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Summary Some livestock breeds face the challenge of reduced genetic variation, increased inbreeding depression owing to genetic drift and selection. Hybridization can reverse these processes and increase levels of productivity and adaptation to various environmental stressors. Samples from American Brangus were used to evaluate the indicine/taurine composition through nine generations (~45 years) after the hybridization process was completed. The purpose was to determine how hybridization alters allelic combinations of a breed over time when genetic factors such as selection and drift are operating. Furthermore, we explored genomic regions with deviations from the expected composition from the progenitor breeds and related these regions to traits under selection. The Brangus composition deviated from the theoretical expectation, defined by the breed association, of 62.5% taurine, showing taurine composition to be 70.4 ± 0.6%. Taurine and indicine proportion were not consistent across chromosomes. Furthermore, these non‐uniform areas were found to be associated with traits that were probably under selection such as intermuscular fat and average daily gain. Interestingly, the sex chromosomes were predominantly taurine, which could be due to the composite being formed particularly in the final cross that resulted in progeny designated as purebred Brangus. This work demonstrated the process of new breed formation on a genomic level. It suggests that factors like genetic drift, selection and complementarity shift the genetic architecture into a uniquely different population. These findings are important to better understand how hybridization and crossbreeding systems shape the genetic architecture of composite populations.

Reducing the prevalence of hypoxia-induced pulmonary hypertension (PH) remains a challenge to high-altitude beef production systems. Previous research and selection strategies have focused on the impact of bulls with PH in gain-test; however, little information is available on heifers that are typically developed in grazing systems. We hypothesized that indicator traits for PH in heifers are genomically associated with growth traits. The objectives of this study were to 1) identify SNP associated with yearling mean pulmonary arterial pressure (YPAP) and growth traits, 2) evaluate sequence variants common to YPAP and growth traits, and 3) identify underlying genes for QTL in Angus cattle. Yearling heifers (n = 1180) grazing in a high-altitude beef production system were measured for YPAP. Additionally, growth measures such as age of dam adjusted birth weight (BW), 205 d weaning weight (WW), 365 d yearling weight (YW), 365 d hip height (HH), and 160 d post-weaning gain (PWG) were also recorded. Isolated DNA from blood, hair, or blood card samples were analyzed using the Ilumina BovineSNP50 Beadchip. Genome-wide association analyses were conducted using an additive multi-locus mixed model with a 5% false discovery rate to account for multiple comparisons. Genotypes adjusted for FDR (P ≤ 1.00E−05; number of SNP) were associated with BW (2), YW (1), PWG (1), and HH (6), but no SNP were associated with YPAP or WW at this significance level. Associated SNP (P ≤ 1.00E−03; number of SNP) were identified for YPAP (37), BW (42), WW (31), YW (38), PWG (36), and HH (65). There was one SNP concordant with YPAP, YW, and HH, another with YPAP, YW, and PWG, and one SNP was concordant between YPAP and BW. Underlying genes within 1 kb of concordant SNP were SLC36A2 and CFAP58 and are involved in small amino acid transportation and cell cycle processes, respectively. Results suggested that 2 genomic regions may co-associate YPAP and growth traits. However, given these SNP accounted for

Precision livestock management has become a new field of study as the result of recent advancements in real-time global positioning system (GPS) tracking, accelerometer and other sensor technologies. Real-time tracking and accelerometer monitoring has the potential to remotely detect livestock disease, animal well-being and grazing distribution issues and notify ranchers and graziers so that they can respond as soon as possible. On-going research has shown that accelerometers can remotely monitor livestock behavior and detect activity changes that are associated with disease and parturition. GPS tracking can also detect parturition by monitoring the distance between a ewe and the remainder of the flock. Tracking also has the potential to detect water system failures. Combinations of GPS tracking and accelerometer monitoring may be more accurate than either device used by itself. Real-time GPS tracking can identify when livestock congregate in environmental sensitive areas which may allow managers the chance to respond before resource degradation occurs. Identification of genetic markers associated with terrain use, decreased cost of GPS tracking and novel tracking data processing should facilitate development of tools needed for genetic selection for cattle grazing distribution. Precision livestock management has potential to improve welfare of livestock grazing rangelands and forested lands, reduce labor costs and improve ranch profitability and improve the condition and sustainability of riparian areas and other environmental sensitive areas on grazing lands around the world.

High Mountain Disease (HMD) in cattle is a consequence of altitude-induced (> 1500 m) pulmonary hypertension (PH). Pulmonary arterial pressure (PAP; mmHg) is an indicator of PH-HMD and moderately heritable. This study analyzed repeated measures of PAP in growing bulls and estimated correlations across elevations and ages. Data included breed, PAP, elevation, weights and ages in spring-born bulls from the Agriculture Research, Development, and Education Center (ARDEC) in Colorado. Five PAP measurements were collected from each bull: 1) Weaning PAP at ARDEC (1,525 m); 2) Yearling PAP at ARDEC (i.e., gain-test); 3) PAP after acclimating for 28 days at Fort Lewis College (FLC; 2,470 m); 4) before returning to ARDEC from FLC after 110 days of grazing; and 5) after re-acclimating for 57 days to the moderate elevation and feeding systems at ARDEC when bulls were 18 months of age. Across these 5 times in Angus (n = 18) and Hereford (n = 12) bulls, PAP measures were: 1) 37.97 ± 0.37; 2) 40.93 ± 0.77; 3) 46.10 ± 1.48; 4) 45.00 ± 1.11; and 5) 42.23 ± 0.67, respectively. Breed and elevation-age were important (P < 0.05) sources of variation. Also, PAP changed (P < 0.05) across the 5 time periods (i.e., increased with altitude and then declined as bulls returned to moderate altitude). Yearling PAP measurements collected at 1,525 m were highly correlated with PAP measures at 2,470 m, as well as a PAP collected at 18.3 ± 0.1 mo of age at 1,525 m (r = 0.93 to 0.99); therefore, suggesting that the yearling PAP measurement collected at 1,525 m in gain-tested bulls was an adequate predictor of PAP at elevations of 1,525 and 2,470 m as bulls aged to 18 months; however, additional study of bovine PAP across elevations, ages, and rates of gain is warranted.

Pulmonary hypertension is a noninfectious disease of cattle at altitudes > 1524 m (5,000 ft). Mean pulmonary arterial pressures (mPAP) ≥ 50 mmHg is used as an indicator for pulmonary hypertension in cattle. Meat quality attribute, such as color, critically influencing consumer purchase decision, is economically significant. However, the effect of pulmonary arterial pressures (PAP) on postmortem beef color has not been investigated. To examine this, instrumental color, metmyoglobin reducing activity (MRA), and lipid oxidation of aged strip loins (longissimus lumborum; LL) steaks from high PAP (98±13; n = 5) and low PAP score (41±3; n = 6) fattened Angus steers (i.e., live weight of ~600 kg) were evaluated during simulated retail display (day 1, 3, 5, 7, 9). A split-plot design was used to analyze the effects of PAP score and display day on instrumental color, MRA, and lipid oxidation. Data analysis was performed using R with the lme4 package as a mixed model, where PAP score (high or low), display day, and their interactions were the fixed effects, and random effect was individual steer. Differences between least square means (P < 0.05) were determined by Tukey’s multiple comparisons. An interaction (P < 0.05) between PAP score and display day for redness (a* value), chroma, hue, and MRA was observed. The LL steaks from high PAP score animal had lower (P < 0.05) redness, chroma, and hue, than from low PAP score steer on day 9. A main effect (P < 0.05) of display day on lipid oxidation of was observed, with lipid oxidation increasing as display days increased. The results of current study indicated that the LL steaks from steers with high PAP score have lower color stability than those from steers with low PAP score during simulated retail display. Research partially supported by USDA-NIFA grant: 2018-67015-28241.

The objective of the study was to evaluate if a genetic relationship exists between pulmonary arterial pressure (PAP) measured at high elevation with traits associated with moderate elevation feedlot and carcass traits. For this analysis, PAP, feed intake, and carcass data were taken from 6,898, 558, and 1,627 animals, respectively. At an elevation of 2,115 m, PAP measurements were collected, then a selective group of steers was relocated to a moderate elevation feedlot (1,500 m) where feed intake data were collected. Genetic relationships were evaluated with 5-trait animal models using REML statistical analysis. For all traits in the analysis, fixed effects and contemporary groups were assigned as well as a direct genetic random effect. For weaning weight, a maternal permanent environmental effect was applied in the analysis. For PAP, the heritability estimate was 0.29 ± 0.03. Genetic correlations between PAP with feedlot traits was positive, with estimates of 0.34 ± 0.20 (average dry matter intake) and 0.05 ± 17 (average daily gain). The strongest genetic correlation between PAP and carcass performance traits were those of rib eye area (-0.30 ± 0.12) and calculated yield grade (0.29 ± 0.13). Genetic correlations between PAP and marbling score, back fat, or hot carcass weight were 0.00 ± 0.13, -0.07 ± 0.13, and 0.14 ± 0.10, respectively. These results suggest a favorable genetic relationship exists between PAP with feedlot and carcass traits.

High altitude disease (HAD) is a hypoxia-influenced pathologic condition experienced by cattle raised at high elevations (> 1,524 m). Pulmonary arterial pressure (PAP) is a common diagnostic tool used as an indicator of susceptibility to develop HAD. Given PAP is moderately heritable, possibilities to genetically reduce the incidence of HAD are feasible. However, an alternative strategy could be given by heterosis, since non-additive genetic effects have been related to survivability and environmental fitness. Therefore, objectives of this study were to determine heterosis and breed percentage effects on PAP measurements. A total of 1,083 cattle with varying percentages of Simmental, Angus, Hereford and Red Angus breeds were used for the study. Such animals’ available information included PAP records, PAP test date, PAP technician, sex, herd of origin and breed percentages of parents. A general linear model was utilized to estimate the effect of heterosis on PAP. Contemporary group (defined as a combination between herd, PAP date, PAP technician and sex) was included as a categorical fixed effect; whereas the age at PAP measurement and the degree of outcross were included as linear covariates. Similarly, breed effects were estimated by including breed percentages of Simmental, Angus, Hereford, Red Angus and “Other” breeds as linear covariates in the model. The general average for PAP measurements in the entire dataset was 41.29 ± 0.22, with range of 26 and 108 mmHg. The estimated regression coefficient for PAP on heterosis was -1.834 ± 1.676 mmHg/percent of outcross (P = 0.276), whereas, the range of breed effects on PAP was 15.08 mmHg. These results suggested that heterosis had no significant effects on PAP measurements. However, further research including other multibreed populations is required in order to better understand if increased levels of heterozygosity could potentially be related to lower PAP scores.

