Estimation of genetic parameters and single-step genome-wide association studies for eating time and rumination time in Holstein dairy cows.

The aims of this study were to estimate genetic parameters and to identify genomic regions associated with eating time (ET) and rumination time (RUT) in Holstein dairy cows. Genetic correlations among ET, RUT, and milk yield traits were also estimated. The data were collected from 2019 to 2022 in 6 dairy herds located in the Walloon Region of Belgium. The dataset consisted of daily ET and RUT records on 284 Holstein cows, from which 41 cows had records only for the first parity (P1), 101 cows had records from both the first and second parities, and 142 cows had records only for the second parity (P2). The number of daily ET and RUT records in the P1 and P2 cows were 18,569 (on 142 cows) and 34,464 (on 243 cows), respectively. Data on 28,994 SNPs located on 29 Bos taurus autosomes (BTA) of 747 animals (435 males) were used. Random regression test-day models were used to estimate genetic parameters through the Bayesian Gibbs sampling method. The SNP solutions were estimated using a single-step genomic best linear unbiased prediction approach. The proportion of genetic variance explained by each 20-SNP sliding window (with an average size of 1.52 Mb) was calculated, and regions accounting for at least 1.0% of the total additive genetic variance were used to search for candidate genes. Mean (standard deviation; SD) averaged daily ET and RUT were 327.0 (85.66) and 559.4 (77.69) min/d for cows in P1 and 316.0 (82.24) and 574.2 (75.42) min/d for cows in P2, respectively. Mean (standard deviation; SD) heritability estimates for daily ET and RUT were 0.42 (0.09) and 0.45 (0.06) for cows in P1 and 0.45 (0.04) and 0.43 (0.02) for cows in P2, respectively. Mean (SD) daily genetic correlations between daily ET and RUT were 0.27 (0.07) for P1 and 0.34 (0.08) for P2. Genome-wide association analyses identified 6 genomic regions distributed over 5 chromosomes (BTA1, BTA4, BTA11, 2 regions of BTA14, and BTA17) associated with ET or RUT. The findings of this study increase our preliminary understanding of the genetic background of feeding behavior in dairy cows; however, larger datasets are needed to determine whether ET and RUT might have the potential to be used in selection programs.

Genetic analysis of milk citrate predicted by milk mid-infrared spectra of Holstein cows in early lactation.

Milk citrate is regarded as an early biomarker of negative energy balance in dairy cows during early lactation and serves as a suitable candidate phenotype for genomic selection due to its wide availability across a large number of cows through milk mid-infrared spectra prediction. However, its genetic background is not well known. Therefore, the objectives of this study were to (1) analyze the genetic parameters of milk citrate; (2) identify genomic regions associated with milk citrate; and (3) analyze the functional annotation of candidate genes and quantitative trait loci (QTL) related to milk citrate in Walloon Holstein cows. In total, 134,517 test-day milk-citrate phenotypes (mmol/L) collected within the first 50 d in milk on 52,198 Holstein cows were used. These milk-citrate phenotypes, predicted by milk mid-infrared spectra, were divided into 3 traits according to the first (citrate1), second (citrate2), and third to fifth parity (citrate3+). Genomic information for 566,170 SNPs was available for 4,479 animals. A multiple-trait repeatability model was used to estimate genetic parameters. A single-step GWAS was used to identify candidate genes for citrate and post-GWAS analysis was done to investigate the relationship and function of the identified candidate genes. The heritabilities estimated for citrate1, citrate2, and citrate3+ were 0.40, 0.37, and 0.35, respectively. The genetic correlations among the 3 traits ranged from 0.98 to 0.99. The genomic correlations among the 3 traits were also close to 1.00 across the genomic regions (1 Mb) in the whole genome, which means that citrate can be considered as a single trait in the first 5 parities. In total, 603 significant SNPs located on 3 genomic regions (chromosome 7, 68.569-68.575 Mb; chromosome 14, 0.15-1.90 Mb; and chromosome 20, 54.00-64.28 Mb), were identified to be associated with milk citrate. We identified 89 candidate genes including GPT, ANKH, PPP1R16A, and 32 QTL reported in the literature related to the identified significant SNPs. These identified QTL were mainly reported associated with milk fatty acids and metabolic diseases in dairy cows. This study suggests that milk citrate in Holstein cows is highly heritable and has the potential to be used as an early proxy for the negative energy balance of Holstein cows in a breeding objective.

