Genetic correlations of direct and indirect genetic components of social dominance with fitness and morphology traits in cattle

BACKGROUND

Within the same species, individuals show marked variation in their social dominance. Studies on a handful of populations have indicated heritable genetic variation for this trait, which is determined by both the genetic background of the individual (direct genetic effect) and of its opponent (indirect genetic effect). However, the evolutionary consequences of selection for this trait are largely speculative, as it is not a usual target of selection in livestock populations. Moreover, studying social dominance presents the challenge of working with a phenotype with a mean value that cannot change in the population, as for every winner of an agonistic interaction there will necessarily be a loser. Thus, to investigate what could be the evolutionary response to selection for social dominance, it is necessary to focus on traits that might be correlated with it. This study investigated the genetic correlations of social dominance, both direct and indirect, with several morphology and fitness traits. We used a dataset of agonistic contests involving cattle (Bos taurus): during these contests, pairs of cows compete in ritualized interactions to assess social dominance. The outcomes of 37,996 dominance interactions performed by 8789 cows over 20 years were combined with individual data for fertility, mammary health, milk yield and morphology and analysed using bivariate animal models including indirect genetic effects.

RESULTS

We found that winning agonistic interactions has a positive genetic correlation with more developed frontal muscle mass, lower fertility, and poorer udder health. We also discovered that the trends of changes in the estimated breeding values of social dominance, udder health and more developed muscle mass were consistent with selection for social dominance in the population.

CONCLUSIONS

We present evidence that social dominance is genetically correlated with fitness traits, as well as empirical evidence of the possible evolutionary trade-offs between these traits. We show that it is feasible to estimate genetic correlations involving dyadic social traits.

Mastitis: What It Is, Current Diagnostics, and the Potential of Metabolomics to Identify New Predictive Biomarkers

Periparturient diseases continue to be the greatest challenge to both farmers and dairy cows. They are associated with a decrease in productivity, lower profitability, and a negative impact on cows’ health as well as public health. This review article discusses the pathophysiology and diagnostic opportunities of mastitis, the most common disease of dairy cows. To better understand the disease, we dive deep into the causative agents, traditional paradigms, and the use of new technologies for diagnosis, treatment, and prevention of mastitis. This paper takes a systems biology approach by highlighting the relationship of mastitis with other diseases and introduces the use of omics sciences, specifically metabolomics and its analytical techniques. Concluding, this review is backed up by multiple studies that show how earlier identification of mastitis through predictive biomarkers can benefit the dairy industry and improve the overall animal health.

Genome-Wide Association Studies for Milk Somatic Cell Score in Romanian Dairy Cattle

Mastitis is one of the most frequently encountered diseases in dairy cattle, negatively affecting animal welfare and milk production. For this reason, contributions to understanding its genomic architecture are of great interest. Genome-wide association studies (GWAS) have identified multiple loci associated with somatic cell score (SCS) and mastitis in cattle. However, most of the studies have been conducted in different parts of the world on various breeds, and none of the investigations have studied the genetic architecture of mastitis in Romanian dairy cattle breeds up to this point in time. In this study, we report the first GWAS for SCS in dairy cattle breeds from Romania. For GWAS, we used an Axiom Bovine v3 SNP-chip (>63,000 Single Nucleotide Polymorphism -SNPs) and 33,330 records from 690 cows belonging to Romanian Spotted (RS) and Romanian Brown (RB) cattle. The results found one SNP significantly associated with SCS in the RS breed and 40 suggestive SNPs with -log₁₀ (p) from 4 to 4.9 for RS and from 4 to 5.4 in RB. From these, 14 markers were located near 12 known genes (AKAP8, CLHC1, MEGF10, SATB2, GATA6, SPATA6, COL12A1, EPS8, LUZP2, RAMAC, IL12A and ANKRD55) in RB cattle, 3 markers were close to ZDHHC19, DAPK1 and MMP7 genes, while one SNP overlapped the HERC3 gene in RS cattle. Four genes (HERC3, LUZP2, AKAP8 and MEGF10) associated with SCS in this study were previously reported in different studies. The most significant SNP (rs110749552) associated with SCS was located within the HERC3 gene. In both breeds, the SNPs and position of association signals were distinct among the three parities, denoting that mastitis is controlled by different genes that are dependent according to parity. The current results contribute to an expansion in the body of knowledge regarding the proportion of genetic variability explained by SNPs for SCS in dairy cattle.

