Hostname: page-component-78c5997874-v9fdk Total loading time: 0 Render date: 2024-11-10T12:08:02.934Z Has data issue: false hasContentIssue false
  • English
  • Français

Genome-wide association study identifies quantitative trait loci regions involved in muscle acidic profile in Large White heavy pigs

Published online by Cambridge University Press:  10 February 2020

G. Catillo ,
M. Zappaterra ,
P. Zambonelli ,
L. Buttazzoni ,
R. Steri ,
G. Minelli  and
R. Davoli
G. Catillo
Affiliation:
Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria (CREA) – Centro di ricerca Zootecnia e Acquacoltura (Research Centre for Animal Production and Aquaculture), Via Salaria 31, I-00015Monterotondo, Italy
M. Zappaterra
Affiliation:
Department of Agricultural and Food Sciences (DISTAL), University of Bologna, Viale Fanin 46, I-40127Bologna, Italy
P. Zambonelli
Affiliation:
Department of Agricultural and Food Sciences (DISTAL), University of Bologna, Viale Fanin 46, I-40127Bologna, Italy
L. Buttazzoni
Affiliation:
Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria (CREA) – Centro di ricerca Zootecnia e Acquacoltura (Research Centre for Animal Production and Aquaculture), Via Salaria 31, I-00015Monterotondo, Italy
R. Steri
Affiliation:
Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria (CREA) – Centro di ricerca Zootecnia e Acquacoltura (Research Centre for Animal Production and Aquaculture), Via Salaria 31, I-00015Monterotondo, Italy
G. Minelli
Affiliation:
Department of Life Sciences, University of Modena and Reggio Emilia, Via G. Amendola 2, I-42122Reggio Emilia, Italy
R. Davoli*
Affiliation:
Department of Agricultural and Food Sciences (DISTAL), University of Bologna, Viale Fanin 46, I-40127Bologna, Italy
*
†E-mail: roberta.davoli@unibo.it
Get access

Abstract

The widespread use of genome-wide association studies resulted in the discovery of genomic regions associated with fatty acid (FA) composition in different porcine tissues, but little information exists about the genes involved in FA composition of meat obtained from heavy pigs selected for the production of Italian dry-cured hams. To this objective, we genotyped with a single nucleotide polymorphism (SNP) panel 795 Italian Large White heavy pigs to identify the markers and genomic regions associated with Semimembranosus muscle FA profile. Heritability estimates for intramuscular fat FA profile were of low-to-moderate magnitude, suggesting that these traits may be improved with genomic selection. On the whole, 45 SNPs were significantly associated with 14 FAs, and 4 of them (ALGA008109, ALGA0081097, CASI0010164 and SIRI0000267) were associated with more than 1 FA. The palmitoleic : palmitic and oleic : stearic ratios displayed the highest number of significant markers and the most significant associations (Bonferroni adjusted P < 5.00E−07). Of particular interest, the palmitoleic : palmitic ratio was strongly associated with markers located at 111 to 114 Mb on chromosome 14, in the same chromosomal region where Stearoyl-CoA desaturase Δ9 (SCD) gene is located. Several significant chromosomal regions were found; some of them harbour key genes playing pivotal roles in FA desaturation and elongation, such as SCD and some members of the Elongation of Very Long-Chain FA (ELOVL) gene family. The results suggest that the identification of causal mutations in these regions may provide a set of markers useful for selection schemes aimed at improving FA composition in pork products.

Keywords

swineintramuscular fatgenetic markersselectionfatty acid
Type
Research Article
Information
animal , Volume 14 , Issue 7 , July 2020 , pp. 1342 - 1350
Copyright
© The Animal Consortium 2020

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

Footnotes

*

These authors contributed equally to this work.

