Search

Estimated breeding values (EBV) for fecal egg counts (FEC) at 42–90 days of age (WFEC) and 91–150 days of age (PFEC) for 84 progeny-tested Katahdin sires were used to identify associations of deregressed EBV with single-nucleotide polymorphisms (SNP) using 388,000 SNP with minor-allele frequencies ≥0.10 on an Illumina high-density ovine array. Associations between markers and FEC EBV were initially quantified by single-SNP linear regression. Effects of linkage disequilibrium (LD) were minimized by assigning SNP to 2,535 consecutive 1-Mb bins and focusing on the effect of the most significant SNP in each bin. Bonferroni correction was used to define bin-based (BB) genome- and chromosome-wide significance. Six bins on chromosome 5 achieved BB genome-wide significance for PFEC EBV, and three of those SNP achieved chromosome-wide significance after Bonferroni correction based on the 14,530 total SNP on chromosome 5. These bins were nested within 12 consecutive bins between 59 and 71 Mb on chromosome 5 that reached BB chromosome-wide significance. The largest SNP effects were at 63, 67, and 70 Mb, with LD among these SNP of r2 ≤ 0.2. Regional heritability mapping (RHM) was then used to evaluate the ability of different genomic regions to account for additive variance in FEC EBV. Chromosome-level RHM indicated that one 500-SNP window between 65.9 and 69.9 Mb accounted for significant variation in PFEC EBV. Five additional 500-SNP windows between 59.3 and 71.6 Mb reached suggestive (p < 0.10) significance for PFEC EBV. Although previous studies rarely identified markers for parasite resistance on chromosome 5, the IL12B gene at 68.5 Mb codes for the p40 subunit of both interleukins 12 and 23. Other immunoregulatory genes are also located in this region of chromosome 5, providing opportunity for additive or associative effects.

Individual and maternal breed additive effects and heterosis exist for most economically important traits in cattle. Crossbreeding may therefore be valuable for emerging and commercial beef farmers in improving the productivity of their herds. Calves were produced by mating Afrikaner, Bonsmara and Nguni cows to Afrikaner, Bonsmara, Nguni, Angus and Simmental bulls. The cows used were from Vaalharts Research Station or were purchased from other herds. Data were collected over three years. Individual and maternal additive effects and individual heterosis were estimated simultaneously as continuous linear variates. The estimated genetic effects were then used to predict production levels that may be achieved through implementation of top-cross, two-breed rotation, and terminal sire crossbreeding systems. The individual estimates of the genetic effects were relatively small and in most cases were not different from zero, with the exception of the maternal additive effects of Nguni on preweaning traits and their individual additive effect on cow weight, which were less than those of Bonsmara. However, the alternative crossbreeding systems differed across traits. The straight-bred breeding system was least efficient, followed by the crisscross system (+2%) and the terminal sire system that utilized Simmental (+4%), with the terminal sire system utilizing Angus being on average most efficient (+8%). The inter-generational genetic differences in cow weight that resulted from the use of different breeds of sire increased its standard deviation by 5 to 6% in rotational crossing. Despite the relatively small magnitude of the genetic effects, advantages of crossbreeding systems became evident.Keywords: breed additive, crossbreeding, heterosis, post-weaning, pre-weaning

Wet carcass syndrome (WCS), which is observed predominantly in sheep, affects carcass quality negatively. After slaughter the carcass appears to be ‘wet’ with a subcutaneous accumulation of watery fluid. Not all animals in a contemporary group are afflicted, and experimental attempts to induce WCS have been unsuccessful. The reported prevalence of WCS in Dorper and Dorper crosses gave rise to the hypothesis that it may have a genetic basis. Therefore, the primary objective of this investigation was to test this hypothesis using a high-density SNP assay to search loci that may predispose sheep to WCS. Muscle samples from 43 afflicted and 41 unafflicted sheep were collected from slaughterhouses in the province of Northern Cape, South Africa, and in southern Namibia. Tests against candidate genes proved uninformative, as did runs of homozygosity. Potential associations between WCS and an autosomal genetic marker were investigated further in a case-control genome-wide association study. Separate analyses for each sex were motivated because single nucleotide polymorphisms (SNPs) on the X chromosome suggested quantitative trait loci. These analyses revealed significant associations between SNP and WCS in males, but not in females. Three SNPs that reached genome-wide significance in males are in strong linkage disequilibrium with the Duchenne muscular dystrophy, 5-hydroxytryptamine receptor 2C, and Teneurin transmembrane protein 1 genes. These genes are identified as positional candidate genes, and the Duchenne muscular dystrophy, 5-hydroxytryptamine receptor 2C genes have biological effects that have been documented in other species, making them plausible functional candidate genes for WCS in sheep.Keywords: association analysis, Dorper, sheep carcass, single nucleotide polymorphisms, X chromosome

Information on body weight and average daily gain (ADG) of growing animals is key not only to monitoring performance, but also for use in genetic evaluations in the pursuit of achieving sustainable genetic gain. Accurate calculation of ADG, however, requires serial measures of body weight over at least 70 days. This can be resource intensive and thus alternative approaches to predicting individual animal ADG warrant investigation. One such approach is the use of continuously collected individual animal partial body weights. The objective of the present study was to determine the utility of partial body weights in predicting both body weight and ADG; a secondary objective was to deduce the appropriate length of test to determine ADG from partial body weight records. The dataset used consisted of partial body weights, predicted body weights and recorded body weights recorded for 8,972 growing cattle from a range of different breed types in 35 contemporary groups. The relationships among partial body weight, predicted body weight and recorded body weight at the beginning and end of the performance test were determined and calculated ADG per animal from each body weight measure were also compared. On average, partial body weight explained 90.7 ± 2.0% of the variation in recorded body weight at the beginning of the postweaning gain test and 87.9 ± 2.9% of the variation in recorded body weight at its end. The GrowSafe proprietary algorithm to predict body weight from the partial body weight strengthened these coefficients of determination to 95.1 ± 0.9% and 94.9 ± 0.8%, respectively. The ADG calculated from the partial body weight or from the predicted body weight were very strongly correlated (r = 0.95); correlations between these ADG values with those calculated from the recorded body weights were weaker at 0.81 and 0.78, respectively. For some applications, ADG may be measured with sufficient accuracy with a test period of 50 days using partial body weights. The intended inference space is to individual trials which have been represented in this study by contemporary groups of growing cattle from different genotypes.

This study evaluated associations of heat shock proteins (HSP) and an oxidative stress protein, protein deglycase (DJ1), with beef quality and tenderness. Samples from the longissimus thoracis (N = 99) were collected pre-rigor (day 0) and after 14-d aging. Warner-Bratzler shear force (WBSF), myofibrillar fragmentation index (MFI), and a trained sensory panel were used to determine meat quality. Protein abundance of DJ1 and 2 HSP—HSPβ1 and HSPA—were assessed. Regression analyses demonstrated that DJ1 abundance after 14 d of aging is a predictor of WBSF (P < 0.001), MFI (P = 0.02), and sensory panel tenderness (P < 0.001). Abundance of HSPβ1 after 14 d of aging is also a predictor of MFI (P = 0.03). Additionally, abundance of both HSPβ1 and DJ1 pre-rigor are predictors of juiciness (P < 0.05). Abundance of HSPβ1 pre-rigor was correlated with WBSF (R = 0.67), sensory panel tenderness (R = −0.44), juiciness (R = −0.30), and umami (R = −0.20). Abundance of DJ1 pre-rigor was also correlated with WBSF (R = 0.72), sensory panel tenderness (R = −0.44), juiciness (R = − 0.24), and umami (R = −0.31). After 14-d aging, HSP β 1 abundance was cor- related with WBSF (R = 0.66), sensory panel tenderness (R = −0.34), juiciness (R = −0.34), umami (R = −0.33), and brown/ roasted (R = −0.30). Abundance of DJ1 after 14-d aging was also correlated with WBSF (R = 0.68), sensory panel tenderness (R = −0.41), juiciness (R = −0.21), and umami (R = −0.28). These results demonstrate that abundance of HSPβ1 and DJ1 both pre-rigor and after 14 d of aging are correlated with meat tenderness and end-product quality as assessed by a trained sensory panel. Regression analyses further reveal that abundance of DJ1 and HSPβ1 after 14 d of aging is causative in development of beef tenderness and juiciness, respectively. Taken together, these results suggest that abundance of DJ1 is a predictor of tenderness, whereas abundance of HSPβ1 is related to meat quality but cannot be used to predict tenderness.

