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Background: Cross-validation techniques in genetic evaluations encounter limitations due to the unobservable nature of breeding values and the challenge of validating estimated breeding values (EBVs) against pre-corrected phenotypes, challenges which the Linear Regression (LR) method addresses as an alternative. Furthermore, beef cattle genetic evaluation programs confront challenges with connectedness among herds and pedigree errors. The objective of this work was to evaluate the LR method's performance under pedigree errors and weak connectedness typical in beef cattle genetic evaluations, through simulation., Methods: We simulated a beef cattle population resembling the Argentinean Brangus, including a quantitative trait selected over six pseudo-generations with a heritability of 0.4. This study considered various scenarios, including: 25% and 40% pedigree errors (PE-25 and PE-40), weak and strong connectedness among herds (WCO and SCO, respectively), and a benchmark scenario (BEN) with complete pedigree and optimal herd connections., Results: Over six pseudo-generations of selection, genetic gain was simulated to be under- and over-estimated in PE-40 and WCO, respectively, contrary to the BEN scenario which was unbiased. In genetic evaluations with PE-25 and PE-40, true biases of - 0.13 and - 0.18 genetic standard deviations were simulated, respectively. In the BEN scenario, the LR method accurately estimated bias, however, in PE-25 and PE-40 scenarios, it overestimated biases by 0.17 and 0.25 genetic standard deviations, respectively. In herds facing WCO, significant true bias due to confounding environmental and genetic effects was simulated, and the corresponding LR statistic failed to accurately estimate the magnitude and direction of this bias. On average, true dispersion values were close to one for BEN, PE-40, SCO and WCO, showing no significant inflation or deflation, and the values were accurately estimated by LR. However, PE-25 exhibited inflation of EBVs and was slightly underestimated by LR. Accuracies and reliabilities showed good agreement between true and LR estimated values for the scenarios evaluated., Conclusions: The LR method demonstrated limitations in identifying biases induced by incomplete pedigrees, including scenarios with as much as 40% pedigree errors, or lack of connectedness, but it was effective in assessing dispersion, and population accuracies and reliabilities even in the challenging scenarios addressed., Competing Interests: Declarations. Ethics approval and consent to participate: Not applicable. Consent for publication: Not applicable. Competing interests: The authors declare that they have no competing interests., (© 2024. The Author(s).)

Gestation length (GL) is a moderately heritable trait in cattle with economic and management implications. This study aimed to characterize the gestation length of an Argentinian Holstein cattle population, understand contributing factors, and explore the GL effect on production performance. Further objectives were to estimate direct and maternal heritabilities for this trait and to identify genomic regions affecting it. Data consisted of GL records from 45,738 births corresponding to 17,004 Holstein cows and heifers. The effects of age and calving season over GL were analyzed using a Student's t-test for homoscedastic samples. The effects of the GL category (GL shorter than 1.5 SD, within ±1.5 SD, and longer than 1.5 SD from the mean) on production performance were studied by analysis of variance. A single-step genome-wide association study was performed using the BLUPF90 suite of programs with genotypes from 654 Holstein animals on 40,339 SNP. The results showed that the younger the age at calving, the shorter the GL. Moreover, gestations ending in warmer seasons were, in general, statistically shorter than those ending in colder seasons for both heifers and cows. Regarding the effect of GL on production performance, cows with gestation periods within ±1.5 SD from the population mean exhibited the highest 305-day cumulative milk, fat, and protein productions. Direct and maternal heritabilities for GL were 0.42 and 0.03, respectively. We detected a SNP suggestively associated with direct gestation length at 57.7 Mb on Bos taurus autosome 18, a locus included in a region described in the literature as associated with the trait. The information obtained on the environmental and genetic factors affecting GL in Argentinian Holstein cows contributes to characterizing the population in pursuit of improving the performance of national dairy cattle breeding systems., Competing Interests: Declaration of competing interest The authors declare that they have no conflict of interest., (Copyright © 2023 Elsevier Inc. All rights reserved.)