Genetic analysis of resilience indicators based on milk yield records in different lactations and at different lactation stages

Resilience is the ability of cows to cope with disturbances, such as pathogens or heat waves. To breed for improved resilience, it is important to know whether resilience genetically changes throughout life. Therefore, the aim was to perform a genetic analysis on 2 resilience indicators based on data from 3 periods of the first lactation (d 11-110, 111-210, and 211-340) and the first 3 full lactations, and to estimate genetic correlations with health traits. The resilience indicators were the natural log-transformed variance (LnVar) and lag-1 autocorrelation (r_auto) of daily deviations in milk yield from an expected lactation curve. Low LnVar and r_auto indicate low variability in daily milk yield and quick recovery, and were expected to indicate good resilience. Data of 200,084 first, 155,784 second, and 89,990 third lactations were used. Heritabilities were similar based on different lactation periods (0.12-0.15 for LnVar, 0.05-0.06 for r_auto). However, the heritabilities of the resilience indicators based on full first lactation were higher than those based on lactation periods (0.20 for LnVar, 0.08 for r_auto), due to lower residual variances. Heritabilities decreased from 0.20 in full lactation 1 to 0.19 in full lactation 3 for LnVar and from 0.08 to 0.06 for r_auto. For LnVar, as well as for r_auto, the strongest genetic correlation between lactation periods was between period 2 and 3 (0.97 for LnVar, 0.96 for r_auto) and the weakest between period 1 and 3 (0.81 for LnVar, 0.65 for r_auto). Similarly, for both traits the genetic correlation between full lactations was strongest between lactations 2 and 3 (0.99 for LnVar, 0.95 for r_auto) and weakest between lactations 1 and 3 (0.91 for LnVar, 0.71 for r_auto). For LnVar, genetic correlations with resilience-related traits, such as udder health, ketosis, and longevity, adjusted for correlations with milk yield, were almost always favorable (-0.59 to 0.02). In most cases these genetic correlations were stronger based on full lactations than on lactation periods. Genetic correlations were similar across full lactations, but the correlation with udder health increased substantially from -0.31 in lactation 1 to -0.51 in lactation 3. For r_auto, genetic correlations with resilience-related traits were always favorable in lactation period 1 and in most full lactations, but not in the other lactation periods. However, correlations were weak (-0.27 to 0.15). Therefore, as a resilience indicator for breeding, LnVar is preferred over r_auto. A multitrait index based on estimated breeding values for LnVar in lactations 1, 2, and 3 is recommended to improve resilience throughout the lifetime of a cow.

Heritability estimates of predicted blood β-hydroxybutyrate and nonesterified fatty acids and relationships with milk traits in early-lactation Holstein cows

At the beginning of lactation, high-producing cows commonly experience an unbalanced energy status that is often responsible for the onset of metabolic disorders and impaired health and performance. Blood β-hydroxybutyrate (BHB) and nonesterified fatty acids (NEFA) are indicators of excessive fat mobilization and circulating ketone bodies. Recently, prediction models based on mid-infrared (MIR) spectroscopy have been developed to assess blood BHB and NEFA from routinely collected individual milk samples. This study aimed to estimate genetic parameters of blood BHB and NEFA predicted from milk MIR spectra and to assess their phenotypic and genetic correlations with milk production and composition traits in early-lactation Holstein cows. The data set comprised the first test-day record within lactation and spectra of individual milk samples (n = 22,718) of 13,106 Holstein cows collected from 5 to 35 d in milk (DIM). Blood BHB and NEFA were predicted from milk MIR spectra using previously developed prediction models. Genetic parameters of blood metabolites and milk traits were estimated for the whole observational period (5-35 DIM) and within 6 classes of DIM. Blood BHB and NEFA showed similar genetic variation across DIM, with the highest heritability in the first 10 d after calving (0.31 ± 0.06 and 0.19 ± 0.05 for BHB and NEFA, respectively). The genetic correlation between BHB and NEFA was moderate (0.51 ± 0.05). Genetic correlations of BHB with milk yield, SCS, protein percentage, lactose percentage, and urea nitrogen content were similar to, or at least in the same direction as, the correlations of NEFA with the same traits, whereas opposite correlations were observed with fat percentage and fat-to-protein ratio. Results of the current study suggest that blood BHB and NEFA predicted from milk MIR spectra have genetic variation that is potentially exploitable for breeding purposes. Therefore, they could be used as indicator traits of hyperketonemia in a selection index aimed to reduce the susceptibility of dairy cows to metabolic disorders in early lactation.

