The ability of livestock to reproduce efficiently is critical to the sustainability of animal agriculture. Antral follicle count (AFC) and reproductive tract scores (RTS) can be used to estimate fertility in beef heifers, but the genetic mechanisms influencing variation in these measures are not well understood. Two genome-wide association studies (GWAS) were conducted to identify the significant loci associated with these traits. In total, 293 crossbred beef heifers were genotyped on the Bovine GGP 50K chip and genotypes were imputed to 836,121 markers. A GWAS was performed with the AFC phenotype for 217 heifers with a multi-locus mixed model, conducted using the year, age at time of sampling and principal component analysis groupings as the covariates. The RTS GWAS was performed with 289 heifers using an additive correlation/trend test comparing prepubertal to pubertal heifers. The loci on chromosomes 2, 3 and 23 were significant in the AFC GWAS and the loci on chromosomes 2, 8, 10 and 11 were significant in the RTS GWAS. The significant region on chromosome 2 was similar between both analyses. These regions contained genes associated with cell proliferation, transcription, apoptosis and development. This study proposes candidate genes for beef cattle fertility, although future research is needed to elucidate the precise mechanisms.
As whole genome sequence (WGS) data sets have become abundant and widely available, so has the need for variant detection and scoring. The aim of this study was to compare the accuracy of commonly used variant calling programs, Freebayes and GATK HaplotypeCaller (GATK-HC), and to use U.S. sheep WGS data sets to identify novel breed-associated SNPs. Sequence data from 145 sheep consisting of 14 U.S. breeds were filtered and biallelic single nucleotide polymorphisms (SNPs) were retained for genotyping analyses. Genotypes from both programs were compared to each other and to genotypes from bead arrays. The SNPs from WGS were compared to the bead array data with breed heterozygosity, principal component analysis and identifying breed associated SNPs to analyze genetic diversity. The average sequence read depth was 2.78 reads greater with 6.11% more SNPs being identified in Freebayes compared to GATK-HC. The genotype concordance of the variant callers to bead array data was 96.0% and 95.5% for Freebayes and GATK-HC, respectively. Genotyping with WGS identified 10.5 million SNPs from all 145 sheep. This resulted in an 8% increase in measured heterozygosity and greater breed separation in the principal component analysis compared to the bead array analysis. There were 1,849 SNPs identified in only the Romanov sheep where all 10 rams were homozygous for one allele and the remaining 135 sheep from 13 breeds were homozygous for the opposite allele. Both variant calling programs had greater than 95% concordance of SNPs with bead array data, and either was suitably accurate for ovine WGS data sets. The use of WGS SNPs improved the resolution of PCA analysis and was critical for identifying Romanov breed-associated SNPs. Subsets of such SNPs could be used to estimate germplasm composition in animals without pedigree information.
The anthelmintic resistance of gastrointestinal nematodes (GINs) poses a significant threat to sheep worldwide, but genomic selection can serve as an alternative to the use of chemical treatment as a solution for parasitic infection. The objective of this study is to conduct genome-wide association studies (GWASs) to identify single nucleotide polymorphisms (SNPs) in Rambouillet (RA) and Dorper × White Dorper (DWD) lambs associated with the biological response to a GIN infection. All lambs were genotyped with a medium-density genomic panel with 40,598 markers used for analysis. Separate GWASs were conducted using fecal egg counts (FECs) from lambs (<1 year of age) that acquired their artificial infections via an oral inoculation of 10,000 Haemonchus contortus larvae (n = 145) or naturally while grazing on pasture (n = 184). A GWAS was also performed for packed cell volume (PCV) in artificially GIN-challenged lambs. A total of 26 SNPs exceeded significance and 21 SNPs were in or within 20 kb of genes such as SCUBE1, GALNT6, IGF1R, CAPZB and PTK2B. The ontology analysis of candidate genes signifies the importance of immune cell development, mucin production and cellular signaling for coagulation and wound healing following epithelial damage in the abomasal gastric pits via H. contortus during GIN infection in lambs. These results add to a growing body of the literature that promotes the use of genomic selection for increased sheep resistance to GINs.
Gastrointestinal nematodes (GIN) are detrimental to the health and productivity of sheep across the world, necessitating genetic selection for improved GIN resistance. In this study, we used genomic analyses across- and within- two important breeds in the United States (US), Rambouillet and Dorper, to investigate physiological mechanisms associated with GIN resistance. Genomic data were evaluated from two experiments where lambs were challenged with GIN, either in a natural environment or artificially. Lambs were genotyped with the Axiom™ Ovine Genotyping Array (50K) with 42,608 single nucleotide polymorphisms (SNP) remaining following quality control for minor allele frequency and variant call rate. In experiment 1, a fecal egg count (FEC) was collected from four- to eight-month-old Dorper and Rambouillet lambs (n=188 total) exposed to GIN on pasture. Using Plink v1.9, a genome-wide association study (GWAS) identified significant SNP (P < 6.0e-5) associated with either an increase or decrease of FEC on chromosomes 1, 2, 3, 4, 12, 15 and 20. In Experiment 2, Rambouillet lambs (n=77) were inoculated with 10,000 Haemonchus contortus L3 larvae and FEC and packed-cell volume (PCV) were recorded. An ensuing GWAS identified significant SNP (P < 2.0e-5) on chromosomes 1, 2, 3, 5, 7, 16, 17 and 23 associated with high and low FEC and SNP on chromosome 10 associated with decreased PCV. Multiple genes were in proximity to the identified SNP, including PIK3 subunits in both experiments. Pathway analysis of reported genes, including PIK3, IMP4, NDST3, MRPL22, HSPA2, TGFA, TGFBR1 and RUNX1 revealed involvement in tissue repair, T-cell differentiation and cytokine signaling in Rambouillet and Dorper sheep more resistant to GIN. Results from this study contribute to the genetic underpinnings of host response to GIN in two important breeds in the US, providing a foundation for future selection of animals more resistant to H. contortus infection.
Rangeland is a valuable resource that can allow producers to cost effectively provide nutrients for grazing cattle. However, grazing behavior of cattle is adversely affected when the temperature humidity index is greater than 72. It is possible to select cattle that exhibit efficient grazing behavior even under mild heat stress. This study evaluated genetic associations with grazing behavior to help producers identify cows that will effectively use their rangeland pastures. Using genome-wide associations, this study identified single nucleotide polymorphisms (SNPs) associated with grazing time, walking time and max slope that cattle utilized while experiencing mild heat load. Data were collected from Angus X Hereford 2-year-old beef cows from UI herd over two years (37 grazing and walking minutes, 38 max slope). Genotypes were obtained using a Bovine GGP 50K SNP marker array and 41,686 markers were used in the analyses. Two SNPs on chromosome 11 are significantly (P = 5.01e-7, P = 6.46e-7) associated with grazing minutes and explain 0.52 proportion of variance (PVE). A SNP on chromosome 3 is significant for walking minutes (P=1.91e-6) with a PVE of 0.48. Additionally, a SNP on chromosome 14 is significantly (P = 8.50e-6) associated with max slope and has a PVE of 0.43. This ongoing project identified significant associations with grazing and walking minutes and maximum slope. This research will be strengthened with the addition of more animals over successive years. Some cattle spend more time grazing, walking, or at a higher elevation in mild heat load. Identifying genetic variants associated with grazing time, walking time, and maximum slope use while under heat stress can enable producers to select for cattle that best fit the rangeland available to them.
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