Exploring a Bayesian sparse factor model-based strategy for the genetic analysis of thousands of MIR-spectra traits for animal breeding.

With the rapid development of animal phenomics and deep phenotyping, we can get thousands of traditional but also molecular phenotypes per individual. However, there is still a lack of exploration regarding how to handle this huge amount of data in the context of animal breeding, presenting a challenge that we are likely to encounter more and more in the future. This study aimed to (1) explore the use of the Mega-scale linear mixed model (MegaLMM), a factor model-based approach, able to simultaneously estimate (co)variance components and genetic parameters in the context of thousands of milk traits, hereafter called thousand-trait (TT) models; (2) compare the phenotype values and genomic breeding values (u) predictions for focal traits (i.e., traits that are targeted for prediction, compared with secondary traits that are helping to evaluate), from single-trait (ST) and TT models, respectively; (3) propose a new approximate method of estimated genomic breeding values (U) prediction with TT models and MegaLMM. 3,421 milk mid-infrared (MIR) spectra wavepoints (called secondary traits) and 3 focal traits [average fat percent (Fat), average methane (CH4), and average somatic cell score (SCS)] collected on 3,302 first-parity Holstein cows were used. The 3,421 milk MIR wavepoints traits were composed of 311 wavepoints in 11 classes (months in lactation). Genotyping information of 564,439 SNP was available for all animals and was used to calculate the genomic relationship matrix. The MegaLMM was implemented in the framework of the Bayesian sparse factor model and solved through Gibbs sampling (Markov chain Monte Carlo). The heritabilities of the studied 3,421 milk MIR wavepoints gradually increased and then decreased in units of 311 wavepoints throughout the lactation. The genetic and phenotypic correlations between the first 311 wavepoints and the other 3,110 wavepoints were low. The accuracies of phenotype predictions from the ST model were lower than those from the TT model for Fat (0.51 vs. 0.93), CH4 (0.30 vs. 0.86), and SCS (0.14 vs. 0.33). The same trend was observed for the accuracies of u predictions: Fat (0.59 vs. 0.86), CH4 (0.47 vs. 0.78), and SCS (0.39 vs. 0.59). The average correlation between U predicted from the TT model and the new approximate method was 0.90. The new approximate method used for estimating U in MegaLMM will enhance the suitability of MegaLMM for applications in animal breeding. This study conducted an initial investigation into the application of thousands of traits in animal breeding and showed that the TT model is beneficial for the prediction of focal traits (phenotype and breeding values), especially for difficult-to-measure traits (e.g., CH4).

The pattern of linkage disequilibrium in Dual-Purpose Belgian Blue cattle.

Quantifying the level of linkage disequilibrium (LD), non-random association of alleles at two or more loci, is important to determine the number of markers needed for genomic selection. The aims of this study were to evaluate the extent of LD in Dual-Purpose Belgian Blue (DPBB) and to compare the level of LD in DPBB with that of Walloon Holstein. Data of 28,427 single nucleotide polymorphisms (SNP), located on 29 Bos taurus autosomes (BTA), of 639 DPBB and 398 Holstein bulls were used. The level of LD between pairwise SNPs separated by up to 10 Mb was evaluated, separately for each breed, using the squared correlation of the alleles at two loci. The analysis of molecular variance showed that the percentage of variation within populations (85.48%) was higher than between populations (14.52%). However, permutation tests showed a significant genetic differentiation between the two studied populations (p < .01). The average LD found between adjacent SNP pairs in DPBB (0.16 (SD = 0.22)) was generally lower than in Holstein (0.23 (SD = 0.27)). The proportion of SNPs in useful LD (r2  > 0.30) within a genomic distance of ≤0.10 Mb between SNPs was 18.58% and 28.23% in DPBB and Holstein bulls, respectively. In both breeds, the effective population size decreased over generations; however, the decline was greater in DPBB than that in Holstein. Based on results, it can be concluded that at least 68,000 SNPs are needed for implementing genomic selection in DPBB cattle with enough accuracy.

Genome-wide association for milk urea concentration in Dual-Purpose Belgian Blue cows.

