Development of a multivariable prediction model to identify dairy calves too young to be transported to auction markets in Canada using simple physical examination and body weight.

Calves born on Eastern Canadian dairy farms that are not kept in the herds are traditionally sold through auction markets and are raised for meat purposes such as veal calves. Since February 2020, a new Canadian federal regulation has forbidden calves <9 d old to be sold through auction markets. However, in the absence of a real-time birth registry consultation system, it would be of interest to look for predictors that could be associated with age to allow identification of calves too young to be transported. In the current retrospective cross-sectional study, 1,178 calves with a declared birth date (411 calves aged <9 d old; 34.9%) were assessed in 2 large Québec auction sites. Easy-to-record covariates [body weight (BW), breed phenotype, and presence of an umbilical cord remnant] as well as other clinical signs (umbilical swelling, enlargement, umbilical pain, wet umbilicus, skin tent, sunken eyes, ocular and nasal secretion, and hide cleanliness) were assessed. Two logistic regression models using age as a dichotomous dependent variable (<9 d old vs ≥9 d old) were built. The first model (model 1) considered all covariates, which were selected after univariable analyses and a backward stepwise selection process, whereas a more pragmatic model (model 2) only included the 3 easy-to-record variables (i.e., BW, breed, umbilical cord). Both models had similar accuracy to detect calves <9 d old (sensitivity of 38.4 and 37.5%, and specificity of 85.7 and 84.6% for model 1 and 2, respectively). Model 2 was subsequently more specifically studied as it employs a faster and easier assessment. Decision thresholds were tested for their robustness based on misclassification cost term (MCT) analysis with various prevalence of calves <9 d old and various costs of false-negative:false-positive ratio. Despite statistical significance, model accuracy, even if refined with MCT analysis, was limited at the individual level, showing the limits of using physical signs and BW or their combination as a reliable proxy of age. The sensitivity of these models to find calves <9 d old was not to be used for monitoring compliance with the Canadian federal regulation. The relatively high model specificity may help to use this model as a rule-in test (i.e., targeting positive calves for further investigation) rather than a rule-out test (due to its low sensitivity).

Genome-wide identification and expression profiling analysis of Wnt family genes affecting adipocyte differentiation in cattle.

The Wnt family features conserved glycoproteins that play roles in tissue regeneration, animal development and cell proliferation and differentiation. For its functional diversity and importance, this family has been studied in several species, but not in the Bovinae. Herein we identified 19 Wnt genes in cattle, and seven other species of Bovinae, and described their corresponding protein properties. Phylogenetic analysis clustered the 149 Wnt proteins in Bovinae, and 38 Wnt proteins from the human and mouse into 12 major clades. Wnt genes from the same subfamilies shared similar protein motif compositions and exon-intron patterns. Chromosomal distribution and collinearity analysis revealed that they were conservative in cattle and five species of Bovinae. RNA-seq data analysis indicated that Wnt genes exhibited tissue-specific expression in cattle. qPCR analysis revealed a unique expression pattern of each gene during bovine adipocytes differentiation. Finally, the comprehensive analysis indicated that Wnt2B may regulate adipose differentiation by activating FZD5, which is worthy of further study. Our study presents the first genome-wide study of the Wnt gene family in Bovinae, and lays the foundation for further functional characterization of this family in bovine adipocytes differentiation.

Copy number variation of bovine DYNC1I2 gene is associated with body conformation traits in chinese beef cattle.

Previous, studies have shown that the dynein transporter compound has a role in diseases such as intellectual disability and cerebral malformations. However, the study of CNV in DYNC1I2 gene has not been reported. Q-PCR and data association analysis were used for DYNC1I2 gene copy in this study. In this study, blood samples were collected from five breeds of Chinese cattle (Qingchuan cattle, Xianan cattle, Yunling cattle, Pinan cattle and Guyuan cattle) for DYNC1I2 gene CNV type detection. SPSS 20.0 software and method of ANOVA were used to analyzed the association between types of CNV and growth traits. Results reveal that the distribution of different copy number types in different cattle breeds is different. Association analysis indicate that CNV of DYNC1I2 gene showed a positive effect in cattle growth: in XN cattle, individuals with deletion types showed better performance on height at hip cross (P < 0.05); individuals with duplication types have better performance on body length (P < 0.05) in PN cattle; individuals with deletion types was significantly correlated with chest width and Hucklebone width (P < 0.05) in QC cattle; individuals with duplication types in Yunling cattle were better than the normal types, and there was a significant correlation between copy number variant and chest depth (P < 0.05). The results showed that CNV markers closely related to cattle production traits were detected at DNA level, which could be used as an important candidate molecular marker for marker-assisted selection of growth traits in Chinese cattle, and provided a new research basis for genetics and breeding of Chinese beef cattle.

