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The Canadian Angus Association recently developed genetic evaluations for teat and udder structure, which impact efficiencies, and animal health and welfare. Genetic selection tools are most effective incorporated into economic selection indexes. An important factor in the development of economic indexes is the estimation of the economic value and discounted gene expression coefficients, and thereby the economic weight, of each trait. Traditional estimation methods, interrogation of previous studies quantifying the impact of the traits and bioeconomic modelling, were reinforced using producer surveys that employed pairwise ranking methods. Estimates of discounted genetic expression coefficients, economic value and economic weight for teat and udder score in Canadian Angus cattle were 0.31 per sire, $52.47, and $16.91 per score change on a per calf born basis, respectively, indicating that functional traits such as teat and udder structure have a significant impact on profitability and should be included in genetic selection programmes. Limitations in previous studies illustrate the need for longitudinal studies on traits that impact efficiencies and animal health and welfare.

Yunling cattle, a three-breed cross consisting of 1/2 Brahman cattle, 1/4 Murray Grey cattle and 1/4 Yunnan Yellow cattle, has advantage of rapid growth, good meat quality, enhanced tolerance towards a hot and humid climate, tick resistance and crude feed forbearance. Here, we investigated the genetic diversity, global and local ancestry proportions by sequencing the genomes of 131 Yungling cattle and 31 Brahman cattle (for control). Furthermore, we used 35 published genomes of ancestry breeds (including Angus cattle [ancestry of Murray Grey], Wannan cattle [ancestry of Yunnan Yellow cattle: Wenshan and Dianzhong], Wenshan and Dianzhong cattle) to characterize the formation process of Yunling cattle. The highest nucleotide diversity was found in the Wannan cattle, followed by Wenshan, Dianzhong, Brahman, Yunling and Angus cattle. The results of LD decay in each breed was largely consistent with the results of nucleotide diversity, except for the faster decay in Angus cattle out of a smaller effective population size and a strong bottleneck during the breed formation. The population-structure analysis revealed that the cross-breed Yunling cattle harboured the ancestry with Angus (0.44), Brahman (0.48) and Wannan cattle (0.08). Subsequently, we used RFmix to infer local ancestry in Yunling cattle and then performed chi-squared test to obtain the segments whose proportions of a certain ancestry were excessive compared with the whole-genome level, leading to 391 Angus, 49 Brahman and 2,312 Wannan segments. Gene annotation and KEGG enrichment analysis revealed that the excessive Angus, Brahman and Wannan segments might contribute to the rapid growth, immune resistance and indigenous adaptation, respectively, in Yunling cattle. Our results help understand ancestry components and formation process in Yunling cattle and will provide an opportunity for selective breeding by molecular approaches in future.

A greater understanding of the rumen microbiota and its function may help find new strategies to improve feed efficiency in cattle. This study aimed to investigate whether the cattle breed affects specific ruminal taxonomic microbial groups and functions associated with feed conversion ratio (FCR), using two genetically related Angus breeds as a model. Total RNA was extracted from 24 rumen content samples collected from purebred Black and Red Angus bulls fed the same forage diet and then subjected to metatranscriptomic analysis. Multivariate discriminant analysis (sparse partial least square discriminant analysis (sPLS-DA)) and analysis of composition of microbiomes were conducted to identify microbial signatures characterizing Black and Red Angus cattle. Our analyses revealed relationships among bacterial signatures, host breeds and FCR. Although Black and Red Angus are genetically similar, sPLS-DA detected 25 bacterial species and 10 functions that differentiated the rumen microbial signatures between those two breeds. In Black Angus, we identified bacterial taxa Chitinophaga pinensis, Clostridium stercorarium and microbial functions with large and small subunits ribosomal proteins L16 and S7 exhibiting a higher abundance in the rumen microbiome. In Red Angus, nonetheless, we identified the poorly characterized bacterial taxon Oscillibacter valericigenes with a higher abundance and pathways related to carbohydrate metabolism. Analysis of composition of microbiomes revealed that C. pinensis and C. stercorarium exhibited a higher abundance in Black Angus compared to Red Angus associated with FCR, suggesting that these bacterial species may play a key role in the feed conversion efficiency of forage-fed bulls. This study highlights how the discovery of signatures of bacterial taxa and their functions can be used to harness the full potential of the rumen microbiome in Angus cattle.

Background Genome-wide association studies (GWAS) are extensively used to identify single nucleotide polymorphisms (SNP) underlying the genetic variation of complex traits. However, much uncertainly often still exists about the causal variants and genes at quantitative trait loci (QTL). The aim of this study was to identify QTL associated with residual feed intake (RFI) and genes in these regions whose expression is also associated with this trait. Angus cattle (2190 steers) with RFI records were genotyped and imputed to high density arrays (770 K) and used for a GWAS approach to identify QTL associated with RFI. RNA sequences from 126 Angus divergently selected for RFI were analyzed to identify the genes whose expression was significantly associated this trait with special attention to those genes residing in the QTL regions. Results The heritability for RFI estimated for this Angus population was 0.3. In a GWAS, we identified 78 SNPs associated with RFI on six QTL (on BTA1, BTA6, BTA14, BTA17, BTA20 and BTA26). The most significant SNP was found on chromosome BTA20 (rs42662073) and explained 4% of the genetic variance. The minor allele frequencies of significant SNPs ranged from 0.05 to 0.49. All regions, except on BTA17, showed a significant dominance effect. In 1 Mb windows surrounding the six significant QTL, we found 149 genes from which OAS2, STC2, SHOX, XKR4, and SGMS1 were the closest to the most significant QTL on BTA17, BTA20, BTA1, BTA14, and BTA26, respectively. In a 2 Mb windows around the six significant QTL, we identified 15 genes whose expression was significantly associated with RFI: BTA20) NEURL1B and CPEB4; BTA17) RITA1, CCDC42B, OAS2, RPL6, and ERP29; BTA26) A1CF, SGMS1, PAPSS2, and PTEN; BTA1) MFSD1 and RARRES1; BTA14) ATP6V1H and MRPL15. Conclusions Our results showed six QTL regions associated with RFI in a beef Angus population where five of these QTL contained genes that have expression associated with this trait. Therefore, here we show that integrating information from gene expression and GWAS studies can help to better understand the genetic mechanisms that determine variation in complex traits.

Zhoushan cattle are an endangered cattle breed in the Zhoushan islands in China. Since Zhoushan cattle have been bred in isolation, they show unique characteristics, such as dark black coat colour. However, no studies have been conducted on the genome of Zhoushan cattle. Here, we performed whole-genome sequencing of seven individuals of Zhoushan cattle and nine cattle in Wenling, geographically close to the Zhoushan islands. By integrating our data and publicly-available data, we found that Zhoushan cattle are genetically highly similar to Bos indicus cattle in south-eastern China. Furthermore, by identifying the genomic regions shared between Zhoushan cattle and Angus cattle, a Bos taurus breed, we found that the p.F195L mutation in melanocyte-stimulating hormone receptor (MC1R) could be associated with their dark black coat colour. Taken together, our results provide a valuable resource for characterising the uniqueness of Zhoushan cattle.

Genomic selection has been adopted nationally and internationally in different livestock and plant species. However, understanding whether genomic selection has been effective or not is an essential question for both industry and academia. Once genomic evaluation started being used, estimation of breeding values with pedigree best linear unbiased prediction (BLUP) became biased because this method does not consider selection using genomic information. Hence, the effective starting point of genomic selection can be detected in two possible ways including the divergence of genetic trends and Realized Mendelian sampling (RMS) trends obtained with BLUP and single-step genomic BLUP (ssGBLUP). This study aimed to find the start date of genomic selection for a set of economically important traits in three livestock species by comparing trends obtained using BLUP and ssGBLUP. Three datasets were used for this purpose: 1) a pig dataset with 117k genotypes and 1.3M animals in pedigree, 2) an Angus cattle dataset consisted of ~842k genotypes and 11.5M animals in pedigree, and 3) a purebred broiler chicken dataset included ~154k genotypes and 1.3M birds in pedigree were used. The genetic trends for pigs diverged for the genotyped animals born in 2014 for average daily gain (ADG) and backfat (BF). In beef cattle, the trends started diverging in 2009 for weaning weight (WW) and in 2016 for postweaning gain (PWG), with little divergence for birth weight (BTW). In broiler chickens, the genetic trends estimated by ssGBLUP and BLUP diverged at breeding cycle 6 for two out of the three production traits. The RMS trends for the genotyped pigs diverged for animals born in 2014, more for ADG than for BF. In beef cattle, the RMS trends started diverging in 2009 for WW and in 2016 for PWG, with a trivial trend for BTW. In broiler chickens, the RMS trends from ssGBLUP and BLUP diverged strongly for two production traits at breeding cycle 6, with a slight divergence for another trait. Divergence of the genetic trends from ssGBLUP and BLUP indicates the onset of the genomic selection. The presence of trends for RMS indicates selective genotyping, with or without the genomic selection. The onset of genomic selection and genotyping strategies agrees with industry practices across the three species. In summary, the effective start of genomic selection can be detected by the divergence between genetic and RMS trends from BLUP and ssGBLUP.