References

Aulchenko, YS, Ripke, S, Isaacs, A and van Duijn, CM 2007. GenABEL: an R library for genome-wide association analysis. Bioinformatics 23, 1294–1296.CrossRefGoogle Scholar
Barrett, JC, Fry, B, Maller, J and Daly, MJ 2005. Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 21, 263–265.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle Scholar
Corominas, J, Ramayo-Caldas, Y, Puig-Oliveras, A, Pérez-Montarelo, D, Noguera, JL, Folch, JM and Ballester, M 2013. Polymorphism in the ELOVL6 gene is associated with a major QTL effect on fatty acid composition in pigs. PLoS ONE 8, e53687.CrossRefGoogle ScholarPubMed
Davoli, R, Catillo, G, Serra, A, Zappaterra, M, Zambonelli, P, Zilio, DM, Steri, R, Mele, M, Buttazzoni, L and Russo, V 2019. Genetic parameters of backfat fatty acids and carcass traits in Large White pigs. Animal 13, 924–932.CrossRefGoogle ScholarPubMed
Folch, J, Lees, M and Sloane Stanley, GH 1957. A simple method for the isolation and purification of total lipides from animal tissues. Journal of Biological Chemistry 226, 497–509.Google ScholarPubMed
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.CrossRefGoogle Scholar
Fontanesi, L, Schiavo, G, Gallo, M, Baiocco, C, Galimberti, G, Bovo, S, Russo, V and Buttazzoni, L 2017. 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.CrossRefGoogle ScholarPubMed
Huang, DW, Sherman, BT and Lempicki, RA 2009. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nature Protocols 4, 44–57.CrossRefGoogle Scholar
Jiménez-Colmenero, F, Carballo, J and Cofrades, S 2001. Healthier meat and meat products: their role as functional foods. Meat Science 59, 5–13.CrossRefGoogle ScholarPubMed
Juárez, M, Dugan, MER, Aldai, N, Aalhus, JL, Patience, JF, Zijlstra, RT and Beaulieu, AD 2011. Increasing omega-3 levels through dietary co-extruded flaxseed supplementation negatively affects pork palatability. Food Chemistry 126, 1716–1723.CrossRefGoogle ScholarPubMed
Kim, YM, Choi, TJ, Ho Cho, K, Cho, ES, Lee, JJ, Chung, HJ, Baek, SY and Jeong, YD 2018. Effects of sex and breed on meat quality and sensory properties in three-way crossbred pigs sired by Duroc or by a synthetic breed based on a Korean native breed. Korean Journal of Food Science and Animal Research 38, 544–553.Google ScholarPubMed
Konovalova, S, Liu, X, Manjunath, P, Baral, S, Neupane, N, Hilander, T, Yang, Y, Balboa, D, Terzioglu, M, Euro, L, Varjosalo, M and Tyynismaa, H 2018. Redox regulation of GRPEL2 nucleotide exchange factor for mitochondrial HSP70 chaperone. Redox Biology 19, 37–45.CrossRefGoogle ScholarPubMed
Lo Fiego, DP, Macchioni, P, Minelli, G and Santoro, P 2010. Lipid composition of covering and intramuscular fat in pigs at different slaughter age. Italian Journal of Animal Science 9, 200–205.CrossRefGoogle Scholar
Lo Fiego, DP, Santoro, P, Macchioni, P and De Leonibus, E 2005. Influence of genetic type, live weight at slaughter and carcass fatness on fatty acid composition of subcutaneous adipose tissue of raw ham in the heavy pig. Meat Science 69, 107–114.CrossRefGoogle Scholar
Park, HB, Han, SH, Yoo, CK, Lee, JB, Kim, JH, Baek, KS, Son, JK, Shin, SM, Lim, HT and Cho, IC 2017. Genome scan linkage analysis identifies a major quantitative trait loci for fatty acid composition in longissimus dorsi muscle in an F2 intercross between Landrace and Korean native pigs. Asian-Australasian Journal of Animal Science 30, 1061–1065.CrossRefGoogle Scholar
Pena, RN, Noguera, JL, García-Santana, MJ, González, E, Tejeda, JF, Ros-Freixedes, R and Ibáñez-Escriche, N 2019. Five genomic regions have a major impact on fat composition in Iberian pigs. Scientific Reports 9, 2031.CrossRefGoogle ScholarPubMed
Pena, RN, Ros-Freixedes, R, Tor, M and Estany, J 2016. Genetic marker discovery in complex traits: a field example on fat content and composition in pigs. International Journal of Molecular Sciences 17, 2100.CrossRefGoogle ScholarPubMed