Machine learning methods were considered efficient in identifying single nucleotide polymorphisms (SNP) underlying a trait of interest. This study aimed to construct predictive models using machine learning algorithms, to identify loci that best explain the variance in milk traits of dairy cattle. Further objectives involved validating the results by comparison with reported relevant regions and retrieving the pathways overrepresented by the genes flanking relevant SNPs. Regression models using XGBoost (XGB), LightGBM (LGB), and Random Forest (RF) algorithms were trained using estimated breeding values for milk production (EBV M ), milk fat content (EBV F ) and milk protein content (EBV P ) as phenotypes and genotypes on 40417 SNPs as predictor variables. To evaluate their efficiency, metrics for actual vs. predicted values were determined in validation folds (XGB and LGB) and out-of-bag data (RF). Less than 4500 relevant SNPs were retrieved for each trait. Among the genes flanking them, signaling and transmembrane transporter activities were overrepresented. The models trained:•Predicted breeding values for animals not included in the dataset.•Were efficient in identifying a subset of SNPs explaining phenotypic variation. The results obtained using XGB and LGB algorithms agreed with previous results. Therefore, the method proposed could be applied for future association studies on milk traits., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2022 The Authors.)

Modified vaccinia Ankara virus (MVA) is extensively used as a vaccine vector. We have previously observed that MVAΔ008, an MVA lacking the gene that codes for interleukin-18 binding protein, significantly increases CD8+ and CD4+ T-cell responses to vaccinia virus (VACV) epitopes and recombinant HIV antigens. However, the efficacy of this vector against pathogens or tumor cells remains unclear. Thus, the aim of this study was to evaluate the cellular immune response and the protection induced by recombinant MVAs encoding the model antigen ovalbumin (OVA). We used the MO5 melanoma tumor model (OVA-expressing tumor) as an approach for evaluating the vector-induced efficacy. Our results show that MVAΔ008-OVA (optimized vector) induced higher in vivo specific cytotoxicity and ex vivo T-cell IFN-γ responses against OVA than the conventional MVA vector. Importantly, the recombinant vectors were capable of controlling MO5 tumor growth. Indeed, the administration of MVAΔ008-OVA or MVA-OVA in prophylactic and therapeutic schemes provided total protection and longer survival of mice, respectively. Overall, our results demonstrate the improved immunogenicity and the protective capacity of MVAΔ008 against a heterologous model antigen. These findings suggest that MVAΔ008 constitutes an excellent candidate for vaccine development against pathogens or cancer therapy., (Copyright © 2021 Elsevier Ltd. All rights reserved.)

The Campero-INTA chicken of Argentina was developed to provide a robust bird that can survive under Argentinian pasture conditions with no significant additional nutrition, producing a source of animal protein for small producers or low-income families. In previous work, we described the AH paternal line of Campero and its Major Histocompatibility Complex B region (MHC-B) variation. In this work we analyzed the three remaining synthetic lines used to produce the Campero-INTA production bird: lines AS, A, and E. Because of the association between variation within the MHC of chickens and disease resistance, MHC variation within this breed is of particular interest. MHC variability within the lines used to produce the Campero-INTA chicken was examined using a 90 SNP panel encompassing the chicken MHC-B region plus the VNTR, LEI0258, located within the chicken MHC. Across all 4lines 12 haplotypes were found, with 7 of these being previously reported in North America/European breeds, reflecting the original breed sources for these birds. Three Campero unique haplotypes were found, 2 of which likely originated from MHC recombination events. MHC-B variation for all lines involved with production of the final Campero-INTA bird has now been determined., (Copyright © 2021 The Authors. Published by Elsevier Inc. All rights reserved.)

