The polygenic nature of fertility, and the reduced ability of common single nucleotide polymorphisms (SNP) to explain a reasonable proportion of the genetic variation, has led to an interest in exploiting whole genome sequence variants for fertility genomic predictions. The objective of this study therefore was to identify whole genome sequence SNPs associated with fertility in multiple breeds; the fertility traits described here were age at first calving and calving interval. Imputation to whole genome sequence was completed using Run6.0 of the 1000 Bulls Genomes Project and predicted transmitting abilities (PTA) on 20,059 multi-breed animals with an effective record contribution ≥1 were used. Whole genomic association analysis was performed using a mixed linear model and the proportion of PTA variance accounted by each chromosome was also estimated. Several genomic regions associated with age at first calving and calving interval were identified when multiple breeds were analysed simultaneously, although stronger genomic associations were identified when breeds were analysed separately. This suggests the existence of breed-specific effects for fertility traits or that the linkage phase between the imputed allele and the causal mutation varies between breeds even at whole genome sequence level. The strongest genomic association (p=1.68 x10-8) identified for age at first calving was an intergenic variant on BTA2. Three genes were located within 500kb of this association (COL5A2, COL3A1 and GULP1), of which the GULP1 gene has been previously identified as a candidate gene for first luteal phase length. Multiple strong associations for calving interval across all breeds were also identified on BTA6, 7 and 23 near quantitative trait loci that have been previously associated with fertility in cattle. Keywords: whole genome sequence, GWAS, fertility, imputation
Proceedings of the World Congress on Genetics Applied to Livestock Production, Volume Biology - Reproduction 2, , 599, 2018
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