Search

The quality grade system used in the United States to identify carcasses with superior eating satisfaction to consumers is based on the amount of marbling within the ribeye and the maturity of the carcass. However, the most important quality attribute for consumers is tenderness. The objective of this study was to investigate the phenotypic correlations between carcass and meat quality traits of strip loin steaks from Brangus steers, particularly the relation between the United States Department of Agriculture (USDA) quality grade and tenderness. Warner–Bratzler shear force (WBSF) values in this study averaged 5.10 ± 0.96 kg, slightly higher than the national average of 4.55 ± 1.14 kg. Average WBSF across all quality grades ranged from 4.90 to 5.27 kg with standard deviations ranging from 0.78 to 1.40 kg. In the present Brangus steer population, there was a weak negative (−0.13) but favorable correlation (P < 0.05) between marbling score and tenderness measured through WBSF. The USDA quality grade had a significant (P = 0.02) effect on WBSF. The WBSF least square means were significantly higher in the Select compared with the Choice¯, and Choiceº quality grades. The Choice⁺ and Prime quality grades were not significantly different from any quality grades regarding the WBSF. The standard quality grade did not have significantly different WBSF least square means from any other quality grade. The range of WBSF values was large, especially in the lower quality grade categories, indicating that there is considerable variation in tenderness, even within quality grade. The high level of variation in tenderness within USDA quality grades highlights the limitation of the USDA grading system to predict eating quality or tenderness.

Bos taurus × Bos indicus crosses are widespread in tropical and subtropical regions, nonetheless, quantitative information about the influence of B. indicus genetics on the reproductive performance of beef cattle is lacking. Herein, we determined the association between level of B. indicus genetics and reproduction from a 31-yr dataset comprising sequential breeding seasons of the University of Florida multibreed herd (n = 6,503 Angus × Brahman cows). The proportion of B. indicus genetics in this herd is evenly distributed by each 1/32nd or approximately 3-percentage points. From 1989 to 2020, the estrous cycle of cows was synchronized for artificial insemination (AI) based on detected estrus or timed-AI (TAI) using programs based on gonadotropin-releasing hormone and prostaglandin, and progestin/progesterone. All cows were exposed to natural service after AI and approximately 90-d breeding seasons, considering the day of AI as day 0. The proportion of B. indicus genetics of cows was associated negatively with pregnancy per AI, ranging from 51.6% for cows with 0%-19% of B. indicus genetics to 37.4% for cows with 81%-100% of B. indicus genetics. Similar association was found for estrous response at the end of the synchronization protocol, ranging from 66.3% to 38.4%, respectively. This reduced estrous response helped to explain the pregnancy results, once the pregnancy to AI of cows showing estrus was 2.3-fold greater than for those not showing estrus and submitted to TAI. Despite reduced pregnancy per AI, the increase in the proportion of B. indicus genetics of cows was not associated with a reduction in the proportion of pregnant cows at the end of the breeding season. Nevertheless, the interval from entering the breeding season to pregnancy was lengthened as the proportion of B. indicus genetics of cows increased. The median days to pregnancy was extended by 25 when the proportion of B. indicus genetics surpassed 78% compared with less than 20%. Thus, the increase in the proportion of B. indicus genetics of cows was related to a reduction in pregnancy per AI and lengthening the interval to attain pregnancy during the breeding season, but not with the final proportion of pregnant cows. As a result, reproductive management strategies directed specifically to cows with a greater proportion of B. indicus genetics are needed to improve the rate of pregnancy in beef herds.Cow–calf operations in the tropics and sub-tropics have benefited from the environmental adaptation provided by Bos indicus genetics. However, reproductive performance has been a cause of concern, although poorly quantified. This study characterized how much the B. indicus genetics in crossbred cows influence herd reproduction. We analyzed data from cows with known proportions of Angus and Brahman genetics, from the same crossbred herd, for 31 sequential breeding seasons. The increase in the proportion of B. indicus genetics reduced estrous response and pregnancy per artificial insemination after estrous synchronization, but not the proportion of pregnant cows at the end of the breeding season. Interval from the beginning of the breeding season to pregnancy was extended by 25 d when the proportion of B. indicus genetics surpassed 78%. In conclusion, reproductive management strategies directed specifically to cows with a greater proportion of B. indicus genetics are needed to improve the rate of pregnancy in beef herds.

Florida Native sheep is among the sheep breeds best adapted to humid and hot climatic conditions such as those of Florida, USA, and have shown a superior ability to regulate nematode burdens. This is one of the oldest sheep breeds in North America and is an endangered species. To ensure genetic diversity and long-term survival of the breed, protection of the current genetic stock is critical and conservation efforts are required to promote its breeding and production. The objective of the present study was to investigate the importance of additive and non-additive genetic effects on resistance to natural Haemonchus contortus infections in Florida Native sheep using a whole genome scan. A total of 200 sheep were evaluated in the present study. Phenotypic records included faecal egg count (FEC, eggs/gram), FAMACHA® score, packed cell volume (PCV, %), body condition score and average daily gain (ADG, kg). Sheep were genotyped using the GGP Ovine 50K SNP chip and 45.2 k single nucleotide polymorphism (SNP) markers spanning the entire genome were available for quality control procedures. Mixed models were used to analyse the response variables and included the identity by state matrix to control for population structure. Bonferroni correction was used to control for multiple testing and a second arbitrary threshold (0.1 × 10−3) was used. Fifteen SNPs with additive and non-additive genetic effects and located in Ovis aries chromosome OAR1, 2, 3, 6, 8, 10, 11, 12, 13 and 21 were associated with FEC, FAMACHA® score, PCV and ADG. These SNPs could be potential genetic markers for resistance to natural H. contortus exposure in Florida Native sheep.

