Uncovering the architecture of selection in two Bos taurus cattle breeds

Selection alters the genome via hard sweeps, soft sweeps, and polygenic selection. However, mapping polygenic selection is difficult because it does not leave clear signatures on the genome like a selective sweep. In populations with temporally-stratified genotypes, the Generation Proxy Selection Mapping (GPSM) method identifies variants associated with generation number (or appropriate proxy) and thus variants undergoing directional allele frequency changes. Here, we use GPSM on two large datasets of beef cattle to detect associations between an animal's generation and 11 million imputed SNPs. Using these datasets with high power and dense mapping resolution, GPSM detected a total of 294 unique loci actively under selection in two cattle breeds. We observed that GPSM has a high power to detect selection in the very recent past (< 10 years), even when allele frequency changes are small. Variants identified by GPSM reside in genomic regions associated with known breed characteristics, such as fertility and maternal ability in Red Angus and carcass merit and coat color in Simmental. Over 60% of the selected loci reside in or near (<50 kb) annotated genes. Additionally, 36% of selected loci overlap known epigenetic marks or putative functional genomic regions. Using RAiSD and nSL, we identify hundreds of putative selective sweeps; however, these sweeps have little overlap with polygenic selected loci. This makes GPSM a complementary approach to sweep detection methods when temporal genotype data are available. The selected loci that we identify across methods demonstrate the complex architecture of selection in domesticated cattle.

Frame Score, Grazing and Delayed Feedlot Entry Effect on Performance and Economics of Beef Steers from Small- and Large-Framed Cows in an Integrated Crop-Livestock System

When selling small-framed steers at weaning, profitability is diminished. The hypothesis is that by using a vertically integrated business model that includes retained ownership, extended grazing, abbreviated feedlot finishing, and selling at slaughter, profitability would increase. Crossbred yearling steers (n = 288) from small size Aberdeen Angus (Lowline) × Red Angus × Angus × Angus cows and moderate to large size Red Angus × Angus × Simmental × Gelbvieh cows calved May−June were randomly assigned (complete randomized design), in a 3 y study, to feedlot control (FLT) and extended grazing (GRZ) frame score treatment groups. Mean frame score for FLT were small frame (SF) 3.82 and large frame (LF) 5.63, and for GRZ, SF: 3.77 and LF: 5.53. Least-square means were utilized to identify levels of effects and to control family-wise error adjusted with Tukey test. The FLT control steers were housed in the feedlot and fed growing diets and subsequently high energy corn-based diets for 218 days. The GRZ steers grazed a sequence of forages (native range, field pea-barley mix, and unharvested corn) for 212 days and then were transferred to the feedlot and fed high energy corn-based finishing diets for 82 days. The SF GRZ steers grew more slowly grazing native range and annual forages compared to GRZ LF steers, but SF steer grazing cost per kg of gain was reduced 7.80%. Grazing steers did not grow to their full genetic potential. Slower growth during grazing allowed LF and SF steers to grow structurally before feedlot entry creating a compensatory feedlot finishing growth response. Overall, grazing steer performance exceeded steer performance of the FLT control treatment and LF grazing steers had the highest rate of gain, and lowest feed cost per kg of gain. The GRZ steer feedlot days on feed were reduced 136 days and total feed intake was reduced resulting in LF and SF grazing steer feed cost reductions of 175.9 and 165.3%, respectively. Extended grazing also resulted in LF and SF grazing steer hot carcass weights to be greater than control LF and SF steers and SF grazing steers had greater dressing percent, and marbling score. Carcass quality grade, meat tenderness, and cooking losses were similar. System net returns were highest for LF (USD 911.58), and SF (USD 866.61) grazing steers. Managerial modification combining retained ownership, extended grazing, and delayed feedlot entry increased profitability and eliminated market bias.