Selective breeding of genetically resistant animals is considered a promising strategy to face the problem of nematode resistance to anthelmintics and mitigate concerns about the presence of chemical residues in animal food products and the environment. Gastrointestinal nematode resistance is a complex, multifactorial trait related to host immunity. However, the mechanisms underlying host resistance and response to infection remain to be fully elucidated. In this context, the objective of this study was to provide insight into the chromosomal regions determining nematode resistance and resilience in Corriedale and resistance in Pampinta sheep breeds. A total of 170 single nucleotide polymorphisms (SNP) from 76 candidate genes for immune response were studied in 624 Corriedale and 304 Pampinta animals. Lambs underwent artificial or natural challenges with infective larvae mainly from Haemonchus contortus. Fecal egg counts, estimated breeding values for fecal egg counts, and rate of packed cell volume change and FAMACHA© score change over the challenge were used, when available, as indicators of host parasite resistance or resilience. Phenotype-genotype association studies were conducted and significance values obtained were adjusted for multiple testing errors. Eight SNPs, located on OARs 3, 6, 12, and 20, reached significance in Corriedale sheep under artificial challenge. Those SNP represent allelic variants from the MHC-Ovine Lymphocyte Antigen-DRA, two C-type lectin domain families, the Interleukin 2 receptor β, the Toll-like receptor 10, the Mannan binding lectin serine peptidase 2, and the NLR family, CARD domain containing 4 genes. On Pampinta lambs under natural challenge, we found three significant SNPs, located in the TIMP metallopeptidase inhibitor 3, the FBJ murine osteosarcoma viral oncogene homolog, and the Interleukin 20 receptor alpha genes, on OARs 3, 7, and 8, respectively. The results obtained herein confirm genomic regions previously reported as associated with nematode resistance in other sheep breeds, reinforcing their role in host response to parasites. These findings contribute to gain knowledge on parasite resistance and resilience in Corriedale sheep and report for the first time SNPs associated with resistance to gastrointestinal parasite infections in Pampinta breed., (Copyright © 2020 Elsevier B.V. All rights reserved.)

Background: Research on loci influencing milk production traits of dairy cattle is one of the main topics of investigation in livestock. Many genomic regions and polymorphisms associated with dairy production have been reported worldwide. In this context, the purpose of this study was to identify candidate loci associated with milk yield in Argentinean dairy cattle. A database of candidate genes and single nucleotide polymorphisms (SNPs) for milk production and composition was developed. Thirty-nine SNPs belonging to 22 candidate genes were genotyped on 1643 animals (Holstein and Holstein x Jersey). The genotypes obtained were subjected to association studies considering the whole population and discriminating the population by Holstein breed percentage. Phenotypic data consisted of milk production values recorded during the first lactation of 1156 Holstein and 462 Holstein x Jersey cows from 18 dairy farms located in the central dairy area of Argentina. From these records, 305-day cumulative milk production values were predicted., Results: Eight SNPs (rs43375517, rs29004488, rs132812135, rs137651874, rs109191047, rs135164815, rs43706485, and rs41255693), located on six Bos taurus autosomes (BTA4, BTA6, BTA19, BTA20, BTA22, and BTA26), showed suggestive associations with 305-day cumulative milk production (under Benjamini-Hochberg procedure with a false discovery rate of 0.1). Two of those SNPs (rs43375517 and rs135164815) were significantly associated with milk production (Bonferroni adjusted p -values < 0.05) when considering the Holstein population., Conclusions: The results obtained are consistent with previously reported associations in other Holstein populations. Furthermore, the SNPs found to influence bovine milk production in this study may be used as possible candidate SNPs for marker-assisted selection programs in Argentinean dairy cattle., Competing Interests: Procedures employed for blood samples collection and for milk production evaluation were approved by the Institutional Committee for Care and Use of Experimental Animals (CICUAE) of the National Institute of Agricultural Technology (INTA) under protocol number 35/2010 and followed the guidelines specified in the institutional manual.Not applicable.The authors declare that they have no competing interests.Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

