Temperature and humidity index (THI) affects salivary cortisol (HC) and dehydroepiandrosterone (DHEA) concentrations in growing bulls following stress generated by performance test procedures.

The hypothalamus-pituitary-adrenal axis response to a challenge was proposed for genetic selection of robust and resilient animals. As ACTH (adrenocorticotropic hormone) test and hormone measurements in blood may result impractical, it may be useful to measure salivary hormones in response to natural stressors, after an accurate biological validation, to control factors that could contribute to the response. We evaluated whether animal handling during performance test affects salivary HC and DHEA secretion and could be used for selection. We tested the effects of habituation to repeated handling and THI as putative bias. Bull calves (N = 273) undergoing performance test were sampled at 8-9 and 11-13 months (N = 101), 8-9 months (N = 131), or 11-13 months (N = 41). On each test day (D0), calves were isolated, conducted to a squeeze chute and immobilized for 6 min. Saliva samples were collected in the morning after feed administration (T0), and after 6 min immobilization in the squeeze chute (T1) for HC and DHEA measurement. Environmental temperature and relative humidity were recorded every hour from 1:00 h to 24:00 h during the 6 days before the performance test and on D0. Salivary HC and DHEA concentrations were higher in T1 (p < 0.01), although a clear individual positive response to handling could be observed in less than 10% of subjects. The mixed model revealed: (i) HC and HC/DHEA were higher in Young bulls (p < 0.05). (ii) The time of T0 sample collection significantly affected DHEA (p < 0.01) and HC/DHEA (p < 0.05). (iii) THI affected both steroids (p < 0.001) but not HC/DHEA. Spearman correlations suggested that THI weakly affected salivary HC at T0 only (ρ = 0.150, p < 0.01), while moderate statistically significant correlations were found between DHEA and THI at T0 (ρ = 0.316, p < 0.001), and T1 (ρ = 0.353, p < 0.001). Salivary HC and DHEA in response to handling procedures might identify subpopulations of subjects with sensitive HPA axis. Habituation to repeated handling played a role, as the hormone response was lower in older animals. Chronic exposure to high THI had a minor effect on salivary HC visible at T0. A more intense THI effect was observed on salivary DHEA concentrations at both T0 and T1, which should be worth of further investigations.

Heritability and genetic correlations of total and differential somatic cell count with milk yield and composition traits in Italian Simmental cows.

Costs of production have deeply increased each year in the last decades, breeders are continuously looking for more cost effective and more efficient ways to produce milk. Despite the major signs of progress in productivity, it is fundamental to optimize rather than maximize the performances of the dairy cows. Mastitis is still a highly prevalent disease in the dairy sector which causes several economic losses and environmental effect. Its accurate and early diagnosis is crucial to improve profitability of dairy cows and contribute to a more sustainable dairy industry. Among mastitis reduction strategies, there is the urgent need to implement breeding objectives to select cows displaying mastitis resistance by investigating the genetic mechanisms at the base of the inflammatory response. Therefore, in this study we aimed to further understand the genetic background of the differential somatic cell count (DSCC), which provides thorough insights on the actual inflammatory status of the mammary glands. The objectives of this study were to estimate on a cohort of 20,215 Italian Simmental cows over a 3-yr period: (1) the heritability and repeatability values of somatic cell score (SCS) and DSCC, (2) the genetic and phenotypic correlations between these 2 traits and milk production and milk composition traits, (3) the heritability and repeatability values of SCS and DSCC within class of udder health status. Heritability was low both for SCS (0.06) and DSCC (0.08), whereas the repeatability values for these traits were 0.43 and 0.36, suggesting that the magnitude of cow permanent environmental effect for these traits is remarkable. The genetic and phenotypic correlation of SCS with DSCC was 0.612 and 0.605, respectively. Because both significantly differed from the unit, we must consider those traits as different ones. This latter aspect corroborates the need to consider the DSCC as a further indicator of inflammatory status which might be implemented in the Simmental breed genetic evaluation. It is worthy to mention that heritability estimates for SCS and DSCC were the highest in healthy cows compared with the other udder health classes. This implies that when the udder health status changes, it is most likely due to environmental factors rather than aspects related to the animal's genetics. In contrast, the highest additive genetic variance and heritability found for SCS and DSCC in the healthy group might reveal the potential to further implement breeding strategies to select for healthier animals.