At altitudes >1500 m, measurements of mean pulmonary arterial pressures (mPAP; mmHg) are a measure of pulmonary hypertension (PH) in cattle. Genotypes of a G/A single nucleotide polymorphism (SNP; rs208684340) in the endothelial PAS domain protein 1 (EPAS1) gene were determined for mPAP categories (low, moderate, high) on Angus cattle. The A allele of this SNP was postulated to be associated with altitude-induced PH. The first objective was to estimate allele and genotypic frequencies in Angus cattle at high- (elevation 1850 to 2800 m) and low-altitude (elevation 91 to 1192 m) ranches (n = 118; random sample of 1275). Percent of cattle at these low elevation ranches with genotypes G/G, G/A, and A/A were 64.4, 33.9, and 1.7%, respectively, and a minor allele frequency (MAF; A allele) of 18.6%. Bulls, steers, and heifers (n = 691) from 4 high-altitude Angus herds in Colorado and Wyoming were genotyped. Percent of cattle with genotypes G/G, G/A, and A/A were 48.6, 34.3, and 17.1%, respectively, with a MAF of 34.2%. Average mPAP was 40.5 ± 8.8 mmHg. Low, moderate, and high-mPAP category MAF were similar (χ2 = 3.03; P = 0.22), with values of 35.4, 31.0, and 37.8%, respectively. Additionally we sought to evaluate the genotype-to-phenotype association of this SNP with mPAP phenotypes (n = 532) from the Colorado State University Beef Improvement Center (elevation 2150 m) Angus herd. Linear mixed model analysis suggested genotype was not a predictor (P = 0.61) of mPAP. Results do not suggest the A allele of SNP in EPAS1 is associated with high altitude-induced PH in yearling Angus cattle.

Over the last 20 yr, global positioning system (GPS) collars have greatly enhanced livestock grazing behavior research. Practices designed to improve livestock grazing distribution can now be accurately and cost effectively monitored with GPS tracking. For example, cattle use of feed supplement placed in areas far from water and on steep slopes can be measured with GPS tracking and corresponding impacts on distribution patterns estimated. Ongoing research has identified genetic markers that are associated with cattle spatial movement patterns. If the results can be validated, genetic selection for grazing distribution may become feasible. Tracking collars have become easier to develop and construct, making them significantly less expensive, which will likely increase their use in livestock grazing management research. Some research questions can be designed so that dependent variables are measured by spatial movements of livestock, and in such cases, GPS tracking is a practical tool for conducting studies on extensive and rugged rangeland pastures. Similarly, accelerometers are changing our ability to monitor livestock behavior. Today, accelerometers are sensitive and can record movements at fine temporal scales for periods of weeks to months. The combination of GPS tracking and accelerometers appears to be useful tools for identifying changes in livestock behavior that are associated with livestock diseases and other welfare concerns. Recent technological advancements may make real-time or near real-time tracking on rangelands feasible and cost-effective. This would allow development of applications that could remotely monitor livestock well-being on extensive rangeland and notify ranchers when animals require treatment or other management.

High altitude disease (HAD) in cattle is historically a consequence of hypoxia-induced pulmonary hypertension at elevations ≥1,500 m. Mean pulmonary arterial pressure (mPAP) is an indicator of an animal’s risk of HAD and is moderately heritable (h2 = 0.26 to 0.34). The objective of this study was to evaluate genetic (i.e., breed) and environmental factors influencing yearling mPAP in growing beef bulls. Data consisting of pen, birth year (BY), breed, end test age, bull test weights, ADG, and mPAP (45.1 ± 12.3 mmHg) measures were obtained from the San Juan Basin Research Center, 4-Corners Bull Test Station (elevation 2,255 m). Records were from 1989 to 2005 (n = 2,426). Bulls of 10 pure and various breed crosses represented 73 different owners. A model of mPAP = Pen_BY + Breed + error was fitted. In an ANOVA for model building, Pen_BY (concatenated fixed effect proxy for contemporary group) and breed were significant (P 0.05). Results also suggested that breed (P < 0.001) was an important factor influencing mPAP. Using a least squares means separation approach, we found an estimated 17.4-mmHg range in mPAP between breeds, where Composite bulls had the lowest adjusted mPAP and Simmental bulls had the highest. Knowledge of genetic (i.e., breed) and environmental factors influencing mPAP could be helpful in reducing the incidence of HAD in beef cattle.

This simulation study used actual SNP genotypes on the first chromosome of Brangus beef cattle to simulate 0.50 genetically correlated two traits with heritabilities of 0.25 and 0.50 determined either by 50, 100, 250 or 500 QTL and then aimed to compare the accuracies of genomic prediction from bivariate linear and artificial neural network with 1 to 10 neurons models based on G genomic relationship matrix. QTL effects of 50, 100, 250 and 500 SNPs from the 3361 SNPs of 719 animals were sampled from a bivariate normal distribution. In each QTL scenario, the breeding values (Σgijβj) of animal i for two traits were generated by using genotype (gij) of animal i at QTL j and the effects (βj) of QTL j from a bivariate normal distribution. Phenotypic values of animal i for traits were generated by adding residuals from a bivariate normal distribution to the breeding values of animal i. Genomic predictions for traits were carried out by bivariate Feed Forward MultiLayer Perceptron ANN-1–10 neurons and linear (GBLUP) models. Three sets of SNP panels were used for genomic prediction: only QTL genotypes (Panel1), all SNP markers, including the QTL (Panel2), and all SNP markers, excluding the QTL (Panel3). Correlations from 10-fold cross validation for traits were used to assess predictive ability of bivariate linear (GBLUP) and artificial neural network models based on 4 QTL scenarios with 3 Panels of SNP panels. Table 1 shows that the trait with high heritability (0.50) resulted in higher correlation than the trait with low heritability (0.25) in bivariate linear (GBLUP) and artificial neural network models. However, bivariate linear (GBLUP) model produced higher correlation than bivariate neural network. Panel1 performed the best correlations for all QTL scenarios, then Panel2 including QTL and SNP markers resulted in better prediction than Panel3.

Progesterone signaling and uterine function are crucial in terms of pregnancy establishment. To investigate how the uterine tissue and its secretion changes in relation to puberty, we sampled tissue and uterine fluid from six pre- and six postpubertal Brahman heifers. Post-pubertal heifers were sampled in the luteal phase. Gene expression of the uterine tissue was investigated with RNA-sequencing, whereas the uterine fluid was used for protein profiling with mass spectrometry. A total of 4034 genes were differentially expressed (DE) at a nominal P-value of 0.05, and 26 genes were significantly DE after Bonferroni correction (P < 3.1 9 10 À6 ). We also identified 79 proteins (out of 230 proteins) that were DE (P < 1 9 10 À5 ) in the uterine fluid. When we compared proteomics and transcriptome results, four DE proteins were identified as being encoded by DE genes: OVGP1, GRP, CAP1 and HBA. Except for CAP1, the other three had lower expression post-puberty. The function of these four genes hypothetically related to preparation of the uterus for a potential pregnancy is discussed in the context of puberty. All DE genes and proteins were also used in pathway and ontology enrichment analyses to investigate overall function. The DE genes were enriched for terms related to ribosomal activity. Transcription factors that were deemed key regulators of DE genes are also reported. Transcription factors ZNF567, ZNF775, RELA, PIAS2, LHX4, SOX2, MEF2C, ZNF354C, HMG20A, TCF7L2, ZNF420, HIC1, GTF3A and two novel genes had the highest regulatory impact factor scores. These data can help to understand how puberty influences uterine function.

Pulmonary hypertension (PH) and subsequent right heart failure is an economic burden for high altitude beef production systems. An indicator of PH is pulmonary arterial pressure (PAP), which has been used to improve tolerance of cattle to high altitude due to its moderate heritability (0.20 to 0.40). A key mediator of myocardial contraction and relaxation is intracellular signaling of calcium. We hypothesized that genes involved in calcium signaling pathways have a role in susceptibility of cattle to PH at high altitude. Right ventricle tissues were collected from Angus steers (age 12 to 14 months; live weight 387 ± 2.5 kg) fed and harvested at high altitude (2,170 m). Experimental groups consisted of low PAP, healthy (average 39 ± 0.2 mm Hg; n = 7) and high PAP, sick/symptomatic of potential heart failure (average 82 ± 2.9 mm Hg; n = 3) steers. Gene expression counts were estimated from RNA-sequence data and then analyzed with DESeq, resulting in 622 differentially expressed genes between experimental groups (Fold change > 2.0; P < 0.05), after a multiple testing correction with the Benjamini-Hochberg procedure. Ingenuity Pathway Analysis revealed the top disease and biological function as cardiovascular malformation represented by 134 of the differentially expressed genes (P < 0.01). The principal intra-pathway genes identified were TGFβ1, an upstream regulator of ventricular chamber hypertrophy and systolic dysfunction leading to heart failure, and EDN1, a vasoconstrictor with downstream regulatory effects on intracellular calcium availability. Two additional genes, FBLN7, a calcium-binding glycoprotein; and ANKRD2, which interacts with calcium-dependent genes, represented the highest expression fold changes. These results support our hypothesis that calcium-dependent gene regulation appears to be influenced by PH (right ventricle malformation) in Angus steers fed at high altitude.

