Growth Endocrine Axis and Bovine Chromosome 5: Association of SNP Genotypes and Reproductive Phenotypes in an Angus, Brahman and Romosinuano Diallele

The growth endocrine axis influences reproduction. A QTL associated with enhanced ovulation exists on chromosome 5 in cattle and there are 6 genes underlying this region involved in the mechanisms of GH action. Resequencing exons, 5’ and 3’ untranslated regions and conserved non-coding regions of these genes in a multibreed resource population revealed 75 SNP usable for genotype to phenotype association studies. In the current study, phenotypes included age at first calving, calving interval, days to calving, and pregnancy rate. Data were collected from developing heifers (n = 650) of a diallele composed of Angus, Brahman, and Romosinuano breeds. A SNP in the promoter of the signal transducer and activator of transcription (STAT)2 gene, which is a second messenger of GH, had minor allele frequency \u3e 10% across the three breeds. This SNP did not deviate from Hardy- Weinberg equilibrium (X2 = 1.00, P \u3e 0.31), so deemed useful for genotype to phenotype association analyses. Since the remaining SNP appeared to predict breed, they were used to correct for population stratification using STRUCTURE, which revealed three distinctive ancestral clusters. No significant association was detected between the STAT2 genotype and reproductive traits in mixed effects analyses using genotype as a fixed term, sire as a random term, and coefficient of ancestry as a covariate; however, the interaction of SNP genotype and ancestral cluster was associated with the traits days to calving (P \u3c 0.05) and calving interval (P \u3c 0.10). Interaction plots revealed a higher estimated effect of heterozygous genotype in cluster 1 (inferred primarily from Brahman) and lower estimates in clusters 2 and 3 (inferred primarily from Bos taurus). The heterozygous genotype extended these trait levels ~100 d. A SNP in the promoter of the STAT2 gene was associated with fertility trait levels in admixed cows of the breeds Angus, Brahman, and Romosinuano. The effect appeared to be a non-additive genetic relationship as heterozygous genotype extended levels of traits indicative of postpartum rebreeding

Growth Endocrine Axis and Bovine Chromosome 5: Association of SNP Genotypes and Reproductive Phenotypes in an Angus, Brahman and Romosinuano Diallele

The growth endocrine axis influences reproduction. A QTL associated with enhanced ovulation exists on chromosome 5 in cattle and there are 6 genes underlying this region involved in the mechanisms of GH action. Resequencing exons, 5’ and 3’ untranslated regions and conserved non-coding regions of these genes in a multibreed resource population revealed 75 SNP usable for genotype to phenotype association studies. In the current study, phenotypes included age at first calving, calving interval, days to calving, and pregnancy rate. Data were collected from developing heifers (n = 650) of a diallele composed of Angus, Brahman, and Romosinuano breeds. A SNP in the promoter of the signal transducer and activator of transcription (STAT)2 gene, which is a second messenger of GH, had minor allele frequency \u3e 10% across the three breeds. This SNP did not deviate from Hardy- Weinberg equilibrium (X2 = 1.00, P \u3e 0.31), so deemed useful for genotype to phenotype association analyses. Since the remaining SNP appeared to predict breed, they were used to correct for population stratification using STRUCTURE, which revealed three distinctive ancestral clusters. No significant association was detected between the STAT2 genotype and reproductive traits in mixed effects analyses using genotype as a fixed term, sire as a random term, and coefficient of ancestry as a covariate; however, the interaction of SNP genotype and ancestral cluster was associated with the traits days to calving (P \u3c 0.05) and calving interval (P \u3c 0.10). Interaction plots revealed a higher estimated effect of heterozygous genotype in cluster 1 (inferred primarily from Brahman) and lower estimates in clusters 2 and 3 (inferred primarily from Bos taurus). The heterozygous genotype extended these trait levels ~100 d. A SNP in the promoter of the STAT2 gene was associated with fertility trait levels in admixed cows of the breeds Angus, Brahman, and Romosinuano. The effect appeared to be a non-additive genetic relationship as heterozygous genotype extended levels of traits indicative of postpartum rebreeding