Stayability in Simmental cattle as affected by muscularity and body condition score between calvings.

The present study aimed to investigate the association between stayability (STAY) traits, muscularity, and body condition score (BCS) in the Italian Simmental dual-purpose cows. Data were collected from 2,656 cows linearly scored in their first lactation from 2002 to 2020 and reared in 324 herds. The binary trait STAY, which is the ability of a cow to stay in the herd, was obtained for each cow-lactation available up to parity 5 (from STAY1-2 to STAY4-5). Analysis of STAY was carried out using logistic regression, considering the fixed effect of energy corrected milk, conception rate, somatic cell score, and muscularity or BCS predicted at different time points. The herd of linear classification and residual error were the random effects. Primiparous cows with a medium BCS and muscularity in early lactation presented a more favorable STAY across life compared to thinner ones (P < 0.05). In fact, cows with an intermediate BCS/muscularity were more likely to stay in the herd after the third lactation (STAY3-4), compared to those presenting a lower BCS/muscularity (P < 0.01). However, cows whose muscularity was high were generally less likely to start the third lactation compared to the others. A potential explanation for this could be the willing to market cows with good conformation for meat purpose. Simmental is in fact a dual-purpose breed known for the good carcass yield and meat quality. This study demonstrates how muscularity and BCS available early in life can be associated with the ability of Simmental cows to stay in the herd.

A transgenerational study on the effect of great-granddam birth month on granddaughter EBV for production traits in Italian Simmental cattle.

Heat tolerance is a key feature of resilient animals. Offspring of animals that suffer environmental stress during pregnancy could show physiological, morphological, and metabolic modifications. This is due to a dynamic reprogramming of the epigenetics of the mammalian genome that occurs in the early life cycle. Thus, the aim of this study was to investigate the extent of the transgenerational effect of heat stress during the pregnancy of Italian Simmental cows. The effects of dam and granddam birth months (as indicator of pregnancy period) on their daughter and granddaughter estimated breeding values (EBV) for some dairy traits as well as of the temperature-humidity index (THI) during the pregnancy were tested. A total of 128,437 EBV (milk, fat, and protein yields, and somatic cell score) were provided by the Italian Association of Simmental Breeders. The best birth months (of both dam and granddam) for milk yield and protein yield were May and June, whereas the worst were January and March. Great-granddam pregnancies developed during the winter and spring seasons positively affected the EBV for milk and protein yields of their great-granddaughters; in contrast, pregnancies during summer and autumn had negative effects. These findings were confirmed by the effects of maximum and minimum THI in different parts of the great-granddam pregnancy on the performances of their great-granddaughters. Thus, a negative effect of high temperatures during the pregnancy of female ancestors was observed. Results of the present study suggest a transgenerational epigenetic inheritance in Italian Simmental cattle due to environmental stressors.

Combined effects of CXCL8 (IL-8) and CXCR2 (IL-8R) gene polymorphisms on deregressed MACE EBV indexes of milk-related traits in Simmental bulls.

CXCL8 (also known as IL-8) is a member of the CXC subfamily of chemokines that binds two of the seven transmembrane G-protein-coupled receptors (GPCRs), CXCR1 and CXCR2, to mediate and regulate leucocyte accumulation and activation at sites of inflammation. They are known to play a critical role in both disease susceptibility and infection outcome. The aim of this study was to investigate the entire sequences of CXCL8 and CXCR2 genes in thirty-one Simmental sires to evaluate the effects of genomic variants on the indexes of the bulls for milk, fat and protein yields, and for somatic cell score (SCS). Five new single nucleotide polymorphisms (SNPs) were found in CXCR2 gene. The analysis of association indicated that one SNP in CXCL8 and two in CXCR2 influenced the considered traits. To evaluate the existence of functional haplotypic effects, combinations among the three genomic variants (SNP 1 in CXCL8, SNP 6 and SNP 7 in CXCR2) were investigated. Four different haplotypic alleles were identified in the experimental population, one of which at a high frequency (61%). Bulls with Hap 4 (G-C-G at SNP 1, SNP 6, and SNP 7 respectively) had more favourable indexes for SCS (P < 0.05). These results suggest that the SNPs in CXCL8 and CXCR2 may be potential genetic markers to improve udder health in the Simmental breed.