Thermal stress limits beef cattle production and a shorter hair coat is a key thermoregulative adaptation that allows cattle to lose heat more efficiently. The objective of this study was to identify genetic variants associated with the length of the undercoat and topcoat of cattle utilizing 1456 Brangus heifers genotyped with the Bovine GGP F250 array. Seven SNPs in the PCCA gene were significantly associated with undercoat length. PCCA belongs to the biotin transport and metabolism pathway. Biotin deficiency has been reported to cause hair loss. Four SNPs in an 110 kb including a missense mutation in the PRLR gene were significantly associated with topcoat length. Whereas the association of this polymorphism with hair length is novel, the SLICK mutation in PRLR has previously been demonstrated to significantly impact hair length in cattle. These newly detected genetic variants may contribute to a shorter hair coat and more thermotolerant animals.

Brahman cattle are used for crossbreeding due to their maternal ability, heat, and parasite tolerance. Brahman displays delayed attainment of puberty compared with taurine breeds. The objective was to identify molecular markers in the blood of prepubertal heifers and bulls that predict early puberty attainment. We hypothesize that Brahmans that attains puberty have a blood metabolite signature that differs from animals that remain prepubertal. Plasma was collected 90 (-90d) and 30 (-30d) days prior to the beginning of the breeding season from 156 yearling Brahman heifers and 28 bulls. Animals were classified as pubertal (pub) or prepubertal (prepub) based on reproductive variables such as the reproductive tract score and pregnancy to insemination for heifers and scrotal circumference and semen quality for bulls. Plasma from 48 pub and 48 prepub heifers and 9 pub and 7 prepub bulls were submitted for quantitative mass spectrometry metabolomics analysis. There was a clear clustering of animals according to puberty status (orthogonal projections of latent structures discriminant analysis). Concentrations of the top three metabolites explaining clustering were analyzed by t-tests. As heifers approached maturity, there was a 3.03-, 11.76- and 2.08-fold change (P < 0.0001) in the concentrations of PC ae C42:3, ProBetaine, and PC ae C42:2 measured at -30 vs. -90 days. Similarly, for bulls, concentrations of HipAcid, C4 and SM (OH) C24:1 were 1.52-, 1.53-, and 1.45-fold greater (P < 0.0001), respectively. Comparing pub vs. prebub heifers on -90 d, there was a 1.26- (P < 0.001), 0.62- (P < 0.01) and 1.11-fold change (P < 0.05) for hArg, Putrescine and AABA concentrations, respectively. Regarding bulls on -90 d, there was a 1.57- (P < 0.01), 1.32- (P < 0.03) and 1.15-fold change (P < 0.03) for FA(18:1), FA(18:2) and DG(16:1_18:2) concentrations, respectively. In conclusion, we discovered potential markers for the prediction of puberty attainment based on plasma metabolomic signatures in Brahman.

Incorporating Brahman genetics into the cow herd alleviates heat stress. This publication discusses Brahman adaptation, challenges and benefits, and recommended Brahman incorporation. Written by Kaitlyn Sarlo Davila, Heather Hamblen, Serdal Dikmen, Peter Hansen, Todd Thrift, and Raluca Mateescu, and published by the UF/IFAS Department of Animal Sciences, October 2021.

Haemonchus contortus infections are an important source of animal production loss to livestock industry. Genetics of helminth resistance involves a complex set of factors related to the host immune response. The increasing use of genetic markers such as single nucleotide polymorphisms (SNPs) in genome wide association studies (GWAS) offers the potential to identify loci or regions associated with nematode resistance in small ruminants. The aims of this study were: (1) to use a targeted sequencing approach to identify SNPs in 100 genes related to immune response during Haemonchus contortus exposure in growing males of St. Croix, Katahdin and Dorper sheep, and in Kiko, Boer and Spanish goats, and (2) to perform an association analysis for fecal egg count (FEC), packed cell volume (PCV), immunoglobulin levels (IgA, IgG and IgM) and average daily gain (ADG) in the populations under study. After quality control (call rate

Beef palatability is a complex concept and could be described through an array of features such as tenderness, juiciness and flavor traits. Improving the eating experience when consuming be...

Carcass and meat quality are two important attributes for the beef industry because they drive profitability and consumer demand. These traits are of even greater importance in crossbred cattle used in subtropical and tropical regions for their superior adaptability because they tend to underperform compared to their purebred counterparts. Many of these traits are challenging and expensive to measure and unavailable until late in life or after the animal is harvested, hence unrealistic to improve through traditional phenotypic selection, but perfect candidates for genomic selection. Before genomic selection can be implemented in crossbred populations, it is important to explore if pleiotropic effects exist between carcass and meat quality traits. Therefore, the objective of this study was to identify genomic regions with pleiotropic effects on carcass and meat quality traits in a multibreed Angus–Brahman population that included purebred and crossbred animals. Data included phenotypes for 10 carcass and meat quality traits from 2,384 steers, of which 1,038 were genotyped with the GGP Bovine F-250. Single-trait genome-wide association studies were first used to investigate the relevance of direct additive genetic effects on each carcass, sensory and visual meat quality traits. A second analysis for each trait included all other phenotypes as covariates to correct for direct causal effects from identified genomic regions with pure direct effects on the trait under analysis. Five genomic windows on chromosomes BTA5, BTA7, BTA18, and BTA29 explained more than 1% of additive genetic variance of two or more traits. Moreover, three suggestive pleiotropic regions were identified on BTA10 and BTA19. The 317 genes uncovered in pleiotropic regions included anchoring and cytoskeletal proteins, key players in cell growth, muscle development, lipid metabolism and fat deposition, and important factors in muscle proteolysis. A functional analysis of these genes revealed GO terms directly related to carcass quality, meat quality, and tenderness in beef cattle, including calcium-related processes, cell signaling, and modulation of cell–cell adhesion. These results contribute with novel information about the complex genetic architecture and pleiotropic effects of carcass and meat quality traits in crossbred beef cattle.