Three Novel Players: PTK2B, SYK, and TNFRSF21 Were Identified to Be Involved in the Regulation of Bovine Mastitis Susceptibility via GWAS and Post-transcriptional Analysis

Bovine mastitis is a common inflammatory disease caused by multiple factors in early lactation or dry period. Genome wide association studies (GWAS) can provide a convenient and effective strategy for understanding the biological basis of mastitis and better prevention. 2b-RADseq is a high-throughput sequencing technique that offers a powerful method for genome-wide genetic marker development and genotyping. In this study, single nucleotide polymorphisms (SNPs) of the immune-regulated gene correlative with mastitis were screened and identified by two stage association analysis via GWAS-2b-RADseq in Chinese Holstein cows. We have screened 10,058 high quality SNPs from 7,957,920 tags and calculated their allele frequencies. Twenty-seven significant SNPs were co-labeled in two GWAS analysis models [Bayesian (P < 0.001) and Logistic regression (P < 0.01)], and only three SNPs (rs75762330, C > T, PIC = 0.2999; rs88640083, A > G, PIC = 0.1676; rs20438858, G > A, PIC = 0.3366) were annotated to immune-regulated genes (PTK2B, SYK, and TNFRSF21). Identified three SNPs are located in non-coding regions with low or moderate genetic polymorphisms. However, independent sample population validation (Case-control study) data showed that three important SNPs (rs75762330, P < 0.025, OR > 1; rs88640083, P < 0.005, OR > 1; rs20438858, P < 0.001, OR < 1) were significantly associated with clinical mastitis trait. Importantly, PTK2B and SYK expression was down-regulated in both peripheral blood leukocytes (PBLs) of clinical mastitis cows and in vitro LPS (E. coli)-stimulated bovine mammary epithelial cells, while TNFRSF21 was up-regulated. Under the same conditions, expression of Toll-like receptor 4 (TLR4), AKT1, and pro-inflammatory factors (IL-1β and IL-8) were also up-regulated. Interestingly, network analysis indicated that PTK2B and SYK are co-expressed in innate immune signaling pathway of Chinese Holstein. Taken together, these results provided strong evidence for the study of SNPs in bovine mastitis, and revealed the role of SYK, PTK2B, and TNFRSF21 in bovine mastitis susceptibility/tolerance.

Genetic correlations of fighting ability with somatic cells and longevity in cattle

The success in competitions may be stressful for animals and costly in terms of immune functions and longevity. Focusing on Aosta Chestnut and Aosta Black Pied cattle, selected for their fighting ability in traditional competitions, this study investigated the genetic relationships of fighting ability with udder health traits (somatic cell score and two threshold traits for somatic cells), longevity (length of productive life and number of calvings) and test-day milk, fat and protein yield. Herdbook information and phenotypic records that have been routinely collected for breeding programs in 16 years were used for the abovementioned traits. Data belonged to 9328 cows and 19 283 animals in pedigree. Single-trait animal model analyses were run using a Gibbs sampling algorithm to estimate the variance components of traits, and bivariate analyses were then performed to estimate the genetic correlations. Moderate positive genetic correlations (ra) were found for fighting ability with somatic cell score (ra=0.255), suggesting that greater fighting ability is genetically related to a detriment in udder health, in agreement with the theory. The high positive genetic correlation between fighting ability and longevity (average ra=0.669) suggests that the economic importance of fighting ability (the winning cows get an higher price at selling) had probably masked the true genetic covariances. The genetic correlation between milk yield traits and fighting ability showed large intervals, but the negative values (average ra=-0.121) agreed with previous research. This study is one of the few empirical studies on genetic correlations for the competitive success v. immune functions and longevity traits. The knowledge of the genetic correlations among productive and functional traits of interest, including fighting ability, is important in animal breeding for a sustainable genetic improvement.

Genetic Selection for Mastitis Resistance

Mastitis is a prevalent and costly disease on dairy farms. Improved management and hygiene can reduce the risk of infection by contagious or environmental pathogens, and genetic selection can confer permanent improvement in mastitis resistance. National veterinary recording systems in the Nordic countries have allowed direct selection for sire families with low incidence of clinical mastitis for 3 decades, whereas other countries have practiced indirect selection for lower somatic cell count. Recently, pooling of producer-recorded data from on-farm herd management software programs has enabled selection for reduced incidence of clinical mastitis in the United States and other leading dairy countries.

Symposium review: Novel strategies to genetically improve mastitis resistance in dairy cattle