Molecular prevalence and risk factors associated with tick-borne pathogens in cattle in western Kenya.

BACKGROUND: Tick-borne pathogens (TBPs) are of global importance, especially in sub-Saharan Africa where they represent a major constraint to livestock production. Their association with human disease is also increasingly recognized, signalling their zoonotic importance. It is therefore crucial to investigate TBPs prevalence in livestock populations and the factors associated with their presence. We set out to identify TBPs present in cattle and to determine associated risk factors in western Kenya, where smallholder livestock production is important for subsistence and market-driven income. RESULTS: Tick-borne pathogen infections in blood samples collected from cattle at livestock markets and slaughterhouses between May 2017 and January 2019 were identified by high-resolution melting analysis and sequencing of PCR products of genus-specific primers. Of the 422 cattle sampled, 30.1% (127/422) were infected with at least one TBP, while 8.8% (37/422) had dual infections. Anaplasma spp. (19.7%) were the most prevalent, followed by Theileria (12.3%), Ehrlichia (6.6%), and Babesia (0.2%) spp. Sequence analysis of the TBPs revealed them to be Anaplasma platys-like organisms (13.5%), Theileria velifera (7.4%), Anaplasma marginale (4.9%), Theileria mutans (3.1%), Theileria parva (1.6%), and Babesia bigemina (0.2%). Ehrlichia ruminantium, Rickettsia spp., and arboviruses were not detected. Exotic breeds of cattle were more likely to be infected with A. marginale compared to local breeds (OR: 7.99, 95% CI: 3.04-22.02, p <  0.001). Presence of ticks was a significant predictor for Anaplasma spp. (OR: 2.18, 95% CI: 1.32-3.69, p = 0.003) and Ehrlichia spp. (OR: 2.79, 95% CI: 1.22-7.23, p = 0.022) infection. Cattle sampled at slaughterhouses were more likely to be positive for Anaplasma spp. (OR: 1.64, 95% CI: 1.01-2.70, p = 0.048) and A. marginale (OR: 3.84, 95% CI: 1.43-12.21, p = 0.012), compared to those sampled at livestock markets. CONCLUSION: This study reports TBP prevalence and associated risk factors in western Kenya, factors which are key to informing surveillance and control measures.

BoLA-DRB3 gene haplotypes show divergence in native Sudanese cattle from taurine and indicine breeds.

Autochthonous Sudanese cattle breeds, namely Baggara for beef and Butana and Kenana for dairy, are characterized by their adaptive characteristics and high performance in hot and dry agro-ecosystems. They are thus used largely by nomadic and semi-nomadic pastoralists. We analyzed the diversity and genetic structure of the BoLA-DRB3 gene, a genetic locus linked to the immune response, for the indigenous cattle of Sudan and in the context of the global cattle repository. Blood samples (n = 225) were taken from three indigenous breeds (Baggara; n = 113, Butana; n = 60 and Kenana; n = 52) distributed across six regions of Sudan. Nucleotide sequences were genotyped using the sequence-based typing method. We describe 53 alleles, including seven novel alleles. Principal component analysis (PCA) of the protein pockets implicated in the antigen-binding function of the MHC complex revealed that pockets 4 and 9 (respectively) differentiate Kenana-Baggara and Kenana-Butana breeds from other breeds. Venn analysis of Sudanese, Southeast Asian, European and American cattle breeds with 115 alleles showed 14 were unique to Sudanese breeds. Gene frequency distributions of Baggara cattle showed an even distribution suggesting balancing selection, while the selection index (ω) revealed the presence of diversifying selection in several amino acid sites along the BoLA-DRB3 exon 2 of these native breeds. The results of several PCA were in agreement with clustering patterns observed on the neighbor joining (NJ) trees. These results provide insight into their high survival rate for different tropical diseases and their reproductive capacity in Sudan's harsh environment.

