Genome-wide association study of infectious bovine keratoconjunctivitis in Angus cattle

Background Infectious Bovine Keratoconjunctivitis (IBK) in beef cattle, commonly known as pinkeye, is a bacterial disease caused by Moraxella bovis. IBK is characterized by excessive tearing and ulceration of the cornea. Perforation of the cornea may also occur in severe cases. IBK is considered the most important ocular disease in cattle production, due to the decreased growth performance of infected individuals and its subsequent economic effects. IBK is an economically important, lowly heritable categorical disease trait. Mass selection of unaffected animals has not been successful at reducing disease incidence. Genome-wide studies can determine chromosomal regions associated with IBK susceptibility. The objective of the study was to detect single-nucleotide polymorphism (SNP) markers in linkage disequilibrium (LD) with genetic variants associated with IBK in American Angus cattle. ResultsThe proportion of phenotypic variance explained by markers was 0.06 in the whole genome analysis of IBK incidence classified as two, three or nine categories. Whole-genome analysis using any categorisation of (two, three or nine) IBK scores showed that locations on chromosomes 2, 12, 13 and 21 were associated with IBK disease. The genomic locations on chromosomes 13 and 21 overlap with QTLs associated with Bovine spongiform encephalopathy, clinical mastitis or somatic cell count. ConclusionsResults of these genome-wide analyses indicated that if the underlying genetic factors confer not only IBK susceptibility but also IBK severity, treating IBK phenotypes as a two-categorical trait can cause information loss in the genome-wide analysis. These results help our overall understanding of the genetics of IBK and have the potential to provide information for future use in breeding schemes

Whole genome analysis of infectious bovine keratoconjunctivitis in Angus cattle using Bayesian threshold models

Infectious bovine keratoconjunctivitis (IBK), also known as pinkeye, is characterized by damage to the cornea and is an economically important, lowly heritable, categorical disease trait in beef cattle. Scores of eye damage were collected at weaning on 858 Angus cattle. SNP genotypes for each animal were obtained from BovineSNP50 Infinium-beadchips. Simultaneous associations of all SNP with IBK phenotype were determined using Bayes-C that treats SNP effects as random with equal variance for an assumed fraction (π=0.999) of SNP having no effect on IBK scores. Bayes-C threshold models were used to estimate SNP effects by classifying IBK into two, three or nine ordered categories. Magnitudes of genetic variances estimated in localized regions across the genome indicated that SNP within the most informative regions accounted for much of the genetic variance of IBK and pointed out some degree of association to IBK. There are many candidate genes in these regions which could include a gene or group of genes associated with bacterial disease in cattle

Cyberinfrastructure for Life Sciences - iAnimal Resources for Genomics and Other Data Driven Biology

Whole genome sequence, SNPs, copy number variation, phenotypes and other “-omics” data underlie evidence-based estimations of breeding value. Unfortunately, the computational resources (data storage, high-performance computing, analysis pipelines, etc.) that exploit this knowledge are limited in availability – many investigations are therefore restricted to the commercial sector or well-funded academic programs. Cyberinfrastructure developed by the iPlant Collaborative (NSF-#DBI0735191) and its extension iAnimal (USDA-#2013-67015-21231) provides the animal breeding community a comprehensive and freely available platform for the storage, sharing, and analyses of large datasets – from genomes to phenotype data. iPlant/iAnimal tools support a variety of genotype-phenotype related analyses in a platform that accommodates every level of user – from breeder to bioinformatician. These tools have been used to develop scalable, accessible versions of common workflows required for applying sequencing to livestock genomics

Quantitative Trait Locus on Sus scrofa Chromosome 4 Associated with Host Response to Experimental Infection with Porcine Reproductive and Respiratory Syndrome Virus

The objective of this study was to conduct a genomewide association study to discover the genetic basis of host response to PRRS virus using data from the PRRS Host Genetics Consortium NPB and PRRS-CAP project. Approximately 1,600 commercial crossbred piglets were experimentally infected with the Porcine Reproductive and Respiratory Syndrome (PRRS) virus. Blood samples and body weights were collected up to 42 days post infection (dpi). Experimental pigs and their parents were genotyped with Illumina’s Porcine 60k BeadChip. Phenotypes analyzed were viral load (VL = area under the curve for log-transformed qRT-PCR based serum virus from 0-21 dpi) and weight gain from 0-42 dpi (WG). Heritabilities estimated using pedigree information were moderate at 0.41 for VL and 0.29 for WG. A 1 Mb region on Sus scrofa chromosome (SSC) 4 was found to be associated with VL and WG and explained a substantial amount of genetic variation. The frequency of the favorable allele for the most significant single nucleotide polymorphism (SNP) was 0.15. These results show that there is a host genetic component to PRRS virus infection and that there is room for genetic improvement