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1.
Front Genet ; 13: 951087, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35910233

RESUMO

Genomic imprinting is an epigenetic phenomenon defined as the silencing of an allele, at least partially, at a given locus based on the sex of the transmitting parent. The objective of the present study was to detect the presence of SNP-phenotype imprinting associations for carcass weight (CW), carcass conformation (CC) and carcass fat (CF) in cattle. The data used comprised carcass data, along with imputed, high-density genotype data on 618,837 single nucleotide polymorphisms (SNPs) from 23,687 cattle; all animal genotypes were phased with respect to parent of origin. Based on the phased genotypes and a series of single-locus linear models, 24, 339, and 316 SNPs demonstrated imprinting associations with CW, CC, and CF, respectively. Regardless of the trait in question, no known imprinted gene was located within 0.5 Mb of the SNPs demonstrating imprinting associations in the present study. Since all imprinting associations detected herein were at novel loci, further investigation of these regions may be warranted. Nonetheless, knowledge of these associations might be useful for improving the accuracy of genomic evaluations for these traits, as well as mate allocations systems to exploit the effects of genomic imprinting.

2.
Sci Rep ; 12(1): 7666, 2022 05 10.
Artigo em Inglês | MEDLINE | ID: mdl-35538182

RESUMO

Respiratory viruses including Respiratory Syncytial Virus, influenza virus and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cause serious and sometimes fatal disease in thousands of people annually. Understanding virus propagation dynamics within the respiratory system is critical because new insights will increase our understanding of virus pathogenesis and enable infection patterns to be more predictable in vivo, which will enhance our ability to target vaccine and drug delivery. This study presents a computational model of virus propagation within the respiratory tract network. The model includes the generation network branch structure of the respiratory tract, biophysical and infectivity properties of the virus, as well as air flow models that aid the circulation of the virus particles. As a proof of principle, the model was applied to SARS-CoV-2 by integrating data about its replication-cycle, as well as the density of Angiotensin Converting Enzyme expressing cells along the respiratory tract network. Using real-world physiological data associated with factors such as the respiratory rate, the immune response and virus load that is inhaled, the model can improve our understanding of the concentration and spatiotemporal dynamics of the virus. We collected experimental data from a number of studies and integrated them with the model in order to show in silico how the virus load propagates along the respiratory network branches.


Assuntos
COVID-19 , SARS-CoV-2 , Humanos , Sistema Respiratório , Vírion
4.
J Anim Breed Genet ; 2022 Apr 29.
Artigo em Inglês | MEDLINE | ID: mdl-35485246

RESUMO

Considerable resources are required to routinely measure detailed milk compositional traits. Hence, an insufficient volume of phenotypic data can hinder genetic progress in these traits within dairy cow breeding programmes. The objective of the present study was to quantify the opportunities for breeding for improved milk protein and free amino acid (FAA) composition by exploiting mid-infrared spectroscopy (MIRS) predictions routinely recorded from milk samples. Genetic parameters for protein fractions and FAA composition were estimated using 134,546 test-day records from 16,166 lactations on 9,572 cows using linear mixed models. Heritability of MIRS-predicted protein fractions ranged from 0.19 (α-lactalbumin) to 0.55 (ß-lactoglobulin A), while heritability of MIRS-predicted FAA ranged from 0.08 for glycine to 0.29 for glutamic acid. Genetic correlations among the MIRS-predicted FAA were moderate to strong ranging from -0.44 (aspartic acid and lysine) to 0.97 (glutamic acid and total FAA). Adjustment of the genetic correlations for the genetic merit of 24-h milk yield did not greatly affect the correlations. Results from the current study highlight the presence of exploitable genetic variation for both protein fractions and FAA in dairy cow milk. Besides, the direction of genetic correlations reveals that breeding programmes directly selecting for greater milk protein concentration carry with them favourable improvement in casein and whey fractions.

