACNB2 gene that has been already associated with loin marbling score in other Duroc pigs. Several regions contained genes that have been already associated with production traits in other pig breeds, including Duroc lines, related to fat deposition or muscle structure. This work reports, for the first time, genome-wide association study results for several traits in Italian Duroc heavy pigs. These results will be useful to dissect the genetic basis for dry-cured ham production traits that determine the total genetic merit index of Italian Duroc pigs.

Keywords

labeled productsmeat qualityseasoningsingle nucleotide polymorphismgenomics
Type
Research Article
Information
animal , Volume 12 , Issue 9 , September 2018 , pp. 1777 - 1784
Copyright
© The Animal Consortium 2018 

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References

Associazione Nazionale Allevatori Suini (ANAS) 2016. ANAS Notizie: La selezione per il prosciutto DOP. Una sfida tecnica per un orizzonte dilungo periodo. Retrieved on 15 January 2018 from http://www.anas.it/circolari/20170001A.PDF Google Scholar
Bosi, P and Russo, V 2004. The production of the heavy pig for high quality processed products. Italian Journal of Animal Science 3, 309–321.Google Scholar
Buttazzoni, L, Gallo, M, Baiocco, C and Carchedi, C 1993. La selezione per la qualità della carne suina destinata alla trasformazione. Rivista di Suinicoltura 34, 139–145.Google Scholar
Carnier, P, Cassandro, M, Knol, E and Padoan, D 1999. Genetic parameters for some carcass and fresh ham traits of crossbred Goland pigs. In Recent progress in animal science (ed. G Piva, G Bertoni, F Masoero, P Bani and L Calamari), pp. 221–223. Franco Angeli Edizioni, Milano, Italy.Google Scholar
Cummings, N, Shields, KA, Curran, JE, Bozaoglu, K, Trevaskis, J, Gluschenko, K, Cai, G, Comuzzie, AG, Dyer, TD, Walder, KR, Zimmet, P, Collier, GR, Blangero, J and Jowett, JB 2012. Genetic variation in SH3-domain GRB2-like (endophilin)-interacting protein 1 has a major impact on fat mass. International Journal of Obesity 36, 201–206.Google Scholar
Ekine, CC, Rowe, SJ, Bishop, SC and de Koning, DJ 2014. Why breeding values estimated using familial data should not be used for genome-wide association studies. G3: Genes, Genomes, Genetics 4, 341–347.Google Scholar
Fernando, R and Garrick, D 2009. GenSel-User manual for a portfolio of genomic selection related analyses. Retrieved on 2 February 2018 from https://static-content.springer.com/esm/art%3A10.1186%2F1471-2105-12-186/MediaObjects/12859_2010_4655_MOESM1_ESM.PDF Google Scholar
Fontanesi, L, Bertolini, F, Scotti, E, Trevisi, P, Buttazzoni, L, Dall’Olio, S, Davoli, R, Bosi, P and Russo, V 2012a. Polymorphisms in an obesity-related gene (PCSK1) are associated with fat deposition and production traits in Italian heavy pigs. Animal 12, 1913–1924.Google Scholar
Fontanesi, L, Davoli, R, Nanni Costa, L, Beretti, F, Scotti, E, Tazzoli, M, Tassone, F, Colombo, M, Buttazzoni, L and Russo, V 2008. Investigation of candidate genes for glycolytic potential of porcine skeletal muscle: association with meat quality and production traits in Italian Large White pigs. Meat Science 80, 780–787.Google Scholar
Fontanesi, L, Schiavo, G, Galimberti, G, Calò, DG and Russo, V 2014. A genome wide association study for average daily gain in Italian Large White pigs. Journal of Animal Science 92, 1385–1394.Google Scholar
Fontanesi, L, Schiavo, G, Galimberti, G, Calò, DG, Scotti, E, Martelli, PL, Buttazzoni, L, Casadio, R and Russo, V 2012b. A genome wide association study for backfat thickness in Italian Large White pigs highlights new regions affecting fat deposition including neuronal genes. BMC Genomics 13, 583.Google Scholar
Fontanesi, L, Schiavo, G, Scotti, E, Galimberti, G, Calò, DG, Samorè, AB, Gallo, M, Russo, V and Buttazzoni, L 2015. A retrospective analysis of allele frequency changes of major genes during 20 years of selection in the Italian Large White pig breed. Journal of Animal Breeding and Genetics 132, 239–246.Google Scholar
Fontanesi, L, Schiavo, G, Galimberti, G, Bovo, S, Russo, V, Gallo, M and Buttazzoni, L 2017a. A genome-wide association study for a proxy of intermuscular fat level in the Italian Large White breed identifies genomic regions affecting an important quality parameter for dry-cured hams. Animal Genetics 48, 459–465.Google Scholar
Fontanesi, L, Schiavo, G, Gallo, M, Baiocco, C, Galimberti, G, Bovo, S, Russo, V and Buttazzoni, L 2017b. Genome-wide association study for ham weight loss at first salting in Italian Large White pigs: towards the genetic dissection of a key trait for dry-cured ham production. Animal Genetics 48, 103–107.Google Scholar
