Identification of quantitative trait loci and associated candidate genes for pregnancy success in Angus – Brahman crossbred heifers
Data files
Sep 14, 2023 version files 132.77 KB
-
GWAS_phenotypes_QH_2.9.23.xlsx
-
README.md
Abstract
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.
README: 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.