5.
Front Genet ; 13: 789270, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35281838

RESUMO

The objective of the present study was to quantify the association between both pedigree and genome-based measures of global heterozygosity and carcass traits, and to identify single nucleotide polymorphisms (SNPs) exhibiting non-additive associations with these traits. The carcass traits of interest were carcass weight (CW), carcass conformation (CC) and carcass fat (CF). To define the genome-based measures of heterozygosity, and to quantify the non-additive associations between SNPs and the carcass traits, imputed, high-density genotype data, comprising of 619,158 SNPs, from 27,213 cattle were used. The correlations between the pedigree-based heterosis coefficient and the three defined genomic measures of heterozygosity ranged from 0.18 to 0.76. The associations between the different measures of heterozygosity and the carcass traits were biologically small, with positive associations for CW and CC, and negative associations for CF. Furthermore, even after accounting for the pedigree-based heterosis coefficient of an animal, part of the remaining variability in some of the carcass traits could be captured by a genomic heterozygosity measure. This signifies that the inclusion of both a heterosis coefficient based on pedigree information and a genome-based measure of heterozygosity could be beneficial to limiting bias in predicting additive genetic merit. Finally, one SNP located on Bos taurus (BTA) chromosome number 5 demonstrated a non-additive association with CW. Furthermore, 182 SNPs (180 SNPs on BTA 2 and two SNPs on BTA 21) demonstrated a non-additive association with CC, while 231 SNPs located on BTA 2, 5, 11, 13, 14, 18, 19 and 21 demonstrated a non-additive association with CF. Results demonstrate that heterozygosity both at a global level and at the level of individual loci contribute little to the variability in carcass merit.

6.
J Anim Sci ; 99(12)2021 Dec 01.
Artigo em Inglês | MEDLINE | ID: mdl-34850954

RESUMO

In growing cattle, the phenotypic and genetic relationships between feeding behavior and both live animal ultrasound measures and subsequent carcass merit are generally poorly characterized. The objective of the current study was to quantify the phenotypic and genetic associations between a plethora of feeding behavior traits with both pre-slaughter ultrasound traits and post-slaughter carcass credentials in crossbred Bos taurus cattle. Carcass data were available on 3,146 young bulls, steers, and heifers, of which 2,795 and 2,445 also had records for pre-slaughter ultrasound muscle depth and intramuscular fat percentage, respectively; a total of 1,548 steers and heifers had information on all of the feeding behavior, ultrasound, and carcass traits. Young bulls were fed concentrates, while steers and heifers were fed a total mixed ration. Feeding behavior traits were defined based on individual feed events or meal events (i.e., individual feed events grouped into meals). Animal linear mixed models were used to estimate (co)variance components. Phenotypic correlations between feeding behavior and both ultrasound and carcass traits were generally weak and not different from zero, although there were phenotypic correlations of 0.40, 0.26, and 0.37 between carcass weight and feeding rate, energy intake per feed event, and energy intake per meal, respectively. Genetically, cattle that had heavier carcass weights, better carcass conformation, or a higher dressing percentage fed for a shorter time per day (genetic correlations [±SE] of -0.46 ± 0.12, -0.39 ± 0.11, and -0.50 ± 0.10, respectively). Genetic correlations of 0.43 ± 0.12 and 0.68 ± 0.13 were estimated between dressing difference (i.e., differential between live weight pre-slaughter and carcass weight) and energy intake per feed event and energy intake per meal, respectively. Neither intramuscular fat percentage measured on live animals nor carcass fat score (i.e., a measure of subcutaneous fat cover of the carcass) was genetically associated with any of the feeding behavior traits. The genetic associations between some feeding behavior traits and both ultrasound and carcass traits herein suggested that indirect responses in the feeding behavior of growing cattle from selection for improved carcass merit would be expected. Such changes in feeding behavior patterns in cattle may be reduced by measuring and including feeding behavior in a multiple-trait selection index alongside carcass traits.


Assuntos
Ingestão de Energia , Comportamento Alimentar , Animais , Composição Corporal/genética , Bovinos/genética , Feminino , Modelos Lineares , Masculino , Carne , Fenótipo , Ultrassonografia/veterinária
7.
Front Vet Sci ; 8: 731894, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34722698