Purcell, S, Neale, B, Todd-Brown, K, Thomas, L, Ferreira, MAR, Bender, D, Maller, J, Sklar, P, de Bakker, PI, Daly, MJ and Sham, PC 2007. PLINK: a tool set for whole-genome association and population-based linkage analyses. America Journal of Human Genetics 81, 559–575.CrossRefGoogle ScholarPubMed
Ros-Freixedes, R, Gol, S, Pena, RN, Tor, M, Ibáñez-Escriche, N, Dekkers, JCM and Estany, J 2016. Genome-wide association study singles out SCD and LEPR as the two main loci influencing intramuscular fat content and fatty acid composition in Duroc pigs. PLoS ONE 11, e0152496.CrossRefGoogle ScholarPubMed
Schönberger, J, Wang, L, Shin, JT, Kim, SD, Depreux, FFS, Zhu, H, Zon, L, Pizard, A, Kim, JB, Macrae, CA, Mungall, AJ, Seidman, JG and Seidman, CE 2005. Mutation in the transcriptional coactivator EYA4 causes dilated cardiomyopathy and sensorineural hearing loss. Nature Genetics 37, 418.CrossRefGoogle ScholarPubMed
Steinberg, SJ, Morgenthaler, J, Heinzer, AK, Smith, KD and Watkins, PA 2000. Very long-chain Acyl-CoA synthetases human “Bubblegum” represents a new family of proteins capable of activating very long-chain fatty acids. Journal of Biological Chemistry 275, 35162–35169.CrossRefGoogle ScholarPubMed
van der Leij, FR, Bloks, VW, Grefhorst, A, Hoekstra, J, Gerding, A, Kooi, K, Gerbens, F, te Meerman, G and Kuipers, F 2007. Gene expression profiling in livers of mice after acute inhibition of β-oxidation. Genomics 90, 680–689.CrossRefGoogle ScholarPubMed
van Son, M, Enger, EG, Grove, H, Ros-Freixedes, R, Kent, MP, Lien, S and Grindflek, E 2017. Genome-wide association study confirm major QTL for backfat fatty acid composition on SSC14 in Duroc pigs. BMC Genomics 18, 369.CrossRefGoogle ScholarPubMed
Vazquez, EJ, Berthiaume, JM, Kamath, V, Achike, O, Buchanan, E, Montano, MM, Chandler, MP, Miyagi, M and Rosca, MG 2015. Mitochondrial complex I defect and increased fatty acid oxidation enhance protein lysine acetylation in the diabetic heart. Cardiovascular Research 107, 453–465.CrossRefGoogle ScholarPubMed
Wiedemann, N, Frazier, AE and Pfanner, N 2004. The protein import machinery of mitochondria. Journal of Biological Chemistry 279, 14473–14476.CrossRefGoogle ScholarPubMed
Wood, JD, Enser, M, Fisher, AV, Nute, GR, Sheard, PR, Richardson, RI, Hughes, SI and Whittington, FM 2008. Fat deposition, fatty acid composition and meat quality: a review. Meat Science 78, 343–358.CrossRefGoogle ScholarPubMed
Wood, JD, Richardson, RI, Nute, GR, Fisher, AV, Campo, MM, Kasapidou, E, Sheard, PR and Enser, M 2004. Effects of fatty acids on meat quality: a review. Meat Science 66, 21–32.CrossRefGoogle ScholarPubMed
Yang, B, Zhang, W, Zhang, Z, Fan, Y, Xie, X, Ai, H, Ma, J, Xiao, S, Huang, L and Ren, J 2013. Genome-wide association analyses for fatty acid composition in porcine muscle and abdominal fat tissues. PLoS ONE 8, e65554.Google ScholarPubMed
Yang, J, Lee, SH, Goddard, ME and Visscher, PM 2011, GCTA: a tool for genome-wide complex trait analysis. American Journal of Human Genetics, 88, 76–82.CrossRefGoogle ScholarPubMed
Zappaterra, M, Ros-Freixedes, R, Estany, J and Davoli, R 2018. Association study highlights the influence of ELOVL fatty acid elongase 6 gene region on backfat fatty acid composition in Large White pig breed. Animal 12, 2443–2452.CrossRefGoogle ScholarPubMed
Zhang, J, Zhang, Y, Gong, H, Cui, L, Huang, T, Ai, H, Ren, J, Huang, L and Yang, B 2017. Genetic mapping using 1.4M SNP array refined loci for fatty acid composition traits in Chinese Erhualian and Bamaxiang pigs. Journal of Animal Breeding and Genetics 134, 472–483.CrossRefGoogle ScholarPubMed
Zhang, W, Zhang, J, Cui, L, Ma, J, Chen, C, Ai, H, Xie, X, Li, L, Xiao, S, Huang, L, Ren, J and Yang, B 2016. Genetic architecture of fatty acid composition in the longissimus dorsi muscle revealed by genome-wide association studies on diverse pig populations. Genetics Selection Evolution 48, 5.CrossRefGoogle ScholarPubMed
Supplementary material: File

Catillo et al. supplementary material

Catillo et al. supplementary material

Download Catillo et al. supplementary material(File)
File 175 KB