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This study evaluated the effectiveness of genetic introgression of the SLICK1 allele derived from Senepol cattle into the Holstein breed to enhance thermotolerance. The SLICK1 allele, located in PRLR gene, confers a short and sleek coat that is inherited as a simple dominant phenotype. Approximately 40 years ago, the University of Florida initiated efforts to introgress this allele into the Holstein population. Here we tracked the introgression of the SLICK1 allele using a medium-density genotyping array and a reference population of both breeds (50 Holstein, 46 Senepol). Among the 31 SLICK1+ Holsteins, there was 15.25% ± 11.11% (mean ± SD) Senepol ancestry on BTA20. Holsteins at the University of Florida descended from slick matings that did not inherit the SLICK1 allele (n=9) exhibited no Senepol ancestry. A secondary introgression of Senepol genetics in SLICK1+ animals was found on BTA4, spanning 54 markers and 15 genes, with 26.67% Senepol ancestry. This region, previously linked to heat stress adaptation, suggests that the introgression extends beyond the SLICK1 allele to incorporate additional beneficial genetics for thermal stress adaptation. These findings indicate that deliberate introgression of the SLICK1 allele enhances specific traits and potentially introduces other adaptive genetic variations. The study demonstrates the successful use of genetic interventions to improve livestock resilience against environmental challenges without significantly disrupting the recipient breed's genetic structure. The introgression of the SLICK1 allele serves as a model for breeding programs aimed at optimizing animal welfare and productivity in the face of global climate change while maintaining breed integrity., (© The Author(s) 2024. Published by Oxford University Press on behalf of The American Genetic Association. All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.)

Here we report the case of a cow with two ovaries that each exhibited hyperplasia but that otherwise had normal gross morphology. Both ovaries had a large number of tertiary follicles on the ovarian surface. Oocytes from one ovary were studied in more detail. The transcriptome was largely similar to other oocytes. Oocytes could undergo cleavage at a rate consistent with other oocytes and result in blastocyst-stage embryo formation after in vitro maturation and fertilization. Review of the literature from cattle and other species did not reveal reports of a similar type of spontaneous ovarian abnormality. Whole genome sequencing revealed many single nucleotide polymorphisms with predicted large effects on protein structure that could potentially be causative for the phenotype. The variant considered most likely to cause the observed alteration in ovarian function was a mutation in the glycoprotein-modifying enzyme MAN1A2., (© 2024. The Author(s), under exclusive licence to Springer Nature B.V.)

Background: Carcass weight (HCW) and marbling (MARB) are critical for meat quality and market value in beef cattle. In composite breeds like Brangus, which meld the genetics of Angus and Brahman, SNP-based analyses have illuminated some genetic influences on these traits, but they fall short in fully capturing the nuanced effects of breed of origin alleles (BOA) on these traits. Focus on the impacts of BOA on phenotypic features within Brangus populations can result in a more profound understanding of the specific influences of Angus and Brahman genetics. Moreover, the consideration of BOA becomes particularly significant when evaluating dominance effects contributing to heterosis in crossbred populations. BOA provides a more comprehensive measure of heterosis due to its ability to differentiate the distinct genetic contributions originating from each parent breed. This detailed understanding of genetic effects is essential for making informed breeding decisions to optimize the benefits of heterosis in composite breeds like Brangus., Objective: This study aims to identify quantitative trait loci (QTL) influencing HCW and MARB by utilizing SNP and BOA information, incorporating additive, dominance, and overdominance effects within a multi-generational Brangus commercial herd., Methods: We analyzed phenotypic data from 1,066 genotyped Brangus steers. BOA inference was performed using LAMP-LD software using Angus and Brahman reference sets. SNP-based and BOA-based GWAS were then conducted considering additive, dominance, and overdominance models., Results: The study identified numerous QTLs for HCW and MARB. A notable QTL for HCW was associated to the SGCB gene, pivotal for muscle growth, and was identified solely in the BOA GWAS. Several BOA GWAS QTLs exhibited a dominance effect underscoring their importance in estimating heterosis., Conclusions: Our findings demonstrate that SNP-based methods may not detect all genetic variation affecting economically important traits in composite breeds. BOA inclusion in genomic evaluations is crucial for identifying genetic regions contributing to trait variation and for understanding the dominance value underpinning heterosis. By considering BOA, we gain a deeper understanding of genetic interactions and heterosis, which is integral to advancing breeding programs. The incorporation of BOA is recommended for comprehensive genomic evaluations to optimize trait improvements in crossbred cattle populations., (© 2024. The Author(s).)

This study evaluated the association between the proportion of Brahman genetics and productivity of Brahman-Angus cows at weaning using a 31-yr dataset containing 6,312 cows and 5,405 pregnancies. Cows were contemporaneously reared and enrolled in yearly breeding seasons under subtropical conditions of North-Central Florida. They were evenly distributed in six-breed groups (G) according to the proportion of Brahman genetics: G0% to 19%, G21% to 34%, G38% (Brangus), G41% to 59%, G63% to 78%, and G81% to 100%. The proportion of cows calving (84.9%) did not differ across the six-breed groups. However, cows in the G81% to 100% weaned fewer calves (90.8%) than cows in the G0% to 19% and G21% to 34% (95.7%, each). The weaning rate of cows in the G38% (94.3%), G41% to 59% (94.2%), and G63% to 78% (93.0%) was intermediate between these three breed groups. The preweaning calf mortality was greater for cows in the G81% to 100% (9.2%) than cows in the G0% to 19% and G21% to 34% (4.3%, each), but intermediate for cows in the G38% (5.7%), G41% to 59% (5.8%), and G63% to 78% (7.0%). Cows in the G81% to 100% also weaned lighter calves (220.6 kg) than cows in the G0% to 19% (245.2 kg), G21% to 34% (250.2 kg), G38% (247.9 kg), G41% to 59% (252.5 kg), and G63% to 78% (245.2 kg). Cows in the G0% to 19% weaned lighter calves than cows with 21% to 78% of Brahman genetics. The 205-d adjusted weaning weight evidenced the less productive results of cows in G0% to 19% and G81% to 100% compared with other genetic groups, as they calved at the fastest and slowest rate, respectively. Thus, the 205-d adjusted weaning weight eliminated this bias. Additionally, younger cows weaned lighter calves; and male calves were heavier at weaning than female calves. Both parity order of cow and calf sex altered the magnitude of the described association between breed group of cows and calf weaning weights. Overall, after adjusting for weaning rate and age of calves at weaning, the number of kilograms produced per cow submitted to reproduction was less for cows in the G0% to 19% (191.1 kg) and G81% to 100 (181.8 kg) compared with cows in the G21% to 34 (197.0 kg), G38 (195.9 kg), G41% to 59 (199.7), and G63% to 78 (196.2). Cows in the G81% to 100% were the least productive. Thus, a proportion of Brahman genetics between 21% and 78% ensured superior productivity of Brahman-Angus cows subjected to subtropical conditions., Competing Interests: The authors report no conflict of interest., (© The Author(s) 2024. Published by Oxford University Press on behalf of the American Society of Animal Science.)