RESUMO

Understanding dairy producer mindset in service sire selection can provide useful information for different junctures along the commercial and extension animal breeding chain. It can aid the targeted marketing of bulls based on farm production systems but also provide useful information for delivering bespoke extension services. The objective of the present study was to examine if differences exist among dairy producers in their choice of dairy and beef service sires depending on the life stage at which the surplus progeny generated from such matings exit the dairy farm. This was predominantly based on evaluating the breed of beef sires used but also their genetic merit for calving difficulty and carcass traits, namely, carcass weight, conformation, and fat score; differences in genetic merit among dairy sires as well as among the dairy cows themselves were also considered. The objective was accomplished through the cross-sectional analyses of progeny fate data from 1,092,403 progeny born in 4,117 Irish dairy herds. Herd-years were categorized into one of four systems based on when the surplus progeny exited the dairy farm: (1) calves sold <70 days of age, (2) cattle sold as yearlings between 250 and 450 days of age, (3) prime cattle sold for finishing (slaughtered between 8 and 120 days of exiting the dairy farm), or (4) prime cattle sold for immediate slaughter (i.e., slaughtered within 7 days of exiting the dairy farm). The mean genetic merit of both the cows and service sires used across the four different systems was estimated using linear mixed models. Of the beef service sires used in herds that sold their surplus progeny as calves, their mean predicted transmitting ability for carcass weight and carcass conformation score was just 2.00 kg and 0.11 scores [scale of 1 (poor) to 15 (excellent)] inferior to the beef service sires used in herds that sold their surplus progeny as prime cattle for immediate slaughter. Similar trends, albeit of smaller magnitude, were evident when comparing the genetic merit of the dairy service sires used in those systems. Cows in herds that sold their surplus progeny as calves were genetically less likely to incur dystocia as well as to have lighter, less-conformed, and leaner carcasses than cows in herds that sold their surplus progeny post-weaning. Hence, results from the present study suggest that diversity in herd strategy regarding when surplus progeny exit the herd influences service sire selection choices in respect of genetic merit for dystocia and carcass attributes. That said, the biological difference based on the current pool of available service sires is small relative to the dairy producers that sell their surplus progeny as young calves; when expressed on a per standard deviation in genetic merit of the beef service sires used across all herds, the difference between extreme systems was, nonetheless, approximately half a standard deviation for carcass weight and conformation.

8.
Front Genet ; 12: 761503, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34795696

RESUMO

The relative contributions of both copy number variants (CNVs) and single nucleotide polymorphisms (SNPs) to the additive genetic variance of carcass traits in cattle is not well understood. A detailed understanding of the relative importance of CNVs in cattle may have implications for study design of both genomic predictions and genome-wide association studies. The first objective of the present study was to quantify the relative contributions of CNV data and SNP genotype data to the additive genetic variance of carcass weight, fat, and conformation for 945 Charolais, 923 Holstein-Friesian, and 974 Limousin sires. The second objective was to jointly consider SNP and CNV data in a least absolute selection and shrinkage operator (LASSO) regression model to identify genomic regions associated with carcass weight, fat, and conformation within each of the three breeds separately. A genomic relationship matrix (GRM) based on just CNV data did not capture any variance in the three carcass traits when jointly evaluated with a SNP-derived GRM. In the LASSO regression analysis, a total of 987 SNPs and 18 CNVs were associated with at least one of the three carcass traits in at least one of the three breeds. The quantitative trait loci (QTLs) corresponding to the associated SNPs and CNVs overlapped with several candidate genes including previously reported candidate genes such as MSTN and RSAD2, and several potential novel candidate genes such as ACTN2 and THOC1. The results of the LASSO regression analysis demonstrated that CNVs can be used to detect associations with carcass traits which were not detected using the set of SNPs available in the present study. Therefore, the CNVs and SNPs available in the present study were not redundant forms of genomic data.

9.
J Anim Sci ; 99(12)2021 Dec 01.
Artigo em Inglês | MEDLINE | ID: mdl-34730184

RESUMO

The identification of different meat cuts for labeling and quality control on production lines is still largely a manual process. As a result, it is a labor-intensive exercise with the potential for not only error but also bacterial cross-contamination. Artificial intelligence is used in many disciplines to identify objects within images, but these approaches usually require a considerable volume of images for training and validation. The objective of this study was to identify five different meat cuts from images and weights collected by a trained operator within the working environment of a commercial Irish beef plant. Individual cut images and weights from 7,987 meats cuts extracted from semimembranosus muscles (i.e., Topside muscle), post editing, were available. A variety of classical neural networks and a novel Ensemble machine learning approaches were then tasked with identifying each individual meat cut; performance of the approaches was dictated by accuracy (the percentage of correct predictions), precision (the ratio of correctly predicted objects relative to the number of objects identified as positive), and recall (also known as true positive rate or sensitivity). A novel Ensemble approach outperformed a selection of the classical neural networks including convolutional neural network and residual network. The accuracy, precision, and recall for the novel Ensemble method were 99.13%, 99.00%, and 98.00%, respectively, while that of the next best method were 98.00%, 98.00%, and 95.00%, respectively. The Ensemble approach, which requires relatively few gold-standard measures, can readily be deployed under normal abattoir conditions; the strategy could also be evaluated in the cuts from other primals or indeed other species.


