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Background  Female 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.    Results  BTA04 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 –log 10 (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.    Conclusion  Screening 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 material  The online version of this article (doi:10.1186/1471-2164-15-790) contains supplementary material, which is available to authorized users.

Fine mapping QTL for female fertility on BTA04 and BTA13 in dairy cattle using HD SNP and sequence data