Background While the adoption of genomic evaluations in livestock has increased genetic gain rates, its effects on genetic diversity and accumulation of inbreeding have raised concerns in cattle populations. Increased inbreeding may affect fitness and decrease the mean performance for economically important traits, such as fertility and growth in beef cattle, with the age of inbreeding having a possible effect on the magnitude of inbreeding depression. The purpose of this study was to determine changes in genetic diversity as a result of the implementation of genomic selection in Angus cattle and quantify potential inbreeding depression effects of total pedigree and genomic inbreeding, and also to investigate the impact of recent and ancient inbreeding. Results We found that the yearly rate of inbreeding accumulation remained similar in sires and decreased significantly in dams since the implementation of genomic selection. Other measures such as effective population size and the effective number of chromosome segments show little evidence of a detrimental effect of using genomic selection strategies on the genetic diversity of beef cattle. We also quantified pedigree and genomic inbreeding depression for fertility and growth. While inbreeding did not affect fertility, an increase in pedigree or genomic inbreeding was associated with decreased birth weight, weaning weight, and post-weaning gain in both sexes. We also measured the impact of the age of inbreeding and found that recent inbreeding had a larger depressive effect on growth than ancient inbreeding. Conclusions In this study, we sought to quantify and understand the possible consequences of genomic selection on the genetic diversity of American Angus cattle. In both sires and dams, we found that, generally, genomic selection resulted in decreased rates of pedigree and genomic inbreeding accumulation and increased or sustained effective population sizes and number of independently segregating chromosome segments. We also found significant depressive effects of inbreeding accumulation on economically important growth traits, particularly with genomic and recent inbreeding.

This experiment was to evaluate a suite of biological traits likely to be associated with genetic variation in residual feed intake (RFI) in Angus cattle. Twenty nine steers and 30 heifers bred to be divergent in postweaning RFI (RFI(p)) and that differed in midparent RFI(p)-EBV (RFI(p)-EBV(mp)) by more than 2 kg DMI/d were used in this study. A 1-unit (1 kg DM/d) decrease in RFI(p)-EBV(mp) was accompanied by a 0.08 kg (SE = 0.03; P < 0.05) increase in ADG, a 0.58 kg/d (0.17; P < 0.01) decrease in DMI, a 0.89 kg/kg (0.22; P < 0.001) decrease in FCR, and a 0.62 kg/d (0.12; P < 0.001) decrease in feedlot RFI (RFI(f)). Ultrasonically scanned depths of subcutaneous fat at the rib and rump sites, measured at the start and end of the RFI test, all had strong positive correlations with RFI(p)-EBV(mp), DMI, and RFI(f) (all r values ≥0.5 and P < 0.001). Variation in RFI(p)-EBV(mp) was significantly correlated (P < 0.05) with flight speed (r = −0.32), number of visits to feed bins (r = 0.45), and visits to exhaled-emission monitors (r = −0.27), as well as the concentrations of propionate (r = −0.32) and valerate (r = −0.31) in rumen fluid, white blood cell (r = −0.51), lymphocyte (r = −0.43), and neutrophil (r = −0.31) counts in blood. RFI(p)-EBV(mp) was also correlated with the cellular immune response to vaccination (r = 0.25; P < 0.1) and heat production in fasted cattle (r = −0.46; P < 0.001). Traits that explained significant variation (P < 0.05) in DMI over the RFI test were midtest metabolic-BW (44.7%), rib fat depth at the end of test (an additional 18%), number of feeder visits (additional 5.7%), apparent digestibility of the ration by animals (additional 2.4%) and white blood-cell count (2.1%), and the cellular immune response to vaccine injection (additional 1.1%; P < 0.1), leaving ~23% of the variation in DMI unexplained. The same traits (BW excluded) explained 33%, 12%, 3.6%, 3.7%, and 3.1%, and together explained 57% of the variation in RFI(f). This experiment showed that genetic variation in RFI was accompanied by variation in estimated body composition, behavior, rumen, fasted heat production, hematology, and immune competence traits, and that variation in feedlot DMI and RFI(f) was due to differences in BW, scanned fatness, and many other factors in these cattle fed ad libitum and able to display any innate differences in appetite, temperament, feeding behavior, and activity.

Heat stress and fescue toxicosis caused by ingesting tall fescue infected with the endophytic fungus Epichloë coenophiala represent two of the most prevalent stressors to beef cattle in the United States and cost the beef industry millions of dollars each year. The rate at which a beef cow sheds her winter coat early in the summer is an indicator of adaptation to heat and an economically relevant trait in temperate or subtropical parts of the world. Furthermore, research suggests that early-summer hair shedding may reflect tolerance to fescue toxicosis, since vasoconstriction induced by fescue toxicosis limits the ability of an animal to shed its winter coat. Both heat stress and fescue toxicosis reduce profitability partly via indirect maternal effects on calf weaning weight. Here, we developed parameters for routine genetic evaluation of hair shedding score in American Angus cattle, and identified genomic loci associated with variation in hair shedding score via genome-wide association analysis (GWAA).Hair shedding score was moderately heritable (hThis work contributes to a continuing trend in the development of genetic evaluations for environmental adaptation. Our results will aid beef cattle producers in selecting more sustainable and climate-adapted cattle, as well as enable the development of similar routine genetic evaluations in other breeds.

For the spring-calving beef herds, late gestation coincides with winter and early spring, when cows are dependent on feed supplements with low quality hay, which is hard to meet their nutrient requirements. However, the effects of deficiencies of metabolizable protein intake during late gestation on offspring beef quality are unclear. Wagyu cattle have excellent marbling, and insemination with Wagyu vs Angus semen is a practical option for beef producers to improve beef quality. To test, Angus cows (621 ± 73 kg) were selected and randomly separated into two groups. Each group was inseminated with either Angus or Wagyu semen. During the last 90 days of gestation, cows in each group were further separated and received either a low protein diet (85% of the NRC metabolizable protein requirement), which was a low quality hay-based diet common in northwestern region of the U.S., or an adequate protein diet (108% NRC requirement). All progeny was managed together and harvested at a final BW of 576.5 ± 16.6 kg. Wagyu-sired offspring had higher marbling scores and quality grades than Angus (P < 0.01). Protein supplementation did not affect Slice Shear Force (SSF) in either breeds (P = 0.60). However, Wagyu-sired cattle had lower SSF than Angus-sired (P < 0.01). In addition, Wagyu-sired cattle had higher intramuscular fat (P < 0.05) and total collagen content (P < 0.05), but Angus-sired had greater mature collagen cross-links, as shown by higher contents of Pyridinoline (P < 0.01) and Ehrlich Chromogen (P < 0.01). Consistently, the mRNA expression of enzymes catalyzing collagen cross-linking was higher in Angus-sired offspring, including Plod 1 (P < 0.05), Plod 2 (P = 0.08), and P4Hα 2 (P < 0.01). In conclusion, Wagyu-sired cattle had greater tenderness and marbling score compared to Angus-sired, which was associated with lower collagen cross-links. Feeding mature grass hay-based diet with relatively low protein content during late gestation had no major effect on beef quality of subsequent cattle.

The stability of genomic evaluations depends on the amount of data and population parameters. When the dataset is large enough to estimate the value of nearly all independent chromosome segments (~10K in American Angus cattle), the accuracy and persistency of breeding values will be high. The objective of this study was to investigate changes in estimated breeding values (EBV) and genomic EBV (GEBV) across monthly evaluations for 1 yr in a large genotyped population of beef cattle. The American Angus data used included 8.2 million records for birth weight, 8.9 for weaning weight, and 4.4 for postweaning gain. A total of 10.1 million animals born until December 2017 had pedigree information, and 484,074 were genotyped. A truncated dataset included animals born until December 2016. To mimic a scenario with monthly evaluations, 2017 data were added 1 mo at a time to estimate EBV using best linear unbiased prediction (BLUP) and GEBV using single-step genomic BLUP with the algorithm for proven and young (APY) with core group fixed for 1 yr or updated monthly. Predictions from monthly evaluations in 2017 were contrasted with the predictions of the evaluation in December 2016 or the previous month for all genotyped animals born until December 2016 with or without their own phenotypes or progeny phenotypes. Changes in EBV and GEBV were similar across traits, and only results for weaning weight are presented. Correlations between evaluations from December 2016 and the 12 consecutive evaluations were ≥0.97 for EBV and ≥0.99 for GEBV. Average absolute changes for EBV were about two times smaller than for GEBV, except for animals with new progeny phenotypes (≤0.12 and ≤0.11 additive genetic SD [SDa] for EBV and GEBV). The maximum absolute changes for EBV (≤2.95 SDa) were greater than for GEBV (≤1.59 SDa). The average(maximum) absolute GEBV changes for young animals from December 2016 to January and December 2017 ranged from 0.05(0.25) to 0.10(0.53) SDa. Corresponding ranges for animals with new progeny phenotypes were from 0.05(0.88) to 0.11(1.59) SDa for GEBV changes. The average absolute change in EBV(GEBV) from December 2016 to December 2017 for sires with ≤50 progeny phenotypes was 0.26(0.14) and for sires with >50 progeny phenotypes was 0.25(0.16) SDa. Updating the core group in APY without adding data created an average absolute change of 0.07 SDa in GEBV. Genomic evaluations in large genotyped populations are as stable and persistent as the traditional genetic evaluations, with less extreme changes.