The objective of this study was to evaluate the effects of various data structures on the genetic evaluation for the binary phenotype of reproductive success. The data were simulated based on an existing pedigree and an underlying fertility phenotype with a heritability of 0.10. A data set of complete observations was generated for all cows. This data set was then modified mimicking the culling of cows when they first failed to reproduce, cows having a missing observation at either their second or fifth opportunity to reproduce as if they had been selected as donors for embryo transfer, and censoring records following the sixth opportunity to reproduce as in a cull-for-age strategy. The data were analyzed using a third-order polynomial random regression model. The EBV of interest for each animal was the sum of the age-specific EBV over the first 10 observations (reproductive success at ages 2–11). Thus, the EBV might be interpreted as the genetic expectation of number of calves produced when a female is given 10 opportunities to calve. Culling open cows resulted in the EBV for 3-yr-old cows being reduced from 8.27 ± 0.03 when open cows were retained to 7.60 ± 0.02 when they were culled. The magnitude of this effect decreased as cows grew older when they first failed to reproduce and were subsequently culled. Cows that did not fail over the 11 yr of simulated data had an EBV of 9.43 ± 0.01 and 9.35 ± 0.01 based on analyses of the complete data and the data in which cows that failed to reproduce were culled, respectively. Cows that had a missing observation for their second record had a significantly reduced EBV, but the corresponding effect at the fifth record was negligible. The current study illustrates that culling and management decisions, and particularly those that affect the beginning of the trajectory of sustained reproductive success, can influence both the magnitude and accuracy of resulting EBV.

Two hundred seventeen grass-finished Braford steers were assessed by ultrasonic scanning and subsequently harvested with their pistol hindquarters fabricated into boneless wholesale cuts. The Longissimus thoracis muscle area and subcutaneous fat depths were measured. The objectives of this study were: 1) to develop prediction equations for weights of the pistol hindquarter and high-value commercial cuts, and 2) to estimate sample size needed for experiments comparing pistol hindquarter retail product weight using either physically or ultrasonically measured carcass traits. Carcass measurements explained 44 % to 94 % of the variation in weights of individual cuts, whereas, measurements that were made using ultrasound explained 42 % to 90 % of the variation in the weights. Models used to predict the weight of pistol hindquarter retail product with carcass measures and ultrasound measures showed high coefficient of determination (R2 = 0.92 and 0.97, respectively). Whether based on carcass or ultrasound measures, models used to estimate weight percentage of fat trimmed from the pistol hindquarter had lack of fit. In general, models for individual cuts weights that used traits measured with ultrasound as independent variables approached the accuracy of models using carcass traits. Thus, only slightly greater samples sizes were required to have equivalent power to detect differences in retail product weights using ultrasound measures. For experiments of equivalent power, differences in the number of animals required may be offset by avoiding costs for slaughter and fabrication. Keywords: cattle, carcass, models, ultrasound Made available in DSpace on 2020-12-08T09:04:59Z (GMT). No. of bitstreams: 1 Cardoso-et-al-2020.pdf: 200863 bytes, checksum: c53212e478f34b7b26120f57f62ac486 (MD5) Previous issue date: 2020

Ultrasound technology provides cattle breeders with a quick, noninvasive, and inexpensive way to measure carcass data on live animals. Ultrasound data are used as indicator traits in cattle genetic evaluations for economically relevant carcass traits. Ultrasound cattle genetic evaluations assume homogeneous additive genetic and residual variance. Thus, the objective was to partition phenotypic variance in ultrasound carcass measurements into components for additive genetic effects, technicians, contemporary groups within technicians, and residual and to examine the homogeneity of these variances among image interpretation laboratories. Records of longissimus muscle area (LMA), percentage of intramuscular fat (IMF), and subcutaneous fat depth (SFD), measured using ultrasound, were provided by the American Angus Association (n = 65,967), American Hereford Association (n = 43,182), and American Simmental Association (n = 48,298). The data also included contemporary group, technician, imaging lab, and a three-generation pedigree for each animal. Variance components for ultrasound carcass measurements were first estimated with univariate animal models for each breed and imaging laboratory using derivative-free restricted maximum likelihood. Then, treating data from each imaging laboratory as separate traits, genetic correlations between laboratories for LMA, percentage of IMF, and subcutaneous fat were estimated with trivariate animal models. The technician explained 12–27%, 5–23%, and 4–26% of the variance for IMF, SFD, and LMA, respectively, across all three breeds. Variance due to technician was often greater than variance due to additive genetic effects but almost always less than that explained by the contemporary group. Within breeds, estimates of additive genetic variance for LMA, SFD, and IMF differed (range divided by mean) among laboratories by 4.5%, 21.5%, and 39.4 % (Angus); 31.6%, 15.0%, and 49.1% (Hereford); and 19.9%, 46.6%, and 55.3% (Simmental), respectively. Likewise, estimates of residual variance for LMA, SFD, and IMF differed among laboratories by 43.4%, 22.9%, and 43.3% (Angus); 24.9%, 15.2%, and 79.2% (Hereford); and 26.4%, 32.5%, and 46.2% (Simmental), respectively. Genetic correlations between labs across breeds ranged from 0.79 to 0.95 for IMF, 0.26 to 0.94 for SFD, and 0.78 to 0.98 for LMA. The impact of the observed heterogeneity of variance between labs on genetic evaluation requires further study.

The objective of the project was to create an economic risk analysis tool for user-defined embryo transfer (ET) programs as an aid in decision-making. Distributions defining the biological uncertainty for many reproductive outcomes are estimated through extensive literature review and limited industry sources. Applying the Latin hypercube variation of Monte Carlo simulation, a sample value from the descriptive distribution associated with each stochastic variable is included in each iteration of the simulation. Through large numbers of iterations with dynamic combinations of variable values, the process culminates in a distribution of possible values for the net present value, annuity equivalent net present value, and return on investment associated with the modeled embryo production scenario. Two options for embryo production, multiple ovulation embryo transfer (MOET) and in vitro embryo production (IVP) from aspirated oocytes, are modeled. Within both MOET and IVP, the use of unsorted or sex-sorted semen is considered, as well as the exception or inclusion of follicular synchronization and/or stimulation before ovum pick-up in IVP procedures. Pretransfer embryo selection through embryo biopsy can also be accounted for when considering in vivo derived embryos. Ample opportunity exists for the commercial application of in-depth, alternative ET scenario assessment afforded through stochastic simulation methodology that the ET industry has not yet fully exploited.

The objective of this study was to estimate economic returns and costs associated with 4 scenarios of genetic evaluation that combine genotypes, phenotypes, and pedigree information from a vertically integrated purebred (PB) and commercial (CM) beef cattle system. Inference was to a genetic evaluation for a production system producing Charolais terminal sires for 10,000 CM cows. The first genetic evaluation scenario, denoted PB_A, modeled a genetic evaluation in which pedigree information and phenotypes are available for PB seedstock animals. Scenario PB_H contained the same information as PB_A with the addition of 25K density (GeneSeek Genomic Profiler LD) single nucleotide polymorphism (SNP) genotypes from PB animals. Scenario PBCM_A contained pedigree records and phenotypes from PB and CM cattle. Scenario PBCM_H contained phenotypes, pedigree, and genotypes from the PB and CM animals. Estimates of prediction error variance, (co)variance, and selection index parameters were used to estimate accuracy of selection candidates (rTI) and genetic gain resulting from selection on an economic index in US dollars (ΔG). Annual costs and incomes were used to determine the 30-yr cumulative net present value (CNPV) per CM calf resulting from selection in these genetic evaluation scenarios. Adding genotypes and CM production phenotypes to genetic evaluation increased the rTI of selection candidates and ΔG across all 4 scenarios. Scenario PBCM_H produced the highest annual ΔG in the PB herd at US$11.91 per head. Including CM phenotypes and parentage testing in the genetic evaluation increased the time to breakeven from 12 yr in PB_A to 19 years in PBCM_A after accounting for the cost of that information. Adding CM phenotypes and genotypes increased the breakeven time from 12 yr in PB_H to 18 yr in PBCM_H. Scenario PB_H produced the highest 30-yr CNPV per slaughtered CM calf at US$371.16. These results using field data indicate that economically relevant rTI and ΔG can be realized by adding 25K SNP genotypes and CM phenotypes to genetic evaluation, but the additional cost of that data significantly delays the economic return to the enterprise.

