Hostname: page-component-586b7cd67f-tf8b9 Total loading time: 0 Render date: 2024-11-24T02:27:05.513Z Has data issue: false hasContentIssue false
  • English
  • Français

Genomic variants associated with the number and diameter of muscle fibers in pigs as revealed by a genome-wide association study

Published online by Cambridge University Press:  15 October 2019

L. Zhang ,
Y. Guo ,
L. Wang ,
X. Liu ,
H. Yan ,
H. Gao ,
X. Hou ,
Y. Zhang ,
H. Guo  and
J. Yue
...Show all authors
L. Zhang
Affiliation:
Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Department of Animal Genetics and Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, 2 Yuanmingyuan West Road, 100193 Beijing, China
Y. Guo
Affiliation:
Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Department of Animal Genetics and Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, 2 Yuanmingyuan West Road, 100193 Beijing, China
L. Wang
Affiliation:
Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Department of Animal Genetics and Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, 2 Yuanmingyuan West Road, 100193 Beijing, China
X. Liu
Affiliation:
Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Department of Animal Genetics and Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, 2 Yuanmingyuan West Road, 100193 Beijing, China
H. Yan
Affiliation:
Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Department of Animal Genetics and Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, 2 Yuanmingyuan West Road, 100193 Beijing, China
H. Gao
Affiliation:
Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Department of Animal Genetics and Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, 2 Yuanmingyuan West Road, 100193 Beijing, China
X. Hou
Affiliation:
Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Department of Animal Genetics and Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, 2 Yuanmingyuan West Road, 100193 Beijing, China
Y. Zhang
Affiliation:
Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Department of Animal Genetics and Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, 2 Yuanmingyuan West Road, 100193 Beijing, China
H. Guo
Affiliation:
Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Department of Animal Genetics and Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, 2 Yuanmingyuan West Road, 100193 Beijing, China
J. Yue
Affiliation:
Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Department of Animal Genetics and Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, 2 Yuanmingyuan West Road, 100193 Beijing, China
J. An
Affiliation:
Department of Animal Genetics and Breeding, Tianjin Institute of Animal Science and Veterinary, 17 km from Jinjing Road, Zhangjiawo Town, 300381 Tianjin, China
L. Wang*
Affiliation:
Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Department of Animal Genetics and Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, 2 Yuanmingyuan West Road, 100193 Beijing, China
*
†E-mail: [email protected]
Get access

Abstract

Muscle fiber characteristics comprise a set of complex traits that influence the meat quality and lean meat production of livestock. However, the genetic and biological mechanisms regulating muscle fiber characteristics are largely unknown in pigs. Based on a genome-wide association study (GWAS) performed on 421 Large White × Min pig F2 individuals presenting well-characterized phenotypes, this work aimed to detect genome variations and candidate genes for five muscle fiber characteristics: percentage of type I fibers (FIB1P), percentage of type IIA fibers (FIB2AP), percentage of type IIB fibers (FIB2BP), diameter of muscle fibers (DIAMF) and number of muscle fibers per unit area (NUMMF). The GWAS used the Illumina Porcine SNP60K genotypic data, which were analyzed by a mixed model. Seven and 10 single nucleotide polymorphisms (SNPs) were significantly associated with DIAMF and NUMMF, respectively (P < 1.10E-06); no SNP was significantly associated with FIB1P, FIB2AP or FIB2B. For DIAMF, the significant SNPs on chromosome 4 were located in the previously reported quantitative trait loci (QTL) interval. Because the significant SNPs on chromosome 6 were not mapped in the previously reported QTL interval, a putative novel QTL was suggested for this locus. None of the previously reported QTL intervals on chromosomes 6 and 14 harbored significant SNPs for NUMMF; thus, new potential QTLs on these two chromosomes are suggested in the present work. The most significant SNPs associated with DIAMF (ALGA0025682) and NUMMF (MARC0046984) explained 12.02% and 11.59% of the phenotypic variation of these traits, respectively. In addition, both SNPs were validated as associated with DIAMF and NUMMF in Beijing Black pigs (P < 0.01). Some candidate genes or non-coding RNAs, such as solute carrier family 44 member 5 and miR-124a-1 for DIAMF, and coiled-coil serine rich protein 2 for NUMMF, were identified based on their close location to the significant SNPs. This study revealed some genome-wide association variants for muscle fiber characteristics, and it provides valuable information to discover the genetic mechanisms controlling these traits in pigs.

Keywords

genotyping beadchipintercross populationlongissimus musclequantitative trait lociswine
Type
Research Article
Information
animal , Volume 14 , Issue 3 , March 2020 , pp. 475 - 481
Copyright
© The Animal Consortium 2019 

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

a

These two authors contributed equally to this work.