Poor teat and udder structure, frequently associated with older cows, impact cow production and health as well as calf morbidity and mortality. However, producer culling, for reasons including age, production, feed availability, and beef markets, creates a bias in teat (TS) and udder scores (US) assessed and submitted to the Canadian Angus Association for genetic evaluations toward improved mammary structure. In addition, due to the infancy of the reporting program, repeated scores are rare. Prior to the adoption of genetic evaluations for TS and US in Canadian Angus cattle, it is imperative to verify that TS and US from young cows are the same traits as TS and US estimated on mature cows. Genetic parameters for TS and US from all cows (n = 4,192) and then from young cows (parities 1 and 2) and from mature cows (parity ≥ 4) were estimated using a single-trait animal model. Genetic correlations for the traits between the two cow age groups were estimated using a two-trait animal model. Estimates of heritability (posterior SD [PSD]) were 0.32 (0.07) and 0.45 (0.07) for young TS and US and 0.27 (0.07) and 0.31 (0.07) for mature TS and US, respectively. Genetic correlation (PSD) between the young and mature traits was 0.87 (0.13) for TS and 0.40 (0.17) for US. Genome-wide association studies were used to further explore the genetic and biological commonalities and differences between the two groups. Although there were no genes in common for the two USs, 12 genes overlapped for TS in the two cow age groups. Interestingly, there were also 23 genes in common between TS and US in mature cows. Based on these findings, it is recommended that producers collect TS and US on their cow herd annually.

Fescue toxicosis is a multifaceted syndrome common in cattle grazing endophyte-infected tall fescue, however, varying symptomatic responses potentially imply genetic tolerance to the syndrome. It was hypothesized that a subpopulation of animals within a herd would develop tolerance to ergot alkaloid toxicity. Therefore, the goals of this study were to develop selection criteria to identify tolerant and susceptible animals within a herd based on animal performance, and then examine responsive phenotypic and cytokine profiles to fescue toxicosis. Angus cows grazed endophyte-infected tall fescue at two locations for 13 weeks starting in mid-April 2016. Forage measurements were collected to evaluate ergot alkaloid exposure during the study. A post hoc analysis of animal performance was utilized to designate cattle into either tolerant or susceptible groups, and weekly physiological measurements and blood samples were collected to evaluate responses to chronic exposure to endophyte-infected tall fescue. Findings from this study support the proposed fescue toxicosis selection method formulated herein, could accurately distinguish between tolerant and susceptible animals based on the performance parameters in cattle chronically exposed to ergot alkaloids, and provides evidence to warrant additional analysis to examine the impact of ergot alkaloids on immune responsiveness in cattle experiencing fescue toxicosis.

Genetic strategies aimed at improving general immune competence (IC) have the potential to reduce the incidence and severity of disease in beef production systems, with resulting benefits of improved animal health and welfare and reduced reliance on antibiotics to prevent and treat disease. Implementation of such strategies first requires that methodologies be developed to phenotype animals for IC and demonstration that these phenotypes are associated with health outcomes. We have developed a methodology to identify IC phenotypes in beef steers during the yard weaning period, which is both practical to apply on-farm and does not restrict the future sale of tested animals. In the current study, a total of 838 Angus steers, previously IC phenotyped at weaning, were categorized as low (n = 98), average (n = 653), or high (n = 88) for the IC phenotype. Detailed health and productivity data were collected on all steers during feedlot finishing, and associations between IC phenotype, health outcomes, and productivity were investigated. A favorable association between IC phenotype and number of mortalities during feedlot finishing was observed with higher mortalities recorded in low IC steers (6.1%) as compared with average (1.2%, P < 0.001) or high (0%, P = 0.018) IC steers. Disease incidence was numerically highest in low IC steers (15.3 cases/100 animals) and similar in average IC steers (10.1 cases/100 animals) and high IC steers (10.2 cases/100 animals); however, differences between groups were not significant. No significant influence of IC phenotype on average daily gain was observed, suggesting that selection for improved IC is unlikely to incur a significant penalty to production. The potential economic benefits of selecting for IC in the feedlot production environment were calculated. Health-associated costs were calculated as the sum of lost production costs, lost capital investment costs, and disease treatment costs. Based on these calculations, health-associated costs were estimated at AUS$103/head in low IC steers, AUS$25/head in average IC steers, and AUS$4/head in high IC steers, respectively. These findings suggest that selection for IC has the potential to reduce mortalities during feedlot finishing and, as a consequence, improve the health and welfare of cattle in the feedlot production environment and reduce health-associated costs incurred by feedlot operators.

This experiment investigated phenotypic and genetic relationships between carbon dioxide production, methane emission, feed intake, and postweaning traits in Angus cattle. Respiration chamber data on 1096 young bulls and heifers from 2 performance recording research herds of Angus cattle were analyzed to provide phenotypic and genetic parameters for carbon dioxide production rate (CPR; n = 425, mean 3,010 ± SD 589 g/d) and methane production rate (MPR; n = 1,096, mean 132.8 ± SD 25.2 g/d) and their relationships with dry matter intake (DMI; n = 1,096, mean 6.15 ± SD 1.33 kg/d), body weight (BW) and body composition traits. Heritability estimates were moderate to high for CPR (0.53 [SE 0.17]), MPR (0.31 [SE 0.07]), DMI (0.49 [SE 0.08]), yearling BW (0.46 [SE 0.08]), and scanned rib fat depth (0.42 [SE 0.07]). There was a strong phenotypic (0.83 [SE 0.02]) and genetic (0.75 [SE 0.10]) correlation between CPR and MPR. The correlations obtained for DMI with CPR and with MPR were high, both phenotypically (rp) and genetically (rg) (rp: 0.85 [SE 0.01] and 0.71 [SE 0.02]; rg (0.95 [SE 0.03] and 0.83 [SE 0.05], respectively). Yearling BW was strongly correlated phenotypically (rp ≥ 0.60) and genetically (rg > 0.80) with CPR, MPR, and DMI, whereas scanned rib fat was weakly correlated phenotypically (rp < 0.20) and genetically (rg ≤ 0.20) with CPR, MPR, and DMI. The strong correlation between both CPR and MPR with DMI confirms their potential use as proxies for DMI in situations where direct DMI recording is not possible such as on pasture.

Functional and enduring mammary structure is pivotal for producer profitability, and animal health and welfare in beef production. Genetic evaluations for teat and udder score in Canadian Angus cattle have previously been developed. The aim of this study was to identify genomic regions associated with teat and udder structure in Canadian Angus cows thereby enhancing knowledge of the biological architecture of these traits. Thus, we performed a weighted single-step genome wide association study (WssGWAS) to identify candidate genes for teat and udder score in 1,582 Canadian Angus cows typed with the GeneSeek® Genomic Profiler Bovine 130K SNP array. Genomically enhanced estimated breeding values (GEBVs) were converted to SNP marker effects using unequal variances for markers to calculate weights for each SNP over three iterations. At the genome wide level, we detected windows of 20 consecutive SNPs that explained more than 0.5% of the variance observed in these traits. A total of 35 and 28 windows were identified for teat and udder score, respectively, with two SNP windows in common for both traits. Using Ensembl, the SNP windows were used to search for candidate genes and quantitative trait loci (QTL). A total of 94 and 71 characterized genes were identified in the regions for teat and udder score, respectively. Of these, 7 genes were common for both traits. Gene network and enrichment analysis, using Ingenuity Pathway Analysis (IPA), signified key pathways unique to each trait. Genes of interest were associated with immune response and wound healing, adipose tissue development and morphology, and epithelial and vascular development and morphology. Genetic architecture from this GWAS confirms that teat and udder score are distinct, polygenic traits involving varying and complex biological pathways, and that genetic selection for improved teat and udder score is possible.

In animal breeding and genetics, the ability to cope with disease, here defined as immune competence (IC), with minimal detriment to growth and fertility is a desired objective which addresses both animal production and welfare considerations. However, defining and objectively measuring IC phenotypes using testing methods which are practical to apply on-farm has been challenging. Based on previously described protocols, we measured both cell-mediated immune response (Cell-IR) and antibody-mediated immune response (Ab-IR) and combined these measures to determine an animal’s IC. Using a population of 2,853 Australian Angus steers and heifers, we compared 2 alternative methods to combine both metrics into a single phenotype to be used as a tool for the genetic improvement of IC. The first method, named ZMEAN, is obtained by taking the average of the individual metrics after subjecting each to a Z-score standardization. The second, ImmuneDEX (IDEX), is a weighted average that considers the correlation between Cell-IR and Ab-IR, as well as the difference in ranking of individuals by each metric, and uses these as weights in the averaging. Both simulation and real data were used to understand the behavior of ZMEAN and IDEX. To further ascertain the relationship between IDEX and other traits of economic importance, we evaluated a range of traits related to growth, feedlot performance, and carcass characteristics. We report estimates of heritability of 0.31 ± 0.06 for Cell-IR, 0.42 ± 0.06 for Ab-IR, 0.42 ± 0.06 for ZMEAN and 0.370 ± 0.06 for IDEX, as well as a unity genetic correlation (rg) between ZMEAN and IDEX. While a moderately positive rg was estimated between Cell-IR and Ab-IR (rg = 0.33 ± 0.12), strongly positive estimates were obtained between IDEX and Cell-IR (rg = 0.80 ± 0.05) and between IDEX and Ab-IR (rg = 0.85 ± 0.04). We obtained a moderately negative rg between IC traits and growth including an rg = −0.38 ± 0.14 between IDEX and weaning weight, and negligible with carcass fat measurements, including an rg = −0.03 ± 0.12 between IDEX and marbling. Given that breeding with a sole focus on production might inadvertently increase susceptibility to disease and associated antibiotic use, our analyses suggest that ImmuneDEX will provide a basis to breed animals that are both highly productive and with an enhanced ability to resist disease.