Assuntos
Inteligência Artificial , Músculos Isquiossurais , Animais , Bovinos , Aprendizado de Máquina , Carne , Redes Neurais de Computação
10.
J Anim Sci ; 99(11)2021 Nov 01.
Artigo em Inglês | MEDLINE | ID: mdl-34673943

RESUMO

The objectives of the present study were to estimate genetic parameters for several feeding behavior traits in growing cattle, as well as the genetic associations among and between feeding behavior and both performance and feed efficiency traits. An additional objective was to investigate the use of feeding behavior traits as predictors of genetic merit for feed intake. Feed intake and live-weight data on 6,088 growing cattle were used of which 4,672 had ultrasound data and 1,548 had feeding behavior data. Feeding behavior traits were defined based on individual feed events or meal events (where individual feed events were grouped into meals). Univariate and bivariate animal linear mixed models were used to estimate (co)variance components. Heritability estimates (± SE) for the feeding behavior traits ranged from 0.19 ± 0.08 for meals per day to 0.61 ± 0.10 for feeding time per day. The coefficient of genetic variation per trait varied from 5% for meals per day to 22% for the duration of each feed event. Genetically heavier cattle, those with a higher daily energy intake (MEI), or those that grew faster had a faster feeding rate, as well as a greater energy intake per feed event and per meal. Better daily feed efficiency (i.e., lower residual energy intake) was genetically associated with both a shorter feeding time per day and shorter meal time per day. In a validation population of 321 steers and heifers, the ability of estimated breeding values (EBV) for MEI to predict (adjusted) phenotypic MEI was demonstrated; EBVs for MEI were estimated using multi-trait models with different sets of predictor traits such as liveweight and/or feeding behaviors. The correlation (± SE) between phenotypic MEI and EBV for MEI marginally improved (P < 0.001) from 0.64 ± 0.03 to 0.68 ± 0.03 when feeding behavior phenotypes from the validation population were included in a genetic evaluation that already included phenotypic mid-test metabolic live-weight from the validation population. This is one of the largest studies demonstrating that significant exploitable genetic variation exists in the feeding behavior of young crossbred growing cattle; such feeding behavior traits are also genetically correlated with several performance and feed efficiency metrics. Nonetheless, there was only a marginal benefit to the inclusion of time-related feeding behavior phenotypes in a genetic evaluation for MEI to improve the precision of the EBVs for this trait.


Assuntos
Ração Animal , Comportamento Alimentar , Ração Animal/análise , Animais , Bovinos/genética , Ingestão de Alimentos/genética , Ingestão de Energia , Feminino , Fenótipo
11.
BMC Genomics ; 22(1): 757, 2021 Oct 23.
Artigo em Inglês | MEDLINE | ID: mdl-34688258

RESUMO

BACKGROUND: The carcass value of cattle is a function of carcass weight and quality. Given the economic importance of carcass merit to producers, it is routinely included in beef breeding objectives. A detailed understanding of the genetic variants that contribute to carcass merit is useful to maximize the efficiency of breeding for improved carcass merit. The objectives of the present study were two-fold: firstly, to perform genome-wide association analyses of carcass weight, carcass conformation, and carcass fat using copy number variant (CNV) data in a population of 923 Holstein-Friesian, 945 Charolais, and 974 Limousin bulls; and secondly to perform separate association analyses of carcass traits on the same population of cattle using the Log R ratio (LRR) values of 712,555 single nucleotide polymorphisms (SNPs). The LRR value of a SNP is a measure of the signal intensity of the SNP generated during the genotyping process. RESULTS: A total of 13,969, 3,954, and 2,805 detected CNVs were tested for association with the three carcass traits for the Holstein-Friesian, Charolais, and Limousin, respectively. The copy number of 16 CNVs and the LRR of 34 SNPs were associated with at least one of the three carcass traits in at least one of the three cattle breeds. With the exception of three SNPs, none of the quantitative trait loci detected in the CNV association analyses or the SNP LRR association analyses were also detected using traditional association analyses based on SNP allele counts. Many of the CNVs and SNPs associated with the carcass traits were located near genes related to the structure and function of the spliceosome and the ribosome; in particular, U6 which encodes a spliceosomal subunit and 5S rRNA which encodes a ribosomal subunit. CONCLUSIONS: The present study demonstrates that CNV data and SNP LRR data can be used to detect genomic regions associated with carcass traits in cattle providing information on quantitative trait loci over and above those detected using just SNP allele counts, as is the approach typically employed in genome-wide association analyses.