References

Ando, T, Yoshida, T, Enomoto, S, Asada, K, Tatematsu, M, Ichinose, M, Sugiyama, T and Ushijima, T 2009. DNA methylation of microRNA genes in gastric mucosae of gastric cancer patients: its possible involvement in the formation of epigenetic field defect. International Journal of Cancer 124, 2367–2374.CrossRefGoogle ScholarPubMed
Ben Gacem, R, Ben Abdelkrim, O, Ziadi, S, Ben Dhiab, M and Trimeche, M 2014. Methylation of miR-124a-1, miR-124a-2, and miR-124a-3 genes correlates with aggressive and advanced breast cancer disease. Tumor Biology 35, 4047–4056.CrossRefGoogle ScholarPubMed
Brooke, MH and Kaiser, KK 1970. Muscle fibers types: how many and what kind? Archives of Neurology 23, 369–379.CrossRefGoogle Scholar
Carty, CL, Keene, KL, Cheng, YC, Meschia, JF, Chen, WM, Nalls, M, Bis, JC, Kittner, SJ, Rich, SS, Tajuddin, S, Zonderman, AB, Evans, MK, Langefeld, CD, Gottesman, R, Mosley, TH, Shahar, E, Woo, D, Yaffe, K, Liu, YM, Sale, MM, Dichgans, M, Malik, R, Longstreth, WT , Jr, Mitchell, BD, Psaty, BM, Kooperberg, C, Reiner, A, Worrall, BB, Fornage, M and COMPASS and METASTROKE Consortia 2015. Meta-analysis of genome-wide association studies identifies genetic risk factors for stroke in African Americans. Stroke 46, 2063–2068.CrossRefGoogle ScholarPubMed
Fiedler, I, Dietl, G, Rehfeldt, C, Wegner, J and Ender, K 2004. Muscle fibre traits as additional selection criteria for muscle growth and meat quality in pigs – results of a simulated selection. Journal of Animal Breeding and Genetics 121, 331–344.CrossRefGoogle Scholar
Frohnert, BI, Laimighofer, M, Krumsiek, J, Theis, FJ, Winkler, C, Norris, JM, Ziegler, AG, Rewers, MJ and Steck, AK 2018. Prediction of type 1 diabetes using a genetic risk model in the Diabetes Autoimmunity Study in the Young. Pediatric Diabetes 19, 277–283.CrossRefGoogle Scholar
Furtado, MB, Merriner, DJ, Berger, S, Rhodes, D, Jamsai, D and O’Bryan, MK 2017. Mutations in the Katnb1 gene cause left-right asymmetry and heart defects. Developmental Dynamics 246, 1027–1035.CrossRefGoogle ScholarPubMed
Hollander, L, Guo, X, Velazquez, H, Chang, J, Safirstein, R, Kluger, H, Cha, C and Desir, GV 2016. Renalase expression by melanoma and tumor-associated macrophages promotes tumor growth through a STAT3-mediated mechanism. Cancer Research 76, 3884–3894.CrossRefGoogle ScholarPubMed
Larzul, C, Lefaucheur, L, Ecolan, P, Gogué, J, Talmant, A, Sellier, P, Le, RP and Monin, G 1997. 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 75, 3126–3137.CrossRefGoogle ScholarPubMed
Lee, EA, Kim, JM, Lim, KS, Ryu, YC, Jeon, WM and Hong, KC 2012. Effects of variation in porcine MYOD1 gene on muscle fiber characteristics, lean meat production, and meat quality traits. Meat Science 92, 36–43.CrossRefGoogle ScholarPubMed
Lefaucheur, L 2010. A second look into fibre typing – relation to meat quality. Meat Science 84, 257–270.CrossRefGoogle ScholarPubMed
Li, WB, Ren, J, Zhu, WC, Guo, BL, Yang, B, Liu, LT, Ding, NS, Ma, JW, Li, L and Huang, LS 2009. Mapping QTL for porcine muscle fibre traits in a White Duroc x Erhualian F2 resource population. Journal of Animal Breeding Genetics 126, 468–474.CrossRefGoogle Scholar
Lopez-Bote, C, Warriss, PD and Brown, SN 1989. The use of muscle protein solubility measurements to assess pig lean meat quality. Meat Science 26, 167–175.CrossRefGoogle ScholarPubMed
Maltin, CA, Warkup, CC, Matthews, KR, Grant, CM, Porter, AD and Delday, MI 1997. Pig muscle fibre characteristics as a source of variation in eating quality. Meat Science 47, 237–248.CrossRefGoogle ScholarPubMed
McIntosh, LA, Marion, MC, Sudman, M, Comeau, ME, Becker, ML, Bohnsack, JF, Fingerlin, TE, Griffin, TA, Haas, JP, Lovell, DJ, Maier, LA, Nigrovic, PA, Prahalad, S, Punaro, M, Rosé, CD, Wallace, CA, Wise, CA, Moncrieffe, H, Howard, TD, Langefeld, CD and Thompson, SD 2017. Genome-wide association meta-analysis reveals novel juvenile idiopathic arthritis susceptibility loci. Arthritis and Rheumatology 69, 2222–2232.CrossRefGoogle ScholarPubMed
