Interleukin-8 haplotype structure from nucleotide sequence variation in commercial populations of US beef cattle

The aim of the present study was twofold: first, to design a panel of 96 si res that reflects the breadth of genetic diversity in U.S. beef cattle, and second, to use this panel to discover nucleotide sequence diversity and ha plotype structures of interleukin (IL)-8 in commercial populations. The lat ter is a requisite for epidemiological studies designed to test whether IL8 alleles are risk factors for acquiring or maintaining bacterial infections in production environments. IL-8 encodes a proinflammatory cytokine that p lays a central role in cell-mediated immunity by attracting and activating neutrophils in the early stages of host defense against bacterial invasion. Seven single-nucleotide polymorphism (SNP) markers were identified by sequ encing two IL8 DNA segments amplified from the panel of 17 popular cattle b reeds (MARC beef cattle diversity panel, version 2.1). Assays for automated genotype scoring by matrix-assisted laser desorption/ ionization time-of-f light mass spectrometry (MALDI-TOF MS) were developed to independently veri fy the seven SNP alleles in the 96 bulls and 313 cattle from the MARC refer ence population. Five haplotype structures, spanning the two IL8 DNA segmen ts, were unambiguously defined for the set of seven IL8 SNPs. Based on the breadth of germplasm in bovine diversity panel, the five haplotype structur es for IL8 are estimated to represent >98% of those present in these DNA se gments in commercial populations of U.S. beef cattle. The frequencies of th e five respective haplotypes in the eight Angus sires of the diversity pane l (0.75, 0.25. 0.00, 0.00, 0.00) were similar to those scored in 150 purebr ed Angus cattle from six herds in four Midwestern states (0.82, 0.18, 0.01, 0.00, 0.00), suggesting that the diversity panel may also be useful for es timating allele frequencies in commercial populations.