New breeds can be developed by combining two or more breeds into a composite population, thereby capitalizing on complementarity and retained heterosis. Evaluation of breed formation across generations has not been performed at the molecular level; therefore, we used Brangus cattle (3/8 Brahman x 5/8 Angus) as a model to identify the dynamics of new breed formation across 10 generations. Genotypic data (777,962 SNP) from 68 Brahman, 95 Angus and 59 Brangus prominent AI sires born from 1970 to 2010 were evaluated. Their pedigrees were used to calculate the number of complete Brangus generations using the OptiSel package in R 3.4.2. After standard SNP data filters and linkage disequilibrium pruning, 158,264 SNP genotypes from 220 bulls were chosen. ADMIXTURE analyses were executed using autosomal markers by chromosome, setting K equal to two and three. Brangus animals had 70.4% of Angus composition in all autosomes versus the expected 62.5% (t-test, P < 0.001). When K = 3, the establishment of the Brangus cluster was observed across the genome with a proportional assignment > 0.5. The sex chromosomes deviated from the autosomal pattern. Chromosome X had a high Angus proportion (83%) conserved across generations and Brahman contributed only to 9% of the Y chromosome. Regression analyses of cluster formation among autosomes and across generations showed (P < 0.001) that Angus (β = -0.07) and Brahman (β = -0.03) clusters decreased while Brangus cluster increased (β = 0.10, R(2) = 0.43). Regressions by each autosome followed a similar pattern. Formation of the Brangus cluster became stable after the 5(th) generation. These results provide a view into the evolution of a new breed. [Image: see text]

High altitude disease (HAD) is an environmentally induced pathologic condition experienced by cattle raised at high elevations (>1,524 m). Physiologically, the disease is a consequence of hypoxia-induced pulmonary hypertension, therefore, susceptibility to HAD can be assessed in cattle by measuring the mean pulmonary arterial pressure (mPAP). The evaluation of a bull’s adaptability to higher altitudes is economically relevant and mPAP has a moderate heritability. Reaction norm models have been successfully applied to measure the change in genetic predictions of individuals in response to changes in environment; therefore, the objective of this study was to evaluate the environmental sensitivity of Angus sires to high altitude disease through the use of reaction norm models. Records of mPAP collected by the same veterinarian between 2009 and 2012 from a total of 382 sixteen-month-old Angus bulls (progeny of 132 sires and unknown dams) were used for the analysis. Each bull was tested twice, first at moderate elevation (~1246 m, Hobson, MT) and approximately two months later at a high elevation (~2173 m, Laramie, WY). Expected progeny difference (EPD) for mPAP were estimated using a reaction norm sire model with Legendre polynomials as the base function. Effects in the model included contemporary group (mPAP date of measurement) and elevation as fixed effects and sire as a random regression term (sire random intercept and slope) on environmental descriptor (elevation). A rank correlation of 0.91 between EPD for mPAP estimated at the two elevation points (moderate and high), revealed a small degree of re-ranking of sires mainly due to the existence of heterogeneous genetic (co)variance components for mPAP studied at the two elevations. The previous implies that sires with advantageous EPD for mPAP at low elevations will not necessarily have advantageous EPD for mPAP at high elevations.

Data were analyzed to compare accuracies from PBLUP and GBLUP in 719 heifers (3/8 Brahman, Bos indicus x 5/8 Angus, Bos taurus). Genotypes were from BovineSNP50 Infinium-beadchips. Phenotypes included growth traits (birth weight, 205-day weight, 365-day weight), pre- and post-weaning average daily gains and yearling carcass measures (longissimus dorsi muscle area, percent fat within longissimus dorsi muscle, fat thickness over the 12(th) rib) collected with real-time ultrasound. For cross-validation strategy, genotyped heifers were first divided into ten mutually exclusive groups using K-means clustering on pedigree estimates of additive genetic relationships between animals. All ten combinations of nine groups were used for model training, with cross-validation performed in the group not used in training. Also, two replicated training-testing sets including ten groups were randomly sampled. Accuracies for all traits based on K-means clustering ranged from 0.06 to 0.179 for PBLUP and from 0.047 to 0.268 for GBLUP. However, accuracies for all traits based on random sampling groups were higher than those from K-means clustering and ranged from 0.148 to 0.331 for PBLUP and from 0.143 to 0.283 for GBLUP. Among the growth traits, the accuracy from PBLUP for 205-day weight (0.084) was higher than birth weight (0.065) and 365-day weight (0.060). However, the accuracy from GBLUP for 205-day weight (0.047) was lower than birth weight (0.110) and 365-day weight (0.121). Accuracies from PBLUP (0.084, 0.179, 0.105) and GBLUP (0.225, 0.268, 0.211) for carcass traits (longissimus dorsi muscle area, percent fat within longissimus dorsi muscle, fat thickness over the 12(th) rib) were higher than growth traits. longissimus dorsi muscle area, percent fat within longissimus dorsi muscle, fat thickness over the 12(th) rib had the highest accuracies among all the studied traits. The accuracies of random sampling groups were considerably higher for all traits than the corresponding accuracies obtained by K-means clustering.

Heat stress greatly influences lactating Holstein cattle in southern Sonora Mexico, where the temperature-humidity index (THI) easily exceeds the cow thermal comfort threshold (>72 THI units) from May through October. Despite such warm conditions, some dairy cows are able to maintain their milk production. Using a regression model, daily milk production as a function of daily THI was used to estimate a heat tolerance indicator (HTI) value. The objective of this study was to identify molecular markers associated with HTI in Holstein cows milked during summer. The study included 676 cows from three dairies located in the Yaqui Valley of Sonora Mexico. An individual blood sample was collected and spotted onto FTA cards, from which DNA was extracted and used to genotype 179 tag SNP within 43 genes of the Prolactin and GH-IGF1 pathways. The association analyses among SNP genotypes and HTI values were performed using a mixed effects model for continuous traits. The model included HTI as the response variable, genotype and herd as fixed effects, sire as a random effect, and days in milk as a covariate. Two SNP, one within the Prolactin Receptor gene (rs135164815) and one within the Signal Transducer and Activator of Transcription-4 gene (rs110344022) were associated with HTI (P < 0.01). Least square means for the rs135164815 genotypes AA, AG and GG were 0.365 ± 0.06, 0.217 ± 0.04 and 0.201 ± 0.03 liters/day, respectively; while least square means for the rs110344022 genotypes CC, CT and TT were 0.296 ± 0.05, 0.235 ± 0.04 and 0.183 ± 0.04 liters/day, respectively. In conclusion, two SNP within the Prolactin and GH-IGF1 pathways were predictors of HTI in lactating Holstein cows during the months of summer heat stress. Such results provide evidence of a genetic basis associated with favorable lactation performance under increasing THI during summer.

Pulmonary arterial pressure (PAP) is an indicator trait for pulmonary hypertension and for the risk of developing high-altitude disease (HAD) in cattle. Pulmonary arterial pressures provide a tool for selection of breeding cattle for tolerance to high altitude in mountainous regions of the United States. The objective of this study was to evaluate relationships between growth performance traits and yearling PAP (42.4 ± 9.9 mmHg; = 5,776; elevation 2,150 m) using data from 1993 to 2014 in the John E. Rouse Colorado State University Beef Improvement Center (CSU-BIC) Angus herd. The breeding program used sires ( = 299) from both low- and high-elevation environments. We hypothesized that little to no genetic relationship exists between PAP and birth weight (BWT; direct and maternal), weaning weight (WW; direct and maternal), yearling weight (YW; direct and maternal), and postweaning gain (PWG). Historic selection of natural service sires from within the herd required a PAP of ≤ 42 mmHg. Outside AI sires ( = 156) used in this breeding program were not PAP tested and therefore were used with little knowledge of these sires' high-altitude adaptability. Performance traits (± SD) routinely recorded included BWT (36.2 ± 5.1 kg; = 8,695), WW (213.5 ± 31.8 kg; = 8,010), YW (345.6 ± 83.8 kg; = 5,580), and PWG (122.0 ± 63.7 kg; = 5,449), where PWG represented the total weight gained from weaning to yearling age. Four-trait analyses using REML were conducted with an animal model. The heritability estimates (± SE) for PAP (0.26 ± 0.03), BWT direct (0.42 ± 0.04) and maternal (0.14 ± 0.02), WW direct (0.29 ± 0.04) and maternal (0.19 ± 0.03), YW direct (0.45 ± 0.04) and maternal (0.23 ± 0.03), and PWG (0.14 ± 0.02) were in the range of those reported in previous literature. Estimates of genetic correlations (± SE) revealed weak relationships between PAP and direct and maternal BWT, direct and maternal WW, direct and maternal YW, and PWG of 0.15 ± 0.09, 0.14 ± 0.10, 0.23 ± 0.09, -0.01 ± 0.10, 0.12 ± 0.08, 0.00 ± 0.09, and -0.10 ± 0.10, respectively. The results of this study suggest that selection for lower PAP measures should have minimal influence on the growth performance of yearling Angus bulls and heifers at the CSU-BIC, supporting our hypothesis.

The objective of this study was to evaluate the effect of altitude on arterial blood-gases and hematocrit in Angus-based calves. It was hypothesized that alveolar ventilation rate, as indicated by arterial pCO, would increase with altitude but hematocrit would not. Five Angus-based herds ( = 30 to 80 per cohort) located at 105 m, 1,470 m, 2,010 m, 2,170 m, and 2,730 m above sea level were enrolled in this prospective cohort study. A portable analyzer measured blood-gas tensions in coccygeal arterial blood. Calves at 1,470 m, 2,170 m, and 2,730 m were sampled twice, at approximately 4 mo and 7 mo of age. Calves at 105 m and 2,010 m were sampled once, at 7 or 4 mo of age, respectively. Linear regression analyses were used to determine the fixed effect of herd (a proxy for altitude) on the 4 outcome variables pCO, pO, pH, and hematocrit, while controlling for age and sex. As hypothesized, alveolar ventilation rate increased with altitude ( < 0.001). Hematocrit, however, did not show a clear association with altitude except for an increase from 105 m to ≥ 1,470 m ( < 0.001). Arterial pO decreased significantly with increasing altitude in calves at 4 mo and 7 mo of age ( < 0.001). The adjusted mean values of the 4 variables studied were similar at 4 and 7 mo of age for all of the herds studied. This indicates that suckling calves show minimal respiratory or erythrocytic adaptation to hypoxemia and hypocapnia with increasing age, regardless of altitude. We propose that the lack of an erythrocytic response in hypoxemic calves born and raised at high altitude prevents a deleterious increase in viscous resistance and, consequently, pulmonary arterial pressure. This physiological response, or lack thereof, may be a survival adaptation in a species predisposed to hypoxia-induced pulmonary hypertension.

