Abstract
BackgroundFemale fertility is important for the maintenance of the production in a dairy cattle herd. Two QTL regions on BTA04 and on BTA13 previously detected in Nordic Holstein (NH) and validated in the Danish Jersey (DJ) and Nordic Red (NR) were investigated further in the present study to further refine the QTL locations. Refined QTL regions were imputed to the full sequence data. The genes in the regions were then studied to ascertain their possible effect on fertility traits.ResultsBTA04 was screened for number of inseminations (AIS), 56-day non-return rate (NRR), days from first to last insemination (IFL), and the interval from calving to first insemination (ICF) in the range of 38,257,758 to 40,890,784 bp, whereas BTA13 was screened for ICF only in the range from 21,236,959 to 46,150,079 with the HD bovine SNP array for NH, DJ and NR. No markers in the DJ and NR breeds reached significance. By analyzing imputed sequence data the QTL position on BTA04 was narrowed down to two regions in the NH. In these two regions a total of 9 genes were identified. BTA13 was analyzed using sequence data for the NH breed. The highest –log10(P-value) was 19.41 at 33,903,159 bp. Two regions were identified: Region 1: 33,900,143-33,908,994 bp and Region 2: 34,051,815-34,056,728 bp. SNPs within and between these two regions were annotated as intergenic.ConclusionScreening BTA04 and BTA13 for female fertility traits in NH, NR and DJ suggested that the QTL for female fertility were specific for NH. A missense mutation in CD36 showed the strongest association with fertility traits on BTA04. The annotated SNPs on BTA13 were all intergenic variants. It is possible that BTA13 at this stage is poorly annotated such that the associated polymorphisms are located in as-yet undiscovered genes. Fertility traits are complex traits as many different biological and physiological factors determine whether a cow is fertile. Therefore it is not expected that there is a simple explanation with an obvious candidate gene but it is more likely a network of genes and intragenic variants that explain the variation of these traits.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-790) contains supplementary material, which is available to authorized users.
Highlights
Female fertility is important for the maintenance of the production in a dairy cattle herd
HD single nucleotide polymorphisms (SNPs) analysis BTA04 and BTA13 were screened with the bovine HD SNP array in the Nordic Holstein (NH), Nordic Red (NR) and Danish Jersey (DJ) breeds, based on the positions on the genome which were chosen due to high significance from Höglund et al [6]
BTA04 was screened for NRRH, IFLH, NRRC, ICF, IFLC, AISH, AISC in a 2,633,026 bp region spanning positions 38,257,758 to 40,890,784 bp (Figure 1: left), whereas BTA13 was screened for ICF only, in the region ranging from 21,236,959 to 46,150,079 bp (Figure 2: left)
Summary
Female fertility is important for the maintenance of the production in a dairy cattle herd. Most of the genetic variants detected by these studies are not causal for the traits themselves. Instead they are in linkage disequilibrium (LD) with the causal polymorphisms. Most GWAS studies in cattle have used data from one breed only In most cases this has been the Holstein Friesian (HF) where the largest datasets are available. The low effective population size in HF has resulted in long-range LD [2,3]. This limits the studies’ ability to distinguish between causal factors and markers in strong LD with causal factors.
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