Background: Thermal stress in subtropical regions is a major limiting factor in beef cattle production systems with around $369 million being lost annually due to reduced performance. Heat stress causes numerous physiological and behavioral disturbances including reduced feed intake and decreased production levels. Cattle utilize various physiological mechanisms such as sweating to regulate internal heat. Variation in these traits can help identify genetic variants that control sweat gland properties and subsequently allow for genetic selection of cattle with greater thermotolerance., Methods: This study used 2,401 Brangus cattle from two commercial ranches in Florida. Precise phenotypes that contribute to an animal's ability to manage heat stress were calculated from skin biopsies and included sweat gland area, sweat gland depth, and sweat gland length. All animals were genotyped with the Bovine GGP F250K, and BLUPF90 software was used to estimate genetic parameters and for Genome Wide Association Study., Results: Sweat gland phenotypes heritability ranged from 0.17 to 0.42 indicating a moderate amount of the phenotypic variation is due to genetics, allowing producers the ability to select for favorable sweat gland properties. A weighted single-step GWAS using sliding 10 kb windows identified multiple quantitative trait loci (QTLs) explaining a significant amount of genetic variation. QTLs located on BTA7 and BTA12 explained over 1.0% of genetic variance and overlap the ADGRV1 and CCDC168 genes, respectively. The variants identified in this study are implicated in processes related to immune function and cellular proliferation which could be relevant to heat management. Breed of Origin Alleles (BOA) were predicted using local ancestry in admixed populations (LAMP-LD), allowing for identification of markers' origin from either Brahman or Angus ancestry. A BOA GWAS was performed to identify regions inherited from particular ancestral breeds that might have a significant impact on sweat gland phenotypes., Conclusions: The results of the BOA GWAS indicate that both Brahman and Angus alleles contribute positively to sweat gland traits, as evidenced by favorable marker effects observed from both genetic backgrounds. Understanding and utilizing genetic traits that confer better heat tolerance is a proactive approach to managing the impacts of climate change on livestock farming., (© 2024. The Author(s).)

Composite breeds, including Brangus, are widely utilized in subtropical and tropical regions to harness the advantages of both Bos t. taurus and Bos t. indicus breeds. The formation and subsequent selection of composite breeds may result in discernible signatures of selection and shifts in genomic population structure. The objectives of this study were to 1) assess genomic inbreeding, 2) identify signatures of selection, 3) assign functional roles to these signatures in a commercial Brangus herd, and 4) contrast signatures of selection between selected and non-selected cattle from the same year. A total of 4035 commercial Brangus cattle were genotyped using the GGP-F250K array. Runs of Homozygosity (ROH) were used to identify signatures of selection and calculate genomic inbreeding. Quantitative trait loci (QTL) enrichment analysis and literature search identified phenotypic traits linked to ROH islands. Genomic inbreeding averaged 5%, primarily stemming from ancestors five or more generations back. A total of nine ROH islands were identified, QTL enrichment analysis revealed traits related to growth, milk composition, carcass, reproductive, and meat quality traits. Notably, the ROH island on BTA14 encompasses the pleiomorphic adenoma (PLAG1) gene, which has been linked to growth, carcass, and reproductive traits. Moreover, ROH islands associated with milk yield and composition were more pronounced in selected replacement heifers of the population, underscoring the importance of milk traits in cow-calf production. In summary, our research sheds light on the changing genetic landscape of the Brangus breed due to selection pressures and reveals key genomic regions impacting production traits., (© 2024. The Author(s), under exclusive licence to Institute of Plant Genetics Polish Academy of Sciences.)

The skin plays an important role in thermoregulation. Identification of genes on the skin that contribute to increased heat tolerance can be used to select animals with the best performance in warm environments. Our objective was to identify candidate genes associated with the heat stress response in the skin of Santa Ines sheep. A group of 80 sheep assessed for thermotolerance was kept in a climatic chamber for 8 days at a stress level temperature of 36 °C (10 am to 04 pm) and a maintenance temperature of 28 °C (04 pm to 10 am). Two divergent groups, with seven animals each, were formed after ranking them by thermotolerance using rectal temperature. From skin biopsy samples, total RNA was extracted, quantified, and used for RNA-seq analysis. 15,989 genes were expressed in sheep skin samples, of which 4 genes were differentially expressed (DE; FDR < 0.05) and 11 DE (FDR 0.05-0.177) between the two divergent groups. These genes are involved in cellular protection against stress (HSPA1A and HSPA6), ribosome assembly (28S, 18S, and 5S ribosomal RNA), and immune response (IGHG4, GNLY, CXCL1, CAPN14, and SAA-4). The candidate genes and main pathways related to heat tolerance in Santa Ines sheep require further investigation to understand their response to heat stress in different climatic conditions and under solar radiation. It is essential to verify whether these genes and pathways are present in different breeds and to understand the relationship between heat stress and other genes identified in this study., (© 2023. The Author(s) under exclusive licence to International Society of Biometeorology.)

Thermotolerance has become an essential factor in the prevention of the adverse effects of heat stress, but it varies among animals. Identifying genes related to heat adaptability traits is important for improving thermotolerance and for selecting more productive animals in hot environments. The primary objective of this research was to find candidate genes in the liver that play a crucial role in the heat stress response of Santa Ines sheep, which exhibit varying levels of heat tolerance. To achieve this goal, 80 sheep were selected based on their thermotolerance and placed in a climate chamber for 10 days, during which the average temperature was maintained at 36 °C from 10 a.m. to 4 p.m. and 28 °C from 4 p.m. to 10 a.m. A subset of 14 extreme animals, with seven thermotolerant and seven non-thermotolerant animals based on heat loss (rectal temperature), were selected for liver sampling. RNA sequencing and differential gene expression analysis were performed. Thermotolerant sheep showed higher expression of genes G Px3, RGS6 , GPAT3, VLDLR , LOC101108817, and EVC. These genes were mainly related to the Hedgehog signaling pathway, glutathione metabolism, glycerolipid metabolism, and thyroid hormone synthesis. These enhanced pathways in thermotolerant animals could potentially mitigate the negative effects of heat stress, conferring greater heat resistance., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2024 The Authors.)

The study of fatty acid (FA) and mineral content in beef is crucial for bridging health and taste. Understanding these components is essential for catering to consumer preferences for nutritious and tasty food, in line with current dietary trends and health recommendations. This holistic view of beef quality is key to helping both producers and consumers make more knowledgeable and health-oriented decisions in meat consumption. The objectives of this study were to 1) characterize the FA composition and mineral concentration of beef from Brangus cattle; 2) estimate their heritability; and 3) calculate the genetic and phenotypic correlations of carcass and meat quality traits to FA composition and mineral concentrations. Brangus steers were evaluated for meat quality and sampled for nutritional content measurements. Brangus cattle had palmitic acid levels as low as 21%, and stearic acid levels as high as 26%, which is notable since stearic acid is considered to have a neutral or potentially beneficial impact on cholesterol levels, unlike other saturated fats. Additionally, Brangus cattle had oleic acid levels as high as 53%, a beneficial monounsaturated fat, and linoleic acid concentrations as high as 12%, an essential omega-6 FA. Saturated FA showed weak negative correlations (-0.06 to -0.15) with hot carcass weight, marbling, and fat over ribeye, similar to polyunsaturated FA which had moderate negative correlations (-0.19 to -0.37) with these traits. Conversely, monounsaturated FA was positively correlated (0.16 to 0.34) with these traits, suggesting that higher levels of monounsaturated FA, particularly oleic acid, are associated with improved meat quality and consumer-desirable traits such as increased marbling. This relationship where higher marbling is linked with increased monounsaturated FA and decreased saturated FA is unique in Brangus cattle, differing from other breeds where increased intramuscular fat typically raises FA saturation levels. The variation in FA observed in Brangus cattle highlights the breed's potential to provide nutritionally enriched beef. With selective breeding, it may be possible to improve both the nutritional value and marbling of the meat, meeting consumer demand for healthier, tastier options. Overall, the study underscores the intricate relationships between FA composition, mineral content, and meat quality, with implications for breeding and nutrition strategies aimed at improving meat quality and healthfulness., (© The Author(s) 2024. Published by Oxford University Press on behalf of the American Society of Animal Science. All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.)