The purposes of this study were to evaluate mean, systolic, and diastolic pulmonary arterial pressures; pulmonary arterial pulse pressures; and systemic oxygen extraction fraction as risk factors for the survival of suckling calves on one ranch located at an altitude of ≥ 2,730 m in Colorado, USA. A prospective cohort study of 58 calves was performed. Pulmonary arterial pressures and systemic oxygen extraction were measured when calves were approximately 3 mo (86 ± 7 d) and 7 mo (197 ± 6 d) of age. Seven of the 58 calves (12%), 4 steers and 3 heifers, were unaccounted for and presumed dead between 3 and 7 mo of age. Calves presumed to have died between 3 and 7 mo of age had significantly greater mean ( = 0.005) and systolic ( = 0.001) pulmonary arterial pressures and greater pulse pressures ( = 0.03) at 3 mo of age than calves that survived to 7 mo. Calves presumed to have died tended to have greater systemic oxygen extraction fractions at 3 mo of age than calves that survived ( = 0.13). Diastolic pressure was not associated with survival ( = 0.27). Mean pulmonary arterial pressure is predominantly determined by static resistance attributable to distal pulmonary arterial remodeling. Pulse pressure and systolic pulmonary arterial pressure represents the dynamic or oscillatory resistance and is determined by the characteristics of ventricular ejection and proximal arterial stiffness. These findings indicate that it may be beneficial to include pressure measurements indicative of both static and dynamic pulmonary arterial resistance in the selection of breeding stock at high altitude.

Puberty onset is a developmental process influenced by genetic determinants, environment, and nutrition. Mutations and regulatory gene networks constitute the molecular basis for the genetic determinants of puberty onset. The emerging knowledge of these genetic determinants presents opportunities for innovation in the breeding of early pubertal cattle. This paper presents new data on hypothalamic gene expression related to puberty in (Brahman) in age- and weight-matched heifers. Six postpubertal heifers were compared with 6 prepubertal heifers using whole-genome RNA sequencing methodology for quantification of global gene expression in the hypothalamus. Five transcription factors (TF) with potential regulatory roles in the hypothalamus were identified in this experiment: , , , , and . These TF genes were significantly differentially expressed in the hypothalamus of postpubertal versus prepubertal heifers and were also identified as significant according to the applied regulatory impact factor metric ( < 0.05). Two of these 5 TF, and , were zinc fingers, belonging to a gene family previously reported to have a central regulatory role in mammalian puberty. The gene belongs to the family of homologues of Drosophila sine oculis () genes implicated in transcriptional regulation of gonadotrope gene expression. Tumor-related genes such as and are known to affect basic cellular processes that are relevant in both cancer and developmental processes. Mutations in were associated with puberty in humans. Mutations in these TF, together with other genetic determinants previously discovered, could be used in genomic selection to predict the genetic merit of cattle (i.e., the likelihood of the offspring presenting earlier than average puberty for Brahman). Knowledge of key mutations involved in genetic traits is an advantage for genomic prediction because it can increase its accuracy.

Bovine respiratory disease complex (i.e., shipping fever and bacterial bronchopneumonia) is a multifaceted respiratory illness influenced by numerous environmental factors and microorganisms. Bovine respiratory disease (BRD) is just one component of BRD complex. Because BRD is moderately heritable, it may be possible to reduce the incidence of BRD through genetic selection. The objectives of this study were to determine the heritability and associative genetic relationships among immune system traits (i.e., cortisol, total IgG, IgG isotypes, and IL-8) in cattle monitored for BRD incidence. At an average of 83 d after weaning (219 d age and mean = 221.7 kg [SD 4.34]), crossbred Bos taurus steer calves (n = 2,869) were received at a commercial feedlot in southeastern Colorado over a 2-yr period. At receiving, jugular blood samples were collected at 212 (yr 1) and 226 d (yr 2) of age for immune trait analyses. The BRD phenotype was defined as a binomial variable (0 = no and 1 = yes) and compared with immune system traits measured at receiving (prior to illness onset). An animal identified as BRD positive exhibited ≥ 2 clinical signs (i.e., eye or nasal discharge, cough, lethargy, rapid breathing, acute interstitial pneumonia, or acute upper respiratory syndrome and/or a rectal temperature > 39.7°C). Heritability and genetic correlation estimates for categorical variable BRD, cortisol, IgG, IgG1, IgG2, and IL-8 were estimated from a sire model using ASREML. Heritability estimates were low to moderate for BRD (0.17 ± 0.08), cortisol (0.13 ± 0.05), IgG (0.15 ± 0.05), IgG1 (0.11 ± 0.05), IgG2 (0.24 ± 0.06), and IL-8 (0.30 ± 0.06). A moderate negative genetic correlation was determined between BRD and cortisol (rg = −0.19 ± 0.32). Moderate positive correlations were found between BRD with IgG (0.42 ± 0.28), IgG1 (0.36 ± 0.32), and IL-8 (rg = 0.26 ± 0.26). Variation in the BRD phenotype and immune system traits suggested herd health improvement may be achieved through genetic selection.

Beef cattle grazing patterns are influenced by topography in that cattle generally select grazing sites near water while avoiding steep, rugged terrain; therefore, forage is often left ungrazed in the mountainous uplands whereas lowland riparian zones can be heavily grazed. Improving uniformity in beef cattle terrain-use provides opportunities to increase forage harvest and sustain sensitive ecosystems. Studies suggest that terrain-use by cattle may be improved using genomic selection as combinations of single nucleotide polymorphisms (SNP) explained approximately 35% of the phenotypic variation in terrain-use indices that combined slope, elevation, and distance traveled from water. The objective of this study was to perform genome-wide association studies (GWAS) for six terrain-use traits (slope, elevation, vertical climb, distance traveled from water, rolling index, and rough index) in which we explored single-SNP associations, surveyed the genome in consecutive, one mega-base windows and examined quantitative trait loci (QTL) and underlying positional and functional candidate genes using bioinformatic tools to identify possible pleiotropic effects with other traits. Global positioning system (GPS) collars were used to track terrain-use patterns for 330 beef cows across 14 rangeland operations located in the western U.S. and Illumina BovineHD and BovineSNP50 SNP arrays were used to collect genomic data. Genotype quality control was conducted using PLINK software and association analyses were performed using BOLT, implementing a BayesC model. Quantitative trait loci detection was based upon the posterior inclusion probability (PIP) for individual loci and the proportion of total genetic variance explained by individual genomic windows. Analyses revealed 19 QTL that have been previously associated with health and production traits in dairy and beef cattle as well as 8 positional putative candidate genes that function in oxygen homeostasis, feed efficiency, and growth. These results suggest that beef cattle terrain-use traits are polygenic and may be pleiotropic with other production traits.

Pulmonary arterial pressure (PAP) score is used to determine the risk for high altitude disease (HAD), a disorder of hypoxia-induced pulmonary hypertension, in beef cattle at high elevation. Given lung development occurs in utero, gestation length (GL) may be a source of variation in PAP score and a predictor of an animal’s susceptibility to HAD later in life. Therefore, the objective was to determine the relationship between GL and PAP in Angus cattle at high elevation. The PAP and GL observations were obtained from the Colorado State University’s Beef Improvement Center near Saratoga, Wyoming (elevation of 2,150 m) using breeding and calving records from the years 2007 to 2016 (n = 1,991 calves). Gestation length was calculated for individuals and verified, with ultrasound up to 50 days after artificial insemination, and subsequent calving records. The data included PAP measurement (43.13 ± 11.23 mmHg), GL (276.8 ± 5.77 days), age of dam (AOD, 5.892 ± 3.30 years), birth year, and calf sex at birth. The relationship between calf GL and PAP was evaluated using both a Pearson correlation coefficient and a simple linear regression model. The linear model for PAP as the dependent variable included GL as a covariate, and sex, birth year, and AOD as categorical fixed effects. The phenotypic correlation was estimated as -0.005 (P > 0.83) between PAP and GL. Regression results suggest no effect of GL (P > 0.50) or AOD (P > 0.85) on yearling PAP score. However, birth year and sex were significant factors (P < 0.001) on yearling PAP score. Results indicate that GL likely has no effect on yearling PAP and gestational age at birth should not increase an animal’s susceptibility to developing HAD into adulthood.

Growth data are often assumed to be normally distributed, but inferences are not robust when the data distributions exhibit heavy tails and outliers. Symmetric heavy-tailed normal/independent distributions are viable alternatives to normal distributions to model the densities of residuals. We compared estimates of genetic parameters fitting symmetric heavy-tailed normal/independent distributions (Normal, Student’s-t and Slash) for residuals in multivariate analysis of birth, 205-day and 365-day weights in beef cattle. Weight and average daily gain (ADG) records of heifers (3/8 Brahman, Bos indicus x 5/8 Angus, Bos taurus; n = 719) were analyzed. Models included fixed effects of contemporary group and age of dam and random effect of animal. Inference was conducted using a Bayesian framework via Markov chain Monte Carlo sampling. The goodness of fit of the models was done by comparing the deviance information criteria (DIC). These indicated that Student’s-t model was the best fitting model for the analysis of growth data but there was no significant difference among models for analysis of ADGs. Results revealed that posterior means for degrees of freedom were 8.4 and 18.1 in Student’s-t error model and 2.6 and 6.9 in Slash error model for weight traits and ADG. Posterior means of heritabilities for weight traits were higher in Student’s-t (0.29, 0.43 and 0.48) when compared to Normal (0.27, 0.39 and 0.46) and Slash (0.28, 0.38 and 0.46) models. However, similar heritability estimates were obtained from the Normal, Student’s-t and Slash models in the analysis of ADG from birth to 205-day weights, and from birth to 365-day weights. Evaluation of 95% posterior probability interval showed that genetic correlations were significant between 205-day and 365-day GW, between birth-205-day-ADGs and birth- 365-day-ADG, between 205-day-365-day-ADG and birth-365-day-ADG. Conclusively, all three models of weight traits, the Student’s-t model outperform the normal model.