MicroRNAs (miRNAs) have been identified in cells as well as in exosomes in biological fluids such as milk. In mammary gland, most of the miRNAs studied have functions related to immunity and show alterations in their pattern of expression during lactation. In mastitis, the inflammatory response caused by Streptococcus uberis alters the expression of miRNAs that may regulate the innate immune system. These small RNAs are stable at room temperature and are resistant to repeated freeze/thaw cycles, acidic conditions and degradation by RNAse, making them resistant to industrial procedures. These properties mean that miRNAs could have multiple applications in veterinary medicine and biotechnology. Indeed, lactoglobulin-free milk has been produced in transgenic cows expressing specific miRNAs. Although plant and animal miRNAs have undergone independent evolutionary adaptation recent studies have demonstrated a cross-kingdom passage in which rice miRNA was isolated from human serum. This finding raises questions about the possible effect that miRNAs present in foods consumed by humans could have on human gene regulation. Further studies are needed before applying miRNA biotechnology to the milk industry. New discoveries and a greater knowledge of gene expression will lead to a better understanding of the role of miRNAs in physiology, nutrition and evolution.

The recurrence and persistence of foot and mouth disease (FMD) could be the consequence of cyclic and massive transportation of calves. For this reason, in South America, vaccination strategies related to livestock dynamic are being promoted. In order to aid the evaluation of such strategies, a method for predicting the risk of transportation of nonvaccinated weaned calves was developed; this method combines expert opinion and empirical evidence using Bayesian estimators. It was applied through Monte Carlo simulation to data of Argentina under four hypothetical vaccination schemes: E1, extended vaccination season of 1/6 of the population of calves each month from July to December without second round vaccination (SRV); E2, extended irregular vaccination from July to December with SRV applied to 70% of the calves resembling the scheme applied in Argentina in 2001; E3, vaccination in November and December without SRV; and E4, vaccination concentrated in November. E1 resulted in probability of transporting non vaccinated calves (tnvc) reaching its maximum in the following year in May with mean=0.0250 and percentile 95% (P95)=0.0404; for the same month tnvc estimates for the other schemes were E2: mean=0.0071; P95=0.0162; E3: mean=0.0017; P95=0.0042 and E4: mean=0.0001; P95=0.0004. Bonferroni multiple comparison for simultaneous assertions for May showed that E4 resulted the best scheme, E1 the worst, and E2 and E3 are intermediate with nonsignificant difference observed between overall (p<0.05). Results were consistent with historical records and quantification for future needs for re-vaccination was made possible. While the ratio "total vaccinated"/"total estimated existences" will give a biased vision of vaccination coverage under the situation of extended vaccination campaigns, a model as the one developed here could allow a more accurate assessment and the design of mitigation plans., (Copyright © 2010 Elsevier B.V. All rights reserved.)

The objectives of this study were to evaluate the effect of somatic cell count (SCC) on functional longevity and to estimate the heritability of functional longevity using survival analysis in Valle del Belice dairy sheep. A total of 4,880 lactations of 2,190 ewes from 11 flocks were used. In this study, SCC was considered as an indication of subclinical mastitis. In case of clinical cases, identified by the technicians at milking time, test-day weights and milk samples of those ewes were not considered. Somatic cells were analyzed as counts, without any transformation, and were grouped in 3 classes based on the observed SCC maximum (mxSCC). The mxSCC classes, expressed as 10(3) cells/mL, were classified as 1 if mxSCC or= 1,000. An increase in SCC was associated with an increased hazard of being culled. Ewes in the highest class of SCC on a test-day had a 20% higher hazard of being culled than those in the lowest class. Therefore, SCC played a role in culling decisions of Valle del Belice dairy sheep farmers. The heritability estimate for functional longevity was 7% on the logarithmic scale and 11% on the real scale, indicating that selection for this trait is possible in sheep. The flock-year-season effect explained 19% of the variation on the logarithmic scale and 27% of the variation on the real scale.