Background: In beef cattle, more than 50% of the energy input to produce a unit of beef is consumed by the female that produced the calf. Development of genomic tools to identify females with high genetic merit for reproductive function could increase the profitability and sustainability of beef production., Results: Genome-wide association studies (GWAS) were performed using a single-step genomic best linear unbiased prediction approach on pregnancy outcome traits from a population of Angus-Brahman crossbred heifers. Furthermore, a validation GWAS was performed using data from another farm. Heifers were genotyped with the Bovine GGP F250 array that contains 221,077 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 3 months. Two phenotypes were analyzed: pregnancy outcome to first-service AI (PAI; n = 1,481) and pregnancy status at the end of the breeding season (PEBS; n = 1,725). The heritability was estimated as 0.149 and 0.122 for PAI and PEBS, respectively. In the PAI model, one quantitative trait locus (QTL), located between 52.3 and 52.5 Mb on BTA7, explained about 3% of the genetic variation, in a region containing a cluster of γ-protocadherin genes and SLC25A2. Other QTLs explaining between 0.5% and 1% of the genetic variation were found on BTA12 and 25. In the PEBS model, a large QTL on BTA7 was synonymous with the QTL for PAI, with minor QTLs located on BTA5, 9, 10, 11, 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 QTLs on BTA10 and 12 were identified., Conclusions: In summary, QTLs and candidate SNPs identified were associated with pregnancy outcomes in beef heifers, 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 predictions of reproductive function in beef cattle. Moreover, additional research is warranted to study the function of candidate genes associated with QTLs., (© 2023. Chinese Association of Animal Science and Veterinary Medicine.)

Cattle lose heat predominantly through cutaneous evaporation at the skin-hair coat interface when experiencing heat stress. Sweating ability, sweat gland properties, and hair coat properties are a few of the many variables determining the efficacy of evaporative cooling. Sweating is a significant heat dissipation mechanism responsible for 85% of body heat loss when temperatures rise above 86⁰F. The purpose of this study was to characterize skin morphological parameters in Angus, Brahman, and their crossbred cattle. Skin samples were taken during the summer of 2017 and 2018 from a total of 319 heifers from six breed groups ranging from 100% Angus to 100% Brahman. Epidermis thickness decreased as the percentage of Brahman genetics increased where the 100% Angus group had a significantly thicker epidermis compared to the 100% Brahman animals. A more extended epidermis layer was identified in Brahman animals due to more pronounced undulations in this skin layer. Breed groups with 75% and 100% Brahman genes were similar and had the largest sweat gland area, indicative of superior resilience to heat stress, compared to breed groups with 50% or lower Brahman genetics. There was a significant linear breed group effect on sweat gland area indicating an increase of 862.0 µm 2 for every 25% increase in Brahman genetics. Sweat gland length increased as the Brahman percentage increased, while the sweat gland depth showed an opposite trend, decreasing from 100% Angus to 100% Brahman. The number of sebaceous glands was highest in 100% Brahman animals which had about 1.77 more sebaceous glands ( p < 0.05) per 4.6 mm 2 area. Conversely, the sebaceous gland area was greatest in the 100% Angus group. This study identified significant differences in skin properties related to heat exchange ability between Brahman and Angus cattle. Equally important, these differences are also accompanied by significant levels of variation within each breed, which is indicative that selection for these skin traits would improve the heat exchange ability in beef cattle. Further, selecting beef cattle for these skin traits would lead to increased resilience to heat stress without disrupting production traits., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Mateescu, Sarlo Davila, Hernandez, Andrade, Zayas, Rodriguez, Dikmen and Oltenacu.)

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., Competing Interests: None declared., (© The Author(s) 2023. Published by Oxford University Press on behalf of the American Society of Animal Science.)

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., (© The Author(s) 2022. Published by Oxford University Press on behalf of the American Society of Animal Science. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Skin and hair coat play important functions in maintaining homeostasis and thermoregulation for cattle, which can affect all modes of heat loss. Our objective was to investigate the effect of hyperthermia experienced in utero during late gestation on postnatal hair length, skin properties, and thermoregulation. Pregnant dams were heat stressed (n = 41) or actively cooled (n = 41) for the last ∼56 d of gestation and gave birth to heifers that were in utero heat stressed (IUHT) or in utero cooled (IUCL), respectively. Hair samples and skin tissue biopsies were collected from neck and rump locations at birth (d 0), 1 wk after weaning (d 63), and at 12 mo. Hair samples were also obtained at 4 and 8 mo. Skin tissue was stained with hematoxylin and eosin to visualize morphology. Hair length (short and long hairs, undercoat and topcoat, respectively), stratum corneum (SC) area, SC thickness, epidermis thickness, sweat gland (SWT) number, SWT cross-sectional area, SWT average size, sebaceous gland (SEB) number, SEB cross-sectional area, SEB average size, and sweat gland depth were assessed. Respiration rate, skin temperature, sweating rate, and rectal temperature was measured weekly from d 7 to 63. Additionally, thermoregulatory patterns were measured every 4 h over a 36-h interval beginning 4 d after weaning. Data were analyzed using PROC MIXED in SAS with a main effect of in utero treatment with location and time points analyzed separately. No difference in hair parameters were detected at d 0 or 12 mo. At d 63, IUHT heifers had longer average hair length (14.8 vs. 13.8 ± 0.2 mm, standard error), shorter undercoats (9.3 vs. 10.4 ± 0.3 mm), longer topcoats (19.6 vs. 17.1 ± 0.3 mm), and a greater difference between topcoat and undercoat (10.1 vs. 7.0 ± 0.4 mm). At 4 mo, IUHT heifers had longer average hair lengths (26.1 vs. 22.2 ± 1.0 mm) and longer topcoats (36.9 vs. 33.9 ± 1.1 mm), and at 8 mo, IUHT had longer average hair lengths (17.9 vs. 16.2 ± 0.6 mm), relative to IUCL. At d 0, IUHT heifers had more (13 vs. 9 ± 2 glands) but smaller average sized SEB (neck: 1,636 vs. 2,238 ± 243 µm 2 ; rump: 2,100 vs. 3,352 ± 379 µm 2 ) and reduced SC area (79,243 vs. 169,419 ± 13,071 µm 2 ). At d 63, IUHT had fewer SEB (11 vs. 15 ± 2 glands), smaller SWT (0.16 vs. 0.23 ± 0.02 mm 2 ), fewer SWT (16 vs. 23 ± 4 glands), and deeper SWT (0.5 vs. 0.4 ± 0.03 mm). At 12 mo, IUHT had greater distance from the skin surface to the most superficial SWT (0.016 vs. 0.015 ± 0.0004 mm), shorter distance to the deepest SWT (0.031 vs. 0.033 ± 0.001 mm), and smaller SWT (81.1 vs. 108.9 ± 10.8 µm 2 ), relative to IUCL. When measured both weekly and hourly, IUHT heifers had higher rectal temperature and sweating rate. Overall, in utero hyperthermia triggers long-lasting hair and skin adaptations, possibly leading to differences in postnatal thermoregulation., (The Authors. Published by Elsevier Inc. and Fass Inc. on behalf of the American Dairy Science Association®. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).)

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., (Copyright © 2021 Australian Society for Parasitology. Published by Elsevier Ltd. All rights reserved.)

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., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Rezende, Rodriguez, Leal-Gutiérrez, Elzo, Johnson, Carr and Mateescu.)

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 in longissimus dorsi muscle. 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&#95;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., Competing Interests: The authors have declared that no competing interests exist.

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., (© 2020 Stichting International Foundation for Animal Genetics.)

Tenderness is a major quality attribute for fresh beef steaks in the United States, and meat quality traits in general are suitable candidates for genomic research. The objectives of the present analysis were to (1) perform genome-wide association (GWA) analysis for marbling, Warner-Bratzler shear force (WBSF), tenderness, and connective tissue using whole-genome data in an Angus population, (2) identify enriched pathways in each GWA analysis; (3) construct a protein-protein interaction network using the associated genes and (4) perform a μ-calpain proteolysis assessment for associated structural proteins. An Angus-sired population of 2,285 individuals was assessed. Animals were transported to a commercial packing plant and harvested at an average age of 457 ± 46 days. After 48 h postmortem, marbling was recorded by graders' visual appraisal. Two 2.54-cm steaks were sampled from each muscle for recording of WBSF, and tenderness, and connective tissue by a sensory panel. The relevance of additive effects on marbling, WBSF, tenderness, and connective tissue was evaluated on a genome-wide scale using a two-step mixed model-based approach in single-trait analysis. A tissue-restricted gene enrichment was performed for each GWA where all polymorphisms with an association p -value lower than 1 × 10 -3 were included. The genes identified as associated were included in a protein-protein interaction network and a candidate structural protein assessment of proteolysis analyses. A total of 1,867, 3,181, 3,926, and 3,678 polymorphisms were significantly associated with marbling, WBSF, tenderness, and connective tissue, respectively. The associate region on BTA29 (36,432,655-44,313,046 bp) harbors 13 highly significant markers for meat quality traits. Enrichment for the GO term GO:0005634 (Nucleus), which includes transcription factors, was evident. The final protein-protein network included 431 interations between 349 genes. The 42 most important genes based on significance that encode structural proteins were included in a proteolysis analysis, and 81% of these proteins were potential μ-Calpain substrates. Overall, this comprehensive study unraveled genetic variants, genes and mechanisms of action responsible for the variation in meat quality traits. Our findings can provide opportunities for improving meat quality in beef cattle via marker-assisted selection., (Copyright © 2020 Leal-Gutiérrez, Rezende, Reecy, Kramer, Peñagaricano and Mateescu.)