Assuntos
Estudo de Associação Genômica Ampla , Polimorfismo de Nucleotídeo Único , Animais , Bovinos/genética , Variações do Número de Cópias de DNA , Masculino , Fenótipo , Locos de Características Quantitativas
12.
Foods ; 10(8)2021 Aug 17.
Artigo em Inglês | MEDLINE | ID: mdl-34441687

RESUMO

The objective of the present study was to determine if animals who were genetically divergent in the predicted tenderness of their meat actually produced more tender meat, as well as what the implications were for other organoleptic properties of the meat. The parental average genetic merit for meat tenderness was used to locate 20 "Tough genotype" heifers and 17 "Tender genotype" heifers; M. longissimus thoracis steaks from all heifers were subjected to sensory affective analysis (140 consumers) and sensory profiling using two trained sensory panels. All sample steaks were treated identically regarding pre- and post-mortem handling, storage, cooking and presentation (i.e., randomised, blind coded). For the affective consumer study, eight steaks were sectioned from the same location of the striploin muscles from each of the heifers. In total, 108 steaks from the Tender genotype and 118 from the Tough genotype were tested in the consumer study to determine the preference or liking of these steaks for appearance, aroma, flavour, tenderness, juiciness and overall acceptability. The consumer study found that the Tender genotype scored higher (p < 0.0001) for liking of tenderness, juiciness, flavour and overall acceptability compared to the Tough genotype. Similar results were generally found for the separate consumer age cohorts (18-64 years) with lower sensory acuity in the 65+ age cohort. For the descriptive analysis, the Tender genotype scored numerically more tender, juicy and flavoursome, although the differences were only significant for one of the panels. The critical outcome from this study is that parental average genetic merit can be used to pre-select groups of animals for tenderness, which, in turn, can be detected by consumers.

13.
Transl Anim Sci ; 5(3): txab126, 2021 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-34430801

RESUMO

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

14.
Animal ; 15(9): 100321, 2021 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-34371469

RESUMO

Genetic evaluations separate phenotypes into their contributing additive genetic effects and non-(additive) genetic effects, with the former termed best linear unbiased predictions, and the latter termed best linear unbiased estimates (BLUEs). For the purpose of the present study, genetic evaluations, along with phenotypic data from 4 137 376 animals, were used to generate herd, year of slaughter and sex contemporary group BLUEs for various slaughter-related traits. These slaughter traits included carcass weight (CW), carcass conformation (CC) and carcass fat (CF). For the 4 665 herds that were consistently slaughtering ≥10 animals/year between the years 2014 and 2018, inclusive, all relevant contemporary group BLUEs were collapsed into a single herd-year value; results herein relate to these herds. The within-year herd-year BLUE correlations between CW and CC, between CW and CF, and between CC and CF were 0.51, 0.10 and -0.04, respectively. The repeatability across years of the herd-year BLUEs for CW, CC and CF was 0.66, 0.59 and 0.50, respectively. Furthermore, when the herds were stratified, within year, on the percentile rank of their herd-year BLUEs, herds had the greatest probability of remaining in the same BLUE stratum from one year to the next. In addition, results from the present study determined that various herd characteristics are associated with differences in the herd BLUEs. Results from the present study could be used to advise beef producers on the most promising strategy to improve the carcass merit of their animals.