Bos taurus indicus cattle have superior ability for regulation of body temperature during heat stress due to a number of physiological and cellular level adaptive traits. The objectives of this study were to quantify the change in body temperature in heifers with various proportions of Brahman genes per unit increase in heat stress as measured by THI and to assess the impact of skin properties on the phenotypic plasticity. A total of 299 two-year old heifers from six breed groups ranging from 100% Angus to 100% Brahman were evaluated under hot and humid conditions during 2017 and 2018 summer days. The plasticity in body temperature of breed groups in response to environmental challenges was estimated using a random regression mixed model. Six mm skin biopsies were collected from the right side of sixth thoracic bone of each heifer. Cross-sections of biopsy samples with a thickness of 7 µm were stained with Hematoxilin–Eosin technique. The number and area of sweat and sebaceous glands and the thickness of dermis and epidermis were determined using the ImageJ program. The 100% Brahman group had the lowest intercept and slope (38.66 and 0.18) representing the body temperature under the low THI conditions and the increase in body temperature for 2 units of THI, respectively. Except for the 100% Angus group, which had a slightly higher intercept (38.68), all other breed groups had lower intercepts. Body temperature in the 100% Angus heifers increases by 0.42 for every 2 units of THI. There was a significant linear effect of Brahman percentage on the sweat gland size, with the 100% Brahman having the largest sweat gland size (203.57µm2) and purebred Angus the smallest (94.31µm2). Effective strategies will require the identification of the genes conferring the superior thermotolerance in Brahman cattle.

Expression QTL mapping provides information about genetic variant with modulatory effects on gene expression which are useful for understanding the genetic architecture of complex phenotypes. This mapping allows for uncovering of genomic regions associated with transcription regulation of genes which can be related to phenotypic variation when they colocalize with QTLs (cis and trans effects), providing a molecular basis for the phenotype-genotype association. The objectives of the present research were to perform eQTL mapping for meat quality traits in longissimus dorsi muscle and to uncover genes whose expression is influenced by local or distant genetic variation. A total of 120 steers from the University of Florida Beef Unit multibreed Angus-Brahman herd born between 2013 and 2014 were used in this study. The first three principal components from a principal component analysis for all meat quality phenotypes were used to construct a meat quality index. Eighty animals were selected based on extreme meat quality index for mRNA sequencing and 100 bp paired-end reads were mapped against to the Btau_4.6.1 reference genome. eQTL mapping was performed using 112,042 SNPs and 8,588 genes. A cis QTL was defined as an SNP located no more than 1 Mb upstream of the transcription start site or downstream of the transcription end site of an annotated gene. Polymorphisms associated with expression of at least 20 genes in the case of eQTL were considered hot spots. The harboring or adjacent gene was defined as master regulators. Multiple cis eQTLs and sQTLs effects were identified and genes such as LSM2, SOAT1, TTN and TEK are a few examples of potential expression and splicing regulatory genes. A total of 27 expression and 13 splicing master regulator genes were uncovered, mainly cytoskeletal or membrane-associated proteins, transcription factors and DNA methylases.

Bos taurus indicus cattle have the superior ability for the regulation of body temperature during heat stress due to a number of physiological and cellular level adaptive traits. The objectives of this study were to quantify the change in body temperature in heifers with various proportions of Brahman genes per unit increase in heat stress as measured by temperature–humidity index (THI) and to assess how different breed groups responded to varying intensity and duration of heat stress. A total of 299 two-yr-old heifers from six breed groups ranging from 100% Angus to 100% Brahman were evaluated under hot and humid conditions during 2017 and 2018 summer days. Two strategies were used to estimate the plasticity in body temperature of breed groups in response to environmental challenges: 1) a random regression mixed model was used to estimate reaction norm parameters for each breed group in response to a specified environmental heat stress and 2) a repeated measures mixed model was used to evaluate the response to different environmental heat loads. The reaction norm model estimated an intercept and slope measuring the change in body temperature per unit increase in THI environmental heat stress for different breed groups of animals and allowed the identification of genotypes which are robust, with low slope values indicative of animals that are able to maintain normal body temperature across a range of environments. The repeated measures mixed model showed that Brahman cattle have an advantage under moderate or high heat stress conditions but both Angus and Brahman breed groups are greatly affected when heat stress is severe. A critical factor appears to be the opportunity to cool down during the night hours more than the number of hours with extreme THI. With heat stress conditions predicted to intensify and expand into currently temperate zones, developing effective strategies to ensure sustainable beef production systems are imperative. Effective strategies will require the identification of the genes conferring the superior thermotolerance in Brahman cattle.

Water is an essential nutrient, but there are few recent studies that evaluate how much water individual beef cattle consume and how environmental factors affect an individual’s water intake (WI). Most studies have focused on WI of whole pens rather than WI of individual animals. Thus, the objective of this study was to evaluate the impact of environmental parameters on individual-animal WI across different seasons and develop prediction equations to estimate WI, including within different environments and management protocols. Individual daily feed intake and WI records were collected on 579 crossbred steers for a 70-d period following a 21-d acclimation period for feed and water bunk training. Steers were fed in 5 separate groups over a 3-yr period from May 2014 to March 2017. Individual weights were collected every 14 d and weather data were retrieved from the Oklahoma Mesonet’s Stillwater station. Differences in WI as a percent of body weight (WI%) were analyzed accounting for average temperature (TAVG), relative humidity (HAVG), solar radiation (SRAD), and wind speed (WSPD). Seasonal (summer vs. winter) and management differences (ad libitum vs. slick bunk) were examined. Regression analysis was utilized to generate 5 WI prediction equations (overall, summer, winter, slick, and ad libitum). There were significant (P < 0.05) differences in WI between all groups when no environmental parameters were included in the model. Although performance was more similar after accounting for all differences in weather variables, significant (P < 0.05) seasonal and feed management differences were still observed for WI%, but were less than 0.75% of steer body weight. The best linear predictors of daily WI (DWI) were dry mater intake (DMI), metabolic body weights (MWTS), TAVG, SRAD, HAVG, and WSPD. Slight differences in the coefficient of determinations for the various models were observed for the summer (0.34), winter (0.39), ad libitum (0.385), slick bunk (0.41), and overall models (0.40). Based on the moderate R2 values for the WI prediction equations, individual DWI can be predicted with reasonable accuracy based on the environmental conditions that are present, MWTS, and DMI consumed, but substantial variation exists in individual animal WI that is not accounted for by these models.