The objectives of this study were to estimate genetic parameters and identify genomic regions associated with milk urea concentration (MU) in Dual-Purpose Belgian Blue (DPBB) cows. The data were 29,693 test-day records of milk yield (MY), fat yield (FY), protein yield (PY), fat percentage (FP), protein percentage (PP) and MU collected between 2014 and 2020 on 2498 first parity cows (16,935 test-day records) and 1939 second-parity cows (12,758 test-day records) from 49 herds in the Walloon Region of Belgium. Data of 28,266 single nucleotide polymorphisms (SNP), located on 29 Bos taurus autosomes (BTA), on 1699 animals (639 males and 1060 females) were used. Random regression test-day models were used to estimate genetic parameters through the Bayesian Gibbs sampling method using a single chain of 100,000 iterations after a burn-in period of 20,000. SNP solutions were estimated using a single-step genomic best linear unbiased prediction approach. The proportion of genetic variance explained by windows of 25 consecutive SNPs (with an average size of ~2 Mb) was calculated, and regions accounting for at least 1.0% of the total additive genetic variance were used to search for candidate genes. The mean (SD) of MU was 22.89 (10.07) and 22.35 (10.07) mg/dl for first and second parity, respectively. The mean (SD) heritability estimates for daily MU were 0.18 (0.01) and 0.22 (0.02), for first and second parity, respectively. The mean (SD) genetic correlations between daily MU and MY, FY, PY, FP and PP were -0.05 (0.09), -0.07 (0.11), -0.03 (0.13), -0.05 (0.08) and -0.03 (0.11) for first parity, respectively. The corresponding values estimated for second parity were 0.02 (0.10), -0.02 (0.09), 0.02 (0.08), -0.08 (0.06) and -0.05 (0.05). The genome-wide association analyses identified three genomic regions (BTA2, BTA3 and BTA13) associated with MU. The identified regions showed contrasting results between parities and among different stages within each parity. This suggests that different groups of candidate genes underlie the phenotypic expression of MU between parities and among different lactation stages within a parity. The results of this study can be used for future implementation and use of genomic evaluation to reduce MU in DPBB cows.

Extracellular Vesicles from Follicular and Ampullary Fluid Isolated by Density Gradient Ultracentrifugation Improve Bovine Embryo Development and Quality.

Extracellular vesicles (EVs) have been isolated from follicular (FF) and ampullary oviduct fluid (AOF), using different isolation methods. However, it is not clear whether different purification methods can affect the functionality of resulting EVs. Here, we compared two methods (OptiPrep™ density gradient ultracentrifugation (ODG UC) and single-step size exclusion chromatography (SEC) (qEV IZON™ single column)) for the isolation of EVs from bovine FF and AOF. Additionally, we evaluated whether the addition of EVs derived either by ODG UC or SEC from FF or AOF during oocyte maturation would yield extra benefits for embryo developmental competence. The characterization of EVs isolated using ODG UC or SEC from FF and AOF did not show any differences in terms of EV sizes (40-400 nm) and concentrations (2.4 ± 0.2 × 1012-1.8 ± 0.2 × 1013 particles/mL). Blastocyst yield and quality was higher in groups supplemented with EVs isolated from FF and AOF by ODG UC, with higher total cell numbers and a lower apoptotic cell ratio compared with the other groups (p < 0.05). Supplementing in vitro maturation media with EVs derived by ODG UC from AOF was beneficial for bovine embryo development and quality.

Genome-wide association for milk production and lactation curve parameters in Holstein dairy cows.

The aim of this study was to identify genomic regions associated with 305-day milk yield and lactation curve parameters on primiparous (n = 9,910) and multiparous (n = 11,158) Holstein cows. The SNP solutions were estimated using a weighted single-step genomic BLUP approach and imputed high-density panel (777k) genotypes. The proportion of genetic variance explained by windows of 50 consecutive SNP (with an average of 165 Kb) was calculated, and regions that accounted for more than 0.50% of the variance were used to search for candidate genes. Estimated heritabilities were 0.37, 0.34, 0.17, 0.12, 0.30 and 0.19, respectively, for 305-day milk yield, peak yield, peak time, ramp, scale and decay for primiparous cows. Genetic correlations of 305-day milk yield with peak yield, peak time, ramp, scale and decay in primiparous cows were 0.99, 0.63, 0.20, 0.97 and -0.52, respectively. The results identified three windows on BTA14 associated with 305-day milk yield and the parameters of lactation curve in primi- and multiparous cows. Previously proposed candidate genes for milk yield supported by this work include GRINA, CYHR1, FOXH1, TONSL, PPP1R16A, ARHGAP39, MAF1, OPLAH and MROH1, whereas newly identified candidate genes are MIR2308, ZNF7, ZNF34, SLURP1, MAFA and KIFC2 (BTA14). The protein lipidation biological process term, which plays a key role in controlling protein localization and function, was identified as the most important term enriched by the identified genes.