Long-term forage and cow-calf performance and economic considerations of two stocking levels on chihuahuan desert rangeland

Forage and cow-calf productivity on two lightly and two conservatively grazed pastures were evaluated over a 15-year period (1997-2011) in the Chihuahuan Desert of south-central New Mexico. Spring-calving Brangus cows were randomly assigned to pastures in January of each year. Pastures were similar in area (1 098 ± 69 ha, mean ± SE) with similar terrain and distance to water. Utilization of primary forage species averaged 27.1 ± 3.0% in lightly stocked pastures and 39.4 ± 4.0% on conservatively stocked pastures. No differences in perennial grass standing crop (163.5 ± 52.2 kg·ha-1) and calf weaning weights (286.1 ± 2.6 kg) were detected (P > 0.10) between light and conservative treatments. Lightly grazed pastures yielded greater (P < 0.05) kg of calf weaned·ha-1 and calf crop percent than conservatively grazed pastures in 1998 due to complete destocking of conservatively grazed pastures during that slight drought (i.e., rainfall was 75% of normal in 1998). After the initial 5 years of study (1997-2001), all pastures were destocked for 4 years (2002-2005) due to drought as rainfall was only 50% or less of normal. Pastures were then restocked for another 6 years (2006-2011). Postdrought, the percentage change in perennial grass standing forage crop (kg·ha-1) was -4.0 and -14.4 ± 2.5 % (P < 0.09) in the light and conservative grazed pastures across the 6 years, respectively. While conservative stocking rates may provide higher net financial returns than light stocking rates during nondrought years as there were more AU per pasture, potential losses from cattle liquidation during short-term (i.e., 1-year) droughts could nullify this advantage. Results suggest that light grazing use of forage is a practical approach for Chihuahuan Desert cow-calf operations to minimize risk of herd liquidation during short-term drought. © 2015 Society for Range Management. Published by Elsevier Inc. All rights reserved.The Rangeland Ecology & Management archives are made available by the Society for Range Management and the University of Arizona Libraries. Contact [email protected] for further information

SNP detection using RNA-sequences of candidate genes associated with puberty in cattle

Fertility traits, such as heifer pregnancy, are economically important in cattle production systems, and are therefore, used ingenetic selection programs. The aim of this study was to identify single nucleotide polymorphisms (SNPs) using RNA-sequencing (RNA-Seq) data from ovary, uterus, endometrium, pituitary gland, hypothalamus, liver, longissimus dorsi muscle, and adipose tissue in 62 candidate genes associated with heifer puberty in cattle. RNA-Seq reads were assembled to the bovine reference genome (UMD 3.1.1) and analyzed in five cattle breeds; Brangus, Brahman, Nellore, Angus, and Holstein. Two approaches used the Brangus data for SNP discovery 1) pooling all samples, and 2) within each individual sample. These approaches revealed 1157 SNPs. These were compared with those identified in the pooled samples of the other breeds. Overall, 172 SNPs within 13 genes (CPNE5, FAM19A4, FOXN4, KLF1, LOC777593, MGC157266, NEBL, NRXN3, PEPT-1, PPP3CA, SCG5, TSG101, and TSHR) were concordant in the five breeds. Using Ensembl’s Variant Effector Predictor, we determined that 12% of SNPs were in exons (71% synonymous, 29% nonsynonymous), 1% were in untranslated regions (UTRs), 86% were in introns, and 1% were in intergenic regions. Since these SNPs were discovered in RNA, the variants were predicted to be within exons or UTRs. Overall, 160 novel transcripts in 42 candidate genes and five novel genes overlapping five candidate genes were observed. In conclusion, 1157 SNPs were identified in 62 candidate genes associated with puberty in Brangus cattle, of which, 172 were concordant in the five cattle breeds. Novel transcripts and genes were also identified

Genome-wide association studies of female reproduction in tropically adapted beef cattle

Genome-wide association studies (GWAS) are a powerful tool for detecting genomic regions explaining variation in phenotype. The objectives of the present study were to identify or refine the positions of genomic regions affecting milk production, milk components and fertility traits in Canadian Holstein cattle, and to use these positions to identify genes and pathways that may influence these traits