The objective of this study was to compare growth from birth to slaughter of different breed groups that were raised in Rio Grande do Sul, Brazil and estimate the consequent breed additive and heterosis effects. Caracu (C), Hereford (H), and Nelore (N) sires were mated with Angus (A) dams, and A sires were mated with H and N dams to produce a first generation of crossbred progeny that was contemporary with purebred A, H, and N calves. Heifers from this first generation (G1) were mated with Brangus (BN) and Braford (BO) sires to produce a second generation (G2) of progeny. Data were analyzed to estimate breed group means, individual and maternal breed additive effects, and heterosis effects on birth weight, weaning weight, preweaning average daily gain, yearling weight, postweaning average daily gain, fattening phase initial weight (around 19 mo), final weight (around 24 mo), average daily gain in the fattening phase, and age at slaughter. In general, crossbred calves outperformed purebred calves. Angus-N and CA crossbred cows weaned heavier calves. Individual taurine-indicine heterosis (Z) significantly increased weaning weight. The AN, NA, and CA steers were heaviest at yearling, whereas NA, CA, AN, and HA had the greatest final weights. However, AH steers were 1 mo older at slaughter than NA contemporaries. Taurine breed effects on postweaning traits and final weight were greater than for N. Maternal breed effects on birth weight and average daily gain in the fattening phase were greater for A and H than for N. In conclusion, heterosis effects were sufficiently large for use of N to be recommended as a component of such systems, despite their relatively low-breed additive effects compared with taurine breeds. Moreover, germplasm from the tropically adapted Bos taurus C may be particularly useful when increased milk production is desired. With the breed and heterosis effects derived in the present study, it is possible to predict the performance and infer which breed and breed crosses will perform better in crossbreeding systems designed for the subtropical conditions of southern Brazil and similar regions.

Shortening the period of recording individual feed intake may improve selection response for feed efficiency by increasing the number of cattle that can be recorded given facilities of fixed capacity. Individual DMI and ADG records of 3,462 steers and 2,869 heifers over the entire intake recording period (range 62 to 154 d; mean 83 d; DMI83 and ADG83, respectively), DMI and ADG for the first 42 d of the recording period (DMI42 and ADG42, respectively), and postweaning ADG based on the difference between weaning and yearling weights (PADG) were analyzed. Genetic correlations among DMI42 and DMI83, ADG42 and ADG83, ADG42 and PADG, and ADG83 and PADG were 0.995, 0.962, 0.852, and 0.822, respectively. Four objective functions [feed:gain ratio in steers (FGS) and heifers (FGH); residual gain (RG); and residual feed intake (RFI)] based on DMI83 and ADG83 were considered. Indices using DMI42 and ADG42 (I42); DMI42 and PADG (IPW); and DMI42, ADG42, and PADG (IALL) were developed. Accuracy of the 5 EBV, 4 objectives, and 12 objective × index combinations were computed for all 12,033 animals in the pedigree. Accuracies of indices (IA) were summarized for animals with accuracies for objectives (OA) of 0.25, 0.5, 0.75, and 1. For the RG objective and animals with OA of 0.75, indices I42, IPW, and IALL had IA of 0.63, 0.55, and 0.67, respectively. Differences in IA increased with increased emphasis on ADG83 in the objective. Differences in IA between I42 and IPW usually increased with OA. Relative efficiency (RE) of selection on 42-d tests compared with 83 d was computed based on differences in IA and selection intensities of 5%, 25%, 50%, and 75% under the 83-d scenario, assuming 65% more animals could be tested for 42 d. For 25% selected for the RG objective, and animals with OA of 0.75, indices I42, IPW, and IALL had RE of 1.02, 0.90, and 1.10, respectively. As % selected, OA, and emphasis on DMI increased, RE increased. Relative efficiency varied considerably according to assumptions. One-half of the scenarios considered had RE > 1.15 with a maximum of 2.02 and 77% RE > 1.0. A shorter period of recording DMI can improve selection response for feed efficiency. Selection for the efficiency objectives would not affect PADG. It will be most effective if ADG over the period coinciding with intake recording and ADG over a much longer period of time are simultaneously included in a multiple-trait genetic evaluation with DMI and used in a selection index for efficiency.

The objective of this study was to estimate genetic parameters and genetic trends of Hereford and Braford breeds for growth traits and visual scores. Data consisting of records for 205-day weight (W205), 550-day weight (W550), 345-day post weaning gain (PWG345), scrotal circumference at 550 days (SC), and muscling (MUS) and frame (FRA) scores also recorded at 550 days of age came from the PampaPlus genetic evaluation system. A series of animal models were fit to the data using Bayesian inference with uninformative priors. Genetic variance for W205 was partitioned into direct (W205 d ) and maternal (W205 m ) components. Posterior means of heritability estimates and 95% support intervals (2.5% ≤ h 2 ≤ 97.5%) for W205 d , W205m, W550, PWG345, SC, MUS, and FRA were 0,12 ≤ 0.13 ≤ 0,14; 0.08 ≤ 0,09 ≤ 0.11; 0.13 ≤ 0.16 ≤ 0.19; 0.04 ≤ 0.10 ≤ 0.18; 0.05 ≤ 0.15 ≤ 0.32; 0.10 ≤ 0.19 ≤ 0.29 and 0.06 ≤ 0.11 ≤ 0.20, respectively. Genetic correlations with W205 d were positive for W550 (0.72 ≤ 0.82 ≤ 0.90), MUS (0.25 ≤ 0.53 ≤ 0.74) and FRA 0.29 ≤ 0.59 ≤ 0.80 and negative for W205 m (− 0.63 ≤ − 0.57 ≤ − 0.50). The genetic correlation of PWG345 and W550 was also positive and large (0.59 ≤ 0.76 ≤ 0.88). Genetic correlations of MUS and FRA with each other (0.30 ≤ 0.53 ≤ 0.73) and with PWG (0.08 ≤ 0.33 ≤ 0.55 and 0.20 ≤ 0.44 ≤ 0.64) and W550 (0.10 ≤ 0.39 ≤ 0.63 and 0.07 ≤ 0.38 ≤ 0.64) were all positive. Use of performance information in selection decisions is supported by positive genetic trends for direct effects on W205 d , PWG345, W550, MUS and FRA. However, the genetic trends were less than the expected gains that would result from use of a recommended selection index, suggesting that the index is not the only criterion currently used in the selection by Pampaplus breeders. It may be concluded that breeders favored larger, more rapidly growing, and more muscular animals in their selection decisions.

An economic selection index was developed for Beefmaster cattle in a general-purpose production system in which bulls are mated to a combination of heifers and mature cows, with resulting progeny retained as replacements or sold at weaning. National average prices from 2010 to 2014 were used to establish income and expenses for the system. Genetic parameters were obtained from the literature. Economic values were estimated by simulating 100,000 animals and approximating the partial derivatives of the profit function by perturbing traits 1 at a time, by 1 unit, while holding the other traits constant at their respective means. Relative economic values for the objective traits calving difficultly direct (CDd), calving difficulty maternal (CDm), weaning weight direct (WWd), weaning weight maternal (WWm), mature cow weight (MW), and heifer pregnancy (HP) were -2.11, -1.53, 18.49, 11.28, -33.46, and 1.19, respectively. Consequently, under the scenario assumed herein, the greatest improvements in profitability could be made by decreasing maintenance energy costs associated with MW followed by improvements in weaning weight. The accuracy of the index lies between 0.218 (phenotypic-based index selection) and 0.428 (breeding values known without error). Implementation of this index would facilitate genetic improvement and increase profitability of Beefmaster cattle operations with a general-purpose breeding objective when replacement females are retained and with weaned calves as the sale end point.