Mastitis is a disease of major economic importance to the dairy cattle sector because of the high incidence of clinical mastitis and prevalence of subclinical mastitis and, consequently, the costs associated with treatment, production losses, and reduced animal welfare. Disease-recording systems compiling data from a large number of farms are still not widely implemented around the world; thus, selection for mastitis resistance is often based on genetically correlated indicator traits such as somatic cell count (SCC), udder depth, and fore udder attachment. However, in the past years, several countries have initiated collection systems of clinical mastitis, based on producers recording data in most cases. The large data sets generated have enabled researchers to assess incidence of this disease and to investigate the genetic background of clinical mastitis itself, as well as its relationships with other traits of interest to the dairy industry. The genetic correlations between clinical mastitis and its previous proxies were estimated more accurately and confirmed the strong relationship of clinical mastitis with SCC and udder depth. New traits deriving from SCC were also studied, with the most relevant findings being associated with mean somatic cell score (SCS) in early lactation, standard deviation of SCS, and excessive test-day SCC pattern. Genetic correlations between clinical mastitis and other economically important traits indicated that selection for mastitis resistance would also improve resistance against other diseases and enhance both fertility and longevity. However, milk yield remains negatively correlated with clinical mastitis, emphasizing the importance of including health traits in the breeding objectives to achieve genetic progress for all important traits. These studies enabled the establishment of new genetic and genomic evaluation models, which are more efficient for selection to mastitis resistance. Further studies that are potential keys for future improvement of mastitis resistance are deep investigation of the bacteriology of mastitis, identification of novel indicator traits and tools for selection, and development of a larger female reference population to improve reliability of genomic evaluations. These cutting-edge studies will result in a better understanding of the genetic background of mastitis resistance and enable a more accurate phenotyping and genetic selection to improve mastitis resistance, and consequently, animal welfare and industry profitability.

Genetic correlations among milk yield, morphology, performance test traits and somatic cells in dual-purpose Rendena breed

Selection in native local breeds needs great carefulness due to the small population size and the risk of inbreeding. Furthermore, most breeds are dual-purpose, and milk and beef attitudes are antagonistic. For preservation purposes functional traits need to be considered. Focusing on the small local Rendena cattle, this study aimed to analyse the genetic correlations among milk, beef and udder health traits and the response to selection predicted under different scenarios. The study considered milk, fat and protein yields (MY), factor scores for udder volume (UV), conformation (UC) and muscularity obtained from type traits scored on primiparous cows, and performance test traits (PT) measured on young bulls at test station: average daily gain, in vivo SEUROP fleshiness, in vivo dressing percentage. Somatic cell score (SCS) was considered as a functional trait, with a possibility of restricting its genetic gain to zero. The study considered 281 497 MY test-day data collected on 16 974 cows, and data from linear type evaluation on 11 992 primiparous cows for factor scores. The PT data were recorded on 1428 young bulls, and SCS obtained from cell counts at milk recording. Bi-trait restricted maximum likelihood animal model analyses were performed to assess genetic parameters. Heritability varied from 0.157 (fat) to 0.442 (dressing percentage). Udder volume and MY resulted positively genetically correlated (average correlation 0.427), whereas the low-negative genetic correlation between MY and UC (-0.141) suggested a negative impact of milk gain on udder form. Beef traits of factor muscularity and PT showed medium-high favourable genetic correlations (from 0.357 to 0.984), excluding a null correlation between daily gain and muscularity. The genetic correlation MY v. muscularity was unfavourable (-0.328 on average), whereas null correlations were found in MY v. PT, apart from fat v. dressing percentage (-0.151). Somatic cell score showed low unfavourable correlations with protein (0.111) and UV (0.092), and favourable correlations with UC (-0.193). Response to selection in different scenarios indicated a good balanced gain for milk and beef when standardized economic weights of 0.66 and 0.34 are given to the two attitudes, and SCS genetic gain is restricted. Current genetic trends (MY and PT increasing, but muscularity lessening) reflect a stronger selection for milk, suggesting a slight progressive change towards a milk conformation. Aiming to preserve the dual-purpose characteristics of a breed, proper breeding policies taking into account the genetic relationships among traits and including functional traits should be applied in local dual-purpose populations.

Bivariate threshold models for genetic evaluation of susceptibility to and ability to recover from mastitis in Danish Holstein cows

Mastitis in dairy cows is an unavoidable problem and genetic variation in recovery from mastitis, in addition to susceptibility, is therefore of interest. Genetic parameters for susceptibility to and recovery from mastitis were estimated for Danish Holstein-Friesian cows using data from automatic milking systems equipped with online somatic cell count measuring units. The somatic cell count measurements were converted to elevated mastitis risk, a continuous variable [on a (0-1) scale] indicating the risk of mastitis. Risk values >0.6 were assumed to indicate that a cow had mastitis. For each cow and lactation, the sequence of health states (mastitic or healthy) was converted to a weekly transition: 0 if the cow stayed within the same state and 1 if the cow changed state. The result was 2 series of transitions: one for healthy to diseased (HD, to model mastitis susceptibility) and the other for diseased to healthy (DH, to model recovery ability). The 2 series of transitions were analyzed with bivariate threshold models, including several systematic effects and a function of time. The model included effects of herd, parity, herd-test-week, permanent environment (to account for the repetitive nature of transition records from a cow) plus two time-varying effects (lactation stage and time within episode). In early lactation, there was an increased risk of getting mastitis but the risk remained stable afterwards. Mean recovery rate was 45% per lactation. Heritabilities were 0.07 [posterior mean of standard deviations (PSD) = 0.03] for HD and 0.08 (PSD = 0.03) for DH. The genetic correlation between HD and DH has a posterior mean of -0.83 (PSD = 0.13). Although susceptibility and recovery from mastitis are strongly negatively correlated, recovery can be considered as a new trait for selection.