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., (© The Author(s) 2020. Published by Oxford University Press on behalf of the American Society of Animal Science. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

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. The objectives of the present research were: 1) to perform eQTL and sQTL mapping analyses for meat quality traits in longissimus dorsi muscle; 2) to uncover genes whose expression is influenced by local or distant genetic variation; 3) to identify expression and splicing hot spots; and 4) to uncover genomic regions affecting the expression of multiple genes., Results: Eighty steers were selected for phenotyping, genotyping and RNA-seq evaluation. A panel of traits related to meat quality was recorded in longissimus dorsi muscle. Information on 112,042 SNPs and expression data on 8588 autosomal genes and 87,770 exons from 8467 genes were included in an expression and splicing quantitative trait loci (QTL) mapping (eQTL and sQTL, respectively). A gene, exon and isoform differential expression analysis previously carried out in this population identified 1352 genes, referred to as DEG, as explaining part of the variability associated with meat quality traits. The eQTL and sQTL mapping was performed using a linear regression model in the R package Matrix eQTL. Genotype and year of birth were included as fixed effects, and population structure was accounted for by including as a covariate the first PC from a PCA analysis on genotypic data. The identified QTLs were classified as cis or trans using 1 Mb as the maximum distance between the associated SNP and the gene being analyzed. A total of 8377 eQTLs were identified, including 75.6% trans, 10.4% cis, 12.5% DEG trans and 1.5% DEG cis; while 11,929 sQTLs were uncovered: 66.1% trans, 16.9% DEG trans, 14% cis and 3% DEG 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 the expression of other genes through cell signaling or by a direct transcriptional activation/repression mechanism., Conclusion: In the present analysis, we show that eQTL and sQTL mapping makes possible positional identification of gene and isoform expression regulators.

Although beef is a nutrient-rich foodstuff excelling in protein, vitamins, and minerals, there is controversy regarding the fat content of beef and its healthfulness in the diet. Although much of the fatty acid (FA) content in beef is considered "healthy fats," many consumers are confused about the different classifications of FA. The objectives of this study were to determine consumers' knowledge about the nutritional value of beef and its importance in purchasing decisions, and to gain a better understanding about preferences for changes in FA composition. Objectives of the study were completed through 2 consumer studies: 1) an online survey and 2) a taste-panel auction. In the online survey, respondents were asked to choose between 2 steaks that varied in polyunsaturated and saturated FA levels, iron content, and price. Respondents were also asked to categorize "Monounsaturated Fat," "Polyunsaturated Fat," "Saturated Fat," and "Trans Fat," as either "healthy" or "unhealthy" both before and after an educational excerpt was provided. The results from the online survey indicated many consumers are unclear about the differences in beef nutritional value, specifically FA content. Initially, only 66.4%, 69.1%, 79.1%, and 79.2% of respondents correctly categorized the monounsaturated, polyunsaturated, saturated, and trans fat, respectively. However, more than 90% of respondents correctly categorized the various FAs after an educational excerpt was provided. After survey respondents better understood the healthfulness of FA in beef, they were also willing to pay a premium for a steak with improved FA composition. However, these premiums diminished when participants had to actually put forth a monetary value for a steak in the taste-panel auction. Research shows that there is variation among cattle for FA composition. This provides opportunity to identify cattle with a favorable composition and market this product to the increasing population of health-conscious consumers. Our results provide insight for beef promotion and marketing opportunities and indicate that relaying information about FA content is extremely important to collect a premium for healthier beef., (© The Author(s) 2019. Published by Oxford University Press on behalf of the American Society of Animal Science. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Automated high-throughput phenotyping with sensors, imaging, and other on-farm technologies has resulted in a flood of data that are largely under-utilized. Drastic cost reductions in sequencing and other omics technology have also facilitated the ability for deep phenotyping of livestock at the molecular level. These advances have brought the animal sciences to a cross-roads in data science where increased training is needed to manage, record, and analyze data to generate knowledge and advances in Agriscience related disciplines. This paper describes the opportunities and challenges in using high-throughput phenotyping, "big data," analytics, and related technologies in the livestock industry based on discussions at the Livestock High-Throughput Phenotyping and Big Data Analytics meeting, held in November 2017 (see: https://www.animalgenome.org/bioinfo/community/workshops/2017/). Critical needs for investments in infrastructure for people (e.g., "big data" training), data (e.g., data transfer, management, and analytics), and technology (e.g., development of low cost sensors) were defined by this group. Though some subgroups of animal science have extensive experience in predictive modeling, cross-training in computer science, statistics, and related disciplines are needed to use big data for diverse applications in the field. Extensive opportunities exist for public and private entities to harness big data to develop valuable research knowledge and products to the benefit of society under the increased demands for food in a rapidly growing population., (Copyright © 2019 Koltes, Cole, Clemmens, Dilger, Kramer, Lunney, McCue, McKay, Mateescu, Murdoch, Reuter, Rexroad, Rosa, Serão, White, Woodward-Greene, Worku, Zhang and Reecy.)

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., (Published by Oxford University Press on behalf of the American Society of Animal Science 2019.)

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 <95% and minor allele frequency ≤0.05. A mixed model was used to analyze the response variables and included the identity by state matrix to control for population structure. A contemporary group (age, group, and sex) was included as fixed effect. Bonferroni correction was used to control for multiple testing. Eighteen SNPs on chromosomes 1, 2, 3, 4, 6, 7, 11, 15, 18, 20, 24, and 26 were significant for different traits. Our results suggest that loci related to Th17, Treg, and Th2 responses play an important role in the expression of resistant phenotypes. Several genes including ITGA4, MUC15, TLR3, PCDH7, CFI, CXCL10, TNF, CCL26, STAT3, GPX2, IL2RB, and STAT6 were identified as potential markers for resistance to natural H. contortus exposure. This is the first study that evaluates potential genetic markers for H. contortus resistance in Florida Native sheep., (© The Author(s) 2019. Published by Oxford University Press on behalf of the American Society of Animal Science. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

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.

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 Author(s) 2019. Published by Oxford University Press on behalf of the American Society of Animal Science. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Background: Meat quality related phenotypes are difficult and expensive to measure and predict but are ideal candidates for genomic selection if genetic markers that account for a worthwhile proportion of the phenotypic variation can be identified. The objectives of this study were: 1) to perform genome wide association analyses for Warner-Bratzler Shear Force (WBSF), marbling, cooking loss, tenderness, juiciness, connective tissue and flavor; 2) to determine enriched pathways present in each genome wide association analysis; and 3) to identify potential candidate genes with multiple quantitative trait loci (QTL) associated with meat quality., Results: The WBSF, marbling and cooking loss traits were measured in longissimus dorsi muscle from 672 steers. Out of these, 495 animals were used to measure tenderness, juiciness, connective tissue and flavor by a sensory panel. All animals were genotyped for 221,077 markers and included in a genome wide association analysis. A total number of 68 genomic regions covering 52 genes were identified using the whole genome association approach; 48% of these genes encode transmembrane proteins or membrane associated molecules. Two enrichment analysis were performed: a tissue restricted gene enrichment applying a correlation analysis between raw associated single nucleotide polymorphisms (SNPs) by trait, and a functional classification analysis performed using the DAVID Bioinformatic Resources 6.8 server. The tissue restricted gene enrichment approach identified eleven pathways including "Endoplasmic reticulum membrane" that influenced multiple traits simultaneously. The DAVID functional classification analysis uncovered eleven clusters related to transmembrane or structural proteins. A gene network was constructed where the number of raw associated uncorrelated SNPs for each gene across all traits was used as a weight. A multiple SNP association analysis was performed for the top five most connected genes in the gene-trait network. The gene network identified the EVC2, ANXA10 and PKHD1 genes as potentially harboring multiple QTLs. Polymorphisms identified in structural proteins can modulate two different processes with direct effect on meat quality: in vivo myocyte cytoskeletal organization and postmortem proteolysis., Conclusion: The main result from the present analysis is the uncovering of several candidate genes associated with meat quality that have structural function in the skeletal muscle.