We carried out a longitudinal study of 122 dairy herds in southwest Sweden to investigate relationships of rearing conditions and health with heifer breeding performance and to estimate the incidence of clinical diseases and survival until 1st calving. A total of 3081 animals born in 1998 (47% Swedish Red; 50% Swedish Holstein breed) were followed from birth until calving, culling or death. Information about housing, management, breeds and dates of birth, breeding and calving was obtained from farmers. Diseases were recorded by farmers and veterinarians; antibiotic treatment was used in < 25% of all cases. Median time to breeding was 17.5 months, 64% of all heifers bred by AI conceived at 1st breeding, and median time to calving was 27.6 months. Age at 1st breeding (log-transformed), conception at 1st breeding (binary), and age at 1st calving (log-transformed) were analysed with three mixed models, accounting for clustering by considering random-intercept and random-slope effects at the herd level. Around 40 potential predictors or confounders were recorded and considered for modelling. Time to breeding and calving increase greatly with the time heifers spend grazing, although up to 5 months of grazing before 1st calving appears to be more favourable than no grazing at all. The effect of grazing differs depending on the season of birth. Zero-grazed heifers calve 20% later if exposed to indoor ammonia concentrations > 10 ppm after start of breeding. There is considerable variation between herds in breeding performance, except for conception at 1st breeding-limiting the potential for improving conception by herd measures. Observed total disease incidence rate was 14 per 100 animal-years from 7 months of age to estimated conception and 4.7 per 100 animal-years from conception to calving, with great variation between herds. Infectious diseases were predominant, and diarrhoea, respiratory disease and ringworm were the most common diagnoses. Eight hundred and fifty-three heifers left the study before calving, due to herd exits (incidence risk 0.073%), selling off live (0.061%), spontaneous deaths (0.050%) or slaughter (0.092%).

In the Mediterranean region, goat milk production is an important economic activity. In the present study, 4 casein genes were genotyped in 5 Sicilian goat breeds to 1) identify casein haplotypes present in the Argentata dell'Etna, Girgentana, Messinese, Derivata di Siria, and Maltese goat breeds; and 2) describe the structure of the Sicilian goat breeds based on casein haplotypes and allele frequencies. In a sample of 540 dairy goats, 67 different haplotypes with frequency >or=0.01 and 27 with frequency >or=0.03 were observed. The most common CSN1S1-CSN2-CSN1S2-CSN3 haplotype for Derivata di Siria and Maltese was FCFB (0.17 and 0.22, respectively), whereas for Argentata dell'Etna, Girgentana and Messinese was ACAB (0.06, 0.23, and 0.10, respectively). According to the haplotype reconstruction, Argentata dell'Etna, Girgentana, and Messinese breeds presented the most favorable haplotype for cheese production, because the casein concentration in milk of these breeds might be greater than that in Derivata di Siria and Maltese breeds. Based on a cluster analysis, the breeds formed 2 main groups: Derivata di Siria, and Maltese in one group, and Argentata dell'Etna and Messinese in the other; the Girgentana breed was between these groups but closer to the latter.

A Bayesian method was developed to handle QTL analyses of multiple experimental data of outbred populations with heterogeneity of variance between sexes for all random effects. The method employed a scaled reduced animal model with random polygenic and QTL allelic effects. A parsimonious model specification was applied by choosing assumptions regarding the covariance structure to limit the number of parameters to estimate. Markov chain Monte Carlo algorithms were applied to obtain marginal posterior densities. Simulation demonstrated that joint analysis of multiple environments is more powerful than separate single trait analyses of each environment. Measurements on broiler BW obtained from 2 experiments concerning growth efficiency and carcass traits were used to illustrate the method. The population consisted of 10 full-sib families from a cross between 2 broiler lines. Microsatellite genotypes were determined on generations 1 and 2, and phenotypes were collected on groups of generation 3 animals. The model included a polygenic correlation, which had a posterior mean of 0.70 in the analyses. The reanalysis agreed on the presence of a QTL in marker bracket MCW0058-LEI0071 accounting for 34% of the genetic variation in males and 24% in females in the growth efficiency experiment. In the carcass experiment, this QTL accounted for 19% of the genetic variation in males and 6% in females.