A disease negatively affecting the swine industry in Mexico is porcine respiratory and reproductive syndrome (PRRS). The disease alters physiology of the pig and decreases performance. Vaccination is the management strategy to protect replacement gilts from PRRS infection; however, their response is highly variable. The research objective was to validate markers associated with indicators of performance in gilts after vaccination against PRRS. Indicator traits included rectal temperature (RT) and average daily gain (ADG). Seventy-five 6-month-old, ¾-Landrace x ¼-Yorkshire replacement gilts were used in the study. Gilts were kept in the quarantine area, vaccinated against PRRS and sampled for genomic analyses using a 10,000 low-density SNP chip. Data were analyzed using SNP and Variation Suite-7 through a multi-locus mixed model that identified 59 SNP associated with indicators of performance. A mixed effects model was used to validate the associative relationship among these SNP with RT and ADG. The SNP ASGA0019551 and M1GA0005374 were associated with RT, whereas ASGA0088990 was associated with ADG (P < 0.01). For ASGA0019551, least square means among genotypes TT, CT and CC were 38.75 ± 0.09, 38.87 ± 0.06 and 39.05 ± 0.06°C; for M1GA0005374, least square means for genotypes GG, AG and AA were 38.81 ± 0.13, 38.79 ± 0.06 and 39.02 ± 0.05°C; and for ASGA0088990, least square means among genotypes TT, CT and CC were 0.55 ± 0.07, 0.53 ± 0.05 and 0.34 ± 0.05kg, respectively. The most favorable alleles for ASGA0019551 and M1GA0005374 reduced RT by 0.16 ± 0.05 and 0.12 ± 0.03°C, respectively; and the most favorable allele for ASGA0088990 increased ADG by 0.12 ± 0.04kg. In conclusion, three SNP were validated to be associated with productive performance in gilts after PRRS vaccination. Therefore, such SNP are proposed as molecular markers for selection of gilts with superior performance after vaccination against PRRS.

Right heart failure secondary to pulmonary hypertension is a leading cause of mortality among suckling beef calves in the Rocky Mountain region. The objective of this study was to track changes in pulmonary arterial pressures (PAP) in healthy calves born and raised at altitudes ranging from 1,470 to 2,730 m. It was hypothesized that calves located at higher altitudes would show a greater increase in mean PAP (mPAP) with age than would be experienced by calves located at lower altitudes. The rationale is that high altitude hypobaric hypoxia causes a greater rate of vascular remodeling and, consequently, greater resistance to blood flow than calves located at lower altitudes. A prospective study was conducted on 5 cohorts of suckling calves from 4 herds located at altitudes of 1,470, 2,010, 2,170, and 2,730 m. In total, 470 PAP measurements were obtained from 258 calves. As hypothesized, calves located at altitudes ≥2,170 m showed a significant increase in mPAP with age ( ≤ 0.002) whereas calves at 1,470 m did not ( = 0.16). Except for calves at 2,170 m ( < 0.001), systolic PAP did not increase with age ( ≥ 0.16). Diastolic PAP increased with age at altitudes ≥ 2,170 m ( ≤ 0.09) but did not change in calves at 1,470 m ( = 0.20). In summary, mPAP and the rate at which mPAP increases with age are positively associated with the altitude at which calves are born and raised.

Pulmonary arterial hypertension due to hypoxia-induced pulmonary vascular remodeling is the predominant cause of right-sided congestive heart failure (CHF) in cattle. Historically, heart failure was problematic only at altitudes over 2,134 m. However, anecdotal reports suggest that the incidence of heart failure is increasing in feedlot cattle at moderate altitude (800 to 1,600 m), with late-fed, or fat, cattle at greatest risk. The goal of this study was to evaluate pulmonary arterial pressures (PAP) in a cohort of male Angus calves from suckling to finishing to better understand why heart failure is particularly problematic in fat cattle. It was hypothesized that mean PAP would increase through the feeding period and that the calves with the greatest pressures at high altitude would have the greatest pressures as fat cattle. A total of 362 PAP measurements were obtained from 153 calves. Calves were tested at altitudes of 2,170 (4 and 6 mo old), 1,560 (13 mo old), and 1,300 m (13 and 18 mo old). Mean PAP were greater in 18-mo-old steers than any other age group (mean = 50.3 mm Hg; 95% confidence interval 48.2 to 52.4; < 0.05). Calves that had the greatest mean pressure at 6 mo of age tended to have the greatest mean pressures at 18 mo of age ( = 0.45, < 0.001). The increase in mean PAP with increasing age and adiposity likely predisposed the steers to an increased risk of CHF during the finishing phase.

The objectives of this research were to compare variance components, genetic parameters, and EBV rankings for birth weight (BW) direct and maternal, weaning weight (WW) direct and maternal, and postweaning gain from 205 d to 365 d (PWG) direct using three genomic–polygenic and one polygenic model representing four plausible beef cattle genetic evaluation scenarios for growth traits under subtropical conditions in the US southern region. In addition, EBV trends as percentage Brahman increased from 0% to 100% were evaluated for each trait and model. The dataset included 5264 animals from a multibreed Angus–Brahman population born from 1987 to 2013. Genomic–polygenic models 1 (GP1; pedigree relationships for all animals; genomic relationships for genotyped animals), 2 (GP2; pedigree relationships for non-genotyped animals; genomic relationships for genotyped animals), and 3 (GP3; no pedigree relationships; genomic relationships for genotyped animals) used actual and imputed genotypes from 46,768 SNP markers. Variance components and genetic parameters were estimated using REML procedures. Variance component and genetic parameter estimates from GP1 were the most similar to those from the polygenic model, followed by those from GP2, and the least similar (especially for maternal traits) were those from GP3. Similarly, the highest rank correlations were those between animal EBV from the polygenic model and GP1, followed by those between animal EBV from GP1 and GP2 and between the polygenic model and GP2. Model GP3 performed poorly for maternal traits due to ignoring calf–dam relationships. These results indicated that the polygenic model and genomic–polygenic model 1 should be preferred. However, high genotyping costs still make the polygenic model preferable for commercial beef cattle operations. Brahman animals tended to have higher EBV for BW direct and WW direct, and lower EBV for PWG direct, BW maternal, and WW maternal. However, low regression coefficients for EBV on Brahman fraction ensured that high, medium, and low EBV animals from all breed compositions existed in this multibreed population.

The Beef Improvement Federation recommends residual feed intake (RFI) be calculated from 70-d tests preceded by a 21-d adjustment period. Individual animal feed intake and gain measurements are expensive and time consuming, which limits the number of animals available for national genetic evaluation of feed intake. If a shorter test period of comparable accuracy could be used, the cost would decrease and more animals could be tested annually. The objective of this study was to determine if data from shortened tests is equally as predictive of average daily DMI (ADMI) and RFI values from 70-d tests. Feed intake and weight measures were collected after weaning from Bos taurus bulls, steers, and heifers (n = 612) during four 70-d performance tests. For each individual, ADMI and RFI were calculated. Residual feed intake was calculated by regressing ADMI on metabolic midweight (MMWT) and ADG with the effect of breed included where appropriate. Based on four 70-d intake tests, ADMI, RFI, ADG, and MMWT were evaluated using shortened test lengths in a post hoc analysis where shortened test lengths were imposed on the full-period tests. The ADMI, RFI, ADG, and MMWT values from the full 70-d test were regressed on ADMI, RFI, ADG, and MMWT values resulting from the constructed shorter data subsets. The 8 subsets ranged from 14 to 56 d in length. The fixed effects of test, breed, animal's origin, and sex were included in each comparison for ADMI, ADG, and MMWT. Estimates for regression coefficients of ADMI values from a full test on various subsets ranged from 0.63 to 1.02. Likewise, estimated coefficients obtained from the regression of full test RFI, ADG, and MMWT values on subsets ranged from 0.50 to 1.00, 0.09 to 0.85, and 0.48 to 1.02, respectively. We conclude that ADMI values from a 42-d test ( < 0.0001) and RFI values from a 56-d test (P < 0.0001) adequately predict ADMI and RFI when compared to a 70-d test. These results suggest that testing periods of 42 d for determining ADMI and 56 d for RFI could ultimately reduce testing costs and result in collection of data on a larger number of animals per year, in turn resulting in more data for genetic evaluation.