Evolution of tissue and developmental specificity of transcription start sites in Bos taurus indicus.

To further the understanding of the evolution of transcriptional regulation, we profiled genome-wide transcriptional start sites (TSSs) in two sub-species, Bos taurus taurus and Bos taurus indicus, that diverged approximately 500,000 years ago. Evolutionary and developmental-stage differences in TSSs were detected across the sub-species, including translocation of dominant TSS and changes in TSS distribution. The 16% of all SNPs located in significant differentially used TSS clusters across sub-species had significant shifts in allele frequency (472 SNPs), indicating they may have been subject to selection. In spleen and muscle, a higher relative TSS expression was observed in Bos indicus than Bos taurus for all heat shock protein genes, which may be responsible for the tropical adaptation of Bos indicus.

Single nucleotide polymorphisms of leptin gene in five Ethiopian indigenous cattle breeds and the Korean Hanwoo breed.

Considering the escalating number of scientific reports on the association between the leptin gene and diverse physiological traits and performance of cattle populations, this study was directed towards identifying SNPs in the leptin gene among five indigenous cattle breeds of Ethiopia. DNA samples were extracted from the nasal swabs of the Ethiopian indigenous cattle breeds: Arsi (n = 18), Horro (n = 20), Begait (n = 21), Boran (n = 19), and Fogera (n = 17) and the Korean Hanwoo (a representative taurine breed) (n = 20), followed by PCR amplification of exon 2 and exon 3 regions of the leptin gene and sequence analysis of the PCR products. Five SNPs, two (generating missense mutations) on exon 2 and three (generating silent mutations) on exon 3 regions, were explicated in this study. Allele frequency and genotype frequency distribution pertaining to the SNPs were recorded for the studied cattle breeds besides the minor allele frequency and deviation from the Hardy-Weinberg equilibrium. Positive FIS index values were recorded for all the markers except SNP2, illustrative of heterozygote deficiency. MEGA X software-based evolutionary divergence analysis of the phylogenetic tree based on the SNP data revealed that the large-sized breeds, Hanwoo, Begait, Boran, and Fogera, were more closely clustered compared to the small-sized Arsi breed. Among the seven haplotypes documented from the various breeds, sequence analysis was suggestive of haplotypes 1 and 2 to be ancestral haplotypes for the leptin gene. This study is envisaged to accelerate molecular breeding programs for the genetic improvement of the Ethiopian cattle breeds.

SNPs with intermediate minor allele frequencies facilitate accurate breed assignment of Indian Tharparkar cattle.

Tharparkar cattle breed is widely known for its superior milch quality and hardiness attributes. This study aimed to develop an ultra-low density breed-specific single nucleotide polymorphism (SNP) genotype panel to accurately quantify Tharparkar populations in biological samples. In this study, we selected and genotyped 72 Tharparkar animals randomly from Cattle & Buffalo Farm of IVRI, India. This Bovine SNP50 BeadChip genotypic datum was merged with the online data from six indigenous cattle breeds and five taurine breeds. Here, we used a combination of pre-selection statistics and the MAF-LD method developed in our laboratory to analyze the genotypic data obtained from 317 individuals of 12 distinct breeds to identify breed-informative SNPs for the selection of Tharparkar cattle. This methodology identified 63 unique Tharparkar-specific SNPs near intermediate gene frequencies. We report several informative SNPs in genes/QTL regions affecting phenotypes or production traits that might differentiate the Tharparkar breed.

Comparative analysis of five different methods to design a breed-specific SNP panel for cattle.