The objectives of this study were to evaluate the effect of diseases on days open (DO), days to first breeding (DFB) and days from first breeding to conception (DFBC) using survival analysis models, and to assess the significance of the sire component and its possible confounding effect. The data consisted of a random sample of 20% of all herds enrolled in Swedish recording system and using 100% artificial insemination with at least 15 Swedish Red and White cows calving in 1991. The follow-up period was from 45 to 145 d after calving. After editing, the data sets had 23,927, 28,197, and 22,089 cows for days open, days to first breeding, and days from first breeding to conception, respectively. The Cox models included parity, calving season, cow milk production and age at first calving as fixed effects, and herd and sire as random effects. Ten disease groups were considered as possible risk factors for the reproductive traits. Disease groups were treated differently if they occurred before or after 45 d postpartum. Diseases occurring in the first 45 d after calving were treated as time-independent covariates and diseases occurring after day 45 were treated as time-dependent covariates for days open and days to first breeding. The percentages of censored cows were 35% for days open, 19% for days to first breeding, and 33% for days from first breeding to conception. Days open increased in cows with dystocia, stillbirth, retained placenta, metritis, or other diseases occurring in the first 45 d after calving, and in cows with metritis, mastitis, or other diseases occurring after 45 d. Days to first breeding increased in cows with stillbirth, retained placenta, milk fever, mastitis, foot and leg problems, or other diseases occurring before day 45, and in cows with metritis, mastitis, foot and leg problems, or other diseases occurring after 45 d. Days to first breeding decreased in cows treated for ovulatory dysfunctions either before or after 45 d. Days from first breeding to conception increased in cows with dystocia, stillbirth, retained placenta, metritis, or ovulatory dysfunctions occurring before first breeding, and in cows with mastitis occurring after first breeding. Although the additive genetic components were significant for all traits considered, the sires did not act as confounders because only a small amount of variability for the traits considered in this study was explained by the sires, with estimated heritabilities of 2% on the logarithmic scale and from 3 to 4% on the real scale.

The purpose of this study was to assess the effect of lameness on dairy cow survival. Cox's proportional hazards regression models were fitted to single-lactation data from 2520 cows in 2 New York State dairy herds. Models were controlled for the time-independent effects of parity, projected milk yield, and calving season, and for the time-dependent effects of lameness and culling. Other common diseases were found to be nonconfounding and so were not included in any of the final models. Survival was measured as the time from calving until death or sale. Cows were censored if they reached the start of the next lactation or end of the study, whichever occurred first. All models were stratified by herd. For all lameness diagnoses combined, survival in the herd decreased for those cows becoming lame during the first half of lactation, with a hazard ratio of up to 2 times that of a nonlame cow. Foot rot diagnosed during the second or third months of lactation decreased survival during the same time period (hazard ratio=5.1; 95% confidence interval=1.6 to 16.2). Sole ulcers diagnosed in the first 4 mo of lactation decreased survival in several subsequent periods in which the strongest association was between diagnosis in the third and fourth months of lactation and exit from the herd during that same period (hazard ratio=2.7; 95% confidence interval=1.3 to 6.0). Foot warts were not associated with decreased survival in this analysis. Lameness was never associated with increased survival in any of the models.

We investigated the effects of dam-related factors (such as calving performance, milk leakage, diseases, milk production, and somatic-cell count (SCC)) on heart girth at birth and the incidence risk of diarrhoea and respiratory disease during the first 90 days in Swedish dairy calves. The effects of these dam-related factors and environmental and management-related (but not dietary) factors on the calves' growth rate during the first 90 days of life also were analysed. The study used nearly 3,000 heifer calves born in 1998 on 122 farms in the south-west of Sweden. Individual health records were kept by the farmers and visiting project veterinarians. The calf's heart girth was measured at birth and weaning. We used generalised linear mixed models for the size of the calf at birth and growth rate. Variables associated with the heart girth at birth were breed, calving performance, mastitis in the dam in the last 49 days before calving, milk production and parity. Variables associated with the growth rate were breed, calving performance, disease in the calf during its first 90 days of life, heart girth at birth, and housing of calves. The effect of the dam on the relative risk of diarrhoea and/or respiratory disease in the calf was evaluated by a generalised linear mixed model with a logit link. Morbidity in the dam during late pregnancy, retained placenta and SCC were associated with the relative risk of respiratory disease in the calf. None of the explanatory variables (other then breed) was associated with the relative risk of diarrhoea.