Consumers demand meat that is both healthy and palatable, 2 attributes of meat that are affected by lipid content. Many cattle in the southern United States are Bos indicus influenced, as this improves the ability to survive and thrive in these subtropical regions. However, these animals tend to have leaner carcasses and less marbled meat products. Thus, the objective of this study was to examine the effect of percent Brahman genetics on carcass characteristics, palatability, fatty acids profile, and minerals content in LM of steers from a multibreed population ranging from 100% Angus to 100% Brahman. Breed effect was significant for birth weight (P = 0.0003), weaning weight (P < 0.0001), HCW (P < 0.0001), dressing percentage (P = 0.0008), ribeye area (P = 0.002), quality grade (P < 0.0001), and marbling score (P < 0.0001), and all these traits except dressing percentage decreased as the percentage of Brahman increased. Among palatability traits, breed group had a significant effect only on tenderness (TEND) and connective tissue (CT) scores (P < 0.0001). Least squares means decreased from Angus (5.75 ± 0.13 TEND score and 6.29 ± 0.14 CT score, respectively) to Brahman (4.84 ± 0.10 TEND score and 5.49 ± 0.11 CT score, respectively) as indicated by a significant linear effect. Breed group significantly affected the percentage of several individual fatty acids, saturated fatty acids (SFA), and polyunsaturated fatty acids (PUFA), but not monounsaturated fatty acids (MUFA). The 100% Angus group had the highest percentage of SFA at 49.92%, which was significantly higher (P < 0.05) than the SFA percentage in the 50%, 75%, and 100% Brahman breed groups. Brangus animals also had an increased SFA percentage compared with the 100% Brahman animals (P < 0.05). No significant effect was identified for the concentration of PUFA across the 6 breed groups (P = 0.14). Least squares means decreased from 100% Angus to 100% Brahman for concentration of total fat, SFA, and MUFA (g/mg meat). The concentration of magnesium (P < 0.0001), phosphorus (P = 0.06), and potassium (P = 0.06) increased as the percentage of Brahman increased. Our study shows that breed has a significant effect on the fatty acid profile of beef. Cattle with high Brahman percentage, which are characterized by lower marbled meat, will present a more favorable healthfulness profile with reduced content of SFA and MUFA but the same content of PUFA as purebred Angus animals.

Heat stress is a cause of major economic losses to cattle producers, especially in tropical and subtropical environments. The objectives of this study were to assess the phenotypic variability in core body temperature and sweating rate and to evaluate the effect of coat type, temperament, and BW on core body temperature and sweating rate in Brangus heifers. During August and September of 2016, 725 Brangus heifers were evaluated on pasture in four separate groups (n = 200, 189, 197, and 139). Environmental measurements of dry bulb temperature (T(db)) and relative humidity (RH) were measured every 15 min during the entire time of data collection and the temperature–humidity index (THI) was used to quantify heat-stress potential. Coat score, sweating rate, chute score, exit score, and live weight were recorded as the animals passed through the chute. Vaginal temperature was recorded every 5 min for five consecutive days. There was significant variation in vaginal temperature between heifers in the same environmental conditions (σ(2)(u) = 0.049), suggesting opportunities for selective improvements. A repeatability of 0.47 and 0.44 was estimated for sweating rate and vaginal temperature, respectively, suggesting that one measurement would be able to adequately describe the sweating capacity or ability to control the body temperature of an individual. Vaginal temperature increased as THI increased, with approximately 1 h lag time in the animal’s response. Vaginal temperature (−0.047 °C, P = 0.015) and sweating rate were lower (−5.49 ± 2.12 g/(m(2)·h), P < 0.01) for heifers that demonstrated a calmer behavior in the chute. Animals with shorter, smoother hair coats had significantly lower vaginal temperatures when compared to animals with longer hair coats (P < 0.01). Also, heavier heifers in this study maintained lower (P < 0.0001) vaginal temperature than the lighter heifers. Our results showed that hair coat, temperament, and weight influenced vaginal temperature regulation.

The Insentec Roughage Intake Control (RIC) system has been validated for the collection of water intake; however, this system has not been validated for water restriction. The objective of this validation was to evaluate the agreement between direct observations and automated intakes collected by the RIC system under both ad libitum and restricted water conditions. A total of 239 crossbred steers were used in a 3-d validation trial, which assessed intake values generated by the RIC electronic intake monitoring system for both ad libitum water intake ( = 122; BASE) and restricted water intake ( = 117; RES). Direct human observations were collected on 4 Insentec water bins for three 24-h periods and three 12-h periods for BASE and RES, respectively. An intake event was noted by the observer when the electronic identification of the animal was read by the transponder and the gate lowered, and starting and ending bin weights were recorded for each intake event. Data from direct observations across each validation period were compared to automated observations generated from the RIC system. Missing beginning or ending weight values for visual observations occasionally occurred due to the observer being unable to capture the value before the monitor changed when bin activity was high. To estimate the impact of these missing values, analyses denoted as OBS were completed with the incomplete record coded as missing data. These analyses were contrasted with analyses where observations with a single missing beginning or end weight (but not both) were assumed to be identical to that which was recorded by the Insentec system (OBS). Difference in mean total intake across BASE steers was 0.60 ± 2.06 kg OBS (0.54 ± 1.99 kg OBS) greater for system observations than visual observations. The comparison of mean total intake across the 3 RES validation days was 0.53 ± 2.30 kg OBS (0.13 ± 1.83 kg OBS) greater for system observations than direct observations. Day was not a significant source of error in this study ( > 0.05). These results indicate that the system was capable of limiting water of individual animals with reasonable accuracy, although errors are slightly higher during water restriction than during ad libitum access. The Insentec system is a suitable resource for monitoring individual water intake of growing, group-housed steers under ad libitum and restricted water conditions.

