Polymorphisms in epigenetic and meat quality related genes in fourteen cattle breeds and association with beef quality and carcass traits.

Xuan Li ,Meng Wu,Xixia Huang,Yachun Wang,Qiang Li,Fanjun Geng,Xu Zhang,Shixin Tan,Chunhua Qin,Yi Zhang,Hongjun Wu,Airong Liu,Zezhao Wang,Lin Liu,Congyong Wang,Ying Yu,Xianzhou Xu,Wanhai Shi,Rui Zhen Tan ,Τahir Usman

doi:10.5713/ajas.13.0837

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.

Highlights

Carcass traits related to beef quality are normallyDuring the last decade two promising single nucleotide polymorphisms (SNPs) have been identified and are being used in selection programs of the economically important traits in the livestock industry
A total of 3 SNPs were found in the exon regions including SNP1 (13154420A>G) in exon and SNP2 in exon (13153987T>C) of DNMT1, and SNP15 (45219258C>T) in exon 4 of CAPN1
Amongst 9 screened and analyzed genes in the present study, SNPs in only 4 genes i.e. DNMT1, DNMT3a, DNMT3b, and CAPN1 were found significantly associated with carcass and beef quality traits

Summary

Introduction

Carcass traits related to beef quality are normally. During the last decade two promising SNPs have been identified and are being used in selection programs of the economically important traits in the livestock industry. One of the SNPs is in the calpain 1 gene (CAPN1, (mu/I) large subunit), which is known to associate with meat tenderness (Smith et al, 2000; White et al, 2005; Casas et al, 2006). The other SNP in the 5'-AMP-activated protein kinase. Sci. 28:467-475 subunit gamma-3 gene (PRKAG3), which affects high glycogen content in porcine skeletal muscle (Li et al, 2012; Ryan et al, 2012)

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