In this study, we aimed to assess the value of genotyping DNA pools as a strategy to generate accurate and cost-effective genomic estimated breeding values (GEBV) of sires in multi-sire mating systems. In order to do that, we used phenotypic records of 2,436 Australian Angus cattle from 174 sires, including yearling weight (YWT; N = 1,589 records), coat score (COAT; N = 2,026 records), and Meat Standards Australia marbling score (MARB; N = 1,304 records). Phenotypes were adjusted for fixed effects and age at measurement and pools of 2, 5, 10, 15, 20, and 25 animals were explored. Pools were created either by phenotype or at random. When pools were created at random, 10 replicates were examined to provide a measure of sampling variation. The relative accuracy of each pooling strategy was measured by the Pearson correlation coefficient between the sire’s GEBV with pooled progeny and the GEBV using individually genotyped progeny. Random pools allow the computation of sire GEBV that are, on average, moderately correlated (i.e., r > 0.5 at pool sizes [PS] ≤ 10) with those obtained without pooling. However, for pools assigned at random, the difference between the best and the worst relative accuracy obtained out of the 10 replicates was as high as 0.41 for YWT, 0.36 for COAT, and 0.61 for MARB. This uncertainty associated with the relative accuracy of GEBV makes randomly assigning animals to pools an unreliable approach. In contrast, pooling by phenotype allowed the estimation of sires’ GEBV with a relative accuracy ≥ 0.9 at PS < 10 for all three phenotypes. Moreover, even with larger PS, the lowest relative accuracy obtained was 0.88 (YWT, PS = 20). In agreement with results using simulated data, we conclude that pooling by phenotype is a robust approach to implementing genomic evaluation using commercial herd data, and PS larger than 10 individuals can be considered.

Pulmonary arterial pressure (PAP) is a diagnostic measure used to determine an individual’s susceptibility to developing high-altitude disease. The importance of PAP measures collected at elevations lower than the intended breeding elevation of the bulls (i.e., ≥1,520 m) is unknown. Therefore, the objective of this study was to determine the genetic relationship between PAP measures collected in a range of elevations using reaction norm models. A total of 9,177 PAP and elevation observations on purebred Angus cattle, which averaged 43.49 ± 11.32 mmHg and 1,878.6 ± 296.8 m, respectively, were used in the evaluation. The average age of the individuals in the evaluation was 434.04 ± 115.9 d. A random regression model containing the effects of sex, a linear covariate of age, a quadratic fixed covariate of elevation, and random effects consisting of a contemporary group and a linear regression of PAP on elevation was used for the evaluation of PAP. Two forms of PAP were evaluated with this model. First, to address the non-normality of the data, PAP was raised to the power of −2.6 (ptPAP) based on the results of a Box–Cox analysis. Second, raw PAP (rPAP) phenotypes were evaluated to compare the results to those obtained from the transformed data. For ptPAP, heritability ranged from 0.25 to 0.37 corresponding to elevations of 1,900 and 1,215 m, respectively. For rPAP, heritability ranged from 0.22 to 0.41 corresponding to elevations of 1,700 and 2,495 m, respectively. Generally, lower elevations corresponded to decreased heritabilities while higher elevations corresponded to increased heritability estimates. For ptPAP, genetic correlations ranged from 0.18 (elevation: 1,215 and 2,495 m) to 1.00. For rPAP, genetic correlations ranged from 0.08 (elevation: 1,215 and 2,495 m) to 1.00. In general, the closer the elevations in which PAP was measured, the greater the genetic relationship. The greater the difference in elevation between PAP measures resulted in lower genetic correlations. The rank correlation between expected progeny differences (EPD) for 1,215 and 2,495 m was 0.65 and 0.49 for the ptPAP and rPAP, respectively. These results suggested that PAP measures collected in lower elevations may be used as an indicator of high-altitude adaptability. In the estimation of EPD to rank sires for their suitability for use in high-elevation production systems, it is important to account for the relationships among varied altitudes.

Made available in DSpace on 2020-12-12T02:41:15Z (GMT). No. of bitstreams: 0 Previous issue date: 2020-04-25 The objectives of this study were to compare ruminal total tract digestibility, bacterial communities, and eating and rumination activity between Holstein and Angus steers fed grain- or forage-based diets. Six Holstein steers (average body weight [BW] = 483 ± 23 kg) and six Angus steers (average BW = 507 ± 29 kg), previously fitted with rumen cannulae, were fed in a crossover design with a 2 × 2 factorial arrangement of four treatments: 1) Holsteins fed a grain-based diet, 2) Holsteins fed a forage-based diet, 3) Angus fed a grain-based diet, and 4) Angus fed a forage-based diet. Each period was 35 d with 26 d of diet adaptation and 9 d of sample collection. On days 1 and 2 of collection, feeding activity was recorded for 48 h. On day 3, rumen contents were sampled to measure ruminal pH at 0, 3, 6, 12, and 18 h after feeding. A portion of the strained ruminal fluid was subsampled at 0, 3, and 6 h for volatile fatty acids (VFA) analysis. Rumen contents were subsampled at 3 h for analysis of bacterial communities. From day 4 to 8, total fecal excretion, feed, and refusals samples were collected and analyzed for dry matter (DM), neutral detergent fiber (NDF), and starch. On days 8 and 9 (0 and 3 h post-feeding, respectively), total reticulorumen evacuation was conducted and contents were weighed. Data were analyzed using the MIXED procedures in SAS (v9.4 SAS Inst. Inc., Cary, NC). Repeated measures were used to analyze changes in ruminal pH and VFA over time. There were no interactions of diet × breed (P ≥ 0.07). While the main effects of diet were expected, unique to these data is the fact that bacterial diversity and richness were reduced (P < 0.01) in cattle fed grain-based diets. There was no main effect (P > 0.34) of breed on total tract DM, organic matter, and starch digestibility, but Angus cattle had greater (P = 0.01) NDF digestibility than Holsteins. The increased NDF digestibility may be associated with a numerical (P = 0.08) increased numbers of bacterial species in Angus steers compared with Holstein steers. Holstein steers also spent more time (P ≤ 0.05) ruminating than Angus steers. There was no effect (P > 0.80) of breed on reticulorumen content at feeding time; however, Holstein steers had greater (P = 0.04) reticulorumen content on a wet basis 3 h post-feeding. Although Holstein steers spent more time ruminating, Angus steers were better able to digest NDF when compared with Holsteins, regardless of basal diet, and this improvement may be related to changes in bacterial communities in the rumen or to rumination activity. Department of Animal Science Pennsylvania State University Department of Animal Production College of Technology and Agricultural Sciences São Paulo State University (UNESP) Department of Animal Production College of Technology and Agricultural Sciences São Paulo State University (UNESP)

Copy number variations (CNVs) recently have been recognized as another important genetic variability followed single nucleotide polymorphisms (SNPs). The guanylate binding protein 2 (GBP2) gene plays an important role in cell proliferation. This study was performed to determine the presence of GBP2 CNV (relative to Angus cattle) in 466 individuals representing six main cattle breeds from China, identify its relationship with growth, and explore the biological effects of gene expression. There were two CNV regions in the GBP2 gene, for three types, CNV1 loss type (relative to Angus cattle) was more frequent in XN than other breeds, and CNV2 loss type (relative to Angus cattle) was more frequent in XN and CDM than other breeds. Though the GBP2 gene copy number presented no correlation with the transcriptional expression of JX (P .05), but the transcriptional expression in heart is higher than other tissues, and the copy number in muscles and fat of JX is higher than others breeds. Statistical analysis revealed that the GBP2 gene CNV1 and CNV2 were significantly associated with growth traits (P .05). In conclusion, this research established the correlations between CNVs of GBP2 gene and growth traits in different cattle breeds, and our results suggested that the CNVs in GBP2 gene may be considered markers for the molecular breeding of Chinese beef cattle.