Environmental Factors Affecting the Reproductive Efficiency of Italian Simmental Young Bulls.

The objectives of the study aimed to evaluate the effect of weather conditions and scrotal circumference (SC) on standard semen characteristics of Italian Simmental young bulls (n = 577), all raised in the same performance station and sampled by the artificial vagina (AV) method. Considering the increasing SC, the results showed a significant increase in quantitative semen parameters (p < 0.05 and p < 0.0001, for sperm concentration and total number of spermatozoa, respectively); for every extra centimeter of SC, 17.5 × 106 spermatozoa/mL and 0.102 × 109 of total spermatozoa were produced. The age of the animal at semen collection (395 and 465 days) had similar positive effects. The effect of the average temperature humidity index (THI limits ≤ 40 and ≥70) in the previous 60, 30, and 10 days before the semen collection was also considered. Sixty days before the semen collection, the increasing THI increased both primary (p < 0.0001) and secondary (p < 0.0001) abnormalities while the percentage of morphologically normal spermatozoa decreased (p < 0.0001). Thirty and ten days before collection, the same effect on morphological traits was maintained, but total and progressive motility was also influenced (p < 0.01) with an unexpected increasing pattern. Thus, environmental conditions can influence semen quality during the entire spermatogenesis and results can guide future research on this breed.

Novel SNPs and haplotypes identified in the CD4 gene and their influence on deregressed MACE EBV indexes of milk-related traits in Simmental breed.

Cluster of differentiation 4 (CD4) is the accessory protein non-covalently bound to the T cell receptor that recognizes an invariant region of MHC class II on antigen presenting cells. Its cytoplasmic tail, physically associated with a protein tyrosine kinase, is important in the activation of helper/inducer T lymphocytes. In Bos taurus, CD4 gene is located on chromosome 5 from which two isoforms are transcribed, with a different number of amino acids due to splicing of exon 7 and variation in the reading frame. The aim of this study was to investigate the sequence of the entire CD4 gene in Simmental sires to evaluate the effects of genomic variants on the indexes of the bulls for milk, fat and protein yields, as well as somatic cell score. The associations among genomic variants and indexes were analysed using the Allele and GLM procedures of SAS 9.4. The analysis indicated that only four of the thirty-one identified SNPs influenced the considered traits. Identified variants insist on coding zones and intronic sequences, where we revealed the presence of sites for transcription factors. To evaluate the existence of haplotypic effects, combinations among the four genomic variants (SNP 3, SNP 8, SNP 11 and SNP 19) were investigated. Six different haplotypic alleles were identified, but only four of them were frequent enough to allow for an evaluation of any haplotypic effect (at least six copies in the examined sample): Hap1, Hap2, Hap3 and Hap6. The analysis of associations between the selected haplotypes in the CD4 gene with milk related indexes showed that bulls with Hap2 (T-A-C-C) had better indexes for milk and protein yields (P < 0.05), whereas the presence of the Hap1 haplotype (A-G-A-T) caused a significant decrease of the index for protein yield (P < 0.05). Frequencies of the two alleles Hap1 and Hap2 (9 and 36% respectively) make them of interest for their possible inclusion in breeding schemes and support the hypothesis of considering this gene as a candidate for the improvement of milk-related traits in the Simmental breed.

Investigation of ß-hydroxybutyrate in early lactation of Simmental cows: Genetic parameters and genomic predictions.

