Polymorphism in promoter of SIX4 gene shows association with its transcription and body measurement traits in Qinchuan cattle

Dawei Wei; Sayed Haidar Abbas Raza; Jiupan Zhang; Linsheng Gui; Siddiq Ur Rahman; Rajwali Khan; Seyed Mahdi Hosseini; Hubdar Ali Kaleri; Linsen Zan

doi:10.1016/j.gene.2018.02.059

Polymorphism in promoter of SIX4 gene shows association with its transcription and body measurement traits in Qinchuan cattle

Gene. 2018 May 20:656:9-16. doi: 10.1016/j.gene.2018.02.059. Epub 2018 Feb 26.

Authors

Dawei Wei¹, Sayed Haidar Abbas Raza¹, Jiupan Zhang², Linsheng Gui³, Siddiq Ur Rahman⁴, Rajwali Khan³, Seyed Mahdi Hosseini⁵, Hubdar Ali Kaleri⁶, Linsen Zan⁷

Affiliations

¹ College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China; National Beef Cattle Improvement Center of Northwest A&F University, Yangling 712100, China.
² Guyuan Branch of Ningxia Academy of Agriculture and Forestry Sciences, 756000 Guyuan, China.
³ College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China.
⁴ College of Life Sciences, Northwest A&F University, 712100 Yangling, China.
⁵ College of Animal Science and Technology, Huazhaong Agricultural University, Wuhan, Hubei 430070, China.
⁶ Department of Animal Science and Aquaculture, Dalhousie University, Canada.
⁷ College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China; National Beef Cattle Improvement Center of Northwest A&F University, Yangling 712100, China. Electronic address: zanlinsen@163.com.

PMID: 29496553
DOI: 10.1016/j.gene.2018.02.059

Abstract

The sine oculis homeobox homolog 4 (SIX4) gene belongs to the SIX gene family, which plays a critical role in muscle regeneration and early stages of ontogeny. This study aimed to detect promoter variations of bovine SIX4 genes in Qinchuan cattle, and to evaluate the effect of transcription regulations and body measurement traits. Quantitative real-time PCR (qPCR) results showed that the mRNA expression levels of SIX4 gene were found significantly highest in longissimus thoracis tissue and individual before attaining the stage of physiological maturity. Using sequencing technology on a total of 428 Qinchuan cattle, seven single nucleotide polymorphisms (SNPs) were identified in the promoter region of SIX4, and seven haplotypes representing 18 potential transcription factor compositions of polymorphic potential cis-acting elements. Association analysis indicated that the H₃-H₃ diplotype performed greater withers height, chest depth, chest circumference, back fat thickness and ultrasound loin muscle area (P < 0.05) than H₅-H₆, which were consistent with the promoter activity of Hap3 haplotype was higher than the Hap5 and Hap6 haplotype in vitro. These potential transcription factor information and combined genotypes H₃-H₃ of the SIX4 gene can be used as a molecular marker for selection of economic traits in Qinchuan cattle.

Keywords: Body measurement traits; Qinchuan cattle; SIX4 gene promoter; SNPs.

MeSH terms

Animals
Body Size / genetics*
Body Weights and Measures
Cattle / genetics*
Cells, Cultured
Female
Genes, Homeobox
Genetic Association Studies
Homeodomain Proteins / genetics*
Linkage Disequilibrium
Male
Mice
Phenotype
Polymorphism, Single Nucleotide*
Promoter Regions, Genetic*
Quantitative Trait, Heritable*
Selection, Genetic
Selective Breeding
Transcription, Genetic

Substances

Homeodomain Proteins