Disclosure of affected breed without disclosure of major progenitors has been the usual practice in scientific papers reporting recessive heritable disorders of cattle. Before molecular genetics, carrier identity could not be used by breeders to control causal mutations because phenotypically normal heterozygotes among genetically related animals could not be detected other than by test mating. Accurate, low-cost DNA tests fundamentally changed this situation. Genomics can provide relief from the old problem of emerging recessive disorders in cattle breeding, but greater transparency of genotype data between breeders is necessary to fully exploit the opportunities for cost-efficient genetic disease control. Effective control of several recessive disorders has been demonstrated in Angus cattle, based entirely on voluntary DNA testing by breeders but mandatory public disclosure of test results and genotype probabilities for all registered animals. When a DNA test is available, major progenitors (particularly bulls from which semen has been distributed) should be identified and disclosed concurrently with the affected breed. As a minimum, whenever possible the closest common ancestors in the pedigrees of the parents of homozygous mutants should be disclosed after confirmation of carrier status. Progenitor disclosure in scientific publications should occur in cooperation with breed societies, which should have the opportunity to advise breeders and initiate management programs before scientific publication. Unless properly managed, genomic enhancement of animal selection using SNP markers may increase inbreeding, co-ancestry and emergence of recessive disorders. The information systems and genotype disclosure policies of some breed societies will be increasingly challenged, particularly with accelerating mutation discovery using next-generation sequencing.

Made available in DSpace on 2018-11-28T04:17:16Z (GMT). No. of bitstreams: 0 Previous issue date: 2017-01-01 Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) UNESP/FCAV, Jaboticabal Embrapa Pecuaria Sudeste With the aim of finding quantitative phenotypic traits that can be used to discriminate the levels of resistance/susceptibility to Babesia bovis, we estimated the repeatability and correlation between the level of infection, determined by the number of copies of a fragment of the gene that encodes cytochrome B (NC mt-cyB) of B. bovis, and the levels of the anti-B. bovis antibodies, in blood samples collected from 51 Angus cattle on two different occasions. Samples with the anticoagulant EDTA were used for DNA extraction and without anticoagulant for separation of the blood serum. The quantification of the NC mt-cyB of B. bovis was carried out by the quantitative PCR technique (qPCR), while the anti-B. bovis IgG antibody titers (S/P) were quantified by the ELISA method. The NC and S/P data were log10-transformed to improve the approximation to the normal distribution and were analyzed using mixed models. The correlations between NC mt-cyB and S/P were estimated, as well as the repeatability values for each trait. The results obtained showed the high sensitivity of the techniques, with 100% of the animals being positive for B. bovis, detected by both the serological and molecular tests. The correlations estimated between NC and S/P were low, 0.10 and 0.12, in the first and second collection, respectively. The repeatability estimated for NC was 0.06, whereas for the SIP it was 0.42. The low correlations between S/P and NC in the two collections demonstrated that the variation in the NC value is independent of the level of antibodies. This results indicated that animals with a higher levels of antibodies against B. bovis in the first collection continued to have a higher levels in the second one. However, the very low values for the repeatability value of NC, and for the correlations between S/P and NC, demonstrates that neither NC or S/P could be used to discriminate animals for resistance/susceptibility to B. bovis. (C) 2016 Elsevier GmbH. All rights reserved. Univ Estadual Julio de Mesquita Filho, Jaboticabal, SP, Brazil Embrapa Suinos & Aves, Concordia, SC, Brazil Univ Fed Sao Carlos, Sao Carlos, SP, Brazil Embrapa Pecuaria Sudeste, Rodovia Washington Luiz,Km 234,CP 339, BR-13560970 Sao Carlos, SP, Brazil Univ Estadual Julio de Mesquita Filho, Jaboticabal, SP, Brazil FAPESP: 2012/00067-5 FAPESP: 2011/23833-2

The objectives of this study were to compare different models for analysing body weight (BW) and average daily feed intake (ADFI) data collected during a 70-day feedlot test period and to explore whether genetic parameters change over time to evaluate the implications of selection response. (Co)variance components were estimated using repeatability and random regression models in 2,071 Angus steers. Models included fixed effects of contemporary group, defined as herd-year-observation_date-age, with additive genetic and permanent environmental components as random effects. Models were assessed based on the log likelihood, Akaike's information criterion and the Bayesian information criterion. For both traits, random regression models (RRMs) presented a better fit, indicating that genetic parameters change over the test period. Using a two-trait RRM, the heritability from day 1 up to day 70 for BW increased from 0.40 to 0.50, while for ADFI, it decreased from 0.44 to 0.33. The genetic correlation increased from 0.53 at day 1 up to 0.79 at day 70. Selection based on an index assuming no change in genetic parameters would yield a 2.78%-3.13% lower selection response compared to an index using parameters estimated with RRMs and assuming these genetic parameters are correct. Results imply that it may be beneficial to implement RRMs to account for the change of parameters across the feedlot period in feed efficiency traits.

Despite their heritability and influence on female productivity, there are currently no genetic evaluations for teat and udder structure in Canadian Angus cattle. The objective of this study was to develop optimal genetic evaluations for these traits in the Canadian Angus population. Guidelines recommended by Beef Improvement Federation (BIF) were used to score teat and udder structure in 1,735 Canadian Angus cows from 10 representative herds. Cows scored ranged in parity from 1 to 13; however, >70% of cows were parity ≤4. Scores ranged from 1 (large, bottle shaped) to 9 (very small) for teats and from 1 (very pendulous) to 9 (very tight) for udders. Consistent with parity distribution, >70% of teat and udder scores were ≥6. Teat and udder scores (TS9 and US9, respectively) were modeled using a multiple trait animal model with random effects of contemporary group (herd-year-season) and additive genetic effect, and fixed effects of breed, parity group, and days between calving and scoring. To test good versus poor structure, a binary classification of 1 or 2 (TS2, US2) [comprised of scores 1 to 5 = 1 (poor structure) and scores 6 to 9 = 2 (good structure)] was created. Further, to assess the impact of grouping less frequently observed poor scores, a 1 to 7 scale (TS7, US7) was created by combining teat and udder scores 1 to 3. Analyses for teat and udder scores on scales TS9, US9, TS7, US7, and TS2, US2 were compared. In addition, both threshold and linear animal models were used to estimate variance components for the traits. Data treatment and models were evaluated based on correlation of resulting estimated breeding value (EBV) with corrected phenotypes, Spearman’s rank correlation coefficient, average EBV accuracies (r), and deviance information criteria (DIC). TS9, US9 scales for teat and udder scores and linear models performed best. Estimates of heritability (SE) for teat and udder score were 0.32 (0.06) and 0.15 (0.04), respectively, indicating these traits were moderately heritable and that genetic improvement for teat and udder scores was possible. Estimates of phenotypic and genotypic correlations for teat and udder score were 0.46 (0.02) and 0.71 (0.09), respectively. Estimates of genotypic correlations with birth weight (BW), weaning weight (WW), and yearling weight (YW), ranged from −0.04 (0.10) to −0.20 (0.12), verifying the importance of selecting for improved teat and udder score as individual traits, alongside performance traits.

Background: Single-step genomic best linear unbiased prediction (SSGBLUP) is a comprehensive method for genomic prediction. Point estimates of marker effects from SSGBLUP are often used for genome-wide association studies (GWAS) without a formal framework of hypothesis testing. Our objective was to implement p-values for singlemarker GWAS studies within the single-step GWAS (SSGWAS) framework by deriving computational algorithms and procedures, and by applying these to a large beef cattle population. Methods: P-values were obtained based on the prediction error (co)variances for single nucleotide polymorphisms (SNPs), which were obtained from the prediction error (co)variances of genomic predictions based on the inverse of the coefficient matrix and formulas to estimate SNP effects. Results: Computation of p-values took a negligible time for a dataset with almost 2 million animals in the pedigree and 1424 genotyped sires, and no inflation of statistics was observed. The SNPs that passed the Bonferroni threshold of 10-5.9 were the same as those that explained the highest proportion of additive genetic variance, but even at the same significance levels and effects, some of them explained less genetic variance due to lower allele frequency. Conclusions: The use of a p-value for SSGWAS is a very general and efficient strategy to identify quantitative trait loci (QTL). It can be used for complex datasets such as those used in animal breeding, where only a proportion of the pedigreed animals are genotyped. Made available in DSpace on 2020-01-06T18:24:04Z (GMT). No. of bitstreams: 1 AguilaretalGSE5128.pdf: 1131067 bytes, checksum: 694d4cc315b780e14aa4cf20808f1e56 (MD5) Previous issue date: 2019

This study determined the impact of selection for greater muscling in Angus cattle on myofibre characteristics, muscle enzymatics, retail colour stability, pH decline and mineral content of the semimembranosus (SM), semitendinosus (ST) and longissimus thoracis (LT). Muscle from 10 low muscled (low) and 11 high muscled (high) steers were analysed. The high steers had myofibres 22% and 24% larger in cross-sectional area in the SM and ST (P < 0.05), and 8.6% less type IIX myofibres in the LT than the low steers (P < 0.05). The highs had 4.9% lower lactate dehydrogenase activity, 10.2% and 12.3% higher citrate synthase and isocitrate dehydrogenase activity than lows (P < 0.05). The highs had 27% more iron in the LT (P < 0.05). The results indicate that the oxidative capacity of muscle can be maintained in more muscular cattle with no detrimental effects to mineral content, pH decline or retail colour stability. Myofibre hypertrophy is one mechanism leading to greater muscle mass of these high muscled cattle.