The objectives of this study were to estimate variance components, genetic parameters, EBV, accuracies, and rankings for nine ultrasound and carcass traits in a multibreed Angus-Brahman population using three genomic-polygenic models and one polygenic model (PM). The genomic-polygenic models used the complete GeneSeek GPF250k SNP set (GPM), top 5% SNP (GPMR1), and 5% SNP evenly spread across the genome (GPMR2). Yearling ultrasound traits were weight (UW), ribeye area (UREA), backfat (UFAT), and percent intramuscular fat (UPIMF). Carcass traits were slaughter age (SLA), hot carcass weight (HCW), ribeye area (REA), backfat thickness (FAT), and marbling score (MAR). The 9-trait GPM, GPMR1, GPMR2, and PM contained fixed contemporary group, age of calf (ultrasound traits only), sex of calf, and direct heterosis effects, and random animal and residual effects. Variance components and genetic parameters were computed using AIREMLF90. Comparable heritabilities were obtained with GPM and PM for UW (GPM: 0.54 ± 0.05; PM: 0.51 ± 0.05), UREA (GPM: 0.36 ± 0.03; PM: 0.34 ± 0.03), UFAT (GPM: 0.12 ± 0.02; PM: 0.11 ± 0.02), UMPIMF (GPM: 0.34 ± 0.03; PM: 0.30 ± 0.03), SLA (GPM: 0.59 ± 0.07, PM: 0.61 ± 0.06), HCW (GPM: 0.58 ± 0.06, PM: 0.52 ± 0.07), REA (GPM: 0.48 ± 0.04, PM: 0.45 ± 0.05), FAT (GPM: 0.41 ± 0.05, PM: 0.30 ± 0.05), and MAR (GPM: 0.56 ± 0.07, PM: 0.51 ± 0.08). Additive genetic correlations between pairs of ultrasound and carcass traits were all between −0.31 and 0.81. The highest positive additive genetic correlations were between UW and UREA, UW and HCW, UW and REA, UREA and HCW, UREA and REA, UFAT and FAT, and between HCW and REA. The largest negative additive genetic correlations were between UREA and UPIMF, UFAT and SLA, UFAT and HCW, UPIMF and REA, and between REA and MAR. High similarity existed among predicted EBV and accuracies from GPM, GPMR1, and GPMR2 as well as high-rank correlations for sires, dams, and progenies. This indicated that the two reduced genotype sets were appropriate alternatives to the complete GPF250k set for genomic-polygenic evaluation and selection in this multibreed Angus-Brahman population. High EBV variability existed among animals of all Angus and Brahman percentages and no specific breed composition was overwhelmingly better or worse for any of the nine traits. This indicated that optimization of genetic progress through selection in multibreed Angus-Brahman populations should be based solely on genetic merit regardless of breed composition.

RNA sequencing (RNA-seq) has allowed for transcriptional profiling of biological systems through the identification of differentially expressed (DE) genes and pathways. A total of 80 steers with extreme phenotypes were selected from the University of Florida multibreed Angus-Brahman herd. The average slaughter age was 12.91±8.69 months. Tenderness, juiciness and connective tissue assessed by sensory panel, along with marbling, Warner-Bratzler Shear Force (WBSF) and cooking loss, were measured inlongissimus dorsimuscle. Total RNA was extracted from muscle and one RNA-seq library per sample was constructed, multiplexed, and sequenced based on protocols by Illumina HiSeq-3000 platform to generate 2×101 bp paired-end reads. The overall read mapping rate using the Btau_4.6.1 reference genome was 63%. A total of 8,799 genes were analyzed using two different methodologies, an expression association and a DE analysis. A gene and exon expression association analysis was carried out using a meat quality index on all 80 samples as a continuous response variable. The expression of 208 genes and 3,280 exons from 1,565 genes was associated with the meat quality index (p-value ≤ 0.05). A gene and isoform DE evaluation was performed analyzing two groups with extreme WBSF, tenderness and marbling. A total of 676 (adjusted p-value≤0.05), 70 (adjusted p-value≤0.1) and 198 (adjusted p-value≤0.1) genes were DE for WBSF, tenderness and marbling, respectively. A total of 106 isoforms from 98 genes for WBSF, 13 isoforms from 13 genes for tenderness and 43 isoforms from 42 genes for marbling (FDR≤0.1) were DE. Cytoskeletal and transmembrane anchoring genes and pathways were identified in the expression association, DE and the gene enrichment analyses; these proteins can have a direct effect on meat quality. Cytoskeletal proteins and transmembrane anchoring molecules can influence meat quality by allowing cytoskeletal interaction with myocyte and organelle membranes, contributing to cytoskeletal structure and architecture maintenance postmortem.

Thermoregulation is important for beef cattle but tends to be negatively correlated with production traits. The objective of this study was to determine the variation in core body temperature and to estimate genetic parameters of skin traits in Angus, Brahman, and different levels of crossbred heifers (n = 337) reared in hot and humid conditions. Core body temperature was recorded as vaginal temperature every 15 minutes for 5 consecutive days. Dry bulb temperature and relative humidity in the pasture were also measured every 15 min and used to calculate a temperature-humidity index (THI). Five mm skin biopsies were collected from the right side of sixth thoracic bone of each heifer. Cross-sections of biopsy samples with a thickness of 7 µm were stained with Hematoxilin–Eosin technique. The number and area of sweat and sebaceous glands, and the thickness of dermis and epidermis were determined using the ImageJ program. Data were analysed using PROC MIXED in SAS 9.4 with a model including the effect of breed, year, and their interaction. Genetic parameters were estimated using WOMBAT. Average core body temperature of Angus, 25%, 37.5%, 50%,75% and 100% Brahman were 39.50±0.05, 39.30±0.04, 39.15±0.05, 39.2±0.0, 39.03±0.05, 39.04±0.05, respectively. Brahman heifers had lower core body temperature compared to Angus heifers (P = 0.0006). Heifers with smaller and more numerous sweat glands had higher (P < 0.01) and more variable core body temperature (P < 0.0001). Heritability of core body temperature under high and low THI was 0.44±0.006 and 0.61±0.003, respectively. Dermis and epidermis thickness had the lowest heritability (0.231±0.002) and the highest heritability (0.75±0.007), respectively. Heritabilities for the number of sweat glands and total sweat gland area were 0.375±0.02 and 0.432±0.006, respectively. In conclusion, thermoregulation was highly correlated with breed composition, number of sweat glands and the average size of sweat glands.