Assuntos
Fenótipo , Animais , Bovinos/genética
15.
BMC Genomics ; 22(1): 343, 2021 May 12.
Artigo em Inglês | MEDLINE | ID: mdl-33980141

RESUMO

BACKGROUND: Bovine TB (bTB), caused by infection with Mycobacterium bovis, is a major endemic disease affecting global cattle production. The key innate immune cell that first encounters the pathogen is the alveolar macrophage, previously shown to be substantially reprogrammed during intracellular infection by the pathogen. Here we use differential expression, and correlation- and interaction-based network approaches to analyse the host response to infection with M. bovis at the transcriptome level to identify core infection response pathways and gene modules. These outputs were then integrated with genome-wide association study (GWAS) data sets to enhance detection of genomic variants for susceptibility/resistance to M. bovis infection. RESULTS: The host gene expression data consisted of RNA-seq data from bovine alveolar macrophages (bAM) infected with M. bovis at 24 and 48 h post-infection (hpi) compared to non-infected control bAM. These RNA-seq data were analysed using three distinct computational pipelines to produce six separate gene sets: 1) DE genes filtered using stringent fold-change and P-value thresholds (DEG-24: 378 genes, DEG-48: 390 genes); 2) genes obtained from expression correlation networks (CON-24: 460 genes, CON-48: 416 genes); and 3) genes obtained from differential expression networks (DEN-24: 339 genes, DEN-48: 495 genes). These six gene sets were integrated with three bTB breed GWAS data sets by employing a new genomics data integration tool-gwinteR. Using GWAS summary statistics, this methodology enabled detection of 36, 102 and 921 prioritised SNPs for Charolais, Limousin and Holstein-Friesian, respectively. CONCLUSIONS: The results from the three parallel analyses showed that the three computational approaches could identify genes significantly enriched for SNPs associated with susceptibility/resistance to M. bovis infection. Results indicate distinct and significant overlap in SNP discovery, demonstrating that network-based integration of biologically relevant transcriptomics data can leverage substantial additional information from GWAS data sets. These analyses also demonstrated significant differences among breeds, with the Holstein-Friesian breed GWAS proving most useful for prioritising SNPS through data integration. Because the functional genomics data were generated using bAM from this population, this suggests that the genomic architecture of bTB resilience traits may be more breed-specific than previously assumed.


Assuntos
Mycobacterium bovis , Tuberculose Bovina , Animais , Bovinos , Estudo de Associação Genômica Ampla , Genômica , Macrófagos Alveolares , Tuberculose Bovina/genética
16.
J Anim Breed Genet ; 138(6): 655-667, 2021 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-34031924

RESUMO

The objective of this study was to determine whether response to selection for carcass weight (CW), conformation (CC) and fat (CF), and the association between heterosis and carcass performance varied by herd environment in cattle. Following edits, carcass information was available for 4,616,761 cattle, of which the majority were some crossbred combination of the following breeds: Angus, Aubrac, Belgian Blue, Blonde d'Aquitaine, Charolais, Hereford, Holstein-Friesian, Jersey, Limousin, Saler, Shorthorn and Simmental. Herd environment was defined separately for each carcass trait using herd solutions outputted from carcass trait genetic evaluations. A total of 3,859 herds were stratified, for each trait, into one of five strata based on their corresponding percentile herd solution rank, with the response to selection and the effect of heterosis then estimated within each stratum. The response in CW and CC from selection on the respective estimated breeding values (EBV) increased between the lowest (0.71 kg and 0.89 CC score increase per unit increase in the respective EBV) and highest (0.99 kg and 1.25 CC score increase per unit increase in the respective EBV) corresponding herd stratum. The response in CF from selection on CF EBV, however, reduced between the lowest and highest CF herd stratum (respective increases of 0.93 and 0.83 CF scores per unit increase in CF EBV). In addition, the effect of a unit increase in heterosis coefficient on CW, CC and CF also varied by herd stratum. Furthermore, results (i.e. the area under relative operating characteristic curves) from the present study demonstrated that the response to selection and heterosis effects estimated for the different herd stratum can be used, along with EBVs and the herd solutions themselves, to improve the accuracy of phenotypic predictions. Results from the present study could help producers to make more informed breeding decisions that are bespoke to their herd.