Highlighting genomic profiles for geographically distinct subpopulations of the same breed may provide insights into adaptation mechanisms to different environments, reveal genomic regions divergently selected, and offer initial guidance to joint genomic analysis. Here, we characterized similarities and differences between the genomic patterns of Angus subpopulations, born and raised in Canada (N = 382) and Brazil (N = 566). Furthermore, we systematically scanned for selection signatures based on the detection of autozygosity islands common between the two subpopulations, and signals of divergent selection, via F

The objective was to examine uterine artery blood flow (UBF) as well as macroscopic and microscopic placentome vascular density in nutrient-restricted Angus and Brahman heifers. Angus (n = 6) and Brahman (n = 6) heifers were bred to a single sire and pregnancy confirmed at 30-d postbreeding. Heifers were randomly assigned to 1 of 2 dietary treatments consisting of 100% (control-fed; CON; n = 6) or 60% (total nutrient-restricted; RES; n = 6) based from net energy requirements for gestating heifers. Nutritional treatments were imposed from days 50 to 180 of gestation. On day 175 of gestation, UBF was collected ipsilateral and contralateral to the conceptus via Doppler ultrasonography. Heifers underwent Cesarean sections for collection of 2 adjacent placentomes on day 180 of gestation. The primary cotyledonary artery of 1 placentome was perfused with Alexa Fluor 647 Con A conjugate to examine macroscopic cotyledonary vascular density via an in vivo imaging system. The second placentome was fixed for microscopic immunofluorescence labeling of capillaries and separated into maternal (caruncle) and fetal (cotyledon) components for determination of angiogenic factor mRNA expression. Main effects of nutritional treatment and breed are reported in the absence of a significant nutritional treatment by breed interaction. Ipsilateral UBF was decreased (P < 0.05) by 48% in RES vs. CON, whereas breed did not influence ipsilateral UBF. Contralateral UBF was not different between nutritional treatments; however, contralateral UBF was decreased (P < 0.05) by 63% in Brahman vs. Angus cattle. Macroscopic cotyledonary vascular density was increased (P < 0.05) by 36% in RES vs. CON and 82% in Brahman vs. Angus heifers. Percent capillary area and capillary perimeter were increased (P < 0.05) in RES vs. CON and increased (P < 0.05) in Brahman vs. Angus heifers. Dietary treatments did not alter angiogenic factor expression; however, transcript abundance of caruncle and cotyledon ANGP1, FLT1, and KDR was increased (P < 0.05) in Brahman vs. Angus heifers. In summary, these data indicate compensatory responses in macroscopic and microscopic placentome blood vessel density during maternal nutrient restriction-induced reductions in UBF. Moreover, a greater macroscopic density of cotyledonary blood vessels was observed in Brahman vs. Angus heifers.

Altitude-induced pulmonary hypertension is a disease once thought to only occur at extremely high elevations (>1,600 m), but recently, it has been observed at moderate elevations of 1,200 to 1,600 m. Pulmonary arterial pressure (PAP) has been used as an indicator of tolerance to high altitude in mountainous beef production systems for over 30 yr. The trait is typically measured on yearling bulls and heifers with values ≤ 41 mmHg being favorable. These observations were historically only considered valid when they were recorded at elevations ≥ 1,600 m; however, if observations from lower (i.e., moderate) elevations were reliable indicators, a greater number of cattle records could be used in genetic improvement programs for high-altitude beef systems. The objectives of this study were to evaluate the relationship between PAP and elevation, as well as to determine whether PAP measures obtained at moderate elevations (ME) less than 1,600 m have a genetic relationship with PAP observations obtained at high elevations (HE) 1,600 m or greater. Elevation and PAP data from purebred Angus cattle (n = 14,665) from 349 contemporary groups were used in the analyses. Elevation and PAP averaged 1,887 ± 1.8 m and 43.0 ± 0.1 mm Hg, respectively. A univariate model containing the effects of sex, age, elevation category (HE vs. ME), elevation (continuous), and elevation category by elevation interaction along with a random direct genetic effect was utilized to determine the relationship between PAP and elevation. In this model, all main effects were found to be significant contributors of variation in PAP (P < 0.001). The interaction between elevation category and elevation was not a significant contributor to variability of PAP (P > 0.05). A bivariate animal model was then used to evaluate the relationship between PAP observations obtained between HE and ME groups. Heritability estimates for these 2 groups were 0.34 ± 0.03 and 0.29 ± 0.09, respectively, and their genetic correlation was 0.83 ± 0.15. Even though this is a strong genetic relationship, results of this study support the hypothesis that PAP observations collected at HE and ME are not perfectly, genetically related. Results suggest that PAP measures collected from 1,219 to 1,600 m may be useful as a correlated trait in a multitrait genetic evaluation to produce EPD useful for selection of animals with reduced susceptibility to pulmonary hypertension.

Background If unmanaged, high rates of inbreeding in livestock populations adversely impact their reproductive fitness. In beef cattle, historical selection strategies have increased the frequency of several segregating fatal autosomal recessive polymorphisms. Selective breeding has also decreased the extent of haplotypic diversity genome-wide. By identifying haplotypes for which homozygotes are not observed but would be expected based on their frequency, candidates for developmentally lethal recessive loci can be localized. This analysis comes without the need for observation of the loss-associated phenotype (e.g., failure to implant, first trimester abortion, deformity at birth). In this study, haplotypes were estimated for 3961 registered Angus individuals using 52,545 SNP loci using findhap v2, which exploited the complex pedigree among the individuals in this population. Results Seven loci were detected to possess haplotypes that were not observed in homozygous form despite a sufficiently high frequency and pedigree-based expectation of homozygote occurrence. These haplotypes were identified as candidates for harboring autosomal recessive lethal alleles. Of the genotyped individuals, 109 were resequenced to an average 27X depth of coverage to identify putative loss-of-function alleles genome-wide and had variants called using a custom in-house developed pipeline. For the candidate lethal-harboring haplotypes present in these bulls, sequence-called genotypes were used to identify concordant variants. In addition, whole-genome sequence imputation of variants was performed into the set of 3961 genotyped animals using the 109 resequenced animals to identify candidate lethal recessive variants at the seven loci. Following the imputation, no variants were identified that were fully concordant with the marker-based diplotypes. Conclusions Selective breeding programs could utilize the predicted lethal haplotypes associated with SNP genotypes. Sequencing and other methods for identifying the causal variants underlying these haplotypes can allow for more efficient methods of management such as gene editing. These two methods in total will reduce the negative impacts of inbreeding on fertility and maximize overall genetic gains.

Mechanisms responsible for excellent marbling in Japanese black cattle, Wagyu, remain to be established. Because both muscle cells and intramuscular adipocytes are developed from mesenchymal progenitor cells during early muscle development, we hypothesized that intramuscular progenitor cells in Wagyu cattle have attenuated myogenic capacity in favor of adipogenesis, leading to high marbling but reduced muscle growth. Biceps femoris muscle biopsy samples were obtained from both Angus (n=3) and Wagyu (n=3) cattle at 12 months of age. Compared with Angus, the density of satellite cells was much lower in Wagyu muscle (by 45.8±10%, P

Bioeconomic models were developed to calculate economic values (EV) for economically important traits in beef cattle, to evaluate the impact of these traits on production profitability, to assess possible market changes with a payment system and to develop economic selection indexes for Angus cattle for two production systems. Two beef cattle production systems were simulated as follows: a cow-calf cycle (CC) and a complete cycle (CoC). Following selection, positive changes in the EV were observed. In the CC, each 1.0% increment in weaning weight (WW), weaning rate (WR) and pregnancy rate (PR) resulted in increases in US$ 1.30, US$ 3.68 and US$ 3.55 per cow/year in profit, respectively. In the CoC, EV of US$ 1.01, US$ 1.79, US$ 1.19, US$ 1.34, US$ 6.84 and US$ 7.86 per cow/year were obtained for WW, year weight, yearling weight, final weight, WR and PR, respectively. The payment system for carcass quality showed that the scenario considering that 100% of the animals displayed uniform carcasses exhibited the highest EV and was considered optimal. Considering the sensitivity analysis, the price paid per animal was the factor that most affected the EV in both systems. The selection indexes obtained may be used in similar production systems, and the use of EV and selection indexes are important tools for any production system with positive change in profit after selection.

Artificial selection towards a desired phenotype/trait has modified the genomes of livestock dramatically that generated breeds that greatly differ in morphology, production and environmental adaptation traits. Angus cattle are among the famous cattle breeds developed for superior beef quality. This paper aimed at exploring genomic regions under selection in Angus cattle that are associated with meat quality traits and other associated phenotypes. The whole genome of 10 Angus cattle was compared with 11 Hanwoo (A-H) and 9 Jersey (A-J) cattle breeds using a cross-population composite likelihood ratio (XP-CLR) statistical method. The top 1% of the empirical distribution was taken as significant and annotated using UMD3.1. As a result, 255 and 210 genes were revealed under selection from A-H and A-J comparisons, respectively. The WebGestalt gene ontology analysis resulted in sixteen (A-H) and five (A-J) significantly enriched KEGG pathways. Several pathways associated with meat quality traits (insulin signaling, type II diabetes mellitus pathway, focal adhesion pathway, and ECM-receptor interaction), and feeding efficiency (olfactory transduction, tight junction, and metabolic pathways) were enriched. Genes affecting beef quality traits (e.g., FABP3, FTO, DGAT2, ACS, ACAA2, CPE, TNNI1), stature and body size (e.g., PLAG1, LYN, CHCHD7, RPS20), fertility and dystocia (e.g., ESR1, RPS20, PPP2R1A, GHRL, PLAG1), feeding efficiency (e.g., PIK3CD, DNAJC28, DNAJC3, GHRL, PLAG1), coat color (e.g., MC1-R) and genetic disorders (e.g., ITGB6, PLAG1) were found to be under positive selection in Angus cattle. The study identified genes and pathways that are related to meat quality traits and other phenotypes of Angus cattle. The findings in this study, after validation using additional or independent dataset, will provide useful information for the study of Angus cattle in particular and beef cattle in general.