It is generally accepted that “temperamental” cattle are more anxious or experience higher stress, causing differences in intake and performance. The objective of this study was to examine whether temperament affects how steers perform during prolonged water restriction, a chronic stressor. Steers from numerous sources in 4 groups (n = 469) were randomly allocated to 2 weight blocks. Steers were fed ad libitum 3 times a day for 70 d. After a 28 d step-down period, steers were maintained at 50% of normal water allotment for 42 d while feed continued to be offered ad libitum. Individual feed and water intake (WI) were measured daily using an Insentec RIC feeding system. Body weight, exit velocity (EV; measured over 1.5m), and chute score (CS; reported on a 1–4 scale) were measured every 14 d. Lower scores indicate calmer temperament. Due to the study design, DMI, ADG, G:F, and WI were split into 7 periods (d 0–28, 28–70, 0–70, 98–140, 98–112, 112–126, and 126–140). Data were analyzed using the MIXED procedure of SAS where the model included EV, CS, the interaction, and block; group was included as a random effect. Gain, DMI, and G:F d 0–28 were affected by both CS and EV. Slow EV steers had higher DMI than fast EV steers (P < 0.02) during d 28–70 and 0–70. During d 28–70, intermediate CS steers had the highest DMI (P < 0.05). During d 0–70 and 98–140, intermediate CS steers had the highest ADG (P < 0.05). All measures of DMI and WI were higher in the heavy weight block (P < 0.05); ADG and G:F were also higher in the heavy weight block during d 0–70 (P < 0.001). This experiment indicates that there may be performance benefits for steers with intermediate CS during long periods of water restriction.

Background Gastrointestinal nematode infection (GNI) is the most important disease affecting the small ruminant industry in U.S. The environmental conditions in the southern United States are ideal for the survival of the most pathogenic gastrointestinal nematode, Haemonchus contortus. Host genetic variation for resistance to H. contortus allows selective breeding for increased resistance of animals. This selection process increases the prevalence of particular alleles in sheep and goats and creates unique genetic patterns in the genome of these species. The aim of this study was to identify loci with divergent allelic frequencies in a candidate gene panel of 100 genes using two different approaches (frequentist and Bayesian) to estimate Fst outliers in three different breeds of sheep and goats exposed to H. contortus. Results Our results for sheep populations showed SNPs under selection in C3AR1, CSF3, SOCS2, NOS2, STAT5B, TGFB2 and IL2RA genes using frequentist and Bayesian approaches. For goats, SNPs in CD1D, ITGA9, IL12A, IL13RA1, CD86 and TGFB2 genes were under selection. Common signatures of selection in both species were observed in NOS2, TGFB2 and TLR4 genes. Directional selection was present in all SNPs evaluated in the present study. Conclusions A total of 13 SNPs within 7 genes of our candidate gene panel related to H. contortus exposure were identified under selection in sheep populations. For goats, 11 SNPs within 7 genes were identified under selection. Results from this study support the hypothesis that resistance to H. contortus is likely to be controlled by many loci. Shared signatures of selection related to mechanisms of immune protection against H. contortus infection in sheep and goats could be useful targets in breeding programs aimed to produce resistant animals with low FEC.

Background: Transcription has a substantial genetic control and genetic dissection of gene expression could help us understand the genetic architecture of complex phenotypes such as meat quality in cattle.Results: A total of 80 steers were selected for phenotyping, genotyping and RNA-seq evaluation. A panel of traits related to meat quality were recorded. Information on 112,042 SNPs and expression data on 8,588 autosomal genes and 87,770 exons from 8,467 genes were included in an expression and splicing quantitative trait loci (QTL) mapping (eQTL and sQTL, respectively). Expression of 1,352 genes was previously identified as associated with meat quality traits using a gene, exon and isoform differential expression (DE) analysis. The R package Matrix eQTL was used to perform the QTL mapping using linear regression. The identified QTLs were classified as cis or trans using 1 Mb as maximum distance between the associated SNP and the gene. Polymorphisms associated with expression of at least 20 genes, and splicing of at least 20 exons were considered QTL hot spots. A total of 8,377 eQTLs were identified, including 75.6% trans, 10.4% cis, 12.5% DE trans and 1.5% DE cis; 11,929 sQTLs were uncovered: 66.1% trans, 16.9% DE trans, 14% cis and 3% DE cis. Twenty seven expression master regulators and 13 splicing master regulators were identified and were classified as membrane associated or cytoskeletal proteins, transcription factors or DNA methylases These genes could control expression of other genes through cell signaling or by a direct transcriptional activation/repression mechanism. The ZNF804A, ALAD, OR13F1 and ENSBTAG00000000336 genes were identified as both expression and splicing master regulators.Conclusion: In the present analysis, we show that eQTL and sQTL mapping makes possible positional identification of gene and isoform expression regulators. Additionally, this mapping provides new insight into the regulatory network architecture in longissimus dorsi muscle in an Angus-Brahman multibreed population.