Fowler, KE, Pong-Wong, R, Bauer, J, Clemente, EJ, Reitter, CP, Affara, NA, Waite, S, Walling, GA and Griffin, DK 2013. Genome wide analysis reveals single nucleotide polymorphisms associated with fatness and putative novel copy number variants in three pig breeds. BMC Genomics 14, 784.Google Scholar
Gondret, F, Vincent, A, Houée-Bigot, M, Siegel, A, Lagarrigue, S, Causeur, D, Gilbert, H and Louveau, I 2017. A transcriptome multi-tissue analysis identifies biological pathways and genes associated with variations in feed efficiency of growing pigs. BMC Genomics 18, 244.Google Scholar
He, Y, Ma, J, Zhang, F, Hou, L, Chen, H, Guo, Y and Zhang, Z 2016. Multi-breed genome-wide association study reveals heterogeneous loci associated with loin eye area in pigs. Journal of Applied Genetics 57, 511–518.Google Scholar
Kouba, M and Sellier, P 2011. A review of the factors influencing the development of intermuscular adipose tissue in the growing pig. Meat Science 88, 216–220.Google Scholar
Lee, KT, Byun, MJ, Kang, KS, Hwang, H, Park, EW, Kim, JM, Kim, TH and Lee, SH 2012. 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 90, 1081–1087.Google Scholar
Lonergan, SM, Huff-Lonergan, E, Rowe, LJ, Kuhlers, DL and Jungst, SB 2001. Selection for lean growth efficiency in Duroc pigs influences pork quality. Journal of Animal Science 79, 2075–2085.Google Scholar
Neustaeter, A, Grossi, DA, Jafarikia, M, Sargolzaei, M and Schenkel, F 2014. Genome-wide Association Study for Loin Marbling Score in Canadian Duroc pigs. Paper presented at the 10th World Congress on Genetics Applied to Livestock Production, 17 to 24 August, Vancouver, BC, Canada.Google Scholar
Ponsuksili, S, Reyer, H, Trakooljul, N, Murani, E and Wimmers, K 2016. Single- and Bayesian multi-marker genome-wide association for haematological parameters in pigs. PLoS One 11, e0159212.Google Scholar
Qualivita-ISMEA 2014. Rapporto 2014 sulle Produzioni Agroalimentari Italiane DOP IGP STG. Edizioni Qualivita, Rome, Italy.Google Scholar
Renaville, B, Piasentier, E, Fan, B, Vitale, M, Prandi, A and Rothschild, MF 2010. Candidate gene markers involved in San Daniele ham quality. Meat Science 85, 441–445.Google Scholar
Russo, V, Nanni Costa, L, Lo Fiego, DP and De Grossi, A 1991. Early estimation of seasoning loss in Parma ham production. Proceedings: 37th International Congress of Meat Science and Technology, Kulmbach, Germany, pp. 926–929.Google Scholar
Samorè, AB, Buttazzoni, L, Gallo, M, Russo, V and Fontanesi, L 2015. Genomic selection in a pig population including information from slaughtered full sibs of boars within a sib-testing program. Animal 9, 750–759.Google Scholar
Sanchez, MP, Tribout, T, Iannuccelli, N, Bouffaud, M, Servin, B, Tenghe, A, Dehais, P, Muller, N, Del Schneider, MP, Mercat, MJ, Rogel-Gaillard, C, Milan, D, Bidanel, JP and Gilbert, H 2014. 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 46, 12.Google Scholar
Sato, S, Uemoto, Y, Kikuchi, T, Egawa, S, Kohira, K, Saito, T, Sakuma, H, Miyashita, S, Arata, S, Kojima, T and Suzuki, K 2016. SNP- and haplotype-based genome-wide association studies for growth, carcass, and meat quality traits in a Duroc multigenerational population. BMC Genetics 17, 60.Google Scholar
Schiavo, G, Galimberti, G, Calò, DG, Samorè, AB, Bertolini, F, Russo, V, Gallo, M, Buttazzoni, L and Fontanesi, L 2016. Twenty years of artificial directional selection have shaped the genome of the Italian Large White pig breed. Animal Genetics 47, 181–191.Google Scholar
Stalder, KJ, Rothschild, MF and Lonergan, SM 2005. Associations between two gene markers and indicator traits affecting fresh and dry-cured ham processing quality. Meat Science 69, 451–457.Google Scholar
Trevaskis, J, Walder, K, Foletta, V, Kerr-Bayles, L, McMillan, J, Cooper, A, Lee, S, Bolton, K, Prior, M, Fahey, R, Whitecross, K, Morton, GJ, Schwartz, MW and Collier, GR 2005. Src homology 3-domain growth factor receptor-bound 2-like (endophilin) interacting protein 1, a novel neuronal protein that regulates energy balance. Endocrinology 146, 3757–3764.Google Scholar
Wang, K, Liu, D, Hernandez-Sanchez, J, Chen, J, Liu, C, Wu, Z, Fang, M and Li, N 2015. Genome wide association analysis reveals new production trait genes in a male Duroc population. PLoS One 10, e0139207.Google Scholar
Wellcome Trust Case Control Consortium 2007. Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 447, 661–683.Google Scholar
Zhang, Z, Ober, U, Erbe, M, Zhang, H, Gao, N, He, J, Li, J and Simianer, H 2014. Improving the accuracy of whole genome prediction for complex traits using the results of genome wide association studies. PLoS One 9, e93017.Google Scholar
Zhou, X and Stephens, M 2012. Genome-wide efficient mixed-model analysis for association studies. Nature Genetics 44, 821–824.Google Scholar
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