Structural equation models involving latent variables are useful tools for formulating hypothesized models defined by theoretical variables and causal links between these variables. The objectives of this study were: (1) to identify latent variables underlying carcass and meat quality traits and (2) to perform whole-genome scans for these latent variables in order to identify genomic regions and individual genes with both direct and indirect effects. A total of 726 steers from an Angus-Brahman multibreed population with records for 22 phenotypes were used. A total of 480 animals were genotyped with the GGP Bovine F-250. The single-step genomic best linear unbiased prediction method was used to estimate the amount of genetic variance explained for each latent variable by chromosome regions of 20 adjacent SNP-windows across the genome. Three types of genetic effects were considered: (1) direct effects on a single latent phenotype; (2) direct effects on two latent phenotypes simultaneously; and (3) indirect effects. The final structural model included carcass quality as an independent latent variable and meat quality as a dependent latent variable. Carcass quality was defined by quality grade, fat over the ribeye and marbling, while the meat quality was described by juiciness, tenderness and connective tissue, all of them measured through a taste panel. From 571 associated genomic regions (643 genes), each one explaining at least 0.05% of the additive variance, 159 regions (179 genes) were associated with carcass quality, 106 regions (114 genes) were associated with both carcass and meat quality, 242 regions (266 genes) were associated with meat quality, and 64 regions (84 genes) were associated with carcass quality, having an indirect effect on meat quality. Three biological mechanisms emerged from these findings: postmortem proteolysis of structural proteins and cellular compartmentalization, cellular proliferation and differentiation of adipocytes, and fat deposition.

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.

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.

Water is an essential nutrient, but the effect it has on performance generally receives little attention. There are few systems and guidelines for collection of water intake (WI) phenotypes in beef cattle, which makes large-scale research on WI a challenge. The Beef Improvement Federation has established guidelines for feed intake (FI) and ADG tests, but no guidelines exist for WI. The goal of this study was to determine the test duration necessary for collection of accurate WI phenotypes. To facilitate this goal, individual daily WI and FI records were collected on 578 crossbred steers for a total of 70 d using an Insentec system at the Oklahoma State University Willard Sparks Beef Research Unit. Steers were fed in five groups and were individually weighed every 14 d. Within each group, steers were blocked by BW (low and high) and randomly assigned to one of four pens containing approximately 30 steers per pen. Each pen provided 103.0 m2 of shade and included an Insentec system containing six feed bunks and one water bunk. Steers were fed a constant diet across groups and DMI was calculated using the average of weekly percent DM within group. Average FI and WI for each animal were computed for increasingly large test durations (7, 14, 21, 28, 35, 42, 49, 56, 63, and 70 d), and ADG was calculated using a regression formed from BW taken every 14 d (0, 14, 28, 42, 56, and 70 d). Intervals for all traits were computed starting from both the beginning (day 0) and the end of the testing period (day 70). Pearson and Spearman correlations were computed for phenotypes from each shortened test period and for the full 70-d test. Minimum test duration was determined when the Pearson correlations were greater than 0.95 for each trait. Our results indicated that minimum test duration for WI, DMI, and ADG were 35, 42, and 70 d, respectively. No comparable studies exist for WI; however, our results for FI and ADG are consistent with those in the literature. Although further testing in other populations of cattle and areas of the country should take place, our results suggest that WI phenotypes can be collected concurrently with DMI, without extending test duration, even if following procedures for decoupled intake and gain tests.

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 (Tdb) 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 (σ2u = 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/(m2·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 objective was to evaluate the influence of varying amounts of Brahman genetics on body temperature under pasture conditions during hot weather. Vaginal temperatures were measured at 5-min intervals for 3 to 5 d on four occasions during August and September from a total of 190 pregnant cows that were either Angus, 2/8 Brahman (remainder Angus), Brangus (3/8 Brahman), 4/8 Brahman, 6/8 Brahman or Brahman. Vaginal temperature was higher for the first two replicates than for the second two replicates. In the first two replicates, average vaginal temperature did not differ between genetic groups, but average vaginal temperature from 1500 to 1900 h was lower for Brahman than other groups. In the second two replicates, average vaginal temperature was lower for cows that were 4/8 or higher Brahman than for cows that were 2/8 Brahman or Angus. Average vaginal temperature from 1500 to 1900 h was lower for cows that were 4/8 or higher Brahman than for cows that were 2/8 Brahman or Angus. In addition, Brahman cows had lower vaginal temperatures than cows that were 4/8 Brahman or 3/8 Brahman (i.e., Brangus). In one replicate, a tracking device was used to map cow location. At 1200 to 1300 h, cows that were 6/8 Brahman or Brahman had fewer observations near the tree line (i.e., in shade) than cows that were 4/8 Brahman or less. At 1500 to 1600 h, cows that were 4/8 or higher Brahman experienced fewer observations near the tree line than cows that contained a lower fraction of Brahman genetics. In summary, a minimum of 4/8 Brahman genetics was required to increase the ability to regulate body temperature and at least 6/8 Brahman when heat stress was severe. It is likely, therefore, that using Brahman genetics to optimize adaptation to thermal stress under conditions of severe heat stress requires a preponderance of Brahman genes.

The effect of Ovar-DRA and Ovar-DRB1 genotypes on faecal egg count (FEC) was determined in sheep and goats infected with Haemonchus contortus. One hundred and forty-three sheep from 3 different breeds (St. Croix, Katahdin and Dorper) and 150 goats from three different breeds (Spanish, Boer and Kiko) were used. Parasitological (FEC), haematological (packed cell volume) and immunological (IgA, IgG and IgM) parameters were measured. Sheep populations showed a higher FEC and humoural response than goat breeds. Genotypes were determined by high-resolution melting assays and by conventional PCR. For Ovar-DRA, sheep and goats carrying the AA genotype showed significant lower FEC than AG and GG genotypes. The additive effect was found to be 115.35 less eggs per gram of faeces for the A allele for goats. For Ovar-DRB1, only in sheep, the GC genotype was associated with low FEC. The additive effect was 316.48 less eggs per gram of faeces for the G allele, and the dominance effect was 538.70 less eggs per gram of faeces. The results indicate that single nucleotide polymorphisms within Ovar-DRA and Ovar-DRB1 could be potential markers to be used in selection programmes for improving resistance to Haemonchus contortus infection., (© 2018 John Wiley & Sons Ltd.)