Miller, SA, Dykes, DD and Polesky, HF 1988. A simple salting out procedure for extracting DNA from human nucleated cells. Nucleic Acids Research 16, 1215.CrossRefGoogle ScholarPubMed
Mishra, P, Varuzhanyan, G, Pham, AH and Chan, DC 2015. Mitochondrial dynamics is a distinguishing feature of skeletal muscle fiber types and regulates organellar compartmentalization. Cell Metabolism 22, 1033–1044.CrossRefGoogle ScholarPubMed
Mishra-Gorur, K, Çağlayan, AO, Schaffer, AE, Chabu, C, Henegariu, O, Vonhoff, F, Akgümüş, GT, Nishimura, S, Han, W, Tu, S, Baran, B, Gümüş, H, Dilber, C, Zaki, MS, Hossni, HA, Rivière, JB, Kayserili, H, Spencer, EG, Rosti, RÖ, Schroth, J, Per, H, Çağlar, C, Çağlar, Ç, Dölen, D, Baranoski, JF, Kumandaş, S, Minja, FJ, Erson-Omay, EZ, Mane, SM, Lifton, RP, Xu, T, Keshishian, H, Dobyns, WB, Chi, NC, Šestan, N, Louvi, A, Bilgüvar, K, Yasuno, K, Gleeson, JG and Günel, M 2014. Mutations in KATNB1 cause complex cerebral malformations by disrupting asymmetrically dividing neural progenitors. Neuron 84, 1226–1239.CrossRefGoogle ScholarPubMed
Nakatani, N, Hattori, E, Ohnishi, T, Dean, B, Iwayama, Y, Matsumoto, I, Kato, T, Osumi, N, Higuchi, T, Niwa, S and Yoshikawa, T 2006. Genome-wide expression analysis detects eight genes with robust alterations specific to bipolar I disorder: relevance to neuronal network perturbation. Human Molecular Genetics 15, 1949–1962.CrossRefGoogle ScholarPubMed
Song, YJ, Choi, JH and Lee, H 2015. Setdb1 is required for myogenic differentiation of C2C12 myoblast cells via maintenance of MyoD expression. Molecules and Cells 38, 362–372.CrossRefGoogle ScholarPubMed
Sugimoto, M, Watanabe, T and Sugimoto, Y 2012. The molecular effects of a polymorphism in the 5’UTR of solute carrier family 44, member 5 that is associated with birth weight in Holsteins. PLoS ONE 7, e41267.CrossRefGoogle ScholarPubMed
Tilli, TM, Castro, CS, Tuszynski, JA and Carels, N 2016. A strategy to identify housekeeping genes suitable for analysis in breast cancer diseases. BMC Genomics 17, 639.CrossRefGoogle ScholarPubMed
Ueda, Y, Ando, T, Nanjo, S, Ushijima, T and Sugiyama, T 2014. DNA methylation of microRNA-124a is a potential risk marker of colitis-associated cancer in patients with ulcerative colitis. Digestive Diseases and Sciences 59, 2444–2451.CrossRefGoogle ScholarPubMed
Wimmers, K, Fiedler, I, Hardge, T, Murani, E, Schellander, K and Ponsuksili, S 2006. QTL for microstructural and biophysical muscle properties and body composition in pigs. BMC Genetics 7, 15.CrossRefGoogle ScholarPubMed
Winkler, C, Krumsiek, J, Buettner, F, Angermüller, C, Giannopoulou, EZ, Theis, FJ, Ziegler, AG and Bonifacio, E 2014. Feature ranking of type 1 diabetes susceptibility genes improves prediction of type 1 diabetes. Diabetologia 57, 2521–2529.CrossRefGoogle ScholarPubMed
Yang, W, Shen, N, Ye, DQ, Liu, Q, Zhang, Y, Qian, XX, Hirankarn, N, Ying, D, Pan, HF, Mok, CC, Chan, TM, Wong, RW, Lee, KW, Mok, MY, Wong, SN, Leung, AM, Li, XP, Avihingsanon, Y, Wong, CM, Lee, TL, Ho, MH, Lee, PP, Chang, YK, Li, PH, Li, RJ, Zhang, L, Wong, WH, Ng, IO, Lau, CS, Sham, PC, Lau, YL and Asian Lupus Genetics Consortium 2010. Genome-wide association study in Asian populations identifies variants in ETS1 and WDFY4 associated with systemic lupus erythematosus. PLoS Genetics 6, e1000841.CrossRefGoogle ScholarPubMed
Zheng, Y, Wang, S and Yan, P 2018. The meat quality, muscle fiber characteristics and fatty acid profile in Jinjiang and F1 Simmental × Jinjiang yellow cattle. Asian-Australasian Journal of Animal Sciences 31, 301–308.CrossRefGoogle Scholar
Zhu, LN, Ren, Y, Chen, JQ and Wang, YZ 2013. Effects of myogenin on muscle fiber types and key metabolic enzymes in gene transfer mice and C2C12 myoblasts. Gene 532, 246–252.CrossRefGoogle ScholarPubMed
Zierath, JR and Hawley, JA 2004. Skeletal muscle fiber type: influence on contractile and metabolic properties. PLoS Biology 2, e348.CrossRefGoogle ScholarPubMed
Supplementary material: File

Zhang et al. supplementary material

Figure S1

Download Zhang et al. supplementary material(File)
File 240.6 KB