Single nucleotide polymorphisms (SNPs) have now replaced microsatellite markers in several species for various genetic investigations like parentage assignment, genetic breed composition, assessment for individuality and, most popularly, as a useful tool in genomic selection. However, such a resource, which can offer to assist breed identification in a cost-effective manner is still not explored in cattle breeding programs. In our study, we have tried to describe methods for reducing the number of SNPs to develop a breed-specific panel. We have used SNP data from Dryad open public access repository. Starting from a global dataset of 178 animals belonging to 10 different breeds, we selected five panels each comprising of similar number of SNPs using different methods i.e., Delta, Pairwise Wright's FST, informativeness for assignment, frequent item feature selection (FIFS) and minor allele frequency-linkage disequilibrium (MAF-LD) based method. MAF-LD based method has been recently developed by us for construction of breed-specific SNP panels. The STRUCTURE software analysis of MAF-LD based method showed appropriate clustering in comparison to other panels. Later, the panel of 591 breed-specific SNPs was called to their respective breeds using Venny 2.1.0 and UGent web tools software. Breed-specific SNPs were later annotated by using various Bioinformatics softwares.

Heifer management characterization in dairy herds from the west of Buenos Aires, Argentina / Caracterização da gestão de novilhas em rebanhos leiteiros do oeste de Buenos Aires, Argentina

The replacement program in a dairy farm represents the second or third largest cost in a dairy operation. This study aimed to characterize and typify the practices related to the dairy heifer replacement program and describe the growth, development, and health parameters during this period in commercial dairy herds in Trenque Lauquen. A cross-sectional observational study was carried out, including 54 randomly selected dairy farms that were visited once to collect data about facilities and management through a semi-structured survey. Cluster and principal coordinates analysis were applied to classify the farms based on all variables collected, grouped in four main areas: pre-fresh cows, colostrum management, pre-weaning calf 's management, and personnel. Additionally, growth, development, and health status were also recorded and described for calves and breeding heifers. Two similar-sized farm clusters were identified with differences in management and facilities in different areas of calves rearing. In one cluster there was a greater proportion of farms having a pre-fresh group, implementing appropriate health (colostrum, vaccination) and feeding management. Also, differences in personnel and technical support were relevant. The estimated body gain was 452 and 774 g/d for calves younger or older than 60 d of age, respectively. The age and weight farm averages in breeding heifers were 21.0 mo (range: 16.7-27.5) and 416.3 kg (range: 336.7-519.3), respectively. Diarrhea and respiratory affections were the major problems in pre-weaning calves and heifer rearing, respectively. The median mortality was 7.3, 7.6, and 2.9% at the calving, pre-weaning, and heifer rearing period, respectively. The results showed an improvement opportunity for producers, the design of precise and high impact programs that could lead to an improved replacement program.(AU)

Nos rebanhos leiteiros, o programa de reposição representa o segundo ou o terceiro maior custo da atividade de produção de leite. O objetivo do presente trabalho foi caracterizar e tipificar as práticas relacionadas ao programa de reposição de novilhas leiteiras e descrever o crescimento, desenvolvimento e parâmetros de saúde durante este período em rebanhos leiteiros comerciais localizados em Trenque Lauquen, oeste de Buenos Aires, Argentina. Foi realizado um estudo observacional transversal incluindo 54 fazendas de produção de leite selecionadas ao acaso e visitadas uma única vez para a colheita de dados relacionados a instalações e manejo empregando-se um questionário semi-estruturado. Foi efetuada a análise dos agrupamentos e das coordenadas principais para classificar as fazendas com base em todas as variáveis colhidas e agrupadas em quatro principais áreas: vacas pré-parto, manejo de colostro, manejo pré-desmame de bezerros e recursos humanos. Os dados referentes ao crescimento, desenvolvimento e estado de saúde dos animais também foram registrados e descritos para bezerros e novilhas. Dois grupos de fazendas de tamanho semelhante foram identificados com diferenças no manejo e instalações em distintas áreas de recria de bezerros. Em um grupo houve uma maior proporção de fazendas que tinham um grupo de vacas pré-parto, com implementação de adequado manejo de saúde (colostro, vacinações) e manejo alimentar. Também foram relevantes as diferenças em termos de pessoal e suporte técnico. O ganho de peso estimado foi de 452 e 774 gramas por dia, respectivamente, para os bezerros jovens e os com idade superior a 60 dias. As médias das fazendas da idade e do peso das novilhas de reprodução foram, respectivamente, 21,0 meses (variação de 16,7 a 27,5) e 416,3 kg (variação de 336,7 a 519,3). A diarreia e as afecções respiratórias foram os maiores problemas de saúde, respectivamente, nos bezerros em pré-desmama e novilhas em recria. A média de mortalidade foi de 7,3; 7,6 e 2,9%, respectivamente, ao parto, na pré-desmama e durante a recria de novilhas. Os resultados obtidos demonstraram a existência de oportunidades de melhoria para os produtores, com o delineamento de programas precisos e de alto impacto que poderão propiciar um programa de reposição aprimorado.(AU)