Carcass data that is collected using ultrasound contributes to national genetic evaluation of beef cattle. Cattle are scanned by many technicians and the resulting images are processed by three laboratories providing data to breed associations. The Ultrasound Guidelines Council certifies technicians and laboratories as being proficient. However, there has been no comprehensive evaluation of non-genetic sources of variation that affect the data. The objective of this study was to partition the variance of ultrasound carcass measurements to animal genetic effects, ultrasound scanning technician and image interpretation laboratory. Ultrasound carcass data for longissimus muscle area, percent intramuscular fat, and subcutaneous fat depth were provided by the American Angus Association (n=65,971), American Hereford Association (n=43,380), and American Simmental Association (n=48,298). For each breed variance components were estimated for additive genetic effects of each animal, technician, contemporary group nested within technician and residual. Genetic correlations were estimated treating measurements from the different interpretation laboratories as separate traits. Across all three breeds, additive genetic effects explained between 15 and 30%, 11 and 25%, and 6 and 13% of the phenotypic variance for IMF, SQF, and LMA, respectively. Similarly, technician explained 12-27%, 4-28%, and 4-26% of the phenotypic variance; contemporary groups within technician accounted for 25-45%, 20-54%, and 43-73% of phenotypic variance. Among the image interpretation laboratories, the ratio of greatest to least residual variance was 3.96, 1.62, and 1.50 for IMF, SQF, and LMA, respectively. Genetic correlations between labs ranged from 0.79 to 0.95 for IMF, 0.64 to 0.94 for SQF and 0.78 to 0.98 for LMA. These results suggest the potential for the residual variances to be heterogeneous, particularly for IMF, depending on the image interpretation laboratory.

International audience; AbstractBackgroundRecessive loss-of-function (LOF) alleles at genes which are essential for life, can result in early embryonic mortality. Cattle producers can use the LOF carrier status of individual animals to make selection and mate allocation decisions.MethodsTwo beef cattle breeding strategies i.e. (1) selection against LOF carriers as parents and (2) simultaneous selection and mate allocation to avoid the occurrence of homozygous offspring in three scenarios, which differed in number and frequency of LOF alleles were evaluated using the mate selection program, MateSel. Scenarios included (a) seven loci with high-frequency LOF alleles, (b) 76 loci with low-frequency LOF alleles, and (c) 50 loci with random high- and low-frequency LOF alleles. In addition, any savings resulting from the information obtained by varying the percentage (0–100%) of the herd genotyped, together with segregation analysis to cover ungenotyped animals, were calculated to determine (1) which percentage optimized net profit for a fixed cost of genotyping ($30/test), and (2) the breakeven cost for genotyping.ResultsWith full knowledge of the LOF alleles carried by selection candidates, the most profitable breeding strategy was always simultaneous selection and mate allocation to avoid homozygous affected offspring (aa) as compared to indiscriminate selection against carrier parents (Aa). The breakeven value of genotyping depended on the number of loci modeled, the LOF allele frequencies, and the mating/selection strategies used. Genotyping was most valuable when it was used to avoid otherwise high levels of embryonic mortalities. As the number of essential loci with LOF alleles increased, especially when some were present at relatively high minor allele frequencies, embryonic losses increased, and profit was maximized by genotyping 10 to 20% of a herd and using that information to reduce these losses.ConclusionsGenotyping 100% of the herd was never the most profitable outcome in any scenario; however, genotyping some proportion of the herd, together with segregation analysis to cover ungenotyped animals, maximized overall profit in scenarios with large numbers of loci with LOF alleles. As more LOF alleles are identified, such a mate selection software will likely be required to optimally select and allocate matings to balance the rate of genetic gain, embryonic losses, and inbreeding.

The objective of this study was to determine breed additive and heterosis effects on growth curves, total milk yield (TMY), calf weaning weight (WW), predicted energy intake (EI), and cow efficiency (CE) of purebred and crossbred beef cows raised in Southern Brazil. The data were from 175 purebred and crossbred cows representing eight genetic groups: Angus (A), Hereford (H), Nelore (N), A × H (AH), H × A (HA), A × N (AN), N × A (NA), and Caracu (C) × A (CA). Growth of the cows was modeled using the nonlinear Brody function and machine milking was used to assess TMY. WW was linearly adjusted to 210 d. EI was predicted with an equation in which the independent variables were estimates of parameters of the Brody function and TMY. The ratio of WW to EI estimated CE. Taurine–indicine heterosis effects were significant for all traits, and greater than those for taurine breed crosses. In general, crossbred cows were heavier at maturity, matured earlier, produced more milk, weaned heavier calves, and were predicted to consume more energy. Thus, they were more efficient than purebred cows, despite their greater predicted feed intake. Among the purebreds, A cows matured most rapidly, weighed the least at maturity, produced the most milk, weaned the heaviest calves, were predicted to consume the least energy; and were therefore most efficient among the breeds that were evaluated. These results are useful as inputs to bioeconomic models that can be used to predict productive and economic outcomes from crossbreeding and to facilitate recommendations for beef producers of southern Brazil and other similar subtropical climatic regions.

Development and long-term retention of replacement beef females in a semi-arid environment are of a major concern for extensive livestock producers. Furthermore, the demand of not only producing a thriving, healthy calf, but having sufficient milk to support that first calf is essential. To address this issue, we conducted a 3-year study measuring milk production and milk constituent yields in primiparous beef heifers (n=48; 16/year reared under two different feeding regimens) raising steer calves. Cows received 1.8 or 1.2 kg/day winter supplementation for ~80 day before parturition and their heifer calves were then randomly assigned to heifer development treatments that provided ad libitum (AL) or 80% (less than ad libitum (LAL)) of ad libitum feed post weaning. Heifers developed on the AL treatment also received 1.8 kg/day winter supplementation for life, whereas heifers developed on the LAL treatment received 1.2 kg/day winter supplementation for life. Milk production of primiparous cows was measured with a portable milking machine every other week from days 27 to 125 postpartum. Milk yield for the 125-day lactation period was calculated from area under the lactation curve approximated by trapezoidal summation. The ANOVA model included in utero winter nutrition, post-weaning heifer development treatment, year and their interaction. Heifers subjected to the AL treatment reached peak milk yield ~12.3 day later (P=0.02) than heifers receiving LAL treatment. In addition, an in utero nutrition×post-weaning heifer treatment×year interaction existed (P⩽0.04) for milk peak yield, average daily milk yield (kg/day) and nutrient composition (protein, lactose, fat, solids non-fat, g/day). These interactions manifest as changes in magnitude and rank across the 3 years of the study. Livestock production in extensive environments is subject to variations in seasonal precipitation patterns and quality and quantity of grazeable forage and these fluctuations have a large impact on milk yield. In summary, the gestational nutritional environment of a heifer's mother may interact with the heifer's nutrient consumption during post-weaning growth and the current year to trigger variation in year-to-year milk production.