Genomic information allows for a more accurate calculation of relationships among animals than the pedigree information, leading to an increase in accuracy of breeding values. Here, we used pedigree-based and single-step genomic approaches to estimate variance components and breeding values for ß-hydroxybutyrate milk content (BHB). Additionally, we performed a genome-wide association study (GWAS) to depict its genetic architecture. BHB concentrations within the first 90 days of lactation, estimated from milk medium infrared spectra, were available for 30,461 cows (70,984 records). Genotypes at 42,152 loci were available for 9,123 animals. Low heritabilities were found for BHB using pedigree-based (0.09 ± 0.01) and genomic (0.10 ± 0.01) approaches. Genetic correlation between BHB and milk traits ranged from -0.27 ± 0.06 (BHB and protein percentage) to 0.13 ± 0.07 (BHB and fat-to-protein ratio) using pedigree and from -0.26 ± 0.05 (BHB and protein percentage) to 0.13 ± 0.06 (BHB and fat-to-protein ratio) using genomics. Breeding values were validated for 344 genotyped cows using linear regression method. The genomic EBV (GEBV) had greater accuracy (0.51 vs. 0.45) and regression coefficient (0.98 vs. 0.95) compared to EBV. The correlation between two subsequent evaluations, without and with phenotypes for validation cows, was 0.85 for GEBV and 0.82 for EBV. Predictive ability (correlation between (G)EBV and adjusted phenotypes) was greater when genomic information was used (0.38) than in the pedigree-based approach (0.31). Validation statistics in the pairwise two-trait models (milk yield, fat and protein percentage, urea, fat/protein ratio, lactose and logarithmic transformation of somatic cells count) were very similar to the ones highlighted for the single-trait model. The GWAS allowed discovering four significant markers located on BTA20 (57.5-58.2 Mb), where the ANKH gene is mapped. This gene has been associated with lactose, alpha-lactalbumin and BHB. Results of this study confirmed the usefulness of genomic information to provide more accurate variance components and breeding values, and important insights about the genomic determination of BHB milk content.

Genome-wide analysis of homozygosity regions in european simmental bulls.

The study of Runs of Homozygosity (ROH) is a useful approach for the characterization of the genome of livestock populations. Due to their high relationship with autozygosity, ROH allow to make inference about population genetic history, to estimate the level of inbreeding, to assess within breed heterogeneity and to detect the footprints of selection on livestock genomes. Aim of this study was to investigate the distribution of runs of homozygosity in bulls belonging to five European Simmental populations and to assess the relationship between three production traits (milk yield, fat and protein contents) and autozygosity. ROH count, distribution and ROH-based coefficient of inbreeding (FROH ) were calculated for 3,845 Simmental bulls of five different European countries: Austria (AT), Switzerland (CH), Czech Republic (CZ), Germany (DE) and Italy (IT). Average values of ROH number per animal, and total genome length covered by ROH were 77.8 ± 20.7 and 205 ± 74.4 Mb, respectively. Bulls from AT, DE and IT exhibited similar ROH characteristics. Swiss animals showed the highest (12.6%), while CZ the lowest (4.6%) FROH coefficient. The relationship between ROH occurrence and milk production traits was investigated through a genome-wide ROH-traits association analysis (GWRA). A total of 34 regions previously associated with milk traits (yield and/or composition) were identified by GWRA. Results of the present research highlight a mixed genetic background in the 5 European Simmental populations, with the possible presence of three subgroups. Moreover, a strong relationship between autozygosity and production traits has been detected.

Beef trait genetic parameters based on old and recent data and its implications for genomic predictions in Italian Simmental cattle.

