title: Polymorphisms in epigenetic and meat quality related genes in fourteen cattle breeds and association with beef quality and carcass traits.
abstract: Improvement for carcass traits related to beef quality is the key concern in beef production. Recent reports found that epigenetics mediates the interaction of individuals with environment and nutrition. The present study was designed to analyze the genetic effect of single nucleotide polymorphisms (SNPs) in seven epigenetic-related genes (DNMT1, DNMT3a, DNMT3b, DNMT3L, Ago1, Ago2, and HDAC5) and two meat quality candidate genes (CAPN1 and PRKAG3) on fourteen carcass traits related to beef quality in a Snow Dragon beef population, and also to identify SNPs in a total of fourteen cattle populations. Sixteen SNPs were identified and genotyped in 383 individuals sampled from the 14 cattle breeds, which included 147 samples from the Snow Dragon beef population. Data analysis showed significant association of 8 SNPs within 4 genes related to carcass and/or meat quality traits in the beef populations. SNP1 (13154420A>G) in exon 17 of DNMT1 was significantly associated with rib-eye width and lean meat color score (p<0.05). A novel SNP (SNP4, 76198537A>G) of DNMT3a was significantly associated with six beef quality traits. Those individuals with the wild-type genotype AA of DNMT3a showed an increase in carcass weight, chilled carcass weight, flank thicknesses, chuck short rib thickness, chuck short rib score and in chuck flap weight in contrast to the GG genotype. Five out of six SNPs in DNMT3b gene were significantly associated with three beef quality traits. SNP15 (45219258C>T) in CAPN1 was significantly associated with chuck short rib thickness and lean meat color score (p<0.05). The significant effect of SNP15 on lean meat color score individually and in combination with each of other 14 SNPs qualify this SNP to be used as potential marker for improving the trait. In addition, the frequencies of most wild-type alleles were higher than those of the mutant alleles in the native and foreign cattle breeds. Seven SNPs were identified in the epigenetic-related genes. The SNP15 in CAPN1 could be used as a powerful genetic marker in selection programs for beef quality improvement in the Snow Dragon Beef population.
authors: Key Laboratory of Agricultural Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
authors: Xuan
authors: X
authors: Liu
authors: Key Laboratory of Agricultural Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China ; Department of Animal Health, The University of Agriculture, Peshawar, Peshawar 25000, Pakistan .
authors: Tahir
authors: T
authors: Usman
authors: Key Laboratory of Agricultural Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
authors: Yachun
authors: Y
authors: Wang
authors: Key Laboratory of Agricultural Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
authors: Zezhao
authors: Z
authors: Wang
authors: Dalian Xuelong Industry Limited Group, Dalian 116001, China .
authors: Xianzhou
authors: X
authors: Xu
authors: Dalian Xuelong Industry Limited Group, Dalian 116001, China .
authors: Meng
authors: M
authors: Wu
authors: Key Laboratory of Agricultural Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
authors: Yi
authors: Y
authors: Zhang
authors: Key Laboratory of Agricultural Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
authors: Xu
authors: X
authors: Zhang
authors: Key Laboratory of Agricultural Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
authors: Qiang
authors: Q
authors: Li
authors: Beijing Dairy Cattle Center, Beijing 100193, China .
authors: Lin
authors: L
authors: Liu
authors: Beijing Dairy Cattle Center, Beijing 100193, China .
authors: Wanhai
authors: W
authors: Shi
authors: Ningxia Sygen BioEngineering Research Center, Yinchuan 750000, China .
authors: Chunhua
authors: C
authors: Qin
authors: Dingyuan Seedstock Bulls Breeding Ltd. Company, Zhengzhou 450000, China .
authors: Fanjun
authors: F
authors: Geng
authors: Dingyuan Seedstock Bulls Breeding Ltd. Company, Zhengzhou 450000, China .
authors: Congyong
authors: C
authors: Wang
authors: Xinjiang General Livestock Service, Urumqi 830000, China .
authors: Rui
authors: R
authors: Tan
authors: College of Animal Science, Xinjiang Agriculture University, Urumqi 830000 China .
authors: Xixia
authors: X
authors: Huang
authors: Xiertala Breeding Farm, Hailaer Farm Buro, Hailaer 021008, China .
authors: Airong
authors: A
authors: Liu
authors: Hailaer Farm Buro, Hailaer 021008, China .
authors: Hongjun
authors: H
authors: Wu
authors: Xinjiang Tianshan Animal Husbandry Bio-Eng. Co. Ltd, Urumqi 830000, China .
authors: Shixin
authors: S
authors: Tan
authors: Key Laboratory of Agricultural Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
authors: Ying
authors: Y
authors: Yu
keywords: Association Study; Beef Quality; CAPN1; Carcass Traits; Epigenetic-related Genes; Protein Kinase Subunit Gamma-3 Gene PRKAG3
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