Background Gastrointestinal nematode infection (GNI) is the most important disease affecting the small ruminant industry in U.S. The environmental conditions in the southern United States are ideal for the survival of the most pathogenic gastrointestinal nematode, Haemonchus contortus. Host genetic variation for resistance to H. contortus allows selective breeding for increased resistance of animals. This selection process increases the prevalence of particular alleles in sheep and goats and creates unique genetic patterns in the genome of these species. The aim of this study was to identify loci with divergent allelic frequencies in a candidate gene panel of 100 genes using two different approaches (frequentist and Bayesian) to estimate Fst outliers in three different breeds of sheep and goats exposed to H. contortus. Results Our results for sheep populations showed SNPs under selection in C3AR1, CSF3, SOCS2, NOS2, STAT5B, TGFB2 and IL2RA genes using frequentist and Bayesian approaches. For goats, SNPs in CD1D, ITGA9, IL12A, IL13RA1, CD86 and TGFB2 genes were under selection. Common signatures of selection in both species were observed in NOS2, TGFB2 and TLR4 genes. Directional selection was present in all SNPs evaluated in the present study. Conclusions A total of 13 SNPs within 10 genes of our candidate gene panel related to H. contortus exposure were identified under selection in sheep populations. For goats, 11 SNPs within 7 genes were identified under selection. Results from this study support the hypothesis that resistance to H. contortus is likely to be controlled by many loci. Shared signatures of selection related to mechanisms of immune protection against H. contortus infection in sheep and goats could be useful targets in breeding programs aimed to produce resistant animals with low FEC.

Background RNA sequencing (RNA-seq) has allowed for transcriptional profiling of biological systems through identification of differentially expressed (DE) genes and pathways. Results A total of 80 steers were selected from the multibreed Angus-Brahman herd of the University of Florida. Sensory panel tenderness, juiciness and connective tissue as well as marbling, WBSF and cooking loss were assessed in longissimus dorsi muscle. Nuclear RNA was extracted from muscle and an RNA-seq library for each sample was constructed, multiplexed, and sequenced based on protocols by Illumina HiSeq 3000 PE100 platform to generate 2 × 101 bp paired-end reads. On average, 34.9 million high-quality paired reads were uniquely mapped to the Btau_4.6.1 reference genome and a total of 8,799 genes were analyzed. Including all 80 animals, gene and exon expression analysis was carried out using a meat quality index as a continuous response variable. The expression of 208 genes and 3,280 exons from 1,565 genes was associated with the meat quality index (p-value ≤ 0.05). Out of the 80 samples sequenced, 40 animals with extreme low and high WBSF, tenderness and marbling values were selected for a differential expression (DE) analysis for gene and isoforms. A total of 676 (adjusted p-value ≤ 0.05), 70 (adjusted p-value ≤ 0.1) and 198 (adjusted p-value ≤ 0.1) genes were DE for WBSF, tenderness and marbling, respectively. A total of 106 isoforms from 98 genes for WBSF, 13 isoforms from 13 genes for tenderness and 43 isoforms from 42 genes for marbling (FDR ≤ 0.1) were DE. Conclusion A number of cytoskeletal and transmembrane anchoring related genes and pathways were identified in the expression, DE and gene enrichment analyses, and these proteins can have a direct effect on meat quality. Cytoskeletal proteins and transmembrane anchoring molecules can influence meat quality by allowing cytoskeletal filament interaction with myocyte and organelle membranes, contributing to cytoskeletal structure, microtubule network stability, and cellular architecture maintenance during the postmortem.

The aim of this study was to identify for the first time single nucleotide polymorphisms (SNPs) associated with Haemonchus contortus resistance in Florida Native sheep, using a targeted sequencing approach. One hundred and fifty-three lambs were evaluated in this study. At the start of the trial, phenotypic records for fecal egg count (FEC), FAMACHA score, body condition score (BCS), and weight were recorded and deworming of sheep with levamisole (18 mg/kg of body weight) was performed. Ten days post-deworming (baseline) and 28 d post-baseline, a full hematogram of each sheep was obtained and FEC, FAMACHA score, BCS, and weight were assessed. Average daily gain was calculated at the end of the trial. Out of 153 animals, 100 sheep were selected for genotyping using a targeted sequencing approach. Targeted sequencing panel included 100 candidate genes for immune response against H. contortus. SNPs were discarded if call rate

In the future, water may not be as readily available due to increases in competition from a growing human population, wildlife, and other agricultural sectors, making selection for water efficiency of beef cattle increasingly important. Substantial selection emphasis has recently been placed on feed efficiency in an effort to reduce production costs, but no emphasis has been placed on making cattle more water efficient due to lack of data. Thus, the objective of this study was to calculate water efficiency metrics for cattle and evaluate their relationship to growth, feed intake (FI), and feed efficiency. Individual daily FI and water intake (WI) records were collected on 578 crossbred steers over a 70-d test period. Animals with low water intake ate less feed, had lower gains, and were more water efficient (as defined by water to gain ratio, W/G, and residual water intake, RWI). However, the amount of water consumed by animals had minimal phenotypic relationship with feed efficiency (residual feed intake [RFI], R2 = 0.1050 and feed to gain ratio (F/G) ratio R2 = 0.0726). Cattle that had low DMI consumed less water, had lower gains, had lower RFI, and had higher F/G. The level of feed consumed had minimal relationship with water efficiency. WI, W/G, RWI, and ADG had moderate heritability estimates of 0.39, 0.39, 0.37, and 0.37, respectively. High heritability estimates were observed for DMI and RFI (0.67 and 0.65, respectively). Feed to gain had a low heritability estimate of 0.16. WI had a strong positive genetic correlation with W/G (0.99) and RWI (0.88), thus selecting for decreased WI should also make cattle more water efficient. The genetic correlation between WI and ADG was 0.05; thus, selecting for low WI cattle should have little effect on growth. There is a low to moderate genetic correlation between WI and DMI (0.34). RWI has a positive genetic correlation with W/G ratio (0.89) and F/G ratio (0.42) and is negatively genetically correlated with RFI (−0.57). Water to gain and F/G had a strong positive genetic correlation (0.68). RFI has a positive genetic correlation with W/G ratio (0.37) and F/G (0.88). Minimal antagonisms seem to be present between WI and ADG, although it should be noted that standard errors were large and often not significantly different from zero due to the small sample size. However, care should be taken to ensure that unintended changes do not occur in DMI or other production traits and incorporation of WI into a selection index would likely prove to be the most effective method for selection.