Frozen-thawed ampullary cell monolayer improves bovine embryo in vitro development and quality.

The aim of this study was to evaluate the effects of different timing for frozen-thawed bovine ampullary epithelial cell (BAEC) and bovine oviductal epithelial cell (BOEC) co-culture on the development and quality of bovine embryos produced in vitro. Embryo development was assessed by day 8 blastocyst yield, whereas embryo quality was determined using blastocyst differential cell count, cryotolerance and the expression of selected genes related to embryo quality. The results showed that the presence of BAECs during the last 6 h of in vitro maturation (IVM) increased blastocyst yield and survival of the vitrified-warmed blastocysts. In addition, embryos produced in the presence of BAECs during the last 6 h of IVM or in the presence of BOECs during the first 4 days of in vitro culture (IVC) showed a greater number of trophectoderm cells and a greater inner cell mass. In terms of gene expression, IFN-T was downregulated and PLAC8, AQP3 and ATP1A1 were upregulated in the presence of the BAECs during the last 6 h of the IVM and/or in the presence of BOECs during the first 4 days of IVC. In conclusion, co-culturing bovine oocytes with a frozen-thawed ampullary cell monolayer during the last 6 h of maturation increased blastocyst yield and quality.

Lactation performances in primiparous Holstein cows following short and normal gestation lengths.

Despite decades of research, little is known regarding physiologic temporal limits for initiation of lactation in pregnant non-lactating cattle the aim of this study was to compare the lactation performances in primiparous Holstein cows after a short gestation length (GL) or abortion to those after a normal GL. The data were collected using an automated data collection system. The 94 herds evaluated were located in Belgium, France, Italy, the Netherlands and Germany. Data from a wide range of physiological cow-life events including birth and calving events, reproduction events (insemination, pregnancy checks, and abortions), and milking events were collected. The GL was defined as the interval between the last insemination and the subsequent calving (or abortion) within a range of 150-297 days. Animals were categorized into one of five categories based on GL quantiles (C-I to C-V). Lactation curve parameters including the scale, ramp, and decay were estimated using the Milkbot model. Then, the derived 305-day milk yield (M305-d), peak yield, and time to peak were compared between different GL categories. Of 13,732 lactations, 15 (0.11%) were found with a GL shorter than 210 days (ranging from 158 to 208 days). The 305-day milk yield was significantly lower in the C-I (7,566 ± 186) and C-II groups (7,802 ± 136 kg), compared to the C-III (8,254 ± 116 kg), C-IV (8,148 ± 119 kg), and C-V (8,255 ± 117 kg) groups. The same trends were found for the scale and peak yield of the lactation; the lowest scale were found for the C-I (31.5 ± 0.73) and C-II (32.8 ± 0.53) groups, and the highest were found for the C-III (34.5 ± 0.46), C-IV (34.9 ± 0.45), and C-V (35.0 ± 0.45) groups. Peak yield increased significantly from C-I (27.8 ± 0.66 kg) and C-II group (28.8 ± 0.48 kg) to the C-III (30.2 ± 0.42 kg) and further to the C-IV (30.6 ± 0.40 kg) and C-V (30.6 ± 0.41 kg) groups. Moreover, primiparous cows in the C-II GL category showed a higher milk yield persistency (decay of 1.30E-4 ± 3.55E-5) compared to those belonging to the C-IV (decay of 1.38E-4 ± 2.51E-5) and C-V (decay of 1.38E-4 ± 2.58E-5) group. In conclusion, results showed that primiparous cows with a shorter GL produced significantly less 305-day milk and peak yields, had a higher lactation persistency, and showed a lower upward slope of the lactation curve compared to those with a normal GL.

Investigation in early growth traits, litter size, and lamb survival in two Iranian fat-tailed sheep breeds.

