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

Orexin is an important neuropeptide that influences livestock's appetite and food intake and is closely related with livestock's growth and development. The variations in the orexin gene 5′ regulatory region might have an influence on the gene expression. Based on the hypothesis, five overlapped fragments including 1 794 bp of orexin gene 5′ regulatory region were investigated for single nucleotide polymorphisms (SNPs) by PCR-SSCP and DNA sequencing in three indigenous cattle populations. A total of five SSCP patterns observed revealed ten SNPs in the region. Two SSCP patterns genotypes (A and B) were exhibited in 0-2 fragment and three (A, B and C) were found in 0-5 fragment. 0-2 contained four SNPs, viz., −583 T>C, −479 OT, −474 A>T, and −451 A>G. In another lous 0-5, six SNPs were identified (-1 610 OG, −1 585 G>A, −1 550 T>C, −1 548 A>C, −1 438 OT, and −1 431 OA). Seven SNPs were found in transcription factor binding sites and four out of them existed in the core sequences. The SNPs at −479, −474 and −451 did not change the putative recognition core sequences of their factors. But the mutation at −583 changed the binding sequence of EVI1 into NFA and created one new binding site for ZFHX simultaneously. In three populations, the frequencies of A, B and C genotypes of 0-2 were 0.2367, 0.4842 and 0.2791, respectively. And the A pattern of 0-5 was preponderant (0.7549) and the other B pattern was not (0.2451). But the frequencies of different SSCP variants varied across three cattle populations. B genotype in 0-2 had significant associations to body weight (BW) and daily weight gain (DWG) in Nanyang cattle 6- and 12-mon aged and might serve as one potential candidate genetic marker for growth and development.