Livestock production impacts food security of developing countries, especially where efficiency of production is compromised by environmental stressors. In South Africa, breeding with indigenous Afrikaner cattle that are genetically well adapted to subtropical environments is considered an essential strategy for sustainable beef production. Today, there is a potential for farmers to participate in commercial systems that join adapted Afrikaner germplasm, used in a specialized maternal role, with exotic terminal sires to optimize production. The objective of this study was to assess productivity of five simulated production systems: 1) straightbred Afrikaner mated naturally, 2) a straight-bred Afrikaner cow herd with two sections; one section to produce replacement females and the other to cross with Charolais terminal sires, both using natural mating, 3) similar to 2, but applying sexed semen to produce replacement females, 4) similar to 2, but using a multi-breed composite dam line with a breed combination of 50% Afrikaner, 25% Hereford and 25% Simmental, and 5) similar to 4, but again applying sexed semen to produce replacement females. Parameter estimates needed to compare these systems were extracted from the scientific literature. Relative to straightbred Afrikaner dams, the simulated composite dams were more fit producing 7.8% more calves and their progeny performance was improved by reducing feed intake (-24.4%) and increasing meat production (+11.7%). The potential benefit of allocating more cows to the terminal sire was insufficient to offset the reduction in pregnancy rate that results with the use of sexed semen. Thus, system 4 had the greatest productivity (+23.1%) while requiring 22.8% less feed for finishing the progeny to be harvested relative to the purebred Afrikaner system. The combination of increased productivity and reduced feed requirement made use of a Charolais terminal sire in conjunction with multi-breed composite females bred by natural service the most efficient system among those studied.

Feral livestock may harbor genetic variation of commercial, scientific, historical or esthetic value. Origins and uniqueness of feral cattle on Chirikof Island, Alaska are uncertain. The island is now part of the Alaska Maritime Wildlife Refuge and Federal wildlife managers want grazing to cease, presumably leading to demise of the cattle. Here we characterize the Chirikof Island cattle relative to extant breeds and discern their origins. Our analyses support the inference that Russian cattle arrived first on Chirikof Island, then approximately 120 years ago the first European taurine cattle were introduced to the island, and finally a large wave of Hereford cattle were introduced on average 40 years ago. While clearly Bos taurus taurus, the Chirikof Island cattle appear at least as distinct as other recognized breeds. Further, this mixture of European and East-Asian cattle is unique compared to other North American breeds and we find evidence that natural selection in the relatively harsh environment of Chirikof Island has further impacted their genetic architecture. These results provide an objective basis for decisions regarding conservation of the Chirikof Island cattle.

Meat is an end-of-life by-product from cows that fail to reproduce. Thus, the objective of this study was to determine breed additive and heterosis effects on carcass traits and characteristics of the meat from beef cows raised in southern Brazil. Angus (A), Hereford (H), Nelore (N), A × H (AH), H × A (HA), A × N (AN), N × A (NA) and Caracu (C) × A (CA) cows were slaughtered when they did not become pregnant for a second season. Slaughter weight (SW), hot carcass weight (CW), carcass yield (CY), ribeye area (REA), pH value, water holding capacity (WHC), tenderness (MT), moisture (MM), ether extract (EE), carcass fat score (CFS), marbling score (MS), subcutaneous fat thickness (SFT) and L*, a* and b* measures of color of the fat and meat color were evaluated. Taurine x taurine heterosis effects increased SW and to a lesser degree CW, and improved MT. Taurine x indicine heterosis increased REA, a* and b*, and decreased L* and EE. Direct breed additive effects attributable to A increased SW but decreased CY and thus had no detectable effect on CW. Direct breed additive effects of C decreased CFS, SFT, CY and MM. Finally, direct breed additive effects of H and C similarly decreased CFS and SFT. Maternal breed additive effects were generally unremarkable except for slight effects of H reducing a* and b*. Thus, SW and MT may be increased by crossbreeding with taurine breeds, while CY and REA can be increased by using zebu-influenced cattle. The desirable carcass composition of CA cows and their MT and color comparable to taurine crossbred cows make this crossbred cow a viable alternative for producers in southern Brazil.

The Guide for the Care and Use of Agricultural Animals in Research and Teaching, commonly known as the Ag Guide, is published jointly by the American Dairy Science Association®, the American Society of Animal Science, and the Poultry Science Association under an open access creative commons license. At present, its 4th edition is under development and out for public comment. When finalized, this edition is intended to replace previous editions from 1988, 1999, and 2010. The first five chapters of the Ag Guide cover subjects that are relevant across species. These are followed by species-specific chapters, which are under the purview of the respective associations dedicated to the species. Authors of the individual chapters, recruited by the associations, were scientists, veterinarians, or engineers with expertise in the species or subjects covered in the respective chapters. All chapters are grounded in the scientific literature. The board of directors of each association approved final drafts of the general chapters and their respective species chapters. The content is intentionally broad so as to cover the diverse research and teaching institutions that use agricultural animals, yet be clear enough to give unambiguous guidance to institutional animal care and use committees (IACUCs) responsible for the care and use of animals in their respective institutions. It is viewed as essential that IACUCs and others who oversee animal care practices use sound professional judgment to achieve appropriate animal welfare outcomes, recognizing that too prescriptive an approach to animal care and use can stifle research and teaching opportunities. The 4th edition of the Ag Guide constitutes a timely and robust updating of guidance pertinent to animal care and use that will be released in 2020.

Hays Converter (HC), the first registered Canadian beef breed, was developed by Harry Hays in the 1950’s as a composite with contributions from Holstein, Hereford, Brown Swiss and with a later introgression of Angus. The breed is well adapted to the Western Canadian climate. Calves reach market weight early, convert feed to gain efficiently, and have excellent carcass quality and yield. The edited data consisted of 21,612 weight records taken at ages 1 to 474 days, from 8,850 animals born at Red Bow Ranching Ltd., Calgary, Alberta between 1970 and 2016. This study aimed to evaluate the genetic parameters and trends in birth, weaning and yearling weights of HC through comparison of different multiple trait models (MTM) with a random regression model (RRM). In MTM scenarios, both adjusted and unadjusted data were examined besides considering contemporary groups (CG) as fixed or random. Estimates of variance components, heritability and genetic correlations from the two approaches were not substantially different and showed similar changes along the growth trajectory. Although there was a considerable reduction in genetic trends from 2004 to 2008, due to weak sire selection, trends generally increased through 2016. Overall, both models performed similarly and fixed CG were preferred.

Genetic variability within and between breeds allows adaptation to a changing environment and consequently prepares producers for the future. Eleven bovine-specific microsatellite markers were used to genotype animals from each of nine South African cattle breeds: Afrikaner (N = 550), Angus (N = 550), Bonsmara (N = 550), Boran (N = 321), Brahman (N = 550), Drakensberger (N = 550), Nguni (N = 550), Simmental (N = 550), and Tuli (N = 311). These breeds were drawn from Bos taurus africanus, Bos taurus, and Bos indicus. Genetic variability estimates included unbiased heterozygosity, effective number of alleles, and inbreeding. Ranges of these parameters were 0.569–0.741, 8.818–11.455, and − 0.001–0.050, respectively. Breed private allele and breed pairwise comparison was also used to characterize the breeds. The analysis of population structure with K = 2 revealed clusters comprised of Sanga-indicine and taurine, while K = 3 included separate clusters of Sanga, indicine, and taurine, and with K = 9 showed the breeds arising from unique progenitor populations. This study broke new ground in molecular cattle genetic diversity by genotyping a large sample size per breed and using a larger number of breeds compared with similar studies that have been conducted in the recent past which have either used a smaller number of breeds or smaller sample sizes but with a larger number of marker loci. Thus, opportunities that arise to explore genetic diversity and relationships in both the livestock and wildlife industries in Southern Africa may capitalize on microsatellite marker databases which remain cost-effective and accessible due to their extensive use for parentage verification.

