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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]
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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 

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Footnotes

a

These two authors contributed equally to this work.

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