The objectives were to estimate additive genetic variance fractions for 4 postweaning ultrasound and weight traits explained by 46,839 actual and imputed SNP genotypes, to compare rankings of calf additive genetic predictions from genomic–polygenic (GP), genomic (G), and polygenic (P) models, and to assess trends for GP, G, and P predicted additive genetic values as functions of calf Brahman fractions in a multibreed Angus–Brahman population. Traits were postweaning ultrasound ribeye area (UREA), backfat thickness (UBF), and percent intramuscular fat (UPIMF), and weight (UW). Phenotypes and Illumina3k genotypes were from 812 bull, heifer, and steer calves housed at the Feed Efficiency Facility of the University of Florida from 2006 to 2010. Program Findhap2 was used to impute from 2899 Illumina3k SNP to 46,839 Illumina50k SNP using a reference population of 828 Brangus heifers. Fixed effects for all models were contemporary group (year-pen), age of dam, sex of calf, age of calf, Brahman fraction of calf, and heterozygosity of calf. Random effects were additive SNP (GP and G models), additive polygenic (GP and P models), and residual. Software GS3 was used to compute variance components and heritabilities, and additive genetic predictions. Additive genetic variance fractions explained by the 46,839 actual and imputed SNP were 0.17 for UREA, 0.32 for UBF, 0.25 for UPIMF, and 0.19 for UW. Heritabilities were 0.33 for UREA, 0.22 for UBF, 0.43 for UPIMF, and 0.54 for UW. These additive genetic variance fractions were 1.8, 1.0, 4.4, and 2.1 times greater and heritabilities were 1.0, 1.2, 1.0, and 1.2 times greater than those obtained for these 4 traits using only the 2899 Illumina3k SNP. Rank correlations between EBV from GP and P models were the highest (0.93 to 0.96), followed by those between EBV from GP and G models (0.81 to 0.94), and by those between EBV from G and P models (0.66 to 0.81). Regression coefficients of EVB on Brahman fraction were small for all traits and models indicating that animals of comparable EBV existed in all breed groups. Imputation from Illumina3k to 50k increased the explained fraction of additive SNP variance resulting in higher rank correlations between additive genetic predictions from G and GP, and from G and P models for all ultrasound traits in this Angus–Brahman multibreed population.

Eighty-seven cows were GPS (Global Positioning System) tracked for 1 to 3 months in mountainous and/or extensive pastures at five ranches located in New Mexico, Arizona, and Montana. The Illumina Bovine HD SNP array, which evaluates approximately 770,000 genetic markers (i.e., single nucleotide polymorphisms; SNPs) across the 30 bovine chromosomes, was used to genotype DNA from these cows and to examine genetic associations with grazing distribution. Terrain use indexes were calculated from tracking data based on normalized averages of slope use, elevation use, and distance travelled from water. Genetic analyses identified a chromosomal region, known as a quantitative trait locus (QTL), associated with these traits. One genetic marker on chromosome 29 identified a gene that has been reported to be involved in locomotion, motivation, and spatial memory. This locus accounted for 24% of the phenotypic variation in use of steep slopes and high elevations, while another QTL on chromosome 17 accounted for 23% of the phenotypic variation. Three other QTLs accounted for 10% to 20% of the variation in terrain use indexes. Using results from the initial high-density genetic marker analyses, a smaller 50-SNP panel was developed targeting previously identified QTL regions and was used to evaluate the 85 cows tracked previously with an additional 73 cows from four ranches. With the 50-SNP panel analyses, multiple genetic markers near or within the gene identified on chromosome 29 confirmed the association with indexes of terrain use. In addition, genetic markers on chromosomes 4, 8, 12, and 17 accounted for a significant portion of the phenotypic variation in terrain use indexes. The associations between terrain use indexes and genetic markers near candidate genes demonstrate that grazing distribution can be inherited and provide a new approach to associate genetic variation with cattle grazing behavior of range beef cattle.

Reproductive performance is the most important component of cattle production from the standpoint of economic sustainability of commercial beef enterprises. Heifer Pregnancy (HPG) and Stayability (STAY) genetic predictions are 2 selection tools published by the Red Angus Association of America (RAAA) to assist with improvements in reproductive performance. Given the importance of HPG and STAY to the profitability of commercial beef enterprises, the objective of this study was to identify QTL associated with both HPG and STAY in Red Angus cattle. A genome-wide association study (GWAS) was performed using deregressed HPG and STAY EBV, calculated using a single-trait animal model and a 3-generation pedigree with data from the Spring 2015 RAAA National Cattle Evaluation. Each individual animal possessed 74,659 SNP genotypes. Individual animals with a deregressed EBV reliability > 0.05 were merged with the genotype file and marker quality control was performed. Criteria for sifting genotypes consisted of removing those markers where any of the following were found: average call rate less than 0.85, minor allele frequency < 0.01, lack of Hardy–Weinberg equilibrium (P < 0.0001), or extreme linkage disequilibrium (r(2) > 0.99). These criteria resulted in 2,664 animals with 62,807 SNP available for GWAS. Association studies were performed using a Bayes Cπ model in the BOLT software package. Marker significance was calculated as the posterior probability of inclusion (PPI), or the number of instances a specific marker was sampled divided by the total number of samples retained from the Markov chain Monte Carlo chains. Nine markers, with a PPI ≥ 3% were identified as QTL associated with HPG on BTA 1, 11, 13, 23, and 29. Twelve markers, with a PPI ≥ 75% were identified as QTL associated with STAY on BTA 6, 8, 9, 12, 15, 18, 22, and 23.

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

Reproductive efficiency is of economic importance in commercial beef cattle production, as failure to achieve pregnancy reduces the number of calves marketed per cow exposed. Identification of genetic markers with predictive merit for reproductive success would facilitate early selection of sires with daughters having improved reproductive rate without increasing generation intervals. To identify regions of the genome harboring variation affecting reproductive success, we applied a genomewide association study (GWAS) approach based on the >700,000 SNP marker assay, using a procedure based on genotyping multianimal pools of DNA to increase the number of animals that could be genotyped with available resources. Cows from several populations were classified according to reproductive efficiency, and DNA was pooled within population and phenotype prior to genotyping. Populations evaluated included a research population at the U.S. Meat Animal Research Center, 2 large commercial ranch populations, and a number of smaller populations (

Reproductive efficiency is arguably the most economically important trait in commercial beef cattle production, as failure to achieve pregnancy reduces the number of calves marketed per cow exposed to breeding. Identification of variation in the genome with predictive merit for reproductive success would facilitate accurate prediction of daughter pregnancy rate in sires enabling effective selection of bulls producing daughters with improved fertility. Copy number variation (CNV) is one form of structural variation that results in abnormal copies of DNA in the genome. Our lab previously reported a region between 25 and 70 Mb on chromosome 5 associated with reproductive efficiency. To further evaluate this region for genomic variations such as CNV, we initially applied a genomewide association approach based on the >700,000 SNP marker assay and PennCNV analysis to 68 Bos indicus cross females from a large commercial ranch in central Florida. A genomic segment located on chromosome 5, spanning the region of approximately 58.37 to 58.44 Mb (Bovine UMD3.1 assembly) was identified as containing a deletion associated with decreased reproductive efficiency. To verify this deletion, a quantitative real-time PCR test was developed to evaluate additional females in the central Florida and U.S. Meat Animal Research Center (USMARC) populations. The frequency of the homozygous deletion was 7% (23/319) in the central Florida population (Bos indicus cross) for females with 2 consecutive failed breeding seasons and 0% in the USMARC population (predominantly Bos taurus) of low reproductive females. To date, we have not identified the deletion in Bos taurus cattle, suggesting that the deletion is specific to Bos indicus cattle. From these data, we have identified a deletion on chromosome 5 associated with reproductive efficiency in Bos indicus-influenced cattle.

The objectives were to estimate the fractions of additive genetic variances for four postweaning feed efficiency and growth traits explained by 46,909 actual and imputed SNP genotypes, to compare rankings of calf additive genetic predictions from genomic–polygenic (GP), genomic (G), and polygenic (P) models, and to determine trends of predicted additive genetic values from calves ranging from 100% Angus to 100% Brahman in a multibreed population. Traits were postweaning residual feed intake (RFI), daily feed intake (DFI), feed conversion ratio (FCR), and weight gain (PWG). Phenotypes were from 807 bull, heifer, and steer calves housed at the Feed Efficiency Facility of the University of Florida from 2006 to 2010. Imputation from 2899 SNP (Illumina3k) to 46,909 SNP (Illumina50k) was done with program findhap2 using a reference population of 828 Brangus heifers. Fixed effects for all models were contemporary group (year–pen), age of dam, sex of calf, age of calf, Brahman fraction of calf, and heterozygosity of calf. Random effects were additive SNP (GP and G models), additive polygenic (GP and P models), and residual. Software GS3 was used to compute variance components and heritabilities, and additive genetic predictions. Heritabilities were 0.30 for RFI, 0.37 for DFI, 0.25 for FCR, and 0.33 for PWG. Fractions of additive variances explained by the 46,909 actual and imputed SNP were 0.48 for RFI, 0.36 for DFI, 0.50 for FCR, and 0.28 for PWG. These fractions were 3.2, 3.2, 2.0, and 1.8 times larger than those previously obtained for these four traits using the 2899 SNP from the Illumina3k chip. Rank correlations between calf additive genetic predictions were high between GP and P and between GP and G models (0.89–0.98; P

Pulmonary hypertension (PH) can cause heart failure in cattle and is measured with pulmonary arterial pressure (PAP). Although historically associated with high elevation (> 1,500 m), PH and heart failure are increasing in moderate altitude feedlots. High elevation production systems wean and stocker calves before placing them in feedlot finishing systems of moderate elevations on the Great Plains of North America. The objective was to evaluate PAP and growth of steers finished at moderate or high elevation with varied lengths of post-weaning grazing. Forty steers from Colorado’s Beef Improvement Center (2,150 m) with PAP averaging 41.5 ± 0.5 mmHg were randomly assigned to one of four management groups: 1) traditional stocker and finishing system (i.e., grown and finished at 1,420 m beginning at 10 months of age), 2) extended stocker grazing at high elevation (2,150 m), but finishing at 1,420 m at 18 months of age, 3) stocker and finishing at high elevation (2,150 m) at 24 months of age, or 4) grass finishing (2,150 m) > 24 months of age. Weight and PAP data were analyzed with a repeated measures model. Effects of group, PAP-date, and their interaction (P < 0.01) were observed. Pre-harvest, steers in the stocker-finishing group at high elevation had higher PAP than the moderate elevation finishing groups (52.9 > 46.5 ± 1.7 mmHg), but PAP (41.1 ± 1.6) was unchanged across dates in the grass finishing group and lower than the grain-fed groups. Pre-harvest live weight averaged 621.6 ± 11.8 kg in all three grain finishing groups, whereas grass finishing steers weighed 436.6 ± 11.5 kg on these dates. In summary, grain-fattening appeared to cause PH independent of elevation. Steers grazing in a high elevation grass finishing system did not experience increased PAP, but required several more months of grazing to reach harvest criteria.