Impact of udder and teat morphometry on udder health in Tharparkar cows under climatic condition of hot arid region of Thar Desert

Prevention of subclinical mastitis (SCM) is an important tool for sustainable dairying and implementing higher production level in animals. The present investigation involved a total of 397 quarters of milk examination of 105 indigenous Tharparkar cows at Livestock Research Centre, Chandan located in the Jaisalmer district of Rajasthan in Thar Desert to study the impact of udder and teat morphometry on udder health. Udder health was examined by somatic cell count to check the status of subclinical mastitis while udder and teat morphometry of 90 udder and 386 quarters, i.e., udder shape and depth, teat end shape, teat length, and teat diameter were examined at individual animal level and quarter level. Data were collected from the record register maintained at the farm and data evaluated by parity (no. of lactation) and stage of lactation. On analysis of variance, result revealed the significantly (P < 0.05) higher incidence of SCM was for pendulous shape udder in respect of regular udder, as well as for inverted and flat teat end shape in respect of pointed teat end shape. Large teat length and upper depth animals had significantly (P < 0.05) more incidence of SCM as compared to small and medium teat length and udder depth group, respectively. Thick teat diameter group animals were significantly (P < 0.01) more prone to infection as compared to medium and thin teat diameter group animals. So, it can be concluded that selection for optimum udder and teat morphometry in breeding program may help to reduce susceptibility for intramammary infections in Tharparkar cows. Microbiological study of milk samples could be helpful in the nearby future for identification of subclinical mastitis.

Genetic parameters for milk fatty acids, milk yield and quality traits of a Holstein cattle population reared under tropical conditions

Information about genetic parameters is essential for selection decisions and genetic evaluation. These estimates are population specific; however, there are few studies with dairy cattle populations reared under tropical and sub-tropical conditions. Thus, the aim was to obtain estimates of heritability and genetic correlations for milk yield and quality traits using pedigree and genomic information from a Holstein population maintained in a tropical environment. Phenotypic records (n = 36 457) of 4203 cows as well as the genotypes for 57 368 single nucleotide polymorphisms from 755 of these cows were used. Covariance components were estimated using the restricted maximum likelihood method under a mixed animal model, considering a pedigree-based relationship matrix or a combined pedigree-genomic matrix. High heritabilities (around 0.30) were estimated for lactose and protein content in milk whereas moderate values (between 0.19 and 0.26) were obtained for percentages of fat, saturated fatty acids and palmitic acid in milk. Genetic correlations ranging from -0.38 to -0.13 were determined between milk yield and composition traits. The smaller estimates compared to other similar studies can be due to poor environmental conditions, which may reduce genetic variability. These results highlight the importance in using genetic parameters estimated in the population under evaluation for selection decisions.

Genetic Analysis of Milk Yield in First-Lactation Holstein Friesian in Ethiopia: A Lactation Average vs Random Regression Test-Day Model Analysis

The development of effective genetic evaluations and selection of sires requires accurate estimates of genetic parameters for all economically important traits in the breeding goal. The main objective of this study was to assess the relative performance of the traditional lactation average model (LAM) against the random regression test-day model (RRM) in the estimation of genetic parameters and prediction of breeding values for Holstein Friesian herds in Ethiopia. The data used consisted of 6,500 test-day (TD) records from 800 first-lactation Holstein Friesian cows that calved between 1997 and 2013. Co-variance components were estimated using the average information restricted maximum likelihood method under single trait animal model. The estimate of heritability for first-lactation milk yield was 0.30 from LAM whilst estimates from the RRM model ranged from 0.17 to 0.29 for the different stages of lactation. Genetic correlations between different TDs in first-lactation Holstein Friesian ranged from 0.37 to 0.99. The observed genetic correlation was less than unity between milk yields at different TDs, which indicated that the assumption of LAM may not be optimal for accurate evaluation of the genetic merit of animals. A close look at estimated breeding values from both models showed that RRM had higher standard deviation compared to LAM indicating that the TD model makes efficient utilization of TD information. Correlations of breeding values between models ranged from 0.90 to 0.96 for different group of sires and cows and marked re-rankings were observed in top sires and cows in moving from the traditional LAM to RRM evaluations.