Impairment of bone growth at a young age leads to dwarfism in adulthood. Dwarfism can be categorised as either proportionate, an overall size reduction without changes in body proportions, or disproportionate, a size reduction in one or more limbs, with changes in body proportions. Many forms of dwarfism are inherited and result from structural disruptions or disrupted signalling pathways. Hormonal disruptions are evident in Brooksville miniature Brahman cattle and Z-linked dwarfism in chickens, caused by mutations in GH1 and GHR. Furthermore, mutations in IHH are the underlying cause of creeper achondroplasia in chickens. Belgian blue cattle display proportionate dwarfism caused by a mutation in RNF11, while American Angus cattle dwarfism is caused by a mutation in PRKG2. Mutations in EVC2 are associated with dwarfism in Japanese brown cattle and Tyrolean grey cattle. Fleckvieh dwarfism is caused by mutations in the GON4L gene. Mutations in COL10A1 and COL2A1 cause dwarfism in pigs and Holstein cattle, both associated with structural disruptions, while several mutations in ACAN are associated with bulldog-type dwarfism in Dexter cattle and dwarfism in American miniature horses. In other equine breeds, such as Shetland ponies and Friesian horses, dwarfism is caused by mutations in SHOX and B4GALT7. In Texel sheep, chondrodysplasia is associated with a deletion in SLC13A1. This review discusses genes known to be involved in these and other forms of dwarfism in livestock.

The qPCR technique with SYBR Green was used to estimate the prevalence and level of Babesia bovis infection in beef cattle raised in areas endemic for babesiosis in Brazil, where the animals were continuously exposed to ticks (Rhipicephalus microplus). This is the first report in which qPCR was used to quantify and compare B. bovis DNA in blood of different cattle breeds. Blood samples were collected from 150 animals (75 cows and 75 calves) of the Angus and Nelore breeds and the first generation of an Angus and Nelore cross (AxN). Blood samples from the jugular vein were used for DNA extraction and determination of packed cell volume (PCV), while samples from peripheral veins were used for microscopic parasite detection. Although no piroplasms of B. bovis were found in blood smears, DNA amplification using qPCR revealed that all of the 150 animals, except two calves and one cow, were positive. The number of copies of B. bovis DNA was higher (p0.05) in the Angus than in the Nelore and AxN animals, for both calves and cows, but no significant difference was found between the Nelore and AxN groups. These results suggest that a heterotic effect was present, since the results from the crossbred animals significantly deviated from the mean of the two parental groups, while closely approaching that of the Nelore group. In the Nelore and AxN groups, calves showed higher infection levels than cows (p0.05), while for the Angus group the difference was found to be non-significant. Within each animal age group, the breed groups with higher infection levels were those with lower PCV values. However, within each breed group, no significant correlations were found between the number of DNA copies and PCV according to animal age. The qPCR method applied here allowed the observation that although there are no differences in the prevalence of infection among breed groups, Nelore and AxN cattle are able to maintain infection by B. bovis at lower levels than the Angus cattle.

Copy number variations (CNVs) have been recently recognized as another important genetic variability complementary to single nucleotide polymorphisms (SNPs). Compelling evidence has indicated that CNVs are responsible for phenotypic traits by changing the copy numbers of functional genes. Myosin heavy chain 3 (MYH3) gene is a critical regulatory factor in skeletal muscle development, and has been detected in the CNVs region by comparative genomic hybridization (CGH) array. This study was conducted to validate and detect the distribution of MYH3 copy numbers (relative to Angus cattle) in four Chinese cattle breeds (NY, QC, LX, and CY), and further to investigate the associations of the copy number changes with its transcriptional expression and cattle growth traits. Substantial genetic differences of MYH3 copy numbers were identified between NY and the other three breeds (P

A genomic relationship matrix (GRM) can be inverted efficiently with the Algorithm for Proven and Young (APY) through recursion on a small number of core animals. The number of core animals is theoretically linked to effective population size (N e ). In a simulation study, the optimal number of core animals was equal to the number of largest eigenvalues of GRM that explained 98% of its variation. The purpose of this study was to find the optimal number of core animals and estimate N e for different species. Datasets included phenotypes, pedigrees, and genotypes for populations of Holstein, Jersey, and Angus cattle, pigs, and broiler chickens. The number of genotyped animals varied from 15,000 for broiler chickens to 77,000 for Holsteins, and the number of single-nucleotide polymorphisms used for genomic prediction varied from 37,000 to 61,000. Eigenvalue decomposition of the GRM for each population determined numbers of largest eigenvalues corresponding to 90, 95, 98, and 99% of variation. The number of eigenvalues corresponding to 90% (98%) of variation was 4527 (14,026) for Holstein, 3325 (11,500) for Jersey, 3654 (10,605) for Angus, 1239 (4103) for pig, and 1655 (4171) for broiler chicken. Each trait in each species was analyzed using the APY inverse of the GRM with randomly selected core animals, and their number was equal to the number of largest eigenvalues. Realized accuracies peaked with the number of core animals corresponding to 98% of variation for Holstein and Jersey and closer to 99% for other breed/species. N e was estimated based on comparisons of eigenvalue decomposition in a simulation study. Assuming a genome length of 30 Morgan, N e was equal to 149 for Holsteins, 101 for Jerseys, 113 for Angus, 32 for pigs, and 44 for broilers. Eigenvalue profiles of GRM for common species are similar to those in simulation studies although they are affected by number of genotyped animals and genotyping quality. For all investigated species, the APY required less than 15,000 core animals. Realized accuracies were equal or greater with the APY inverse than with regular inversion. Eigenvalue analysis of GRM can provide a realistic estimate of N e .

Copy number variations (CNVs) recently have been recognized as an important source of genetic variability. Compelling evidence has indicated that CNVs are responsible for phenotypic traits by altering the copy numbers of functional genes. The molecule interacting with CasL-like protein 2 (MICAL-L2) gene plays a critical role in muscle fiber development and has been identified in the CNV region by comparative genomic hybridization array. In the present study, we detected the different distributions of MICAL-L2 gene copy numbers in four Chinese cattle breeds (QC, NY, LX, and CY) and investigated the functional effects of MICAL-L2 CNVs on the gene’s expression level and the phenotypic traits in QC and NY cattle. The results showed that the copy number loss (relative to Angus cattle) was more frequent in CY than in the other breeds. The MICAL-L2 gene copy number presented a moderate negative correlation with the transcriptional expression in fetal skeletal muscles (P < 0.05). Statistical analysis revealed that the MICAL-L2 CNVs were significantly associated with body weight, body height, and body length of NY cattle in the early stages (6 and 12 months old), and the copy number loss showed better traits than the gain and/or median groups (P < 0.05). No significance was found at the late stages in QC (24 months old) and NY cattle (18 and 24 months old). These observations provided further insight into the associations between cattle CNVs and economic traits, suggesting that the CNVs may be considered promising markers for the molecular breeding of Chinese beef cattle.

Residual feed intake (RFI) has been adopted in Australia for the purpose of genetic improvement in feed efficiency in beef cattle. RFI is the difference between the observed feed intake of an animal and the predicted feed intake based on its size and growth rate over a test period. Gene expression of eight candidate genes (AHSG, GHR, GSTM1, INHBA, PCDH19, S100A10, SERPINI2 and SOD3), previously identified as differentially expressed between divergent lines of high- and low-RFI animals, was measured in an unselected population of 60 steers from the Angus Society Elite Progeny Test Program using quantitative real-time PCR. Results showed that the levels of gene expression were significantly correlated with RFI. The genes explain around 33.2% of the phenotypic variance in RFI, and prediction equations using the expression data are reasonably accurate estimators of RFI. The association of these genes with economically important traits, such as other feed efficiency-related traits and fat, growth and carcass traits, was investigated as well. The expression of these candidate genes was significantly correlated with feed conversion ratio and daily feed intake, which are highly associated with RFI, suggesting a functional role for these genes in modulating feed utilisation. The expression of these genes did not show any association with average daily gain, eye muscle area and carcass composition.