Influence of beef genotypes on animal performance, carcass traits, meat quality and sensory characteristics in grazing or feedlot-finished steers

A 2-yr study was conducted to evaluate the effects of beef genotypes and feeding systems on performance, carcass traits, meat quality, and sensory attributes. A 2×2 factorial experiment was used to randomly allocate 60 steers in year 1 (YR1) and 44 steers in year 2 (YR2). The two beef genotypes evaluated were Red Angus (RA), and RA x Akaushi (AK) crossbreed. The steers were allotted to two finishing feeding systems: grazing, a multi-species forage mixture (GRASS) and feedlot finishing, conventional total mixed ration (GRAIN). All steers were slaughtered on the same day, at 26 and 18 mo of age (GRASS and GRAIN, respectively), and carcass data were collected 48 h postmortem. Growth and slaughter characteristics were significantly impacted by the finishing system (P &lt; 0.01), with the best results presented by GRAIN. Beef genotype affected dressing percent (P &lt; 0.01), ribeye area (P = 0.04), and marbling score (P = 0.01). The AK steers had a tendency (P = 0.09) for lower total gain; however, carcass quality scores were greater compared to RA. There was a genotype by system interaction for USDA yield grade (P &lt; 0.01), where it was lower in GRASS compared to GRAIN in both genotypes, and no difference was observed between the two genotypes for any GRASS or GRAIN systems. There was no difference in meat quality or sensory attributes (P &gt; 0.10) between the two genotypes, except that steaks from AK tended to be juicier than RA (P = 0.06). Thawing loss and color variables were impacted by the finishing system (P &lt; 0.01). L* (lightness) and hue angle presented greater values while a* (redness), b* (yellowness), and chroma presented lower values in GRAIN compared to GRASS. Sensory attributes were scored better in GRAIN than GRASS beef (P &lt; 0.01). There was a genotype by system interaction for flavor (P = 0.02), where beef from RA had a lower flavor rating in GRASS than in GRAIN, and no difference was observed for AK. Within each system, no difference was observed for flavor between RA and AK. Beef from steers in GRASS had greater (P &lt; 0.01) WBSF than those from GRAIN. These results indicate that steers from GRAIN had superior performance and carcass merit and that AK enhanced these traits to a greater degree compared to RA. Furthermore, the beef finishing system had a marked impact on the steaks’ sensory attributes and consumer acceptability. The favorable results for texture and juiciness in GRAIN, which likely impacted overall acceptability, may be related to high marbling.

PSXV-28 Late-Breaking: Impact of beef genotypes and finishing systems on beef consumer acceptability and the effect of demographic factors on consumer sensory preferences

Beef genotypes and diets can improve the eating quality and consistency of beef. A 2-yr study was conducted to evaluate the effects of beef genotypes and diet on consumer acceptability of beef. Steaks were from Red Angus (RA) and RA x Akaushi (AK) crossbreed, fed one of two finishing systems: grazing (GRASS) and feedlot (GRAIN). Consumers (n = 105 in each year) evaluated cooked steaks for flavor, tenderness, juiciness, and overall acceptability using a 9-point hedonic scale. Demographical information was collected and used as covariates in the statistical model. There was no difference in sensory attributes (P &gt; 0.05) between the genotypes, except that steaks from AK tended to be juicier than RA (P = 0.06). Sensory attributes were scored better in GRAIN than GRASS beef (P &lt; 0.01) for all variables. There was a genotype by system interaction for flavor (P = 0.02), where beef from RA had a lower flavor rating in GRASS than in GRAIN, and no difference was observed for AK. Demographic effects showed that gender and beef consumption location had significant effects on flavor. Flavor scores were higher for females than males (6.1 vs 5.7, P = 0.02), and higher from consumers who eat beef in restaurants than consumers who do not eat beef in restaurants (6.6 vs 5.3, P &lt; 0.01). Juiciness scores were impacted by the frequency of beef consumption. Panelists who eat beef once every 2–3 weeks rated the steaks juicier than those who eat beef once every 2–3 months (6.5 vs 4.3, P = 0.04), and consumers who eat grass-fed beef twice a year rated the steaks worse than those who eat it less than once a year (P = 0.02). Our results suggest that the beef finishing system had a marked impact on consumer acceptability, and AK might produce meat juicier than RA. Some demographic factors may influence consumer perceptions of beef.