Lethal recessive alleles that act prenatally may be detected from the absence of homozygous individuals in a population. However, these alleles may be maintained at relatively low frequencies in populations as heterozygotes. In pigs, they may reduce litter size. This study aimed to detect putative lethal variants in the Duroc breed. Phenotypes for the numbers of piglets born (TNB), born live (BA), alive at 24 h (L24), stillborn (SB), and born as mummified fetuses (MM) were available from 5340 recorded litters which resulted from mating of 192 genotyped boars with sows of unknown genotype (dataset 1). An additional 50 litters were produced from parents that were both genotyped (dataset 2). Imputed genotypes of 650K SNPs for 1359 Duroc boars were used in this study. One significant SNP (Bonferroni corrected P = 5.5E-06) was located on SSC14 with 45.3 homozygous individuals expected but none observed. This SNP was significant for mummified fetuses. One hundred fifty two haplotypes were also found to potentially harbor recessive lethal mutations. Twenty-one haplotypes had a significant harmful effect on at least one trait. Two regions, located on SSC8 (144.9–145.5 Mb) and SSC9 (19–19.4 Mb) had significant effects on fertility traits in both datasets. Additionally, regions on SSC1 (82.0–82.8 Mb), SSC3 (73.3–73.7 and 87.1–87.5 Mb) and SSC12 (35.8–36.2 and 50.0–50.5 Mb) had significant deleterious effects on TNB or BA or L24 in dataset 1. Finally, a region on SSC17 (28.7–29.3 Mb) had significant effects on TNB, BA and L24 in dataset 2. A few candidate genes identified within these regions were described as being involved in spermatogenesis and male fertility (TEX14, SEP4, and HSF5), or displayed recessive lethality (CYP26B1, SCD5, and PCF11) in other species. The putative loci detected in this study provide valuable information to potentially increase Duroc litter size by avoiding carrier-by-carrier matings in breeding programs. Further study of the identified candidate genes responsible for such lethal effects may lead to new insights into functions regulating pig fertility.

Genomic selection for feed efficiency in beef cattle offers an opportunity to reduce feed costs and greenhouse gas (GHG) emissions while increasing profitability and environmental sustainability in beef production. Data from a selection experiment using three beef cattle populations maintained at the University of Alberta Roy Berg Kinsella Research Ranch namely, the Kinsella beef composite (KC - split into efficient and control lines), purebred Angus (AN), and purebred Charolais (CH) were analyzed following three years of selection (2013–2016) to obtain an evaluation of selection responses. Selection was carried out using multiple trait selection indexes based on molecular breeding values (MBVs). For the KC and AN population, a maternal profitability index (MPI) for improved feed efficiency, i.e. low residual feed intake (RFI), higher direct (DWWT) and maternal weaning weights (MWWT) was applied, while for the CH population a feedlot profitability index (FPI) for low RFI, low dry matter intake (DMI), higher average daily gain (ADG), greater carcass marbling (CMAR), greater hot carcass weight (HCW), increased lean meat yield (LMY), and increased average back fat thickness (AFAT) was applied. Across the three populations, average estimated breeding values (EBVs) obtained from a multivariate animal model showed significant differences at P

Our goal was to define a breeding objective for Brangus beef cattle in Brazil. Bioeconomic models were produced and used to estimate economic values (EVs). The scenarios simulated were typical full-cycle beef production systems that are used in tropical and subtropical regions. The breeding objective contained pregnancy rate (PR), warm carcass weight (WCW), mature cow weight (MCW), number of nematode eggs per gram of faeces (EPG) and tick count (TICK). Two models were used in series to estimate the EV. A deterministic model was used to simulate effects of PR, WCW and MCW on profitability with a constant parasite load. Subsequently, stochastic models were used to estimate economic values for TICK and EPG as consequences of their environmental effects on weight gains, mortality and health costs. The EV of PR, WCW, MCW, EPG and TICK, was US$1.59, US$2.11, -US$0.24, -US$5.35 and -US$20.88, respectively. Results indicate positive emphasis should be placed on PR (12.49%) and WCW (65.07%) with negative emphasis on MCW (13.92%), EPG (2.77%) and TICK (5.75%). In comparison with the indexes usually used, these results suggest a reformulation in the selection indexes of the beef production system in tropical and subtropical regions in order to obtain greater profitability.

The objective of this study was to estimate economic returns and costs associated with 4 scenarios of genetic evaluation that combine genotypes, phenotypes, and pedigree information from a vertically integrated purebred (PB) and commercial (CM) beef cattle system. Inference was to a genetic evaluation for a production system producing Charolais terminal sires for 10,000 CM cows. The first genetic evaluation scenario, denoted PB_A, modeled a genetic evaluation in which pedigree information and phenotypes are available for PB seedstock animals. Scenario PB_H contained the same information as PB_A with the addition of 25K density (GeneSeek Genomic Profiler LD) single nucleotide polymorphism (SNP) genotypes from PB animals. Scenario PBCM_A contained pedigree records and phenotypes from PB and CM cattle. Scenario PBCM_H contained phenotypes, pedigree, and genotypes from the PB and CM animals. Estimates of prediction error variance, (co)variance, and selection index parameters were used to estimate accuracy of selection candidates (rTI) and genetic gain resulting from selection on an economic index in US dollars (ΔG). Annual costs and incomes were used to determine the 30-yr cumulative net present value (CNPV) per CM calf resulting from selection in these genetic evaluation scenarios. Adding genotypes and CM production phenotypes to genetic evaluation increased the rTI of selection candidates and ΔG across all 4 scenarios. Scenario PBCM_H produced the highest annual ΔG in the PB herd at US$11.91 per head. Including CM phenotypes and parentage testing in the genetic evaluation increased the time to breakeven from 12 yr in PB_A to 19 years in PBCM_A after accounting for the cost of that information. Adding CM phenotypes and genotypes increased the breakeven time from 12 yr in PB_H to 18 yr in PBCM_H. Scenario PB_H produced the highest 30-yr CNPV per slaughtered CM calf at US$371.16. These results using field data indicate that economically relevant rTI and ΔG can be realized by adding 25K SNP genotypes and CM phenotypes to genetic evaluation, but the additional cost of that data significantly delays the economic return to the enterprise.

Porcine reproductive and respiratory syndrome virus (PRRSv) is the costliest swine disease of North America. Vaccines and management alone have not been effective at controlling this disease and genetic selection may be a complimentary approach to controlling PRRSv-infection. The objective of this study was to estimate performance differences between two groups of pigs from the same commercial line following infection with PRRSv 1-7-4: 1) pigs sired by boars selected based on a standard index (STD), which emphasizes feed efficiency and carcass quality; and 2) pigs sired by boars selected based on an experimental index (EXP), with emphasis on feed intake, piglet vitality, and robustness. Pigs (n~730 per group) were housed in a commercial research wean-to-finish barn. Average daily gain (ADG) and average daily feed intake (ADFI) were recorded from birth-to-slaughter. At weaning, pigs were placed in pens by group and balanced by sex. To facilitate collection of feed intake data, the experimental unit was pen, with 27 pens representing each group. Four weeks post-wean, all pigs were experimentally infected with 2mL of 1-7-4 PRRSv at 3.5 logs of TCID50 per mL. Statistical analyses were performed using a linear mixed model with group (STD or EXP) as a fixed effect and block as a random effect. No significant difference was detected between groups for wean-to-finish or 0 to 42 days post-infection (dpi) ADG. The ADFI was 0.06 kg/day greater for the EXP group than the STD group from 0 to 42 dpi (P = 0.01). Feed conversion ratio (FCR) was 0.03 (P = 0.03) less for the EXP group from wean-to-finish and 0 to 42 dpi, respectively. Pigs sired by boars selected using the experimental index showed no significant difference in ADG, but had greater ADFI post-challenge, while pigs sired by boars selected based on the standard index had significantly better FC.

An objective of commercial beef cattle crossbreeding programs is to simultaneously optimize use of additive (breed differences) and non-additive (heterosis) effects. A total of 6,794 multibreed and crossbred beef cattle with phenotype and Illumina BovineSNP50 genotype data were used to predict genomic heterosis for growth and carcass traits by applying two methods assumed to be linearly proportional to heterosis. The methods were as follows: 1) retained heterozygosity predicted from genomic breed fractions (HET1) and 2) deviation of adjusted crossbred phenotype from midparent value (HET2). Comparison of methods was based on prediction accuracy from cross-validation. Here, a mutually exclusive random sampling of all crossbred animals (n = 5,327) was performed to form five groups replicated five times with approximately 1,065 animals per group. In each run within a replicate, one group was assigned as a validation set, while the remaining four groups were combined to form the reference set. The phenotype of the animals in the validation set was assumed to be unknown; thus, it resulted in every animal having heterosis values that were predicted without using its own phenotype, allowing their adjusted phenotype to be used for validation. The same approach was used to test the impact of predicted heterosis on accuracy of genomic breeding values (GBV). The results showed positive heterotic effects for growth traits but not for carcass traits that reflect the importance of heterosis for growth traits in beef cattle. Heterosis predicted by HET1 method resulted in less variable estimates that were mostly within the range of estimates generated by HET2. Prediction accuracy was greater for HET2 (0.37-0.98) than HET1 (0.34-0.43). Proper consideration of heterosis in genomic evaluation models has debatable effects on accuracy of EBV predictions. However, opportunity exists for predicting heterosis, improving accuracy of genomic selection, and consequently optimizing crossbreeding programs in beef cattle.