This study aimed to evaluate the changes in variance components over time to identify a subset of data from the Italian Simmental (IS) population that would yield the most appropriate estimates of genetic parameters and breeding values for beef traits to select young bulls. Data from bulls raised between 1986 and 2017 were used to estimate genetic parameters and breeding values for four beef traits (average daily gain [ADG], body size [BS], muscularity [MUS], and feet and legs [FL]). The phenotypic mean increased during the years of the study for ADG, but it decreased for BS, MUS, and FL. The complete dataset (ALL) was divided into four generational subsets (Gen1, Gen2, Gen3, and Gen4). Additionally, ALL was divided into two larger subsets: the first one (OLD) combined data from Gen1 and Gen2 to represent the starting population, and the second one (CUR) combined data from Gen3 and Gen4 to represent a subpopulation with stronger ties to the current population. Genetic parameters were estimated with a four-trait genomic animal model using a single-step genomic average information restricted maximum likelihood algorithm. Heritability estimates from ALL were 0.26 ± 0.03 for ADG, 0.33 ± 0.04 for BS, 0.55 ± 0.03 for MUS, and 0.23 ± 0.03 for FL. Higher heritability estimates were obtained with OLD and ALL than with CUR. Considerable changes in heritability existed between Gen1 and Gen4 due to fluctuations in both additive genetic and residual variances. Genetic correlations also changed over time, with some values moving from positive to negative or even to zero. Genetic correlations from OLD were stronger than those from CUR. Changes in genetic parameters over time indicated that they should be updated regularly to avoid biases in genomic estimated breeding values (GEBV) and low selection accuracies. GEBV estimated using CUR variance components were less biased and more consistent than those estimated with OLD and ALL variance components. Validation results indicated that data from recent generations produced genetic parameters that more appropriately represent the structure of the current population, yielding accurate GEBV to select young animals and increasing the likelihood of higher genetic gains.

Variance components using genomic information for 2 functional traits in Italian Simmental cattle: Calving interval and lactation persistency.

Functional traits, such as fertility and lactation persistency, are becoming relevant breeding goals for dairy cattle. Fertility is a key element for herd profitability and animal welfare; in particular, calving interval (CIN) is an indicator of female fertility that can be easily recorded. Lactation persistency (LPE; i.e., the ability of a cow to maintain a high milk yield after the lactation peak) is economically important and is related to several other traits, such as feed efficiency, health, and reproduction. The selection of these functional traits is constrained by their low heritability. In this study, variance components for CIN and LPE in the Italian Simmental cattle breed were estimated using genomic and pedigree information under the single-step genomic framework. A data set of 594,257 CIN records (from 275,399 cows) and 285,213 LPE records (from 1563,389 cows) was considered. Phenotypes were limited up to the third parity. The pedigree contained about 2 million animals, and 7,246 genotypes were available. Lactation persistency was estimated using principal component analysis on test day records, with higher values of the second extracted principal component (PC2) values associated with lower LPE, and lower PC2 values associated with higher LPE. Heritability of CIN and LPE were estimated using single-trait repeatability models. A multiple-trait analysis using CIN and production traits (milk, fat, and protein yields) was performed to estimate genetic correlations among these traits. Heritability for CIN in the single-trait model was low (0.06 ± 0.002). Unfavorable genetic correlations were found between CIN and production traits. A measure of LPE was derived using principal component analysis on test day records. The heritability and repeatability of LPE were 0.11 ± 0.004 and 0.20 ± 0.02, respectively. Genetic correlation between CIN and LPE was weak but had a favorable direction. Despite the low heritability estimates, results of the present work suggest the possibility of including these traits in the Italian Simmental breeding program. The use of a single-step approach may provide better results for young genotyped animals without their own phenotypes.

A practical approach to detect ancestral haplotypes in livestock populations.

BACKGROUND: The effects of different evolutionary forces are expected to lead to the conservation, over many generations, of particular genomic regions (haplotypes) due to the development of linkage disequilibrium (LD). The detection and identification of early (ancestral) haplotypes can be used to clarify the evolutionary dynamics of different populations as well as identify selection signatures and genomic regions of interest to be used both in conservation and breeding programs. The aims of this study were to develop a simple procedure to identify ancestral haplotypes segregating across several generations both within and between populations with genetic links based on whole-genome scanning. This procedure was tested with simulated and then applied to real data from different genotyped populations of Spanish, Fleckvieh, Simmental and Brown-Swiss cattle. RESULTS: The identification of ancestral haplotypes has shown coincident patterns of selection across different breeds, allowing the detection of common regions of interest on different bovine chromosomes and mirroring the evolutionary dynamics of the studied populations. These regions, mainly located on chromosomes BTA5, BTA6, BTA7 and BTA21 are related with certain animal traits such as coat colour and milk protein and fat content. CONCLUSION: In agreement with previous studies, the detection of ancestral haplotypes provides useful information for the development and comparison of breeding and conservation programs both through the identification of selection signatures and other regions of interest, and as indicator of the general genetic status of the populations.