Type

Journal Article

Authors

Donagh P. Berry
Francis J Kearney
Ross D Evans
Daniel G Bradley
Deirdre C Purfield

Subjects

Veterinary

Topics
single snp regression cattle calving difficulty perinatal mortlaity genomic association genome wide association study dairy cattle cattle production systems

Genome-wide association study for calving performance using high-density genotypes in dairy and beef cattle (2015)

Abstract BackgroundCalving difficulty and perinatal mortality are prevalent in modern-day cattle production systems. It is well-established that there is a genetic component to both traits, yet little is known about their underlying genomic architecture, particularly in beef breeds. Therefore, we performed a genome-wide association study using high-density genotypes to elucidate the genomic architecture of these traits and to identify regions of the bovine genome associated with them. Results Genomic regions associated with calving difficulty (direct and maternal) and perinatal mortality were detected using two statistical approaches: (1) single-SNP (single nucleotide polymorphism) regression and (2) a Bayesian approach. Data included high-density genotypes on 770 Holstein-Friesian, 927 Charolais and 963 Limousin bulls. Several novel or previously identified genomic regions were detected but associations differed by breed. For example, two genomic associations, one each on chromosomes 18 and 2 explained 2.49 % and 3.13 % of the genetic variance in direct calving difficulty in the Holstein-Friesian and Charolais populations, respectively. Imputed Holstein-Friesian sequence data was used to refine the genomic regions responsible for significant associations. Several candidate genes on chromosome 18 were identified and four highly significant missense variants were detected within three of these genes (SIGLEC12, CTU1, and ZNF615). Nevertheless, only CTU1 contained a missense variant with a putative impact on direct calving difficulty based on SIFT (0.06) and Polyphen (0.95) scores. Using imputed sequence data, we refined a genomic region on chromosome 4 associated with maternal calving difficulty in the Holstein-Friesian population and found the strongest association with an intronic variant in the PCLO gene. A meta-analysis was performed across the three breeds for each calving performance trait to identify common variants associated with these traits in the three breeds. Our results suggest that a portion of the genetic variation in calving performance is common to all three breeds. Conclusion The genomic architecture of calving performance is complex and mainly influenced by many polymorphisms of small effect. We identified several associations of moderate effect size but the majority were breed-specific, indicating that breed-specific alleles exist for calving performance or that the linkage phase between genotyped allele and causal mutation varies between breeds.
Collections Ireland -> Teagasc -> Animal & Bioscience
Ireland -> Teagasc -> Teagasc publications in Biomed Central

Full list of authors on original publication

Donagh P. Berry, Francis J Kearney, Ross D Evans, Daniel G Bradley, Deirdre C Purfield

Experts in our system

1
D P Berry
Teagasc
Total Publications: 243
 
2
Francis Kearney
Teagasc
Total Publications: 9
 
3
R. D. Evans
Teagasc
Total Publications: 44
 
4
Daniel Bradley
Trinity College Dublin
Total Publications: 84
 
5
Deirdre C Purfield
Teagasc
Total Publications: 23