Genetic analysis of clinical mastitis data for Holstein cattle in the Czech Republic

Abstract. Cases of mastitis were recorded from 22 812 lactations of 10 294 cows on seven farms in the Czech Republic from 2000 to 2012. The per cow number of clinical mastitis (CM) cases per lactation (CM1), number of days of CM per lactation (CM2), and CM considered as an all-or-none trait (CM3) with values of 0 (no CM case) or 1 (at least 1 CM case) were analyzed with linear animal models. Bivariate linear animal models were used for estimation of genetic correlations between CM traits and average lactation somatic cell score (SCS305), average 305-day milk (MY305), fat (FY305) and protein (PY305) yield, and interval between calving and first insemination (INT) and days open (DO). Factors included in the model of choice were parity, herd effect, year of calving, calving season, permanent environmental effect of the cow, and additive genetic effect of the cow. Estimated heritabilities for CM traits were in the range of 0.09 to 0.10. Genetic correlations of SCS305 with CM traits 1, 2, and 3 were 0.22 ± 0.062, 0.23 ± 0.064, and 0.29 ± 0.086, respectively; those of MY305 with the three CM traits were 0.80 ± 0.037, 0.79 ± 0.040, and 0.83 ± 0.038, respectively; those of INT with the three CM traits were 0.19 ± 0.087, 0.17 ± 0.089, and 0.26 ± 0.091, respectively; and those of DO with the three CM traits were 0.28 ± 0.089, 0.22 ± 0.091, and 0.27 ± 0.091, respectively. Knowledge of genetic parameters of mastitis incidence and assessment of the economic importance of the disease is necessary to design breeding programs to improve udder health.

Estimation of Genetic Parameters for Somatic Cell Scores of Holsteins Using Multi-trait Lactation Models in Korea

The study was conducted to analyze the genetic parameters of somatic cell score (SCS) of Holstein cows, which is an important indicator to udder health. Test-day records of somatic cell counts (SCC) of 305-day lactation design from first to fifth lactations were collected on Holsteins in Korea during 2000 to 2012. Records of animals within 18 to 42 months, 30 to 54 months, 42 to 66 months, 54 to 78 months, and 66 to 90 months of age at the first, second, third, fourth and fifth parities were analyzed, respectively. Somatic cell scores were calculated, and adjusted for lactation production stages by Wilmink's function. Lactation averages of SCS (LSCS1 through LSCS5) were derived by further adjustments of each test-day SCS for five age groups in particular lactations. Two datasets were prepared through restrictions on number of sires/herd and dams/herd, progenies/sire, and number of parities/cow to reduce data size and attain better relationships among animals. All LSCS traits were treated as individual trait and, analyzed through multiple-trait sire models and single trait animal models via VCE 6.0 software package. Herd-year was fitted as a random effect. Age at calving was regressed as a fixed covariate. The mean LSCS of five lactations were between 3.507 and 4.322 that corresponded to a SCC range between 71,000 and 125,000 cells/mL; with coefficient of variation from 28.2% to 29.9%. Heritability estimates from sire models were within the range of 0.10 to 0.16 for all LSCS. Heritability was the highest at lactation 2 from both datasets (0.14/0.16) and lowest at lactation 5 (0.11/0.10) using sire model. Heritabilities from single trait animal model analyses were slightly higher than sire models. Genetic correlations between LSCS traits were strong (0.62 to 0.99). Very strong associations (0.96 to 0.99) were present between successive records of later lactations. Phenotypic correlations were relatively weaker (<0.55). All correlations became weaker at distant lactations. The estimated breeding values (EBVs) of LSCS traits were somewhat similar over the years for a particular lactation, but increased with lactation number increment. The lowest EBV in first lactation indicated that selection for SCS (mastitis resistance) might be better with later lactation records. It is expected that results obtained from these multi-trait lactation model analyses, being the first large scale SCS data analysis in Korea, would create a good starting step for application of advanced statistical tools for future genomic studies focusing on selection for mastitis resistance in Holsteins of Korea.

Farmer-observed health data around calving--Genetic parameters and association with veterinarian diagnoses in Austrian Fleckvieh cows