Crossbreeding is a common strategy used in tropical and subtropical regions to enhance beef production, and having accurate knowledge of breed composition is essential for the success of a crossbreeding program. Although pedigree records have been traditionally used to obtain the breed composition of crossbred cattle, the accuracy of pedigree-based breed composition can be reduced by inaccurate and/or incomplete records and Mendelian sampling. Breed composition estimation from genomic data has multiple advantages including higher accuracy without being affected by missing, incomplete, or inaccurate records and the ability to be used as independent authentication of breed in breed-labeled beef products. The present study was conducted with 676 Angus-Brahman crossbred cattle with genotype and pedigree information to evaluate the feasibility and accuracy of using genomic data to determine breed composition. We used genomic data in parametric and non-parametric methods to detect population structure due to differences in breed composition while accounting for the confounding effect of close familial relationships. By applying principal component analysis (PCA) and the maximum likelihood method of ADMIXTURE to genomic data, it was possible to successfully characterize population structure resulting from heterogeneous breed ancestry, while accounting for close familial relationships. PCA results offered additional insight into the different hierarchies of genetic variation structuring. The first principal component was strongly correlated with Angus-Brahman proportions, and the second represented variation within animals that have a relatively more extended Brangus lineage-indicating the presence of a distinct pattern of genetic variation in these cattle. Although there was strong agreement between breed proportions estimated from pedigree and genetic information, there were significant discrepancies between these two methods for certain animals. This was most likely due to inaccuracies in the pedigree-based estimation of breed composition, which supported the case for using genomic information to complement and/or replace pedigree information when estimating breed composition. Comparison with a supervised analysis where purebreds are used as the training set suggest that accurate predictions can be achieved even in the absence of purebred population information.

Autogenous proteolytic enzymes of the calpain family are implicated in myofibrillar protein degradation. As a result, the μ-calpain gene and its specific inhibitor, calpastatin, have been repeatedly investigated for their association with meat quality traits in cattle; however, no functional mutation has been identified for these two genes. The objectives of this study were: (1) to assess breed composition effect on tenderness; (2) to perform a linkage disequilibrium (LD) analysis in μ-calpain and calpastatin genes as well as an association analyses with tenderness; and (3) to analyze putative functional SNPs inside the significant LD block for an effect on tenderness. Tenderness measurements and genotypes for 16 SNPs in μ-calpain gene and 28 SNPs in calpastatin gene from 673 steers were analyzed. A bioinformatic analysis identified "putative functional SNPs" inside the associated LD block - polymorphisms able to produce a physical and/or chemical change in the DNA, mRNA, or translated protein in silico . Breed composition had a significant ( P < 0.0001) effect on tenderness where animals with more than 80% Angus composition had the most tender meat. One 11-kb LD-block and three LD-blocks of 37, 17, and 14 kb in length were identified in the μ-calpain and calpastatin genes, respectively. Out of these, the LD-block 3 in calpastatin, tagged by SNPs located at 7-98566391 and 7-98581038, had a significant effect on tenderness with the TG-CG diplotype being approximately 1 kg more tender than the toughest diplotype, TG-CG. A total of 768 SNPs in the LD-block 3 of calpastatin were included in the bioinformatic analysis, and 28 markers were selected as putative functional SNPs inside the LD-block 3 of calpastatin; however, none of them were polymorphic in this population. Out of 15 initial polymorphisms segregating inside the LD-block 3 of calpastatin in this population, markers ARSUSMARC116, Cast5, rs730723459, and rs210861835 were found to be significantly associated with tenderness.

The objective of this study was to determine the influence of Brahman genetics on muscle contractile and metabolic phenotype and postmortem proteolysis. Cattle used in this study represent a continuous spectrum of Angus-Brahman genetic variation. Steers were harvested and Longissimus samples were collected at 1.5h, 24h, and 14d postmortem. Proteolysis during the 14d aging period was evaluated, along with Warner-Bratzler shear force (WBSF) and trained sensory panel tenderness. Myosin heavy chain composition and enzymatic activity were used to evaluate fiber type characteristics. As Brahman influence increased, WBSF increased and sensory tenderness decreased. Calpain-1 autolysis decreased as Brahman percentage increased, and corresponded with reduced degradation of troponin-T, desmin, and titin. Increasing Brahman percentage was associated with greater citrate synthase activity and greater cross-sectional area of type IIx fibers. Brahman-influenced cattle produced tougher steaks and exhibited decreased protein degradation. Thus, Brahman genetics impacted not only the calpain-calpastatin system, but also muscle fiber size and metabolic properties., (Copyright © 2017 Elsevier Ltd. All rights reserved.)

Improvements in eating satisfaction will benefit consumers and should increase beef demand which is of interest to the beef industry. Tenderness, juiciness, and flavor are major determinants of the palatability of beef and are often used to reflect eating satisfaction. Carcass qualities are used as indicator traits for meat quality, with higher quality grade carcasses expected to relate to more tender and palatable meat. However, meat quality is a complex concept determined by many component traits making interpretation of genome-wide association studies (GWAS) on any one component challenging to interpret. Recent approaches combining traditional GWAS with gene network interactions theory could be more efficient in dissecting the genetic architecture of complex traits. Phenotypic measures of 23 traits reflecting carcass characteristics, components of meat quality, along with mineral and peptide concentrations were used along with Illumina 54k bovine SNP genotypes to derive an annotated gene network associated with meat quality in 2,110 Angus beef cattle. The efficient mixed model association (EMMAX) approach in combination with a genomic relationship matrix was used to directly estimate the associations between 54k SNP genotypes and each of the 23 component traits. Genomic correlated regions were identified by partial correlations which were further used along with an information theory algorithm to derive gene network clusters. Correlated SNP across 23 component traits were subjected to network scoring and visualization software to identify significant SNP. Significant pathways implicated in the meat quality complex through GO term enrichment analysis included angiogenesis, inflammation, transmembrane transporter activity, and receptor activity. These results suggest that network analysis using partial correlations and annotation of significant SNP can reveal the genetic architecture of complex traits and provide novel information regarding biological mechanisms and genes that lead to complex phenotypes, like meat quality, and the nutritional and healthfulness value of beef. Improvements in genome annotation and knowledge of gene function will contribute to more comprehensive analyses that will advance our ability to dissect the complex architecture of complex traits.

The fatty acid profile of beef is a complex trait that can benefit from gene-interaction network analysis to understand relationships among loci that contribute to phenotypic variation. Phenotypic measures of fatty acid profile from triacylglycerol and phospholipid fractions of longissimus muscle, pedigree information, and Illumina 54 k bovine SNP genotypes were utilized to derive an annotated gene network associated with fatty acid composition in 1,833 Angus beef cattle. The Bayes-B statistical model was utilized to perform a genome wide association study to estimate associations between 54 k SNP genotypes and 39 individual fatty acid phenotypes within each fraction. Posterior means of the effects were estimated for each of the 54 k SNP and for the collective effects of all the SNP in every 1-Mb genomic window in terms of the proportion of genetic variance explained by the window. Windows that explained the largest proportions of genetic variance for individual lipids were found in the triacylglycerol fraction. There was almost no overlap in the genomic regions explaining variance between the triacylglycerol and phospholipid fractions. Partial correlations were used to identify correlated regions of the genome for the set of largest 1 Mb windows that explained up to 35% genetic variation in either fatty acid fraction. SNP were allocated to windows based on the bovine UMD3.1 assembly. Gene network clusters were generated utilizing a partial correlation and information theory algorithm. Results were used in conjunction with network scoring and visualization software to analyze correlated SNP across 39 fatty acid phenotypes to identify SNP of significance. Significant pathways implicated in fatty acid metabolism through GO term enrichment analysis included homeostasis of number of cells, homeostatic process, coenzyme/cofactor activity, and immunoglobulin. These results suggest different metabolic pathways regulate the development of different types of lipids found in bovine muscle tissues. Network analysis using partial correlations and annotation of significant SNPs can yield information about the genetic architecture of complex traits.