Background Heterosis has been suggested to be caused by dominance effects. We performed a joint genome-wide association analysis (GWAS) using data from multi-breed and crossbred beef cattle to identify single nucleotide polymorphisms (SNPs) with significant dominance effects associated with variation in growth and carcass traits and to understand the mode of action of these associations. Methods Illumina BovineSNP50 genotypes and phenotypes for 11 growth and carcass traits were available for 6796 multi-breed and crossbred beef cattle. After performing quality control, 42,610 SNPs and 6794 animals were used for further analyses. A single-SNP GWAS for the joint association of additive and dominance effects was conducted in purebred, crossbred, and combined datasets using the ASReml software. Genomic breed composition predicted from admixture analyses was included in the mixed effect model to account for possible population stratification and breed effects. A threshold of 10% genome-wide false discovery rate was applied to declare associations as significant. The significant SNPs with dominance association were mapped to their corresponding genes at 100 kb. Results Seven SNPs with significant dominance associations were detected for birth weight, weaning weight, pre-weaning daily gain, yearling weight and marbling score across the three datasets at a false discovery rate of 10%. These SNPs were located on bovine chromosomes 1, 3, 4, 6 and 21 and mapped to six putative candidate genes: U6atac, AGBL4, bta-mir-2888-1, REPIN1, ICA1 and NXPH1. These genes have interesting biological functions related to the regulation of gene expression, glucose and lipid metabolism and body fat mass. For most of the identified loci, we observed over-dominance association with the studied traits, such that the heterozygous individuals at any of these loci had greater genotypic values for the trait than either of the homozygous individuals. Conclusions Our results revealed very few regions with significant dominance genetic effects across all the traits studied in the three datasets used. Regarding the SNPs that were detected with dominance associations, further investigation is needed to determine their relevance in crossbreeding programs assuming that dominance effects are the main cause of (or contribute usefully to) heterosis. Electronic supplementary material The online version of this article (10.1186/s12711-018-0405-y) contains supplementary material, which is available to authorized users.

The objectives of this study were to evaluate statistical models of potential utility for genetic evaluation of feed intake and to estimate the (co)variance components and genetic parameters that would be necessary for their use in a national cattle evaluation scheme. Data were from Afrikaner bulls that were tested between 1974 and 2016 in Phases C (n = 1 250) and D (n = 11 083) of the National Beef Recording and Improvement Scheme. Statistical analyses in which the number of traits varied and contemporary group effects were considered either random or fixed were conducted using multiple-trait derivative-free restricted maximum likelihood. Contemporary group effects were important. When they were considered random, the estimated phenotypic variance of feed intake increased and its heritability reduced from approximately 0.43 ± 0.09 to approximately 0.30 ± 0.06. Use of average daily gain, recorded either concurrently with the feed intake measure (ADG C ) or from related bulls reared on-farm (ADG D ), had relatively little effect on estimated heritability of feed intake. Thus, considering contemporary group effects random consistently increased the accuracy of the estimated breeding values. Relatively small genetic correlations between ADG C and ADG D complicated the ultimate application of data recorded in Phase C and the use of data recorded in Phase D in decoupling the phenotypes for feed intake and growth in an evaluation of feed efficiency. Some modification of testing procedures may be necessary to facilitate this application of the results. Keywords: accuracy, contemporary group, genetic parameters, performance testing

Data from a total of 4842 animals were used to test whether the regular dry matter intake (DMI) data collection and residual feed intake (RFI) estimation period could be decreased. Eighty-three sho...

This study examined the feasibility and accuracy of using Illumina BovineSNP50 genotypes to estimate individual cattle breed composition and heterosis relative to estimate from pedigree. First, ped...

The Afrikaner is an indigenous South African breed of "Sanga" type beef cattle along with breeds such as the Drakensberger and Nguni. Six composite breeds have been developed from crosses with the Afrikaner. Additionally, Afrikaner has been the base from which exotic breeds were established in South Africa through backcrossing. The study examined genetic diversity of Afrikaner cattle by genotyping 1257 animals from 27 herds in different geographic areas of South Africa and Namibia using 11 microsatellite markers. Multiple-locus assignment, performed using the Bayesian clustering algorithm of STRUCTURE, revealed three underlying genotypic groups. These groups were not geographically localized. Across herds and markers, the proportion of unbiased heterozygosity ranged from 0.49 to 0.72 averaging 0.57; mean number of alleles per locus ranged from 3.18 to 7.09, averaging 4.81; and allelic richness ranged from 2.35 to 3.38, averaging 2.67. It is concluded that a low inbreeding level of 2.7% and a moderate to high degree of variation still persists within the Afrikaner cattle breed, despite the recent decline in numbers of animals.

Feral cattle residing in Chirikof Island, Alaska, are relatively distinct from breeds used in commercial production in North America. However, preliminary evidence suggested that they exhibit substantial genetic relationship with cattle from Yakutian region of Siberia. Thus, our objective was to further elucidate quantify the origins, admixture and divergence of the Chirikof Island cattle relative to cattle from Siberia and USA. Subject animals were genotyped at 15 microsatellite loci. Compared with Turano–Mongolian and North American cattle, Chirikof Island cattle had similar variation, with slightly less observed heterozygosity, fewer alleles per locus and a positive fixation index. Analysis of the genetic distances revealed two primary clusters; one that contained the North American breeds and the Kazakh White head, and a second that contained the Yakutian and Kalmyk breeds, and the Chirikof population. Thus, it is suggested that Chirikof Island cattle may be a composite of British breeds emanating from North America and Turano–Mongolian cattle. A potential founder effect, consistent with historical records of the Russian–American period, may contribute to the adaptation of the Chirikof Island cattle to their harsh high-latitude environment. Further study of adaptive mechanisms manifest by these cattle is warranted., published version, peerReviewed

This study evaluated the use of molecular breeding values (MBVs) for carcass traits to sort steers into quality grid and lean meat yield groups. A training set of 2300 animals with genotypes and phenotypes was used to predict MBVs for lean meat yield (LMY) and marbling score (MBS) for 299 Angus, 181 Charolais and 638 Kinsella composite steers using the genomic best linear unbiased prediction method. Steers were placed into MBV-Quality, MBV-Lean, MBV-Marbling and MBV-Other groups on the basis of predicted MBV for LMY and MBS being jointly greater or less than the mean MBV values for both traits. Carcass phenotypes of the steers were then collected and evaluated for consistency with the assigned group using descriptive statistics. Also, the accuracy of genomic predictions was assessed as the additive genetic correlation from a bivariate animal model that fits the observed carcass phenotype and the predicted MBV. The number of steers that met the expected carcass outcome was counted to produce actual percentages for each MBV group. Results showed that on average, MBV-Quality and MBV-Marbling groups had heavier carcasses, greater backfat and more marbling across the three populations while MBV-Lean had leaner carcasses. For most traits, the coefficient of variation suggested less variability and uniform carcass in the MBV-Marbling followed by MBV-Lean and MBV-Quality groups. Greater than 70% of the steers in the MBV-Quality, MBV-Lean and MBV-Marbling groups reached the desired carcass outcome of 70:70 Quality Grid and Y1-lean meat yield in Angus and Charolais but not for Kinsella composite. The accuracy of genomic prediction showed that the MBVs could predict from 60 to 80% of the observed carcass trait values. Thus, genomic profiles can potentially help to streamline the feedlot-finishing process and improve the quality and consistency of beef carcasses.