Ancient genomes reveal tropical bovid species in the Tibetan Plateau contributed to the prevalence of hunting game until the late Neolithic.

Local wild bovids have been determined to be important prey on the northeastern Tibetan Plateau (NETP), where hunting game was a major subsistence strategy until the late Neolithic, when farming lifestyles dominated in the neighboring Loess Plateau. However, the species affiliation and population ecology of these prehistoric wild bovids in the prehistoric NETP remain unknown. Ancient DNA (aDNA) analysis is highly informative in decoding this puzzle. Here, we applied aDNA analysis to fragmented bovid and rhinoceros specimens dating ∼5,200 y B.P. from the Neolithic site of Shannashuzha located in the marginal area of the NETP. Utilizing both whole genomes and mitochondrial DNA, our results demonstrate that the range of the present-day tropical gaur (Bos gaurus) extended as far north as the margins of the NETP during the late Neolithic from ∼29°N to ∼34°N. Furthermore, comparative analysis with zooarchaeological and paleoclimatic evidence indicated that a high summer temperature in the late Neolithic might have facilitated the northward expansion of tropical animals (at least gaur and Sumatran-like rhinoceros) to the NETP. This enriched the diversity of wildlife, thus providing abundant hunting resources for humans and facilitating the exploration of the Tibetan Plateau as one of the last habitats for hunting game in East Asia.

Comparative analyses of copy number variations between Bos taurus and Bos indicus.

BACKGROUND: Bos taurus and Bos indicus are two main sub-species of cattle. However, the differential copy number variations (CNVs) between them are not yet well studied. RESULTS: Based on the new high-quality cattle reference genome ARS-UCD1.2, we identified 13,234 non-redundant CNV regions (CNVRs) from 73 animals of 10 cattle breeds (4 Bos taurus and 6 Bos indicus), by integrating three detection strategies. While 6990 CNVRs (52.82%) were shared by Bos taurus and Bos indicus, large CNV differences were discovered between them and these differences could be used to successfully separate animals into two subspecies. We found that 2212 and 538 genes uniquely overlapped with either indicine-specific CNVRs and or taurine-specific CNVRs, respectively. Based on FST, we detected 16 candidate lineage-differential CNV segments (top 0.1%) under selection, which overlapped with eight genes (CTNNA1, ENSBTAG00000004415, PKN2, BMPER, PDE1C, DNAJC18, MUSK, and PLCXD3). Moreover, we obtained 1.74 Mbp indicine-specific sequences, which could only be mapped on the Bos indicus reference genome UOA_Brahman_1. We found these sequences and their associated genes were related to heat resistance, lipid and ATP metabolic process, and muscle development under selection. We further analyzed and validated the top significant lineage-differential CNV. This CNV overlapped genes related to muscle cell differentiation, which might be generated from a retropseudogene of CTH but was deleted along Bos indicus lineage. CONCLUSIONS: This study presents a genome wide CNV comparison between Bos taurus and Bos indicus. It supplied essential genome diversity information for understanding of adaptation and phenotype differences between the Bos taurus and Bos indicus populations.

Whole genome analysis of water buffalo and global cattle breeds highlights convergent signatures of domestication.