Product quality is a high priority for the beef industry because of its importance as a major driver of consumer demand for beef and the ability of the industry to improve it. A 2-prong approach based on implementation of a genetic program to improve eating quality and a system to communicate eating quality and increase the probability that consumers' eating quality expectations are met is outlined. The objectives of this study were 1) to identify the best carcass and meat composition traits to be used in a selection program to improve eating quality and 2) to develop a relatively small number of classes that reflect real and perceptible differences in eating quality that can be communicated to consumers and identify a subset of carcass and meat composition traits with the highest predictive accuracy across all eating quality classes. Carcass traits, meat composition, including Warner-Bratzler shear force (WBSF), intramuscular fat content (IMFC), trained sensory panel scores, and mineral composition traits of 1,666 Angus cattle were used in this study. Three eating quality indexes, EATQ1, EATQ2, and EATQ3, were generated by using different weights for the sensory traits (emphasis on tenderness, flavor, and juiciness, respectively). The best model for predicting eating quality explained 37%, 9%, and 19% of the variability of EATQ1, EATQ2, and EATQ3, and 2 traits, WBSF and IMFC, accounted for most of the variability explained by the best models. EATQ1 combines tenderness, juiciness, and flavor assessed by trained panels with 0.60, 0.15, and 0.25 weights, best describes North American consumers, and has a moderate heritability (0.18 ± 0.06). A selection index (I= -0.5[WBSF] + 0.3[IMFC]) based on phenotypic and genetic variances and covariances can be used to improve eating quality as a correlated trait. The 3 indexes (EATQ1, EATQ2, and EATQ3) were used to generate 3 equal (33.3%) low, medium, and high eating quality classes, and linear combinations of traits that best predict class membership were estimated using a predictive discriminant analysis. The best predictive model to classify new observations into low, medium, and high eating quality classes defined by the EATQ1 index included WBSF, IMFC, HCW, and marbling score and resulted in a total error rate of 47.06%, much lower than the 60.74% error rate when the prediction of class membership was based on the USDA grading system. The 2 best predictors were WBSF and IMFC, and they accounted for 97.2% of the variability explained by the best model.

The objective of this study was to estimate genetic parameters for intramuscular fatty acids from triacylglycerol (TAG) and phospholipid (PL) fractions in beef LM tissue. Longissimus muscle samples were obtained from 1,833 Angus cattle to determine the intramuscular fatty acid composition for 31 lipids and lipid classes from TAG and PL fractions and were classified by structure into saturated (SFA), monounsaturated (MUFA), polyunsaturated (PUFA), omega-3 (n-3), and omega-6 (n-6) fatty acids. An atherogenic index (AI) was also determined as a measure of the unsaturated fatty acid to SFA ratio. Restricted maximum likelihood methods combined with pedigree data were used to estimate variance components with the WOMBAT software package. Heritability estimates ranged from 0.00 to 0.63 for the major classes of fatty acids. Heritability estimates differed between the TAG and PL fractions, with higher estimates for TAG up to 0.64 and lower estimates for PL that ranged from 0.00 to 0.14. Phenotypic and genetic correlations among individual fatty acids were determined for the TAG fraction as well as among carcass traits, including rib eye area, numerical marbling score, yield grade, ether fat, and Warner-Bratzler shear force value. Strong negative or positive genetic correlations were observed among individual fatty acids in the TAG fraction, which ranged from -0.99 to 0.97 ( < 0.05). Moderate correlations between carcass traits and fatty acids from the TAG fraction ranged from -0.43 to 0.32 ( < 0.05). These results indicate that fatty acids prominent in beef tissues show significant genetic variation as well as genetic relationships with carcass traits.

The objective of this study was to estimate heritabilities for sensory traits and genetic correlations among sensory traits and with marbling score (MS), Warner-Bratzler shear force (WBSF), and intramuscular fat content (IMFC). Samples of LM from 2,285 Angus cattle were obtained and fabricated into steaks for laboratory analysis and 1,720 steaks were analyzed by a trained sensory panel. Restricted maximum likelihood procedures were used to obtain estimates of variance and covariance components under a multitrait animal model. Estimates of heritability for MS, IMFC, WBSF, tenderness, juiciness, and connective tissue traits were 0.67, 0.38, 0.19, 0.18, 0.06, and 0.25, respectively. The genetic correlations of MS with tenderness, juiciness, and connective tissue were estimated to be 0.57 ± 0.14, 1.00 ± 0.17, and 0.49 ± 0.13, all positive and strong. Estimated genetic correlations of IMFC with tenderness, juiciness, and connective tissue were 0.56 ± 0.16, 1.00 ± 0.21, and 0.50 ± 0.15, respectively. The genetic correlations of WBSF with tenderness, juiciness, and connective tissue were all favorable and estimated to be -0.99 ± 0.08, -0.33 ± 0.30 and -0.99 ± 0.07, respectively. Strong and positive genetic correlations were estimated between tenderness and juiciness (0.54 ± 0.28) and between connective tissue and juiciness (0.58 ± 0.26). In general, genetic correlations were large and favorable, which indicated that strong relationships exist and similar gene and gene networks may control MS, IMFC, and juiciness or WBSF, panel tenderness, and connective tissue. The results from this study confirm that MS currently used in selection breeding programs has positive genetic correlations with tenderness and juiciness and, therefore, is an effective indicator trait for the improvement of tenderness and juiciness in beef. This study also indicated that a more objective measure, particularly WBSF, a trait not easy to improve through phenotypic selection, is an excellent candidate trait for genomic selection aimed at improving eating satisfaction.

The objective of this study was to characterize variation and identify SNP and chromosomal regions associated with mineral concentrations in LM of Angus beef cattle. Samples of LM from 2,285 Angus cattle were obtained, and concentrations of 7 minerals, including iron, magnesium, manganese, phosphorus, potassium, sodium, and zinc, were quantified. Genomic DNA extracted from the ground beef sample used for mineral composition was genotyped with the Bovine SNP50 Infinium II BeadChip, and effects of SNP on each trait were estimated using the Bayes-Cπ module of GenSel software. Pedigree-based estimates of heritabilities and corresponding genetic variances indicate iron was the only mineral concentration that could be considered a good candidate for manipulation by genomic selection. The amount of variation that could be accounted for by SNP genotypes was concordant with pedigree-based heritabilities and varied from very low for potassium and sodium (<0.09) to medium high (0.37) for iron. Although significant chromosomal regions were identified for all minerals analyzed in this study, further study focused on iron. Seven regions on 6 chromosomes (1, 2, 7, 10, 15, and 28) were identified to have a major effect on the iron content of LM in Angus cattle. The accuracy of direct genomic values (DGV) for iron concentration was estimated using a 5-fold cross-validation strategy. The accuracy of DGV estimated as the genetic correlation between DGV and the phenotype (iron concentration) adjusted for contemporary groups was 0.59. A bivariate animal model was used to estimate genetic correlations between iron concentrations and a reduced set of economically important carcass traits: HCW, rib eye area, calculated USDA yield grade, percent KPH, and marbling score. The genetic correlations between iron concentration and HCW, percentage KPH, marbling score, and rib eye area were small (-0.19 to 0.15) and nonsignificant. Although still weak (0.22), a positive significant genetic correlation was identified between iron content and USDA calculated yield grade. Beef is a major contributor of iron and zinc in the human diet, and this study found that iron content might be effectively manipulated through marker-assisted selection programs, without compromising other carcass and palatability traits.

The objective of this study was to estimate genetic parameters for concentrations of minerals in LM and to evaluate their associations with beef palatability traits. Samples of LM from 2,285 Angus cattle were obtained and fabricated into steaks for analysis of mineral concentrations and for trained sensory panel assessments. Nine minerals, including calcium, copper, iron, magnesium, manganese, phosphorus, potassium, sodium, and zinc, were quantified. Restricted maximum likelihood procedures were used to obtain estimates of variance and covariance components under a multiple-trait animal model. Estimates of heritability for mineral concentrations in LM varied from 0.01 to 0.54. Iron and sodium were highly and moderately heritable, respectively, whereas the other minerals were lowly heritable except for calcium, copper, and manganese, which exhibited no genetic variation. Strong positive genetic correlations existed between iron and zinc (0.49, P < 0.05), between magnesium and phosphorus (0.88, P < 0.05), between magnesium and sodium (0.68, P < 0.05), and between phosphorus and potassium (0.69, P < 0.05). Overall tenderness assessed by trained sensory panelists was positively associated with manganese, potassium, and sodium and negatively associated with phosphorus and zinc concentrations (P < 0.05). Juiciness assessed by trained sensory panelists was negatively associated with magnesium and positively associated with manganese and sodium concentrations (P < 0.05). Livery or metallic flavor was not associated with any of the minerals (P > 0.05). Beefy flavor was positively associated with calcium, iron, and zinc and negatively associated with sodium concentration, whereas a painty or fishy flavor was positively associated with sodium and negatively associated with calcium and potassium concentrations (P < 0.05). Beef is a major contributor of iron and zinc in the human diet, and these results demonstrate sufficient genetic variation for these traits to be improved through marker-assisted selection programs without compromising beef palatability.