Concentrated grazing may destroy wildlife habitat, reduce forage harvest, and degrade riparian areas; therefore, it is necessary to develop tools to improve grazing distribution for extensive pastures in beef production systems. A previous genome-wide association study identified 5 QTL on BTA 4, 12, 17, and 29 that were associated with grazing distribution indices (rolling and rough). The objective of this study was to validate these QTL using additional association analyses with a Bayesian approach. Global positioning system (GPS) technology was used to collect grazing distribution phenotypes from 80 beef cows on 5 ranches in New Mexico, Montana, and Arizona. Percent slope, elevation, and distance from water were calculated using GPS coordinates and incorporated into two terrain-use indices (rough and rolling). Cows were genotyped with 777,962 SNP and after applying standard SNP quality filters, 733,713 SNP from 75 cows were available for analysis. A single chromosome (BTA 4, 12, 17, 29) association analysis was performed for both the rough and rolling indices using Bayes C (within the BOLT software package. The posterior inclusion probability (PIP) for each SNP was estimated. The association between rs109619368 on BTA 17 and the rough index was confirmed (PIP = 2.1%); however, the QTL on BTA 4, 12, and 29 were not verified. To further investigate this, 50 SNP spanning 0.2 MB on BTA 29 were analyzed with the rolling index. Two SNP were confirmed in this analysis: rs42161939 (PIP = 54.9%) and rs43744222 (PIP = 21.6%). The Bayesian approach applied in this study, in which markers are simultaneously fit in the model, revealed 3 QTL concordant with previous analyses which used a single-marker regression approach. These results suggest that grazing distribution traits are under genetic control; however, a greater number of observations are needed to confirm the QTL associated with grazing distribution (SW15-015).

Excess nitrogen excretion is viewed as a worldwide environmental problem, and blood urea nitrogen (BUN; mg/dl) has been shown to be a predictor of nitrogen excretion in cattle. As a result, the objective of this study was to identify factors influencing BUN in a cohort of Angus cattle. Steers (n = 98) were born between February and June of 2016 and entered Colorado State University’s Feed Intake Unit (FIU) in May 2017 at an average age of 394.6 ± 21.0 d. While in the FIU, steers were fed a growing diet consisting primarily of corn silage and alfalfa hay. Animals were subjected to a 20 d warm-up period and a 54 d individual feed intake test period. Blood samples were collected on d 50 of the test. A generalized linear regression model was used to determine factors important in the determination of BUN concentrations of individual animals. Factors considered were sire, BUN assay date, age, initial test weight, birth weight, weaning weight, average daily gain, dry matter intake, residual feed intake, pulmonary arterial pressure, ultrasound ribeye area, ultrasound back fat, ultrasound percent intramuscular fat, and feedlot pen. Sire (P < 0.0005; partial r(2) = 0.47), BUN assay date (P < 0.00005; partial r(2) = 0.46) and age (P < 0.005; partial r(2) = 0.18) were all important sources of variation of BUN concentration levels. Sire and assay date explained the largest proportion of variability in BUN concentration as evidenced by their partial r(2) values. Sample process date and age are factors in which cattle producers would have little control in mitigating BUN concentrations, but that could be adjusted for with proper data recording. Differences amongst sires, however, indicate genetic differences may be exploited to reduce BUN concentrations.

The objectives of this study were to estimate the proportion of additive genetic and phenotypic variances explained by the SNP markers in the Illumina3K chip for 4 postweaning ultrasound carcass and weight traits, to compare rankings of calf predicted additive genetic values with 3 models, and to evaluate trends of calf predictions as Brahman fraction increased from 0 to 1. Traits were postweaning ultrasound measures of ribeye area (UREA), backfat thickness (UFAT), intramuscular fat (UPIMF), and body weight at time of ultrasound (UW). Models were genomic-polygenic, genomic, and polygenic. Phenotypes and genotypes were from 623 bulls, heifers, and steers ranging in breed composition from 100% Angus to 100% Brahman fed for 90 d at a GrowSafe automated feeding facility from 2006 to 2010. Variance components were estimated with Markov Chain Monte Carlo procedures (option VCE, program GS3) using a single-trait genomic-polygenic model. Fixed effects were contemporary group (year-pen), age of dam, sex of calf, age of calf, Brahman fraction of calf, and heterozygosity of calf. Random effects were additive SNP, animal polygenic, and residual effects. Models without polygenic effects were used for genomic predictions, and without additive SNP effects for polygenic predictions. Fractions of additive genetic variances explained by the SNP in the Illumina3K chip were 9% for UREA, 38% for UBF, 6% for UPIMF, and 8% for UW. Phenotypic variance fractions explained by Illumina3K SNP were 3.7% for UREA, 9.7% for UBF, 3.2% for UPIMF, and 4.6% for UW. Substantially higher rank correlations existed between genomic-polygenic and polygenic models (0.89 to 0.99) than between genomic-polygenic and genomic (0.64 to 0.79), and genomic and polygenic (0.51 to 0.65) models. Genomic-polygenic, genomic, and polygenic predicted values tended to decrease as Brahman fraction of calf increased suggesting that calves with higher percentage Brahman grew more slowly and had less desirable ultrasound carcass traits. However, there were calves with high, medium, and low predicted genetic values across the Angus–Brahman spectrum, suggesting that selection of animals with desirable postweaning ultrasound carcass and growth traits using a genomic-polygenic strategy would be effective in this multibreed population. Insofar as this multibreed herd represents commercial operations in Florida and the Southern region of the US, selection of commercial calves for these postweaning traits would likely increase their rate of improvement in Brahman and Brahman crossbred populations.

Brangus [3/8 Brahman (Bos indicus) × 5/8 Angus (Bos taurus); n ≈ 800] heifers from 67 sires were used to estimate heritability and conduct a genome-wide association study (GWAS) for 2 binary fertility traits: first service conception (FSC) and heifer pregnancy (HPG). Genotypes were from 53,692 loci on the BovineSNP50 (Infinium Bead Chips, Illumina, San Diego, CA). Yearling heifers were estrous synchronized, bred by AI, and then exposed to natural service breeding. Reproductive ultrasound and DNA-based parentage testing were used to determine if the heifer conceived by AI or natural service, and code for FSC and HPG traits. Success rates for FSC and HPG were 53.3% and 78.0% ± 0.01%, and corresponding heritability estimates were 0.18 ± 0.07 and 0.10 ± 0.06, respectively. The models used in obtaining these heritability estimates and GWAS included fixed effects of year (i.e., 2005 to 2007), birth location, calving season, age of dam, and contemporary group. In GWAS, simultaneous associations of 1 Mb SNP windows with phenotype were undertaken with Bayes C analyses using GenSel software. The 1 Mb windows contained 21.3 ± 1.1 SNP. Analyses fitted a mixture model that treated SNP effects as random, with an assumed fraction pi = 0.9995 having no effect on phenotype. The windows that accounted for 1.0% of genetic variance were considered as QTL associated with FSC or HPG. Eighteen QTL existed on 15 chromosomes for the 2 traits. On average, each QTL accounted for 2.43% ± 0.2% of the genetic variance. Chromosome 8 harbored 2 QTL for FSC and 1 for HPG; however, these regions did not overlap. Chromosomes 3, 15, 16, 19, 24, 26, 27, 29, and X included QTL only for FSC, whereas chromosomes 2, 4, 10, 13, and 20 contained QTL only for HPG. The multitude of QTL detected for FSC and HPG in this GWAS involving Brangus heifers exemplifies the complex regulation of variation in heifer fertility traits of low heritability.

Many traits affecting profitability and sustainability of meat, milk, and fiber production are polygenic, with no single gene having an overwhelming influence on observed variation. No knowledge of the specific genes controlling these traits has been needed to make substantial improvement through selection. Significant gains have been made through phenotypic selection, enhanced by pedigree relationships and continually-improving statistical methodology. Genomic selection, recently enabled by assays for dense SNP located throughout the genome, promises to increase selection accuracy and accelerate genetic improvement by emphasizing the SNP most strongly correlated to phenotype, although the genes and sequence variants affecting phenotype remain largely unknown. These genomic predictions theoretically rely on linkage disequilibrium (LD) between genotyped SNP and unknown functional variants, but familial linkage may increase effectiveness when predicting individuals related to those in the training data. Genomic selection with functional SNP genotypes should be less reliant on LD patterns shared by training and target populations, possibly allowing robust prediction across unrelated populations. While the specific variants causing polygenic variation may never be known with certainty, a number of tools and resources can be employed to identify those most likely to affect phenotype. Associations of dense SNP genotypes with phenotype provide a one-dimensional approach for identifying genes affecting specific traits; in contrast, associations with multiple traits allow defining networks of genes interacting to affect correlated traits. Such networks are especially compelling when corroborated by existing functional annotation and established molecular pathways. The SNP occurring within network genes, obtained from public databases or derived from genome and transcriptome sequences, may be classified according to expected effects on gene products. As illustrated by functionally informed genomic predictions being more accurate than naive whole-genome predictions of beef tenderness, coupling evidence from livestock genotypes, phenotypes, gene expression and genomic variants with existing knowledge of gene functions and interactions may provide greater insight into the genes and genomic mechanisms affecting polygenic traits, and facilitate functional genomic selection for economically important traits.