The insulin-like growth factor 1 (IGF-1) is considered to be a factor that mainly regulates growth, differentiation, and the maintenance of various function in numerous tissues through binding to a family of transmembrane tyrosine kinase receptors, signaling primarily through the insulin-like growth factor 1 receptor (IGF-1R) encoded by the IGF1R gene. The objectives of the present study were to estimate the allele and genotype frequencies of the IGF1R/MspI (silent mutation within exon 12) and the IGF1R/TaqI (within the 3' untranslated region, 3'UTR) gene polymorphisms in beef cattle and to determine associations between these polymorphisms and growth traits. In a preliminary study on 310 Angus calves, association analyses with three production traits (birth weight, BWT; weaning weight adjusted to 210 days, WWT210; and average daily gain, ADG) were conducted. The GG genotype of the IGF1R/e12/MspI polymorphism was significantly associated (P ≤ 0.05) with a higher WWT210 (+5.06 kg) compared to the AG genotype. Polymorphism within the 3'UTR had no significant effect on growth traits. The effect of combined genotypes was also examined. At WWT(210), calves with the GG/AA and GG/AG combinations were heavier than calves with the AG/AA and AG/AG combined genotypes (P ≤ 0.05). To our knowledge, this is the first report of a polymorphism within the coding region of the Bos taurus IGF1R gene.

Gastrointestinal nematode (GIN) infection is a major cause of production losses in cattle. This study was carried out to evaluate the natural resistance against nematode infection in Crioulo Lageano and crossbred Angus male calves. Crioulo Lageano is a local cattle breed in the state of Santa Catarina, in southern Brazil. Ten weaned calves of each breed were grazed together on pasture and naturally infected with nematodes between July 2009 and December 2010. Once every 28 days, we collected fecal and blood samples for parasitological and immunological tests, as well as recording body weights. After 19 samplings, all animals were slaughtered for quantification and identification of GINs. We found that the animals had been infected with the following nematode species, in decreasing order by the mean number of specimens: Trichostrongylus axei, Cooperia punctata, Ostertagia ostertagi, Haemonchus placei, Oesophagostomum radiatum, and Trichuris spp. There were no significant differences between the Crioulo Lageano and crossbred Angus groups in terms of worm burden or nematode fecal egg count, nor in terms of the mean levels of immunoglobulin (G and A) against C. punctata and H. placei antigens, except in IgA mean level in abomasal mucus against H. placei adult worms that was significantly higher in crossbred Angus cattle (p

The analysis of infection by Paramphistomidae trematodes was conducted in two agricultural regions with different knowledge on this parasitosis. Faecal and blood samples were collected from 374 cattle in Salto (NW Uruguay) where there is a lack of information about paramphistomosis. A total of 429 cattle from Galicia (NW Spain), an area with previous records of infection by gastric flukes, were sampled. Diagnostics of trematodosis was developed by using a copromicroscopic probe and an ELISA with excretory/secretory antigens collected from adult Calicophoron daubneyi (Paramphistomidae) specimens. Results were evaluated according intrinsic and extrinsic factors. In the Uruguay, the percentage of cattle passing Paramphistomidae-eggs by faeces was 7% (95% Confidence Interval 5, 10). A significantly higher prevalence of paramphistomosis in the Hereford × Angus cattle (OR = 3.5) was recorded, as observed for the oldest ruminants (>3.5. years). An overall seroprevalence of 29% (25, 34) was obtained by ELISA, with the highest values in the Friesians (OR = 3), the youngest bovines (

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

The sensory attributes and flavor chemistry of grilled beef striploins (M. longissimus lumborum, n = 42) varying widely in marbling from commercial production types typical for Southern Australia were extensively characterized. Striploins from Angus grass-fed yearlings (5.2-9.9% intramuscular fat), Angus grain-finished steers (10.2-14.9%), and Wagyu grass-fed heifers (7.8-17.5%) were evaluated. Inherent differences between samples from grass- and grain-fed Angus cattle were minimal when the intramuscular fat content was above ∼5%. After adjusting for intramuscular fat, Wagyu samples had more intense flavor and higher tenderness and juiciness compared to Angus grass-fed samples. Grilled beef flavor, dairy fat, and sweetness increased with the marbling level, and sourness and astringency decreased. Tenderness and juiciness increased with the marbling level and were correlated with Warner-Bratzler peak force measurements. Trained panel sensory differences in flavor corresponded with increases in aroma volatiles and changes in nonvolatile flavor compounds. Unsaturated fatty acids with potential health benefits (vaccenic, oleic, and rumenic acids) increased with the level of marbling.

The traditional techniques to measure heat production (HP) are calorimetry (direct and indirect) and comparative slaughter. Both methods are expensive and require extensive amounts of time and infrastructure. Infrared thermography (IRT) could be a faster and less expensive alternative to estimate cattle HP. The objective of this project was to evaluate the use of the IRT technique as an indicator of HP in cattle. A total of 24 bulls (12 Nellore and 12 Black Angus) with initial BW of 380 ± 7 kg were used. Initially, 4 animals of each breed were harvested (baseline animals) and simple regressions were developed for each breed from these baseline animals to estimate the initial chemical composition of the remaining bulls. Eight animals of each breed were fed a silage/concentrate diet for ad libitum intake in individual stalls. On the 25th, 50th, and 75th experimental day, infrared thermal images (Fluke Ti 55ft; Fluke Corporation) were taken of each animal's face to access skin and ocular surface temperatures. A metabolism trial was conducted to estimate the ME intake (MEI). After 84 experimental days, the cattle were harvested and retained energy (RE) and HP were calculated. The data were analyzed using the MIXED and REG procedures of SAS adopting a significance level of 0.05. Angus cattle had a greater daily MEI, HP, and skin and eye temperatures than Nellore. We found significant correlations ( ≤ 0.005) between daily HP and maximum ( = 0.65) and average skin temperatures ( = 0.65) and maximum ( = 0.65) and average ocular surface ( = 0.69) temperatures recorded on d 50. Infrared thermography has potential to be used to evaluate HP in cattle.

Improvement in feed conversion efficiency can improve the sustainability of beef cattle production, but genomic selection for feed efficiency affects many underlying molecular networks and physiological traits. This study describes the differences between steer progeny of two influential Angus bulls with divergent genomic predictions for residual feed intake (RFI). Eight steer progeny of each sire were phenotyped for growth and feed intake from 8 mo. of age (average BW 254 kg, with a mean difference between sire groups of 4.8 kg) until slaughter at 14-16 mo. of age (average BW 534 kg, sire group difference of 28.8 kg). Terminal samples from pituitary gland, skeletal muscle, liver, adipose, and duodenum were collected from each steer for transcriptome sequencing. Gene expression networks were derived using partial correlation and information theory (PCIT), including differentially expressed (DE) genes, tissue specific (TS) genes, transcription factors (TF), and genes associated with RFI from a genome-wide association study (GWAS). Relative to progeny of the high RFI sire, progeny of the low RFI sire had -0.56 kg/d finishing period RFI (P = 0.05), -1.08 finishing period feed conversion ratio (P = 0.01), +3.3 kg^0.75 finishing period metabolic mid-weight (MMW; P = 0.04), +28.8 kg final body weight (P = 0.01), -12.9 feed bunk visits per day (P = 0.02) with +0.60 min/visit duration (P = 0.01), and +0.0045 carcass specific gravity (weight in air/weight in air-weight in water, a predictor of carcass fat content; P = 0.03). RNA-seq identified 633 DE genes between sire groups among 17,016 expressed genes. PCIT analysis identified >115,000 significant co-expression correlations between genes and 25 TF hubs, i.e. controllers of clusters of DE, TS, and GWAS SNP genes. Pathway analysis suggests low RFI bull progeny possess heightened gut inflammation and reduced fat deposition. This multi-omics analysis shows how differences in RFI genomic breeding values can impact other traits and gene co-expression networks.

The objectives of this work were to assess alternative linear reaction norm (RN) models for genetic evaluation of Angus cattle in Brazil. That is, we investigated the interaction between genotypes and continuous descriptors of the environmental variation to examine evidence of genotype by environment interaction (G×E) in post-weaning BW gain (PWG) and to compare the environmental sensitivity of national and imported Angus sires. Data were collected by the Brazilian Angus Improvement Program from 1974 to 2005 and consisted of 63,098 records and a pedigree file with 95,896 animals. Six models were implemented using Bayesian inference and compared using the Deviance Information Criterion (DIC). The simplest model was M1, a traditional animal model, which showed the largest DIC and hence the poorest fit when compared with the 4 alternative RN specifications accounting for G×E. In M2, a 2-step procedure was implemented using the contemporary group posterior means of M1 as the environmental gradient, ranging from −92.6 to +265.5 kg. Moreover, the benefits of jointly estimating all parameters in a 1-step approach were demonstrated by M3. Additionally, we extended M3 to allow for residual heteroskedasticity using an exponential function (M4) and the best fitting (smallest DIC) environmental classification model (M5) specification. Finally, M6 added just heteroskedastic residual variance to M1. Heritabilities were less at harsh environments and increased with the improvement of production conditions for all RN models. Rank correlations among genetic merit predictions obtained by M1 and by the best fitting RN models M3 (homoskedastic) and M5 (heteroskedastic) at different environmental levels ranged from 0.79 and 0.81, suggesting biological importance of G×E in Brazilian Angus PWG. These results suggest that selection progress could be optimized by adopting environment-specific genetic merit predictions. The PWG environmental sensitivity of imported North American origin bulls (0.046 ± 0.009) was significantly larger (P < 0.05) than that of local sires (0.012 ± 0.013). Moreover, PWG of progeny of imported sires exceeded that of native sires in medium and superior production levels. On the other hand, Angus cattle locally selected in Brazil tended to be more robust to environmental changes and hence be more suitable when production environments for potential progeny is uncertain.