Detection of SNPs in the TBC1D1 gene and their association with carcass traits in chicken

Yan Wang; Heng-Yong Xu; Elizabeth R Gilbert; Xing Peng; Xiao-Ling Zhao; Yi-Ping Liu; Qing Zhu

doi:10.1016/j.gene.2014.06.061

Detection of SNPs in the TBC1D1 gene and their association with carcass traits in chicken

Gene. 2014 Sep 1;547(2):288-94. doi: 10.1016/j.gene.2014.06.061. Epub 2014 Jun 27.

Authors

Yan Wang¹, Heng-Yong Xu¹, Elizabeth R Gilbert², Xing Peng¹, Xiao-Ling Zhao³, Yi-Ping Liu¹, Qing Zhu⁴

Affiliations

¹ Farm Animal Genetic Resource Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu Campus, Chengdu 611130, China.
² Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA.
³ College of Animal Science and Technology, Sichuan Agricultural University, Ya'an, Sichuan 625014, China.
⁴ College of Animal Science and Technology, Sichuan Agricultural University, Ya'an, Sichuan 625014, China. Electronic address: zhuqing5959@163.com.

PMID: 24979340
DOI: 10.1016/j.gene.2014.06.061

Abstract

TBC1D1 plays an important role in numerous fundamental physiological processes including muscle metabolism, regulation of whole body energy homeostasis and lipid metabolism. The objective of the present study was to identify single nucleotide polymorphisms (SNPs) in chicken TBC1D1 using 128 Erlang mountainous chickens and to determine if these SNPs are associated with carcass traits. The approach consisted of sequencing TBC1D1 using a panel of DNA from different individuals, revealing twenty-two SNPs. Among these SNPs, two polymorphisms (g.69307744C>T and g.69307608T>G) of block 1, four polymorphisms (g.69322320C>T, g.69322314G>A, g.69317290A>G and g.69317276T>C) of block 2 and four polymorphisms of block 3 (g.69349746G>A, g.69349736C>G, g.69349727C>T and g.69349694C>T) exhibited a high degree of linkage disequilibrium in all test populations. An association analysis was performed between the twenty-two SNPs and seven performance traits. SNPs g.69307744C>T, g.69340192G>A and g.69355665T>C were demonstrated to have a strong effect on liveweight (BW), carcass weight (CW), semi-eviscerated weight (SEW) and eviscerated weight (EW) and g.69340070C>T polymorphism was related to BW, SEW and BMW in chicken populations. However, for the other SNPs, there were no significant correlations between different genotypes and carcass traits. Meanwhile, haplotype CT-TG of block 1 and combined genotype AG-TT-AC-CT of block 3 were significantly associated with BW, CW, SEW and EW. Overall, our results provide evidence that polymorphisms in TBC1D1 are associated with carcass traits and would be a useful candidate gene in selection programs for improving carcass traits.

Keywords: Carcass traits; Chicken; Haplotype; SNPs; TBC1D1.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Chickens / genetics*
Food Quality
GTPase-Activating Proteins / genetics*
Polymorphism, Single Nucleotide*
Poultry Products / standards*

Substances

GTPase-Activating Proteins