Breed and heterotic effects for mature weight in beef cattle

Mature cow weight (MWT) is heritable and affects the costs and efficiency of a breeding operation. Cow weight is also influenced by the environment, and the relationship between the size and profitability of a cow varies depending on production system. Producers therefore need tools to incorporate MWT in their selection of cattle breeds and herd replacements. The objective of this study was to estimate breed and heterotic effects for MWT using weight-age data on crossbred cows. Cow’s MWT at 6 yr was predicted from the estimated parameter values—asymptotic weight and maturation constant (k)—from the fit of the Brody function to their individual data. Values were obtained for 5,156 crossbred cows from the U.S. Meat Animal Research Center (USMARC) Germplasm Evaluation Program using 108,957 weight records collected from approximately weaning up to 6 yr of age. The cows were produced from crosses among 18 beef breeds. A bivariate animal model was fitted to the MWT and k obtained for each cow. The fixed effects were birth year-season contemporary group, and covariates of direct and maternal breed fractions, direct and maternal heterosis, and age at final weighing. The random effects were direct additive and residual. A maternal additive random effect also was fitted for k. In a separate analysis from that used to estimate breed effects and (co)variances, cow MWT was regressed on sire yearling weight (YWT) EPD by its addition as a covariate to the animal model fitted for MWT. That regression coefficient was then used to adjust breed solutions for sire selection in the USMARC herd. Direct heterosis was 15.3 ± 2.6 kg for MWT and 0.000118 ± 0.000029 d-1 for k. Maternal heterosis was -5.7 ± 3.0 kg for MWT and 0.000130 ± 0.000035 d-1 for k. Direct additive heritabilities were 0.56 ± 0.03 for MWT and 0.23 ± 0.03 for k. The maternal additive heritability for k was 0.11 ± 0.02. The direct additive correlation between MWT and k was negligible (0.08 ± 0.09). Adjusted for sire sampling, Angus was heaviest at maturity of the breeds compared. Deviations from Angus ranged from -8.9 kg (Charolais) to 136.7 kg (Braunvieh). Ordered by decreasing MWT, the breeds ranked Angus, Charolais, Hereford, Brahman, Salers, Santa Gertrudis, Simmental, Maine Anjou, Limousin, Red Angus, Brangus, Chiangus, Shorthorn, Gelbvieh, Beefmaster, and Braunvieh. These breed effects for MWT can inform breeding programs where cow size is considered a key component of overall profitability.

131 Zilpaterol Hydrochloride and Heat Stress Each Alter the Cattle Adipose Transcriptome and Predicted to Alter Molecular Pathways After 21 Days

Heat stress reduces livestock performance while supplementation of beta-adrenergic agonists (βAA) such as zilpaterol hydrochloride (ZH) improve production efficiency; both stimulate lipolysis. The objective of this study was to understand the effects (independent, interacting) of heat stress and ZH on the subcutaneous adipose transcriptome in fed steers. 24 Red Angus steers were assigned to thermoneutral (TN; THI=68) or heat stress (HS; THI=83) conditions and fed no supplement (NS) or ZH (8.33 mg/kg/day) for 21d in a 2x2 factorial. TN steers were pair-fed the HS daily average. Subcutaneous adipose samples were collected at day -3, 3, 10, and 21. RNA was isolated and sequenced using 3’ Tag-Seq reads to a depth of 3.6 million reads/sample. Transcripts were mapped to ARS-UCD1.2 and quantified. After quality control, differential expression (DE) analyses were performed in DESeq2 with a significance threshold (FRD) of 0.05. Pathway analysis was used to explore pathways affected by HS, ZH, and their interaction using DE loci (P &lt; 0.05). The acute phase response signaling pathway was predicted to be activated at 3d, but inhibited at 10d and 21d by the combination of HS and ZH. At multiple time points, inflammatory pathways including those for interferon and IL-8 were predicted to be activated by HS. Mitochondrial function pathways including oxidative phosphorylation, mitochondrial dysfunction, and TCA cycle II were altered by ZH. Adipose centric pathways for phospholipase-C and protein kinase-A signaling were altered by HS/ZH interaction while glycolysis was altered solely by HS. These data support the hypothesis that exposing cattle to HS conditions and ZH supplementation alters the subcutaneous adipose transcriptome, but not necessarily in an additive fashion. These data provide information regarding the supplementation of βAA in heat stress environments, especially if it mediates the effects of HS.

PSV-5 Effect of Breed and Barn Location on Semen Quality at an Artificial Insemination Facility

