DOI: 10.5061/dryad.h70rxwdp5
title: Identification of quantitative trait loci and associated candidate genes for pregnancy success in Angus – Brahman crossbred heifers

description: Development of genomic tools to identify females with high genetic merit
 for reproductive function could increase the profitability and
 sustainability of beef production. Here, genome-wide association studies
 (GWAS) were performed on pregnancy outcome traits from a population of
 Angus – Brahman crossbred heifers. Furthermore, a validation GWAS was
 performed using data from another location. Heifers were genotyped with
 the Bovine GGP F250 array that contains ~250,000 SNPs. In the discovery
 population, heifers were bred in winter breeding seasons involving a
 single round of timed artificial insemination (AI) followed by natural
 mating for three months. Three phenotypes were analyzed: pregnancy outcome
 to first-service AI (PAI; n = 1481), pregnancy status at the end of the
 breeding season (PEBS; n = 1725), and pregnancy score (Pregscore where 1 =
 pregnant to first-service AI, 2 = pregnant to bull, 3 = not pregnant; n
 =1481). The heritability for PAI was estimated as 0.149. One large
 quantitative trait locus (QTL) that explained ~3% of the genetic variation
 for PAI was found on BTA7, in a region containing a cluster of
 γ-protocadherin genes and SLC25A2. Other QTLs explaining between 0.5-1% of
 the genetic variation were found on BTA12 and 25. The heritability of PEBS
 was estimated at 0.122. A large QTL on BTA7 was synonymous with the QTL
 for PAI, with minor QTL located on BTA5, 9, 10, 11, 19, and 20. Estimated
 heritability for Pregscore was 0.189. There was a large QTL on BTA7
 synonymous with the other two traits as well as smaller QTLs on BTA1, 10,
 15, 18, 19, and 20. The validation population for pregnancy status at the
 end of the breeding season were Angus-Brahman crossbred heifers bred by
 natural mating. In concordance with the discovery population, the large
 QTL on BTA7 and QTL on BTA10, 12 and 18 were identified. In summary, QTL
 and candidate SNPs associated with pregnancy outcomes in beef heifers were
 identified, including a large QTL associated with a group of protocadherin
 genes. Confirmation of these associations with larger populations could
 lead to the development of genomic estimates of reproductive function in
 beef cattle.
description: # Identification of quantitative trait loci and associated candidate genes
 for pregnancy success in Angus – Brahman crossbred heifers --- Data are
 individual values for the following traits of Angus - Brahman crossbred
 heifers: * Animal ID, Population * Replicate * Weight 5 Months Before
 Breeding (lb) * Pregnancy Score * Pregnant to First-Service AI (yes or no)
 * Pregnant at End of Breeding Season (yes or no) * Brahman Percentage Data
 are coded as follows: Pregnancy Score key 1= pregnant to first-service AI
 2= pregnant to bull 3= not pregnant at end of breeding season PAI/PEBS key
 1= pregnant 0= not pregnant Population key 1= Discovery population 2=
 Validation population ## Description of the data and file structure These
 data are phenotypes of 2730 heifers arranged in columns in an Excel file.
 SNP genotypes of these animals will be deposited in the European Variation
 Archive. ## Sharing/Access information The link to SNP data will be
 provided when available and will also be included in the final
 publication. * Data was derived from the following sources: * Research
 data collected from cooperating ranches in Florida by University of
 Florida researchers.