The objective of this study was to investigate if farmer-observed health data around calving can be used together with veterinarian diagnoses for genetic evaluations. Four diseases are recorded by farmers: retained placenta, downer cow syndrome, mastitis, and lameness. Mean disease frequencies were 4.7, 3.8, and 1.8% for retained placenta, downer cow syndrome, and mastitis, respectively. Lameness had a very low frequency (0.7%) and a preliminary analysis revealed a heritability close to zero for this trait. Therefore, lameness was not considered in the analysis. For genetic analyses, univariate and bivariate linear animal models were fitted. Heritabilities for retained placenta, downer cow syndrome, and mastitis were 0.01, 0.03, and 0.003, respectively. Genetic correlations among the investigated disease traits were low to moderate and not significantly different from zero. Pearson correlations between estimated breeding values for disease traits and other routinely evaluated traits were computed, which revealed mostly favorable relationships to fertility, maternal calving ease, muscling, and longevity. In addition, a moderate favorable association was found between mastitis and somatic cell score. Heritability estimates of farmer-observed health traits were comparable to estimates based on veterinarian diagnoses. Genetic correlations between the investigated diseases based on farmer observations and veterinarian diagnoses were almost 1, with estimates ranging from 0.98 to 0.99. These results suggest that farmer recorded health data could be used together with veterinarian diagnoses for genetic evaluations.

Invited review: overview of new traits and phenotyping strategies in dairy cattle with a focus on functional traits

For several decades, breeding goals in dairy cattle focussed on increased milk production. However, many functional traits have negative genetic correlations with milk yield, and reductions in genetic merit for health and fitness have been observed. Herd management has been challenged to compensate for these effects and to balance fertility, udder health and metabolic diseases against increased production to maximize profit without compromising welfare. Functional traits, such as direct information on cow health, have also become more important because of growing concern about animal well-being and consumer demands for healthy and natural products. There are major concerns about the impact of drugs used in veterinary medicine on the spread of antibiotic-resistant strains of bacteria that can negatively impact human health. Sustainability and efficiency are also increasingly important because of the growing competition for high-quality, plant-based sources of energy and protein. Disruptions to global environments because of climate change may encourage yet more emphasis on these traits. To be successful, it is vital that there be a balance between the effort required for data recording and subsequent benefits. The motivation of farmers and other stakeholders involved in documentation and recording is essential to ensure good data quality. To keep labour costs reasonable, existing data sources should be used as much as possible. Examples include the use of milk composition data to provide additional information about the metabolic status or energy balance of the animals. Recent advances in the use of mid-infrared spectroscopy to measure milk have shown considerable promise, and may provide cost-effective alternative phenotypes for difficult or expensive-to-measure traits, such as feed efficiency. There are other valuable data sources in countries that have compulsory documentation of veterinary treatments and drug use. Additional sources of data outside of the farm include, for example, slaughter houses (meat composition and quality) and veterinary labs (specific pathogens, viral loads). At the farm level, many data are available from automated and semi-automated milking and management systems. Electronic devices measuring physiological status or activity parameters can be used to predict events such as oestrus, and also behavioural traits. Challenges concerning the predictive biology of indicator traits or standardization need to be solved. To develop effective selection programmes for new traits, the development of large databases is necessary so that high-reliability breeding values can be estimated. For expensive-to-record traits, extensive phenotyping in combination with genotyping of females is a possibility.

Genetic associations of test-day fat:protein ratio with milk yield, fertility, and udder health traits in Nordic Red cattle

Interest is growing in finding indicator traits for the evaluation of nutritional or tissue energy status of animals directly at the individual animal level. The development and subsequent use of such traits in practice demands a clear understanding of the genetic and phenotypic associations with the various production and functional traits. In this study, the relationships during lactation between milk fat:protein ratio (FPR) and production and functional traits were estimated for Nordic Red cattle, in which published information is scarce. The objectives of this study were to estimate genetic associations of FPR with milk yield (MY), fertility, and udder health traits during different stages of lactation. Traits included in the analyses were MY, 4 fertility traits-days from calving to insemination (DFI), days open (DO), number of inseminations (NI), and nonreturn rate to 56 d (NRR)-and 2 udder health traits-test-day somatic cell score (SCS) and clinical mastitis (CM). Data were from a total of 22,422 first-lactation cows. Random regression models were used to estimate genetic parameters and associations between traits. The mean FPR in first-lactation cows was 1.28 and ranged from 1.25 to 1.45. During first lactation, the heritability of FPR ranged from 0.14 to 0.25. Genetic correlations between FPR and MY in early lactation (until 50 d in milk) were positive and ranged from 0.05 to 0.22; later in lactation, they were close to zero or negative, indicating that cows may have come out of the negative state of energy balance. The strength of genetic associations between FPR and fertility traits varied during lactation. In early lactation, correlations between FPR and the interval fertility traits DFI and DO were positive and ranged from 0.14 to 0.28. Genetic correlations between FPR and the udder health traits SCS and CM in early lactation ranged from 0.09 to 0.20. Milk fat:protein ratio is a heritable trait and easily available from routine milk-recording schemes. It can be used as a low-cost monitoring tool of poor health and fertility in the most critical phases of lactation and as an important indicator trait to improve robustness in dairy cows through selection.