A better understanding of the factors that influence collection and semen quality for AI sires is needed. Our objectives were to evaluate the effect of breed and environmental factors on semen characteristics from 49,086 ejaculates analyzed by a single technician at a beef semen collection facility. Bulls were housed in one of 5 barns based on health testing and purpose of semen collection. Multiple ejaculate characteristics were evaluated using regression models; fixed effects included breed, age, and barn. Ejaculate volume differed (P &lt; 0.001) between Angus (8.5 ml) and Horned Hereford (7.5 ml). Concentration of spermatozoa was lower (P &lt; 0.001) for Angus compared with Simmental, Charolais, and Horned Hereford (1009, 1100, 1252, and 1197 x 106/ml, respectively). Horned Hereford had greater (P &lt; 0.01) concentration of spermatozoa compared with Red Angus (1197 and 1046 x 106/ml, respectively). Simmental had greater (P &lt; 0.01) pre-freeze motility when compared with Angus, Red Angus, and Horned Hereford (54, 50, 49 and 49%, respectively). Average production of 0.5 CC frozen straws per collection was greater (P &lt; 0.001) for Simmental (244) when compared with Red Angus (205) and Angus (223). Pre-freeze motility (% motile) varied from 48% to 53% between the five barns (P &lt; 0.001). The average concentration of spermatozoa varied from 1000 (x 106/ml) to 1155 (x 106/ml), with Barn 1 producing the lowest per ejaculate (P &lt; 0.001). Bulls in Barn 1 produced a greater amount (P &lt; 0.001) of primary abnormalities than Barn 4 and more (P &lt; 0.001) secondary abnormalities than Barn 3. Overall, Simmental, when compared with Angus bulls, produced the greatest number of straws per collection, with the highest pre-freeze motility. Recognizing breed differences and the effect of barn location may help improve overall efficiency, and producer expectations of semen collection at this facility.

Correlation between L-Lactate Concentrations in Beef Cattle, Obtained Using a Hand-Held Lactate Analyzer and a Lactate Assay Colorimetric Kit

Lactate is a product of anaerobic glycolysis, used in animal research as an indicator of muscle fatigue. Therefore, it has been used as an indicator of cattle response to long distance transportation. The aim of this study was to assess the relationship of L-lactate concentrations measured using a Lactate Scout+ analyzer and a traditional lactate assay colorimetric kit. Blood samples were collected by venipuncture from 96 steers (Black or Red Angus × Hereford/Simmental and Black or Red Angus × Charolais; 247 ± 38.2 kg BW) prior to loading (LO1) and after 36 h of transport, and prior to reloading and after an additional 4 h of road transportation, and on d 1, 2, 3, 5, 14, and 28 after transport. The Lactate Scout+ analyzer strip was dipped in blood at the time of sampling, while blood samples were collected into sodium fluoride tubes for use in the colorimetric analysis. Pearson correlations were calculated to assess the strength of the relationship between the experimental methods for the quantification of L-lactate concentrations. The magnitude and direction of the correlation, and the level of statistical significance varied over the observed time points, ranging from r = −0.03 (p = 0.75; LO1) to r = 0.75 (p < 0.0001; d 3). The correlation for the pooled data was weak but statistically significant (r = 0.33, p < 0.0001). Based on the low magnitude of the correlation due to variability across sampling time points in this study, the Lactate Scout+ analyzer is not a suitable alternative to a lab-based assay (considered the gold standard) for measuring L-lactate in transported cattle.

X-Linked Hypohidrotic Ectodermal Dysplasia in Crossbred Beef Cattle Due to a Large Deletion in EDA

X-linked hypohidrotic ectodermal dysplasia-1 (ECTD1) in people results in a spectrum of abnormalities, most importantly hypotrichosis, anodontia/oligodontia, and absent or defective ectodermally derived glands. Five Red Angus-Simmental calves born over a 6-year period demonstrated severe hypotrichosis and were diagnosed as affected with ECTD1-like syndrome. Two died of severe pneumonia within a week of birth. The skin of three affected calves revealed a predominance of histologically unremarkable small-caliber hair follicles. Larger follicles (>50 µm) containing medullated hairs (including guard and tactile hairs) were largely restricted to the muzzle, chin, tail, eyelids, tragus and distal portions of the limbs and tail. The mean histological density of hair follicles in flank skin of two affected calves was slightly greater than that in two unaffected calves. One affected calf was examined postmortem at 10 days of age to better characterize systemic lesions. Nasolabial, intranasal and tracheobronchial mucosal glands were absent, whereas olfactory glands were unaffected. Mandibular incisor teeth were absent. Premolar teeth were unerupted and widely spaced. Other than oligodontia, histological changes in teeth were modest, featuring multifocal disorganization of ameloblasts, new bone formation in dental alveoli, and small aggregates of osteodentin and cementum at the margins of the enamel organ. A 52,780 base pair deletion spanning six out of eight coding exons of EDA and all of AWAT2 was identified. Partial deletion of the EDA gene is the presumed basis for the reported X-chromosomal recessive inherited genodermatosis.