Abstract
Heifer conception rate (HCR) is defined as the percentage of inseminated heifers that become pregnant at each service. The genome-wide association analyses in this study focused on identifying the loci associated with Holstein heifer (n = 2013) conception rate at first service (HCR1) and the number of times bred (TBRD) to achieve a pregnancy. There were 348 unique loci associated (p < 5 × 10−8) with HCR1 and 615 unique loci associated (p < 5 × 10−8) with TBRD. The two phenotypes shared 302 loci, and 56 loci were validated in independent cattle populations. There were 52 transcription factor binding sites (TFBS) and 552 positional candidate genes identified in the HCR1- and TBRD-associated loci. The positional candidate genes and the TFBS associated with HCR1 and TBRD were used in the ingenuity pathway analysis (IPA). In the IPA, 11 pathways, 207 master regulators and 11 upstream regulators were associated (p < 1.23 × 10−5) with HCR1 and TBRD. The validated loci associated with both HCR1 and TBRD make good candidates for genomic selection and further investigations to elucidate the mechanisms associated with subfertility and infertility.
Highlights
The United States dairy industry has struggled with subfertility since the 1950s
The objectives of this study were to identify (1) the loci associated with heifer conception rate in U.S Holstein heifers; (2) the positional candidate genes and transcription factor binding sites (TFBS) within the associated loci; (3) the potential interactions and functions of the positional candidate genes and regulatory elements of the loci associated with Heifer conception rate (HCR); and (4) the validated loci associated with HCR
This study focused on identifying and analyzing the loci associated with heifer conception rate in U.S Holstein cattle
Summary
The United States dairy industry has struggled with subfertility since the 1950s. Poor reproductive performance leads to decreased productivity and profitability due to elevated veterinary costs, additional inseminations and increased culling rates [1,2]. Due to the importance of fertility, dairy producers use several measures of reproductive performance for cows and heifers. Daughter pregnancy rate, defined as the percentage of a bull’s daughters who become pregnant in a 21-day period, is one of those measures [4]. Another reproductive performance measure is conception rate, defined as the percentage of inseminated cows and heifers that become pregnant at each service. Heifer conception rate (HCR) declined from approximately 60% in 1950 to 52% in the early 2000s [5] This decline is likely due, in part, to selection for production traits without emphasis on selection for fertility traits [6,7,8]
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