Polymorphisms in the 5' upstream region of the CXCR1 chemokine receptor gene, and their association with somatic cell score in Holstein cattle in Canada.

Identification of regulatory elements in 5' regions of chemokine genes is fundamental for understanding chemokine gene expression in response to infection diseases. The CXCR1 receptor is expressed on the surface of neutrophils and interacts primarily with CXCL8 (IL-8), the most potent chemoattractant for neutrophils. The aim of this study was to characterize the 5' upstream region (2.1 kb) of the bovine CXCR1 chemokine receptor gene for polymorphism content and to identify in silico potential transcription-factor binding sites. The 5' flanking region was found by mining the NCBI GenBank (www.ncbi.nlm.nih.gov/). A DNA sequence from the whole genome shotgun sequence project with reference number AC150887.4 contained the CXCR1 5' flanking sequence. Computer analysis revealed potential binding sites for the transcription factors nuclear factor kappaB (NF-kappaB), binding factor GATA-1, barbiturate inducible element (Barbie), nuclear factor of activated T-cells, and activator protein 1. Polymorphism discovery in this region was conducted by constructing an inclusive DNA pool including 2 phenotypic extreme groups, 20 bulls with high estimated breeding values (EBV) for somatic cell score (SCS), and 20 bulls with low EBV for SCS. Independent amplicons along the 5' flanking region of bovine CXCR1 were generated for polymorphism discovery by sequencing. Three novel single nucleotide polymorphisms (SNP), CXCR1c.-344T>C, CXCR1c.-1768T>A, and CXCR1c.-1830A>G, and a previously identified SNP in the coding region, CXCR1c.777G>C, were identified. The 4 SNP were genotyped in Canadian Holstein bulls (n = 338) using tetra-primer amplification refractory mutation system (ARMS)-PCR. Average allele substitution effects were estimated to investigate associations between the 4 SNP and EBV for SCS in first, second, and third and later lactations. Multiple trait analysis revealed that the SNP CXCR1c.-1768T>A was associated with EBV for SCS in the first and second lactations and over all 3 lactations. Haplotype analysis substantiated this association with EBV for SCS in the first lactation. Given the location of SNP CXCR1c.-1768T>A and the surrounding potential binding recognition sequences for NF-kappaB, GATA-1, and Barbie transcription-factors, this SNP may be implicated in gene regulation and warrants further research.