In the present study, 1,635 lambing records of Ghezel (n=766) and Mehraban (n=869) breeds were used to evaluate the early growth traits, litter size, and lamb survival in sheep reared in Fars Province, southern Iran, during a 5-year-long period. The least squares means (± SE) of lamb birth weight for Ghezel were 5.27 (± 0.22), 5.02 (± 0.22), and 3.98 (± 0.23) kg for single males, single females, and twin lambs, respectively; whereas, the corresponding values for Mehraban were 4.39 (± 0.18), 4.18 (± 0.18), and 3.50 (± 0.19) kg. The least squares means of pre-weaning lamb growth (gram per day) for Ghezel were 239 (± 15), 218 (± 15), and 181 (± 16) for single males, single females, and twin lambs, respectively, and the corresponding values for Mehraban were 204 (± 12), 187 (± 12), and 156 (± 13). Lambs from 2 year old ewes or younger were on average lighter at birth and at weaning and had a lower average daily gain than those from older ewes (P<0.05). The percentage of twin births increased from 1.1 and 1.3 % for ewes aged ≤ 2 years to 19 and 12 % for those aged ≥ 6 years old in Ghezel and Mehraban, respectively (P<0.05). The mean pre-weaning lamb mortality was 7.1 and 4.1 % for Ghezel and Mehraban, respectively.

Trends in the reproductive performance of Holstein dairy cows in Iran.

The study was undertaken to determine the trends in the reproductive performance of Holstein dairy cows in Iran during 1994 to 2008. Reproductive performance data for 528,034 lactations of 246,132 cows in 1,822 Holstein dairy herds of Iran were used. The potential effect of calving season, herd, parity, calving year, as well as herd size and 305-day milk production on reproductive performance traits was investigated using multiple regression models. The least squares means of age at first calving decreased by 3.1 (± 0.06) days per year from 806.5 (± 96.3) days in 1994 to 788 (± 89.9) days in 2008. The least squares means of calving interval increased 1.02 (± 0.03) days per year from 394.1 (± 65) days in 1994 to 413.2 (± 81) days in 2008. Greater 305-day milk production was associated with an average increase of 6.55 (± 0.08) days in calving interval per 1,000-kg increase in milk yield. Larger herd size was associated with an average decrease of 0.22 (± 0.02) days in calving interval per 50 cows per herd. The mean number of days dry was 88.6 (± 51.3) days and increased by 0.82 (± 0.02) days per year. In conclusion, reproductive performance in Holstein dairy herds has generally decreased, whereas herd size and milk production have increased over time. Producers may make significant improvements in herd reproduction by reviewing management strategies including the sire selection, reproductive management, inseminator training and techniques, and improved estrous detection. Moreover, it may be advisable for the fertility traits to be included in the genetic selection indices to reduce the rate of reproductive decline.

Prevalence, risk factors and consequent effect of dystocia in holstein dairy cows in iran.

The objective of this research was to determine the prevalence, risk factors and consequent effect of dystocia on lactation performance in Holstein dairy cows in Iran. The data set consisted of 55,577 calving records on 30,879 Holstein cows in 30 dairy herds for the period March 2000 to April 2009. Factors affecting dystocia were analyzed using multivariable logistic regression models through the maximum likelihood method in the GENMOD procedure. The effect of dystocia on lactation performance and factors affecting calf birth weight were analyzed using mixed linear model in the MIXED procedure. The average incidence of dystocia was 10.8% and the mean (SD) calf birth weight was 42.13 (5.42) kg. Primiparous cows had calves with lower body weight and were more likely to require assistance at parturition (p<0.05). Female calves had lower body weight, and had a lower odds ratio for dystocia than male calves (p<0.05). Twins had lower birth weight, and had a higher odds ratio for dystocia than singletons (p<0.05). Cows which gave birth to a calf with higher weight at birth experienced more calving difficulty (OR (95% CI) = 1.1(1.08-1.11). Total 305-d milk, fat and protein yield was 135 (23), 3.16 (0.80) and 6.52 (1.01) kg less, in cows that experienced dystocia at calving compared with those that did not (p<0.05).

Genome-Wide Association Study for Lactation Performance in the Early and Peak Stages of Lactation in Holstein Dairy Cows.