Data from developing Brangus heifers (3/8 Brahman-Bos indicus × 5/8 Angus-Bos taurus; n ≈ 802 from 67 sires) registered with International Brangus Breeders Association were analyzed to detect QTL associated with growth traits and ultrasound measures of carcass traits. Genotypes were from BovineSNP50 (Infinium BeadChip, Illumina, San Diego, CA; 53,692 SNP). Phenotypes included BW collected at birth and ∼205 and 365 d of age, and yearling ultrasound assessment of LM area, percent intramuscular fat, and depth of rib fat. Simultaneous association of SNP windows with phenotype were undertaken with Bayes C analyses, using GenSel software. The SNP windows were ≈ 5 SNP in length. Analyses fitted a mixture model that treated SNP effects as random, with an assumed fraction pi = 0.999 having no effect on phenotype. Bootstrap analyses were used to obtain significance values for the SNP windows with the greatest contribution to observed variation. The SNP windows with P < 0.01 were considered as QTL associated with a trait in which case their location was queried from dbSNP and the presence of a previously reported QTL in that location was checked in CattleQTLdb. For 9 traits, QTL were mapped to 139 regions on 25 chromosomes. Forty-one of these QTL were already described in CattleQTLdb, so 98 are new additions. The SNP windows on chromosomes 1, 3, and 6 were associated with multiple traits (i.e., 205- and 365- d BW, and ADG from birth to 205 and 365 d of age). Several chromosomes harbored regions associated with multiple traits; however, the SNP that comprised the window often varied among traits (i.e., chromosomes 1, 3, 4, 5, 6, 7, 9, 10, 11, 13, 14, 15, 16, 20, 21, 22, 24, 28, and 29). Results from whole genome association of SNP with growth and ultrasound carcass traits in developing Brangus heifers confirmed several published QTL and detected several new QTL.

Measures of heifer fertility are economically relevant traits for beef production systems and knowledge of candidate genes could be incorporated into future genomic selection strategies. Ten traits related to growth and fertility were measured in 890 Brangus heifers (3/8 Brahman × 5/8 Angus, from 67 sires). These traits were: BW and hip height adjusted to 205 and 365 d of age, postweaning ADG, yearling assessment of carcass traits (i.e., back fat thickness, intramuscular fat, and LM area), as well as heifer pregnancy and first service conception (FSC). These fertility traits were collected from controlled breeding seasons initiated with estrous synchronization and AI targeting heifers to calve by 24 mo of age. The BovineSNP50 BeadChip was used to ascertain 53,692 SNP genotypes for ∼802 heifers. Associations of genotypes and phenotypes were performed and SNP effects were estimated for each trait. Minimally associated SNP (P < 0.05) and their effects across the 10 traits formed the basis for an association weight matrix and its derived gene network related to FSC (57.3% success and heritability = 0.06 ± 0.05). These analyses yielded 1,555 important SNP, which inferred genes linked by 113,873 correlations within a network. Specifically, 1,386 SNP were nodes and the 5,132 strongest correlations (|r| ≥ 0.90) were edges. The network was filtered with genes queried from a transcriptome resource created from deep sequencing of RNA (i.e., RNA-Seq) from the hypothalamus of a prepubertal and a postpubertal Brangus heifer. The remaining hypothalamic-influenced network contained 978 genes connected by 2,560 edges or predicted gene interactions. This hypothalamic gene network was enriched with genes involved in axon guidance, which is a pathway known to influence pulsatile release of LHRH. There were 5 transcription factors with 21 or more connections: ZMAT3, STAT6, RFX4, PLAGL1, and NR6A1 for FSC. The SNP that identified these genes were intragenic and were on chromosomes 1, 5, 9, and 11. Chromosome 5 harbored both STAT6 and RFX4. The large number of interactions and genes observed with network analyses of multiple sources of genomic data (i.e., GWAS and RNA-Seq) support the concept of FSC being a polygenic trait.

The objectives of this study were to determine the fraction of additive genetic variance explained by the SNP from the Illumina Bovine3K chip; to compare the ranking of animals evaluated with genomic-polygenic, genomic, and polygenic models; and to assess trends in predicted values from these 3 models for residual feed intake (RFI), daily feed intake (DFI), feed conversion ratio (FCR), and postweaning BW gain (PWG) in a multibreed Angus-Brahman cattle population under subtropical conditions. Data consisted of phenotypes and genotypes from 620 bulls, steers, and heifers ranging from 100% Angus to 100% Brahman. Phenotypes were collected in a GrowSafe automated feeding facility (GrowSafe Systems, Ltd., Airdrie, Alberta, Canada) from 2006 to 2010. Variance components were estimated using single-trait genomic-polygenic mixed models with option VCE (Markov chain Monte Carlo) of the program GS3. Fixed effects were contemporary group (year-pen), age of dam, sex of calf, age of calf, Brahman fraction of calf, and heterozygosity of calf. Random effects were additive SNP, animal polygenic, and residual effects. Genomic predictions were computed using a model without polygenic effects and polygenic predictions with a model that excluded additive SNP effects. Heritabilities were 0.20 for RFI, 0.31 for DFI, 0.21 for FCR, and 0.36 for PWG. The fraction of the additive genetic variance explained by SNP in the Illumina 3K chip was 15% for RFI, 11% for DFI, 25% for FCR, and 15% for PWG. These fractions will likely differ in other multibreed populations. Rank correlations between genomic-polygenic and polygenic predictions were high (0.95 to 0.99; P < 0.0001), whereas those between genomic-polygenic and genomic predictions were low (0.65 to 0.74; P < 0.0001). Genomic-polygenic, genomic, and polygenic predictions for all traits tended to decrease as Brahman fraction increased, indicating that calves with greater Brahman fraction were more efficient but grew more slowly than calves with greater Angus fraction. Predicted SNP values were small for all traits, and those above and below 0.2 SNP SD were in multiple chromosomes, supporting the contention that quantitative traits are determined by large numbers of alleles with small effects located throughout the genome.

Reproductive efficiency is of economic importance in commercial beef cattle production, since failure to achieve pregnancy reduces the number of calves marketed. Identification of genetic markers with predictive merit for reproductive success would facilitate early selection of females and avoid inefficiencies associated with sub-fertile cows. To identify regions of the genome harboring variation affecting reproductive success, we applied a genome-wide association approach based on the >700,000 SNP marker assay. To include the largest number of individuals possible under the available budget, cows from several populations were assigned to extremes for reproductive efficiency, and DNA was pooled within population and phenotype before genotyping. Surprisingly, pools prepared from DNA of low reproductive cattle returned fluorescence intensity data intermediate between fertile females and males for SNP mapped to the Y chromosome (i.e., male sex chromosome). The presence of Y-associated material in low reproductive heifers or cows was confirmed by Y-directed PCR, which revealed that 21 to 29% of females in the low reproductive category were positive by a Y chromosome PCR test normally used to sex embryos. The presence of the Y chromosome anomaly was further confirmed with application of additional Y-specific PCR amplicons, indicating the likelihood of the presence of some portion of male sex chromosome in female cattle in various beef cattle herds across the U.S. Discovery of this Y anomaly in low reproductive females may make an important contribution to management of reproductive failures in beef cattle operations.

Grazing distribution can be improved by using adapted cattle breeds that travel to distant areas of extensive pastures. A 2-yr study was conducted to evaluate grazing distribution and diet quality of Angus, Brangus, and Brahman cows (seven cows per breed group) in the Chihuahuan Desert during three seasons (winter, early summer, and late summer) using three pastures. Two GPS collars were randomly assigned to each breed group and cow positions were logged every 10 min for 10- to 14-d periods in each pasture (3 periods · season -1 ). In 2008, breed groups were evaluated in separate pastures and data were analyzed as a 3 × 3 Latin square design. In 2009, all breed groups were evaluated at the same time in the same pastures. Fecal samples were collected in 2008 and analyzed using near infrared spectroscopy (NIRS) to estimate diet quality. If positions recorded when cows were resting were excluded, Brahman cows traveled greater distances per day than Angus cows throughout the study and greater ( P ≤ 0.10) than Brangus cows in all but one season during 2009. No differences in average distance to water were detected ( P s 0.10) among breed groups. During early summer in 2008 and early and late summer in 2009, Angus cows maintained a more linear grazing path ( P ≤ 0.10) than Brangus or Brahman cows. Brahman cows displayed more sinuous grazing paths ( P ≤ 0.10) than other breeds during early and late summer seasons in 2009. In 2008, no differences in crude protein content of diets were detected ( P s 0.10) among breed groups during all seasons. Spatial movement patterns of Brahman cows appeared to differ from Angus and Brangus cows; however, there was no evidence to suggest that there was any advantage in use of areas far from water by any breed group.

The promise of genomic selection is accurate prediction of the genetic potential of animals from their genotypes. Simple DNA tests might replace low-accuracy predictions for expensive or lowly heritable measures of puberty and fertility based on performance and pedigree. Knowing with some certainty which DNA variants (e.g., SNP) affect puberty and fertility is the best way to fulfill the promise. Several SNP from the BovineSNP50 assay have tentatively been associated with reproductive traits including age at puberty, antral follicle count, and pregnancy observed on different sets of heifers. However, sample sizes are too small and SNP density is too sparse to definitively determine genomic regions harboring causal variants affecting reproductive success. Additionally, associations between individual SNP and similar phenotypes are inconsistent across data sets, and genomic predictions do not appear to be globally applicable to cattle of different breeds. Discrepancies may be a result of different QTL segregating in the sampled populations, differences in linkage disequilibrium (LD) patterns such that the same SNP are not correlated with the same QTL, and spurious correlations with phenotype. Several approaches can be used independently or in combination to improve detection of genomic factors affecting heifer puberty and fertility. Larger samples and denser SNP will increase power to detect real associations with SNP having more consistent LD with underlying QTL. Meta-analysis combining results from different studies can also be used to effectively increase sample size. High-density genotyping with heifers pooled by pregnancy status or early and late puberty can be a cost-effective means to sample large numbers. Networks of genes, implicated by associations with multiple traits correlated with puberty and fertility, could provide insight into the complex nature of these traits, especially if corroborated by functional annotation, established gene interaction pathways, and transcript expression. Example analyses are provided to demonstrate how integrating information about gene function and regulation with statistical associations from whole-genome SNP genotyping assays might enhance knowledge of genomic mechanisms affecting puberty and fertility, enabling reliable DNA tests to guide heifer selection decisions.