Background Gastrointestinal nematode infection (GNI) is the most important disease affecting the small ruminant industry in U.S. The environmental conditions in the southern United States are ideal for the survival and growth of the most pathogenic gastrointestinal nematode, Haemonchus contortus. Host genetic variation for resistance to H. contortus allows selective breeding for increased resistance of animals. This selection process increases the prevalence of particular alleles in sheep and goats and creates unique genetic patterns in the genome of these species. The aim of this study was to identify loci with divergent allelic frequencies using Fst statistic in three different breeds of sheep and goats previously exposed to H. contortus. Results Our results for sheep populations showed loci under selection on chromosomes 1, 2, 3, 6, 11, 12, 14, and 19. For goats, loci on chromosome 1, 2, 3, 5, 11, 12, 16, 18, 24 and 26 were under selection. SNPs under selection in CD86, NOS2, TGFB2 and TLR2 genes were identified in both species. Conclusions SNPs within immune response genes related to H. contortus exposure were identified under selection in sheep and goat populations. Results from this study support the hypothesis that resistance to H. contortus is likely to be controlled by many loci. Shared signatures of selection related to mechanisms of immune protection against H. contortus infection in sheep and goats could be useful targets in breeding programs aimed to produce resistant animals with low FEC.

Thermal stress limits beef cattle production and results in a loss of $370 million in the U.S. annually due to reduced animal performance. A shorter hair coat is a key thermoregulative adaptation that allows cattle to lose heat more efficiently through conductive, convective, and evaporative cooling at the hair-skin interface. The objective of this study was to identify genetic variants associated with the length of the topcoat and undercoat of cattle. Hair samples were collected from the shoulder, 4 inches down from the spine from 2,161 heifers in 2016, 2017 and 2018. ImageJ software was used to measure hair length. The length of the topcoat and undercoat were evaluated for each individual by averaging five long and five short hairs, respectively. DNA was extracted from blood samples and genotyped with the Bovine GGP F250 array. After quality control, 132,225 SNP were available for association analyses using Golden Helix SVS. Year of collection was fitted as a fixed effect and the genomic relationship matrix was fitted to account for the genetic covariance among animals. To correct for multiple tests, the Benjamini-Hochberg false discovery rate was constrained to 0.1. Four SNP in the PRLR gene were significantly associated with topcoat length, including a missense mutation that explained 4% of the variation in topcoat length. PRLR has previously been demonstrated to significantly impact hair length in cattle. Seven SNP in the PCCA gene were significantly associated with undercoat length. PCCA belongs to the biotin transport and metabolism pathway. Biotin deficiency has been reported to cause hair loss. These genetic variants may contribute to a shorter hair coat and more thermotolerant animals.

Thermal stress in hot humid conditions limits cattle production. The objectives for this study were to estimate genetic parameters for hair characteristics and core body temperature under low and high temperature humidity index (THI) conditions. Hair samples were collected and measured for length and diameter. Core body temperature was measured as vaginal temperature every 15 min over a 5-d period using an iButton temperature measuring device implanted in a blank CIDR in 336 heifers from the University of Florida multibreed herd (ranging from 100% Angus to 100% Brahman). Restricted maximum likelihood procedures were used to estimate heritabilities from multiple bivariate animal models using the WOMBAT program. Estimates of heritability for hair diameter, undercoat length, topcoat length, body temperature under low THI conditions, and body temperature under high THI conditions were 0.50, 0.67, 0.42, 0.32, and 0.26, respectively. The genetic parameters estimated in this study indicate a large, exploitable genetic variance which can be selected upon to improve tolerance in cattle. Breed effects for differing compositions of Brahman and Angus were also estimated. As Brahman breed composition increased by 25% undercoat length, topcoat length, body temperature under low THI conditions, and body temperature under high THI conditions decreased by 1.32 mm, 2.94 mm, 0.11 °C, and 0.14 °C, respectively. Under both low and high THI conditions, cattle with 25% Brahman breed composition or greater maintained a significantly lower body temperature than the 100% Angus breed group. The incorporation of Brahman germplasm is recommended for herds that often experience heat stress conditions in order to increase resilience to heat stress.

The quality grade system used in the United States to identify carcasses with superior eating satisfaction to consumers is based on the amount of intramuscular fat (marbling) within the ribeye and the maturity of the carcass. However, the most important quality attribute for consumers is tenderness. The objective of this study was to investigate the relationship between quality grade and tenderness assessed by slice shear force in strip loin steaks from Brangus cattle. Brangus steers (n = 860) were harvested when they reached approximately 1.27 cm fat over the ribeye. Hot carcass weight (HCW), dressing percentage (DP), marbling score (MARB; 100 to 199 = practically devoid, 200 to 299 = traces, 300 to 399=slight, 400 to 499=small, 500 to 599=modest, 600 to 699=moderate, 700 to 799=slightly abundant, 800 to 899=moderately abundant, and 900 to 999=abundant), ribeye area (REA), fat over the eye (FOE), and kidney pelvic and heart fat percentage (KPH) were evaluated for each animal. Quality grades and yield grades were calculated according to industry standards. A steak from the longissimus lumborum muscle was collected from each carcass, aged for 14 d and used for slice shear force testing to determine the tenderness. Data was analyzed with a general linear model with cooking loss, ranch, and feedlot as fixed effects. The quality grades ranged from high standard to average prime and the average of slice shear force values was 26.09 ± 8.76 kg. Quality grade had a significant effect on Slice Shear Force values (P = 0.0078), showing that quality grade significantly impacts tenderness. However, there was a high level of variation in Slice Shear Force values within quality grades. This indicates that carcasses with high quality grades could have meat with unacceptable tenderness, which could affect the demand for beef products.