Fatty acid profiles and intramuscular expression of genes involved in fatty acid metabolism were characterized in concentrate- (CO) and forage- (FO) based finishing systems. Intramuscular samples from the adductor were taken at slaughter from 99 heifers finished on a CO diet and 58 heifers finished on a FO diet. Strip loins were obtained at fabrication to evaluate fatty acid profiles of LM muscle for all 157 heifers by using gas chromatography fatty acid methyl ester analysis. Composition was analyzed for differences by using the General Linear Model (GLM) procedure in SAS. Differences in fatty acid profile included a greater atherogenic index, greater percentage total MUFA, decreased omega-3 to omega-6 ratio, decreased percentage total PUFA, and decreased percentage omega-3 fatty acids in CO- compared with FO-finished heifers (P<0.05). Fatty acid profiles from intramuscular samples were ranked by the atherogenic index, and 20 heifers with either a high (HAI; n=10) or low (LAI; n=10) atherogenic index were selected for gene expression analysis using real-time PCR (RT-PCR). Gene expression data for the 20 individuals were analyzed as a 2 by 2 factorial arrangement of treatments using the GLM procedure in SAS. There was no significant diet × atherogenic index interaction identified for any gene (P>0.05). Upregulation was observed for PPARγ, fatty acid synthase (FASN), and fatty acid binding protein 4 (FABP4) in FO-finished compared with CO-finished heifers in both atherogenic index categories (P<0.05). Upregulation of diglyceride acyl transferase 2 (DGAT2) was observed in FO-finished heifers with a HAI (P<0.05). Expression of steroyl Co-A desaturase (SCD) was upregulated in CO-finished heifers with a LAI, and downregulated in FO-finished heifers with a HAI (P<0.05). Expression of adiponectin (ADIPOQ) was significantly downregulated in CO-finished heifers with a HAI compared with all other categories (P<0.05). The genes identified in this study which exhibit differential regulation in response to diet or in animals with extreme fatty acid profiles may provide genetic markers for selecting desirable fatty acid profiles in future selection programs.

The objective of this study was to estimate genetic parameters for carnitine, creatine, creatinine, carnosine, and anserine concentration in LM and to evaluate their associations with Warner-Bratzler shear force (WBSF) and beef palatability traits. Longissimus muscle samples from 2,285 Angus cattle were obtained and fabricated into steaks for analysis of carnitine, creatine, creatinine, carnosine, anserine, and other nutrients, and for trained sensory panel and WBSF assessments. Restricted maximum likelihood procedures were used to obtain estimates of variance and covariance components under a multiple-trait animal model. Estimates of heritability for carnitine, creatine, creatinine, carnosine, and anserine concentrations in LM from Angus cattle were 0.015, 0.434, 0.070, 0.383, and 0.531, respectively. Creatine, carnosine, and anserine were found to be moderately heritable, whereas almost no genetic variation was observed in carnitine and creatinine. Moderate positive genetic (0.25, P < 0.05) and phenotypic correlations (0.25, P < 0.05) were identified between carnosine and anserine. Medium negative genetic correlations were identified between creatine and both carnosine (-0.53, P < 0.05) and anserine (-0.46, P < 0.05). Beef and livery/metallic flavor were not associated with any of the 5 compounds analyzed (P > 0.10), and carnitine concentrations were not associated (P > 0.10) with any of the meat palatability traits analyzed. Carnosine was negatively associated with overall tenderness as assessed by trained sensory panelists. Similar negative associations with overall tenderness were identified for creatinine and anserine. Painty/fishy was the only flavor significantly and negatively associated with creatinine and carnosine. These results provide information regarding the concentration of these compounds, the amount of genetic variation, and evidence for negligible associations with beef palatability traits in LM of beef cattle.

Beef is considered to be an excellent source of dietary iron. However, little is known about the genetic control of beef iron content. We hypothesized that genetic polymorphisms in transferrin receptor 2 (TFR2) and solute carrier family 40 (iron-regulated transporter), member 1 (SLC40A1) could influence skeletal muscle iron content. The objective of this study was to use Angus cattle to identify single-nucleotide polymorphisms (SNPs) in the exons and flanking regions of the bovine TFR2 and SLC40A1 genes and to evaluate the extent to which genetic variation in them was associated with bovine longissimus dorsi muscle iron content. Ten novel SNPs were identified in TFR2, of which one SNP tended to be associated (P < 0.013) with skeletal muscle iron content. Nine novel SNPs in SLC40A1, NC007300: rs133108154, rs137140497, rs135205621, rs136600836, rs134388440, rs136347850, rs134186279, rs134621419 and rs137555693, were identified, of which SNPs rs134388440, rs136347850 and rs137555693 were significantly associated (P < 0.007) with skeletal muscle iron content. High linkage disequilibrium was observed among SLC40A1 SNPs rs134388440, rs136347850 and rs137555693 (R(2)  > 0.99), from which two haplotypes, TGC and CAT, were defined. Beef from individuals that were homozygous for the TGC haplotype had significantly (P < 0.001) higher iron content than did beef from CAT homozygous or heterozygous individuals. The estimated size of effect of the identified haplotypes was 0.3% of the phenotypic variance. In conclusion, our study provides evidence for genetic control of beef iron concentration. Moreover, SNPs identified in SLC40A1, rs134388440, rs136347850 and rs137555693 might be useful markers for the selection of Angus cattle for altered iron content., (© 2011 The Authors, Animal Genetics © 2011 Stichting International Foundation for Animal Genetics.)

Thirty-three steer calves were used to determine the effect of sire breed (Angus or Charolais), time of weaning [normal weaned at approximately 210 d of age (NW) or late weaned at approximately 300 d of age (LW)], and muscle type [LM and semitendinosus muscle (STN)] on fatty acid composition. The whole plot consisted of a 2 (sire breed) × 2 (time of weaning) treatment arrangement, and the subplot treatment was muscle type. Body weights were recorded at 28-d intervals to determine animal performance. Muscle biopsies were collected on d 127 and 128 of finishing. All calves were slaughtered on d 138, and carcass data were collected. Angus-sired steers had lighter initial BW (271 vs. 298 kg; P = 0.02), and LW steers were heavier (351 vs. 323 kg; P = 0.03) on d 28, but no other differences in BW were noted. Charolais-sired steers had larger LM area (P = 0.03), reduced yield grades (P = 0.01), less 12th-rib fat (P < 0.01), and less marbling (P < 0.01) than Angus-sired steers. Carcass measures overall indicate Angus-sired steers were fatter. Hot carcass weight was heavier (348 vs. 324 kg; P = 0.04) in LW steers than NW steers. No other differences (P > 0.05) were observed for feedlot performance or carcass characteristics. Total lipids were extracted from muscle biopsies, derivatized to their methyl esters, and analyzed using gas chromatography. The LM had greater SFA (43.94 vs. 35.76%; P < 0.01) and decreased unsaturated fatty acids (UFA; 56.90 vs. 66.19%; P < 0.01) compared with the STN. Percent total MUFA was greater in STN than LM (51.05 vs. 41.98%; P < 0.01). Total SFA, UFA, and MUFA did not differ due to sire breed or time of weaning. Total PUFA differed (P = 0.04) due to a sire breed × time of weaning interaction but did not differ due to muscle type, with greater PUFA in NW Charolais than any other sire breed × time of weaning combination. Observed changes in percent MUFA may be a result of greater Δ(9)-desaturase activity. The calculated desaturase index suggests STN has a greater Δ(9)-desaturase activity than LM, but no differences (P > 0.05) between sire breed or time of weaning were observed. These results indicate that sire breed, time of weaning, and muscle type all affect fatty acid composition in beef. This information provides insight into factors for manipulation of beef fatty acids. More research is needed to identify beef cuts based on fatty acid profile and healthfulness.