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Background  Neuropeptide Y is a key neurotransmitter of the central nervous system which plays a vital role in the feed energy homeostasis in mammals. Mutations in the regulatory and coding regions of the bovine  NPY  gene can potentially affect the neuronal regulation of appetite and feeding behaviour in cattle. The objectives of this experiment were to: a) fully characterize the bovine  NPY  gene transcript and b) identify the SNP diversity in both coding and non-coding regions of the  NPY  gene in a panel of  Bos taurus  and  B. indicus  cattle.    Results  Bovine  NPY  gene consists of four exons (99, 188, 81 and 195 nucleotides) and three introns. The promoter region of the  NPY  gene consists of TATA and GC boxes which are separated from the transcription start site (TSS) by 29 and ~100 nt, respectively. Analyses of the tissue specific expression of the bovine  NPY  gene revealed the presence of highly abundant  NPY  gene transcripts in the arcuate nucleus, cerebral and cerebellar regions of the bovine brain. We identified a total of 59 SNPs in the 8.4 kb region of the bovine  NPY  gene. Seven out of nine total SNPs in the promoter region affect binding of putative transcription factors. A high level of nucleotide diversity was evident in the promoter regions (2.84 × 10 -3 ) compared to the exonic (1.44 × 10 -3 ), intronic (1.30 × 10 -3 ) and 3' untranslated (1.26 × 10 -3 ) regions.    Conclusion  The SNPs identified in different regions of bovine  NPY  gene may serve as a basis for understanding the regulation of the expression of the bovine  NPY  gene under a variety of physiological conditions and identification of genotypes with high feed energy conversion efficiency.

Mapping of the transcription start site (TSS) and identification of SNPs in the bovine neuropeptide Y (NPY) gene