This study aimed to detect genomic loci associated with the lactation performance during 9 to 50 days in milk (DIM) in Holstein dairy cows. Daily milk yield (MY), fat yield (FY), and protein yield (PY) during 9 to 50 DIM were recorded on 134 multiparous Holstein dairy cows distributed in four research herds. Fat- and protein-corrected milk (FPCM), fat-corrected milk (FCM), and energy-corrected milk (ECM) were predicted. The records collected during 9 to 25 DIM were put into the early stage of lactation (EARLY) and those collected during 26 to 50 DIM were put into the peak stage of lactation (PEAK). Then, the mean of traits in each cow included in each lactation stage (EARLY and PEAK) were estimated and used as phenotypic observations for the genome-wide association study. The included animals were genotyped with the Illumina BovineHD Genotyping BeadChip (Illumina Inc., San Diego, CA, USA) for a total of 777,962 single nucleotide polymorphisms (SNPs). After quality control, 585,109 variants were analyzed using GEMMA software in a mixed linear model. Although there was no SNP associated with traits included at the 5% genome-wide significance threshold, 18 SNPs were identified to be associated with milk yield and composition at the suggestive genome-wide significance threshold. Candidate genes identified for milk production traits showed contrasting results between the EARLY and PEAK stages of lactation. This suggests that differential sets of candidate genes underlie the phenotypic expression of the considered traits in the EARLY and PEAK stages of lactation. Although further functional studies are needed to validate our findings in independent populations, it can be concluded that in any genomic study it should be taken into account that the genetic effects of genes related to the lactation performance are not constant during the lactation period.

An Origanum majorana Leaf Diet Influences Myogenin Gene Expression, Performance, and Carcass Characteristics in Lambs.

Myogenin is a protein in the myogenic regulatory factor family that plays an important role in determining carcass and meat traits and is vital for the growth and development of livestock muscles. The objective of this study was to determine the impact of Origanum majorana leaf (MOL) on the myogenin gene expression of lambs. Twenty-four male Kermani lambs were used in a completely randomized design using two experimental groups (0% Origanum majorana L. = MOL0 and 4% Origanum majorana L. = MOL4). Final weight, average daily gain, hot and cold carcass weight, feed conversion ratio, empty body weight, hot and cold dressing percentage, the weight of the shoulder, loin, leg, and lean meat, and the lean/bone ratio were measured. A standard kit was used for extracting total RNA from the loin, leg, and shoulder muscles of the lambs' tissues. The cDNA was synthesized, a real-time PCR was performed, and the obtained data were analyzed. The results of this study showed that the effect of MOL4 on dry matter intake is not significant. The MOL4 diet increased final weight by 8.22%, average daily gain by 28.57%, hot carcass weight by 11.38%, cold carcass weight by 13.43%, feed conversion ratio by 31.03%, empty body weight by 9.38%, hot dressing percentage by 2.92%, cold dressing percentage by 3.75%, shoulder weight by 56.70%, loin weight by 8.98%, leg weight by 10.90%, lean meat weight by 14.62%, and the lean/bone ratio by 2.85% (p < 0.05) compared to the MOL0. Along with adding MOL4 in the lambs' diets, in comparison with MOL0, there was higher expression of myogenin in the loin (3.5 times), leg (3.9 times), and shoulder (3.6 times) muscles of the lambs. Due to the fact that adding Origanum majorana to the diet of the lambs enhanced the expression of the myogenin gene in the loin, leg, and shoulder muscles and increased parameters related to growth, it can be used to improve the parameters related to growth and to increase myogenin gene expression in the muscle of lambs.

Genetic Aspects of Somatic Cell Count in Holstein Dairy Cows in Iran.

The aim of this study was to estimate the genetic parameters of somatic cell count (SCC) and its relationship with production traits in the first three parities in Iranian Holstein dairy cows. Data were 1,891,559 test-day records of SCC, milk yield, and milk compositions on 276,217 lactations on 147,278 cows distributed in 134 herds. The number of test-day records in the first, second and third parities were 995,788 (on 147,278 cows), 593,848 (on 85,153 cows), and 301,923 (on 43,786 cows), respectively. Test-day SCCs were transformed to somatic cell scores (SCS). A random regression test-day animal model through four-trait three-lactation was used to estimate variance components for test-day records of SCS and lactation traits were included. Gibbs sampling was used to obtain marginal posterior distributions for the various parameters using a single chain of 200,000 iterates in which the first 50,000 iterates of each chain were regarded as a burn-in period. The mean heritability estimates for SCS (0.15 to 0.18) were lower than those for milk yield (0.36 to 0.38), fat yield (0.30 to 0.31), protein yield (0.31 to 0.32), fat percentage (0.21 to 0.25), and protein percentage (0.21 to 0.22). Low negative genetic correlations ranging from -0.05 to -0.30 were found between SCS and yield traits (milk, fat, and protein yields). The genetic correlation found between SCS and fat percentage was close to zero, however, a low positive genetic correlation ranging from 0.12 to 0.17 was found between SCS and protein percentage. Based on the results, it can be concluded that genetic selection for decreasing SCS would also increase lactation yield. The estimates found in this study can be used to perform breeding value estimations for national genetic evaluations in Iranian Holsteins using a multiple-trait, multiple-lactation random regression model.