Assuntos
Vigor Híbrido , Animais , Bovinos/genética , Fenótipo
17.
J Anim Sci ; 99(7)2021 Jul 01.
Artigo em Inglês | MEDLINE | ID: mdl-33974695

RESUMO

Awareness and interest in calf health and wellbeing is intensifying, prompting change in the management and breeding decisions of producers and associated policy-makers. The objectives of the present study were to 1) quantify the risk factors associated with subjectively measured scores of vigor and birth size as well as diagnoses of scour and pneumonia in a large national dataset of beef calves, and 2) to estimate the contribution of genetic variance to such phenotypic measures. After edits, the data consisted of health and birth size data subjectively scored by producers on 88,207 calves born in 6,126 Irish beef herds. Vigor was recorded on a scale of 1 (very poor) to 5 (very good). Birth size was also scored on a scale of 1 (very small) to 5 (very large). Scour and pneumonia were both scored independently based on the suspected number of occurrence of each (0 = no occurrence, 1 = one occurrence, or 2 = more than one occurrence). On average, 14.7% of calves were recorded as having had at least one occurrence of scour within the first 5 mo of life, whereas 6.4% of calves were recorded as having had at least one occurrence of pneumonia within the first 5 mo of life. Relative to female calves, male calves had a worse vigor score and a suspected greater incidence of both scour and pneumonia. Relative to singletons, twins were, on average, smaller at birth, they had a worse vigor score, and they were more prone to scour. Calves born in the later periods of the calving season (i.e., late and very late) had a greater incidence of scour relative to calves in the herd born earlier in the calving season. Heritability estimates for vigor, birth size, and pneumonia were 0.12 (0.02), 0.33 (0.03), and 0.08 (0.02), respectively; no genetic variance was detected for scour. Breeding for vigorous calves that are less susceptible to pneumonia could provide producers with an additional strategy to ensure consumer concerns regarding food quality, safety, and calf wellbeing are being met.


Assuntos
Parto , Animais , Bovinos/genética , Feminino , Incidência , Masculino , Fenótipo , Gravidez , Fatores de Risco , Estações do Ano
18.
J Anim Sci ; 99(7)2021 Jul 01.
Artigo em Inglês | MEDLINE | ID: mdl-33860324

RESUMO

A major obstacle in applying genomic selection (GS) to uniquely adapted local breeds in less-developed countries has been the cost of genotyping at high densities of single-nucleotide polymorphisms (SNP). Cost reduction can be achieved by imputing genotypes from lower to higher densities. Locally adapted breeds tend to be admixed and exhibit a high degree of genomic heterogeneity thus necessitating the optimization of SNP selection for downstream imputation. The aim of this study was to quantify the achievable imputation accuracy for a sample of 1,135 South African (SA) Drakensberger cattle using several custom-derived lower-density panels varying in both SNP density and how the SNP were selected. From a pool of 120,608 genotyped SNP, subsets of SNP were chosen (1) at random, (2) with even genomic dispersion, (3) by maximizing the mean minor allele frequency (MAF), (4) using a combined score of MAF and linkage disequilibrium (LD), (5) using a partitioning-around-medoids (PAM) algorithm, and finally (6) using a hierarchical LD-based clustering algorithm. Imputation accuracy to higher density improved as SNP density increased; animal-wise imputation accuracy defined as the within-animal correlation between the imputed and actual alleles ranged from 0.625 to 0.990 when 2,500 randomly selected SNP were chosen vs. a range of 0.918 to 0.999 when 50,000 randomly selected SNP were used. At a panel density of 10,000 SNP, the mean (standard deviation) animal-wise allele concordance rate was 0.976 (0.018) vs. 0.982 (0.014) when the worst (i.e., random) as opposed to the best (i.e., combination of MAF and LD) SNP selection strategy was employed. A difference of 0.071 units was observed between the mean correlation-based accuracy of imputed SNP categorized as low (0.01 < MAF ≤ 0.1) vs. high MAF (0.4 < MAF ≤ 0.5). Greater mean imputation accuracy was achieved for SNP located on autosomal extremes when these regions were populated with more SNP. The presented results suggested that genotype imputation can be a practical cost-saving strategy for indigenous breeds such as the SA Drakensberger. Based on the results, a genotyping panel consisting of ~10,000 SNP selected based on a combination of MAF and LD would suffice in achieving a <3% imputation error rate for a breed characterized by genomic admixture on the condition that these SNP are selected based on breed-specific selection criteria.