More people globally depend on the water buffalo than any other domesticated species, and as the most closely related domesticated species to cattle they can provide important insights into the shared evolutionary basis of domestication. Here, we sequence the genomes of 79 water buffalo across seven breeds and compare patterns of between breed selective sweeps with those seen for 294 cattle genomes representing 13 global breeds. The genomic regions under selection between cattle breeds significantly overlap regions linked to stature in human genetic studies, with a disproportionate number of these loci also shown to be under selection between water buffalo breeds. Investigation of potential functional variants in the water buffalo genome identifies a rare example of convergent domestication down to the same mutation having independently occurred and been selected for across domesticated species. Cross-species comparisons of recent selective sweeps can consequently help identify and refine important loci linked to domestication.

Grouping crossbred Holstein x Gyr heifers according to different feed efficiency indexes and its effects on energy and nitrogen partitioning, blood metabolic variables and gas exchanges.

The objectives of this study were: i) to classify animals into groups of high and low feed efficiency (FE) using three FE indexes (Residual feed intake (RFI), Residual weight gain (RG) and Feed conversion efficiency (FCE)), and ii) to evaluate whether crossbreed Holstein x Gyr heifers divergent for FE indexes exhibit differences in nutrient intake and digestibility, energy partitioning, heat production, methane emissions, nitrogen partitioning and blood parameters. Thirty-five heifers were housed in a tie-stall, received ad libitum TMR (75:25, corn silage: concentrate) and were ranked and classified into high (HE) or low efficiency (LE) for RFI, RG and FCE. The number of animals for each HE group were 13 (< 0.5 standard deviation (SD) for RFI, 11 for RG and 11 for FCE (> 0.5 SD) and for the LE were 10 (> 0.5 SD) for RFI, 11 for RG and 12 for FCE (< 0.5 SD). Gas exchanges (O2 consumption, CO2 and CH4 production) in open-circuit respiratory chambers and whole tract digestibility trial was performed. A completely randomized experimental design was used and the data were analyzed by ANOVA and correlation study. High efficiency animals for RFI produced less CO2, consumed less O2 and had lower heat production (HP). Methane production was positively correlated with RFI. High efficiency RG had higher O2 consumption and CO2 production in relation to LE-RG. High efficiency FCE had greater NFC digestibility, higher positive energy balance (EB) and excreted (11.4 g/d) less nitrogen in urine. High efficiency RG and FCE groups emitted less CH4 per kg of weight gain than LE animals. Animals HE for RFI and FCE had lower ß-hydroxybutyrate and higher glucose concentrations, respectively. The differences in intake, digestibility, energy and nitrogen partition, CH4 emission, blood metabolic variables and heat production between the HE and LE groups varied according to the efficiency indexes adopted. The HP (kcal/d/BW0.75) was lower for HE animals for RFI and FCE indexes.

The genetic heritage of Alpine local cattle breeds using genomic SNP data.

BACKGROUND: Assessment of genetic diversity and population structure provides important control metrics to avoid genetic erosion, inbreeding depression and crossbreeding between exotic and locally-adapted cattle breeds since these events can have deleterious consequences and eventually lead to extinction. Historically, the Alpine Arc represents an important pocket of cattle biodiversity with a large number of autochthonous breeds that provide a fundamental source of income for the entire regional economy. By using genotype data from medium-density single nucleotide polymorphism (SNP) arrays, we performed a genome-wide comparative study of 23 cattle populations from the Alpine Arc and three cosmopolitan breeds. RESULTS: After filtering, we obtained a final genotyping dataset consisting of 30,176 SNPs for 711 individuals. The local breeds showed high or intermediate values of genetic diversity compared to the highly selected cosmopolitan breeds. Patterns of genetic differentiation, multidimensional scaling, admixture analysis and the constructed phylogenetic tree showed convergence, which indicates the presence of gene flow among the breeds according to both geographic origin and historical background. Among the most differentiated breeds, we identified the modern Brown cattle. In spite of admixture events, several local breeds have preserved distinctive characteristics, which is probably due to differences in genetic origin and geographic location. CONCLUSIONS: This study represents one of the most comprehensive genome-wide analysis of the Alpine cattle breeds to date. Using such a large dataset that includes the majority of the local breeds found in this region, allowed us to expand knowledge on the evaluation and status of Alpine cattle biodiversity. Our results indicate that although many of the analyzed local breeds are listed as endangered, they still harbor a large amount of genetic diversity, even when compared to some cosmopolitan breeds. This finding, together with the reconstruction of the phylogeny and the relationships between these Alpine Arc cattle breeds, provide crucial insights not only into the improvement of genetic stocks but also into the implementation of future conservation strategies.