Genetic parameters for milk urea and its relationship with milk yield and compositions in Holstein dairy cows.

The aim was to estimate genetic parameters for milk urea (MU) concentration and its relationship with milk yield and compositions in Holstein dairy Cows. Edited data were 90,594 test-day records of milk yield and composition collected during 2015 to 2018 on 13,737 lactations obtained from 7,850 Holstein cows in 50 herds. Random regression test-day model was used to estimate genetic parameters. (Co)variance components were estimated with the Bayesian Gibbs sampling method using a single chain of 400,000 iterates. The first 50,000 iterates of each chain were regarded as a burn-in period. Mean (SD) of MU was 23.03 (5.99) and 22.41 (5.74) mg/dl in primiparous and multiparous cows, respectively. Average heritability estimates for daily MU was 0.33 (SD = 0.02) ranged 0.29 to 0.36 and 0.32 (SD = 0.03) ranged 0.27 to 0.34, respectively, for primiparous and multiparous cows. The mean (SD) genetic correlation between MU and milk yield, fat yield, protein yield, lactose yield, fat percentage, protein percentage, lactose percentage, and somatic cell score was, respectively, -0.02 (0.03), -0.02 (0.01), 0.01 (0.04), 0.01 (0.03), 0.00 (0.07), -0.03 (0.04), 0.00 (0.01), -0.11 (0.06) in primiparous cows. The corresponding values in multiparous cows were -0.01 (0.02), -0.01 (0.03), -0.04 (0.04), -0.04 (0.04), 0.04 (0.04), 0.04 (0.07), -0.03 (0.09), 0.06 (0.11), respectively. The results indicate that selection on MU is possible with no effect on milk yield or compositions, however, relationships between MU and other important traits such as longevity, metabolic diseases, and fertility are needed.

Association between age at first calving and lactation performance, lactation curve, calving interval, calf birth weight, and dystocia in Holstein dairy cows.

In the present study, records on 115,291 heifers distributed in 113 herds were used to investigate the association between age at the first calving (AFC) and lactation performance, lactation curve, the length of the first calving interval (CI), calf birth weight (CBW), and the incidence of dystocia in Holstein heifers in Iran. Based on the AFC, the heifers were classified into eight classes: AFC of 541 to 690 d, 691 to 720 d, 721 to 750 d, 751 to 780 d, 781 to 810 d, 811 to 840 d, 841 to 900 d, and 901 to 1200 d (AFC1 to AFC8, respectively). Multiple regression mixed models were used to investigate the association between AFC and lactation curve parameters, partial and 305-d lactation performance, 100- and 305-d SCS, and the length of the first calving (CI) interval. The mean (SD) and median AFC across all heifers was 760.2 (74.01) and 750 d, respectively. Of 115,291 heifers included, 28,192 and 7,602 heifers were, respectively, ≤ 720 and > 900 d when calving for the first time. More than 44% of the heifers were at 691 to 750 d (23 to 25 months) of age when calving for the first time. An increased AFC was associated with increased partial and 305-d lactation performance, 100- and 305-d SCS, initial milk yield, milk production at the peak of lactation, upward and downward slopes of the lactation curve. The 305-d fat percentage was associated with AFC; however, there was no association between AFC and 305-d protein percentage. An increased AFC was also associated with decreased milk production persistency, delayed peak time, longer CI, and higher calf birth weight. Compared to heifers calving for the first time between 691 to 780 d (23 to 26 months) of age, both increasing and decreasing AFC were associated with increased risk of dystocia. Controlling AFC is an important management factor in achieving a lower risk of dystocia, higher lactation performance, lower SCS, and shorter length of the calving interval.

Reproductive and embryological toxicity of lead acetate in male mice and their offspring and mitigation effects of quercetin.