A total of 84% of South Africa’s land is available for agriculture, of which 13% is cultivated and 71% is only suitable for extensive livestock farming. Beef cattle farming is dominating these areas. The type of production strategy to be followed, e.g. purebreeding with adapted genotypes or crossbreeding, will depend primarily on the environment and level of management. A crossbreeding project with specialized sire lines (Angus and Simmentaler) and dam breed bulls, mated to Afrikaner, Bonsmara and Nguni females (mated in all possible combinations) is being conducted in Northern Cape, producing 15 genotypes. The climate is semi-arid, characterized by hot summers (average maximum temperature 32°C) and cold winters (average lowest temperature –0.5°C), with an annual rainfall is 440 millimeters. The 5 bull breeds are mated to 8 females from each of the breeds. The mating season is from 15 December until 28 February. Predicted means of Afrikaner, Bonsmara, and Nguni calves for preweaning traits, and for dam weight at weaning of their calves, corrected to 7 years of age for the first three seasons are reported. At birth, Nguni calves weighed less (32.9kg ± 0.6), than either Afrikaner (36.0 ± 0.9) or Bonsmara (37.3 ± 0.7) calves. The respective 205-day corrected weaning weights for the different breeds were (192.0kg ± 9.0) for the Afrikaner; (218. ± 13.0) for the Bonsmara and (185. ± 6.0) for Nguni. The cow weight of the Nguni (365.0kg ± 7.0) was significantly different from that of the Afrikaner (446.0kg ± 10.0) and Bonsmara (454.0kg ± 10.0). Performances of the calves sired by the various breeds of sire varied from 187. ± 7.0 in Afrikaner x Nguni to 224. ± 13.0 in Angus x Bonsmara. A study to estimate all the crossbreeding effects on cow efficiency and component traits is currently underway.

Knowledge on the extent of linkage disequilibrium (LD) in livestock populations is essential to determine the minimum distance between markers required for effective coverage when conducting genome-wide association studies (GWAS). This study evaluated the extent of LD, persistence of allelic phase and effective population size (Ne) for four Sanga cattle breeds in South Africa including the Afrikaner (n = 44), Nguni (n = 54), Drakensberger (n = 47), and Bonsmara breeds (n = 46), using Angus (n = 31) and Holstein (n = 29) as reference populations. We found that moderate LD extends up to inter-marker distances of 40-60 kb in Angus (0.21) and Holstein (0.21) and up to 100 kb in Afrikaner (0.20). This suggests that genomic selection and association studies performed within these breeds using an average inter-marker r (2)≥ 0.20 would require about 30,000-50,000 SNPs. However, r (2)≥ 0.20 extended only up to 10-20 kb in the Nguni and Drakensberger and 20-40 kb in the Bonsmara indicating that 75,000 to 150,000 SNPs would be necessary for GWAS in these breeds. Correlation between alleles at contiguous loci indicated that phase was not strongly preserved between breeds. This suggests the need for breed-specific reference populations in which a much greater density of markers should be scored to identify breed specific haplotypes which may then be imputed into multi-breed commercial populations. Analysis of effective population size based on the extent of LD, revealed Ne = 95 (Nguni), Ne = 87 (Drakensberger), Ne = 77 (Bonsmara), and Ne = 41 (Afrikaner). Results of this study form the basis for implementation of genomic selection programs in the Sanga breeds of South Africa.

Four semen traits: volume (VOL), concentration (CON), progressive motility of spermatozoa (MOT), and abnormal spermatozoa (ABN) provide complementary information on boar fertility. Assessment of the impact of selection for semen traits is hindered by limited information on economic parameters. Objectives of this study were to estimate economic values for semen traits and to evaluate the genetic gain when these traits are incorporated into traditional selection strategies in a 3-tier system of swine production. Three-way (maternal nucleus lines A and B and paternal nucleus line C) and 4-way (additional paternal nucleus line D) crossbreeding schemes were compared. A novel population structure that accommodated selection for semen traits was developed. Three selection strategies were simulated. Selection Strategy I (baseline) encompassed selection for maternal traits: number of pigs born alive (NBA), litter birth weight (LBW), adjusted 21-d litter weight (A21), and number of pigs at 21 d (N21); and paternal traits: number of days to 113.5 kg (D113), backfat (BF), ADG, feed efficiency (FE), and carcass lean % (LEAN). Selection Strategy II included Strategy I and the number of usable semen doses per collection (DOSES), a function of the 4 semen traits. Selection Strategy III included Strategy I and the 4 semen traits individually. The estimated economic values of VOL, CON, MOT, ABN, and DOSES for 7 to 1 collections/wk ranged from $0.21 to $1.44/mL, $0.12 to $0.83/10 spermatozoa/mm, $0.61 to $12.66/%, -$0.53 to -$10.88/%, and $2.01 to $41.43/%, respectively. The decrease in the relative economic values of semen traits and DOSES with higher number of collections per wk was sharper between 1 and 2.33 collections/wk than between 2.33 and 7 collections/wk. The higher economic value of MOT and ABN relative to VOL and CON could be linked to the genetic variances and covariances of these traits. Average genetic gains for the maternal traits were comparable across strategies. Genetic gains for paternal traits, excluding semen traits, were greater in selection Strategy I than Strategies III and II. Genetic gains for paternal and maternal traits were greater in the 4- and 3-way schemes, respectively. The selection strategy including the 4 semen traits is recommended because this approach enables genetic gains for these traits without compromising the genetic gains for maternal traits and with minimal losses in genetic gains for paternal traits.

The role of preovulatory estradiol on post-fertilization embryo survival and pregnancy establishment has not been well characterized in beef cows. We hypothesized that preovulatory estradiol is important for embryo survival and pregnancy establishment in beef cows. Twenty-four ovariectomized multiparous cows were used in a replicated 3×3 Latin Square design. Cows received estradiol cypionate (ECP) 36h, estradiol benzoate (EB) 12h, or no estradiol (CON) before a gonadotropin-releasing hormone (d 0) induced LH surge. Luteal phase progesterone was mimicked with twice daily progesterone injections from d 3 to 6. On d 7 cows received one embryo and progesterone was supplemented with progesterone-releasing devices (CIDR). Expression of interferon stimulated genes, ISG15, MX2, and OAS1, in leukocytes was determined on d 17, 19, 21, and 28 to determine capability of embryonic signaling. Pregnancy specific protein B concentrations were measured in serum samples from d 17 through 29 to determine embryonic attachment. Transrectal ultrasonography was performed on d 29 and 32 to determine pregnancy viability (heartbeat). Serum estradiol profiles during simulated proestrus/estrus were different (P

The objective of this study was to discern opportunities for improving leather-making properties of hides originating from beef production systems based on indigenous Afrikaner cattle via crossbreeding. Data were previously unpublished breed means from purebred Afrikaner, Brahman, Charolais, Hereford and Simmental, top-crosses of Brahman, Charolais, Hereford, and Simmental sires on (1) Afrikaner dams producing F1 progenies and (2) Brahman × Afrikaner, Charolais × Afrikaner, Hereford × Afrikaner, and Simmental × Afrikaner F1 females producing both backcross and three-breed cross progenies. Hide yield (%), leather yield (dm2/kg), force 20% extension (Mpa), extension grain crack (%), extension break (%), force break (Mpa), slit tear force (N/mm), distension grain crack (%), and force grain crack (N/mm) were evaluated. Breed direct effects and individual heterosis, but not maternal effects, may be important for most of these traits. Direct effects due to the exotic breeds reduced hide yield but generally improved leather properties relative to the indigenous Afrikaner. For both hide and leather yields, individual heterosis effects arose primarily from indicus × taurus crosses with the Hereford × Brahman effect being most pronounced. Thus, there may be opportunities to improve leather yield and quality through crossbreeding relative to the straightbred Afrikaner. A top-cross mating plan may be recommended to enhance production by subsistence level farmers having access to Afrikaner females, provided that management can ensure appropriate use of the terminal sires.