Assuntos
Nucleotídeos , Polimorfismo de Nucleotídeo Único , Animais , Bovinos/genética , Frequência do Gene , Genótipo , Desequilíbrio de Ligação
19.
J Anim Sci ; 99(5)2021 May 01.
Artigo em Inglês | MEDLINE | ID: mdl-33677555

RESUMO

Sexual dimorphism, the phenomenon whereby males and females of the same species are distinctive in some aspect of appearance or size, has previously been documented in cattle for traits such as growth rate and carcass merit using a quantitative genetics approach. No previous study in cattle has attempted to document sexual dimorphism at a genome level; therefore, the objective of the present study was to determine whether genomic regions associated with size and muscularity in cattle exhibited signs of sexual dimorphism. Analyses were undertaken on 10 linear-type traits that describe the muscular and skeletal characteristics of both males and females of five beef cattle breeds: 1,444 Angus (AA), 6,433 Charolais (CH), 1,129 Hereford, 8,745 Limousin (LM), and 1,698 Simmental. Genome-wide association analyses were undertaken using imputed whole-genome sequence data for each sex separately by breed. For each single-nucleotide polymorphism (SNP) that was segregating in both sexes, the difference between the allele substitution effect sizes for each sex, in each breed separately, was calculated. Suggestively (P ≤ 1 × 10-5) sexually dimorphic SNPs that were segregating in both males and females were detected for all traits in all breeds, although the location of these SNPs differed by both trait and breed. Significantly (P ≤ 1 × 10-8) dimorphic SNPs were detected in just three traits in the AA, seven traits in the CH, and three traits in the LM. The vast majority of all segregating autosomal SNPs (86% in AA to 94% in LM) had the same minor allele in both males and females. Differences (P ≤ 0.05) in allele frequencies between the sexes were observed for between 36% (LM) and 66% (AA) of the total autosomal SNPs that were segregating in both sexes. Dimorphic SNPs were located within a number of genes related to muscularity and/or size including the NAB1, COL5A2, and IWS1 genes on BTA2 that are located close to, and thought to be co-inherited with, the MSTN gene. Overall, sexual dimorphism exists in cattle at the genome level, but it is not consistent by either trait or breed.


Assuntos
Estudo de Associação Genômica Ampla , Caracteres Sexuais , Animais , Bovinos/genética , Feminino , Genoma , Estudo de Associação Genômica Ampla/veterinária , Genômica , Masculino , Fenótipo , Polimorfismo de Nucleotídeo Único
20.
Mol Biol Evol ; 38(3): 838-855, 2021 03 09.
Artigo em Inglês | MEDLINE | ID: mdl-32941615

RESUMO

How animals, particularly livestock, adapt to various climates and environments over short evolutionary time is of fundamental biological interest. Further, understanding the genetic mechanisms of adaptation in indigenous livestock populations is important for designing appropriate breeding programs to cope with the impacts of changing climate. Here, we conducted a comprehensive genomic analysis of diversity, interspecies introgression, and climate-mediated selective signatures in a global sample of sheep and their wild relatives. By examining 600K and 50K genome-wide single nucleotide polymorphism data from 3,447 samples representing 111 domestic sheep populations and 403 samples from all their seven wild relatives (argali, Asiatic mouflon, European mouflon, urial, snow sheep, bighorn, and thinhorn sheep), coupled with 88 whole-genome sequences, we detected clear signals of common introgression from wild relatives into sympatric domestic populations, thereby increasing their genomic diversities. The introgressions provided beneficial genetic variants in native populations, which were significantly associated with local climatic adaptation. We observed common introgression signals of alleles in olfactory-related genes (e.g., ADCY3 and TRPV1) and the PADI gene family including in particular PADI2, which is associated with antibacterial innate immunity. Further analyses of whole-genome sequences showed that the introgressed alleles in a specific region of PADI2 (chr2: 248,302,667-248,306,614) correlate with resistance to pneumonia. We conclude that wild introgression enhanced climatic adaptation and resistance to pneumonia in sheep. This has enabled them to adapt to varying climatic and environmental conditions after domestication.


Assuntos
Adaptação Biológica/genética , Resistência à Doença/genética , Introgressão Genética , Ovinos/genética , Animais , Evolução Biológica , Mudança Climática , Variação Genética , Filogeografia , Pneumonia/imunologia , Ovinos/imunologia
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