Effects of vulvar width and antral follicle count on oocyte quality, in vitro embryo production and pregnancy rate in Bos taurus taurus and Bos taurus indicus cows.

It was hypothesized that Brahman cows have greater in vitro embryo production than Simmental cows, and that regardless of breed, antral follicle count (AFC) and vulvar width (VW) are positively associated with oocyte quality, embryo number and pregnancy rate. Brahman (Bos taurus indicus, n = 184) and Simmental (Bos taurus taurus, n = 99) cows were classified as having a large AFC (Brahman: ≥50, Simmental: ≥25); intermediate AFC (Brahman: >30 and ≤49; Simmental: >16 and <24) and small AFC (Brahman: <30, Simmental: ≤15). The VW was considered to be large (Brahman: >123 mm, Simmental: >80 mm); intermediate (Brahman: >102 mm and ≤123 mm; Simmental: >65 mm and ≤80 mm) and small (Brahman: ≤102 mm and Simmental: ≤65 mm). For each group of cows, ovum pick up, oocyte in vitro maturation, fertilization and embryo culture were performed. Embryo transfers were subsequently performed and pregnancy rate was evaluated. Brahman cows had a larger number of viable oocytes, greater efficiency of embryo production and greater pregnancy rate (P < 0.05) than Simmental cows. Pregnancy percentages in Simmental cows with a small AFC were greater than those cows with an intermediate and large AFC. With the Brahman cows, there was no difference in pregnancy rate among the cows with different AFC classifications. In contrast to Simmental cows, Brahman cows with an intermediate VW had a greater pregnancy percentage than those with a small and large AFC. In conclusion, Brahman cows have a larger AFC, number of viable oocytes, and pregnancy rate than Simmental cows.

In silico validation of pooled genotyping strategies for genomic evaluation in Angus cattle.

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.

Breed- and trait-specific associations define the genetic architecture of calving performance traits in cattle.

Reducing the incidence of both the degree of assistance required at calving, as well as the extent of perinatal mortality (PM) has both economic and societal benefits. The existence of heritable genetic variability in both traits signifies the presence of underlying genomic variability. The objective of the present study was to locate regions of the genome, and by extension putative genes and mutations, that are likely to be underpinning the genetic variability in direct calving difficulty (DCD), maternal calving difficulty (MCD), and PM. Imputed whole-genome single-nucleotide polymorphism (SNP) data on up to 8,304 Angus (AA), 17,175 Charolais (CH), 16,794 Limousin (LM), and 18,474 Holstein-Friesian (HF) sires representing 5,866,712 calving events from descendants were used. Several putative quantitative trait loci (QTL) regions associated with calving performance both within and across dairy and beef breeds were identified, although the majority were both breed- and trait-specific. QTL surrounding and encompassing the myostatin (MSTN) gene were associated (P < 5 × 10-8) with DCD and PM in both the CH and LM populations. The well-known Q204X mutation was the fifth strongest association with DCD in the CH population and accounted for 5.09% of the genetic variance in DCD. In contrast, none of the 259 segregating variants in MSTN were associated (P > × 10-6) with DCD in the LM population but a genomic region 617 kb downstream of MSTN was associated (P < 5 × 10-8). The genetic architecture for DCD differed in the HF population relative to the CH and LM, where two QTL encompassing ZNF613 on Bos taurus autosome (BTA)18 and PLAG1 on BTA14 were identified in the former. Pleiotropic SNP associated with all three calving performance traits were also identified in the three beef breeds; 5 SNP were pleiotropic in AA, 116 in LM, and 882 in CH but no SNP was associated with more than one trait within the HF population. The majority of these pleiotropic SNP were on BTA2 surrounding MSTN and were associated with both DCD and PM. Multiple previously reported, but also novel QTL, associated with calving performance were detected in this large study. These also included QTL regions harboring SNP with the same direction of allele substitution effect for both DCD and MCD thus contributing to a more effective simultaneous selection for both traits.