Single Nucleotide Polymorphism (SNP) Analysis of orexin Gene 5´ Regulatory Region in Chinese Indigenous Cattle Populations

• Published in: Journal of Integrative Agriculture Vol. 10; no. 8; pp. 1273 - 1279
• Main Author: ZHANG Ai-ling, ZHANG Li, ZHANG Liang-zhi, LAN Xian-yong, ZHANG Cun-lei, ZHANG Cun-fang, CHEN Hong (School of Agriculture and Biology, Shanghai Jiao Tong University)
• Format: Journal Article
• Language: English
• Published: Science Press 15.08.2011; Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University,Yangling 712100, P.R.China; College of Life Sciences, Xuzhou Normal University, Xuzhou 221000, P.R.China; Guangdong Provincial Key Laboratory ofAgro-Anirmal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, P.R. China%Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University,Yangling 712100, P.R.China; Agricultural College, Guangdong Ocean University, Zhanjiang 524000, P.R. China%Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University,Yangling 712100, P.R.China%College of Life Sciences, Xuzhou Normal University, Xuzhou 221000, P.R.China%Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University,Yangling 712100, P.R.China
• Subjects: orexin gene promoter SNP cattle; promoter; cattle; orexin gene; SNP
• ISSN: 2095-3119; 2352-3425

Orexin is an important neuropeptide that influences livestock’s appetite and food intake and is closely related withlivestock’s growth and development. The variations in the orexin gene 5´ regulatory region might have an influence onthe gene expression. Based on the hypothesis, five overlapped fragments including 1 794 bp of orexin gene 5´ regulatoryregion were investigated for single nucleotide polymorphisms (SNPs) by PCR-SSCP and DNA sequencing in threeindigenous cattle populations. A total of five SSCP patterns observed revealed ten SNPs in the region. Two SSCP patternsgenotypes (A and B) were exhibited in O-2 fragment and three (A, B and C) were found in O-5 fragment. O-2 contained fourSNPs, viz., -583 T>C, -479 C>T, -474 A>T, and -451 A>G. In another lous O-5, six SNPs were identified (-1 610 C>G,-1 585 G>A, -1 550 T>C, -1 548 A>C, -1 438 C>T, and -1 431 C>A). Seven SNPs were found in transcription factor bindingsites and four out of them existed in the core sequences. The SNPs at -479, -474 and -451 did not change the putativerecognition core sequences of their factors. But the mutation at -583 changed the binding sequence of EVI1 into NFA andcreated one new binding site for ZFHX simultaneously. In three populations, the frequencies of A, B and C genotypesof O-2 were 0.2367, 0.4842 and 0.2791, respectively. And the A pattern of O-5 was preponderant (0.7549) and the other Bpattern was not (0.2451). But the frequencies of different SSCP variants varied across three cattle populations. Bgenotype in O-2 had significant associations to body weight (BW) and daily weight gain (DWG) in Nanyang cattle 6- and12-mon aged and might serve as one potential candidate genetic marker for growth and development.