Exposure to heavy metals not only impacts on fertility in males, it may also affect the offspring. The aim of the present study was to examine the toxic effects of lead acetate on fertility in male mice and their offspring, and the potential effect of quercetin on mitigating the likely effects. Experimental mice were randomly divided into three groups and administered with (i) distilled water (control); (ii) lead acetate (150 mg/kg BW/day); (iii) lead acetate (150 mg/kg BW/day) with quercetin (75 mg/kg BW/day). Lead acetate administration in male mice adversely affected their fertility through changes in sperm motility, viability, morphology, maturity, membrane integrity, and intracellular reactive oxygen species (P <  0.05). Similar findings were observed in the offspring of the lead-treated male mice. Early embryonic development and implantation rate were also adversely influenced in both the sires and offspring when male mice were treated with lead acetate (P <  0.05). The data demonstrated that down-regulation of Cks2 (CDC28 protein kinase regulatory subunit-2) in sperm had an association with early embryonic development in lead acetate treated group. In conclusion, lead acetate administration adversely impacted on the fertility of the male mice and their male offspring fertility; on the other hand, paternal quercetin co-administration somewhat ameliorated the adverse effects of lead on male mice and their offspring.

Systems Biology-Derived Genetic Signatures of Mastitis in Dairy Cattle: A New Avenue for Drug Repurposing.

Mastitis, a disease with high incidence worldwide, is the most prevalent and costly disease in the dairy industry. Gram-negative bacteria such as Escherichia coli (E. coli) are assumed to be among the leading agents causing acute severe infection with clinical signs. E. Coli, environmental mastitis pathogens, are the primary etiological agents of bovine mastitis in well-managed dairy farms. Response to E. Coli infection has a complex pattern affected by genetic and environmental parameters. On the other hand, the efficacy of antibiotics and/or anti-inflammatory treatment in E. coli mastitis is still a topic of scientific debate, and studies on the treatment of clinical cases show conflicting results. Unraveling the bio-signature of mastitis in dairy cattle can open new avenues for drug repurposing. In the current research, a novel, semi-supervised heterogeneous label propagation algorithm named Heter-LP, which applies both local and global network features for data integration, was used to potentially identify novel therapeutic avenues for the treatment of E. coli mastitis. Online data repositories relevant to known diseases, drugs, and gene targets, along with other specialized biological information for E. coli mastitis, including critical genes with robust bio-signatures, drugs, and related disorders, were used as input data for analysis with the Heter-LP algorithm. Our research identified novel drugs such as Glibenclamide, Ipratropium, Salbutamol, and Carbidopa as possible therapeutics that could be used against E. coli mastitis. Predicted relationships can be used by pharmaceutical scientists or veterinarians to find commercially efficacious medicines or a combination of two or more active compounds to treat this infectious disease.

A Genome-Wide Association Study for Calving Interval in Holstein Dairy Cows Using Weighted Single-Step Genomic BLUP Approach.

The aim of the present study was to identify genomic region(s) associated with the length of the calving interval in primiparous (n = 6866) and multiparous (n = 5071) Holstein cows. The single nucleotide polymorphism (SNP) solutions were estimated using a weighted single-step genomic best linear unbiased prediction (WssGBLUP) approach and imputed high-density panel (777 k) genotypes. The effects of markers and the genomic estimated breeding values (GEBV) of the animals were obtained by five iterations of WssGBLUP. The results showed that the accuracies of GEBVs with WssGBLUP improved by +5.4 to +5.7, (primiparous cows) and +9.4 to +9.7 (multiparous cows) percent points over accuracies from the pedigree-based BLUP. The most accurate genomic evaluation was provided at the second iteration of WssGBLUP, which was used to identify associated genomic regions using a windows-based GWAS procedure. The proportion of additive genetic variance explained by windows of 50 consecutive SNPs (with an average of 165 Kb) was calculated and the region(s) that accounted for equal to or more than 0.20% of the total additive genetic variance were used to search for candidate genes. Three windows of 50 consecutive SNPs (BTA3, BTA6, and BTA7) were identified to be associated with the length of the calving interval in primi- and multiparous cows, while the window with the highest percentage of explained genetic variance was located on BTA3 position 49.42 to 49.52 Mb. There were five genes including ARHGAP29, SEC24D, METTL14, SLC36A2, and SLC36A3 inside the windows associated with the length of the calving interval. The biological process terms including alanine transport, L-alanine transport, proline transport, and glycine transport were identified as the most important terms enriched by the genes inside the identified windows.