Genetic correlations of days open with production traits and contents in milk of major fatty acids predicted by mid-infrared spectrometry

The objective of this study was to estimate the genetic relationships between days open (DO) and both milk production traits and fatty acid (FA) content in milk predicted by mid-infrared spectrometry. The edited data set included 143,332 FA and production test-day records and 29,792 DO records from 29,792 cows in 1,170 herds. (Co)variances were estimated using a series of 2-trait models that included a random regression for milk production and FA traits. In contrast to the genetic correlations with fat content, those between DO and FA content in milk changed considerably over the lactation. The genetic correlations with DO for unsaturated FA, monounsaturated FA, long-chain FA, C18:0, and C18:1 cis-9 were positive in early lactation but negative after 100 d in milk. For the other FA, genetic correlations with DO were negative across the whole lactation. At 5 d in milk, the genetic correlation between DO and C18:1 cis-9 was 0.39, whereas the genetic correlations between DO and C6:0 to C16:0 FA ranged from -0.37 to -0.23. These results substantiated the known relationship between fertility and energy balance status, explained by the release of long-chain FA in early lactation, from the mobilization of body fat reserves, and the consequent inhibition of de novo FA synthesis in the mammary gland. At 200 d in milk, the genetic correlations between DO and FA content ranged from -0.38 for C18:1 cis-9 to -0.03 for C6:0. This research indicates an opportunity to use FA content in milk as an indicator trait to supplement the prediction of genetic merit for fertility.

Somatic cell score genetic parameter estimates of dairy cattle in Portugal using fractional polynomials

Milk somatic cell count is an indicator trait for mastitis resistance. Genetic parameters for somatic cell score in the Portuguese Holstein-Friesian population were estimated by modeling the pattern of genetic correlation over the first 3 lactations (days in milk) with a random regression model. Data records from the first 3 lactations were from the national database of the Portuguese Holstein Association herds. Heritability estimates ranged from 0.05 at the beginning of the lactation for the 3 lactations, to 0.07 at the end of the lactation period for the first and third lactations, to 0.09 for the second lactation. This increase in the heritability values was due to an increase in the genetic variance and a decrease in the residual variances. Genetic correlations evaluated for monthly time points were high (0.65 to 0.99) for all 3 lactations, whereas phenotypic correlations were much less than the genetic correlations (0.13 to 0.62).

The effect of management system on mortality and other welfare indicators in Pennsylvania dairy herds

The objective of this study was to identify farm characteristics that were associated with cow (Bos taurus) welfare outcomes, including mortality rate, culling by 60 days of lactation, survival to ≥ 6 years of age and ≥ 5th parity (aged cows), somatic cell score, milk yield, and milk composition. Data were collected on housing systems, feeding systems, pasture strategies, bedding type, labour management practices and other farm characteristics in face-to-face interviews with 314 Pennsylvania dairy herd owners where performance records were available. Five herd management systems were identified in the sample: free-stalls with complete confinement (n = 37); free-stalls that allowed outdoor access (n = 76); tie-stalls with complete confinement (n = 52); tie-stalls with outdoor access and that fed a total mixed ration (n = 72); and tie-stalls with outdoor access and that did not feed a total mixed ration (n = 77). Welfare outcomes were evaluated with multivariable linear regression models and marginal means were estimated for herd management system. Tie-stalls that allowed outdoor access and that did not feed total mixed rations had the lowest mortality rate (2.0%), culling in the first 60 days of lactation (5.1%), and the highest proportion of aged cows (13.8%). Those herds also had high lifetime-to-date milk yield, a low proportion of fat-protein inversions, and low somatic cell scores. Free-stalls with complete confinement had significantly higher levels of mortality (8.3%), culling in the first 60 days of lactation (9.7%), and fewer aged cows (6.4%). It was concluded that shifts toward more efficient herd management systems have not benefited cow health and welfare. This suggests that cow welfare has been compromised to facilitate the economic survival of dairy farms.

Comparison of different models for genetic analysis of clinical mastitis in Austrian Fleckvieh dual-purpose cows

The performance of different models for genetic analyses of clinical mastitis in Austrian Fleckvieh dual-purpose cows was evaluated. The main objective was to compare threshold sire models (probit and logit) with linear sire and linear animal models using REML algorithm. For comparison, data were also analyzed using a Bayesian threshold sire model. The models were evaluated with respect to ranking of sires and their predictive ability in cross-validation. Only minor differences were observed in estimated variance components and heritability from Bayesian and REML probit models. Heritabilities for probit and logit models were 0.06 and 0.08, respectively, whereas heritabilities for linear sire and linear animal models were lower (0.02). Correlations among ranking of sires from threshold and linear sire models were high (>0.99), whereas correlations between any sire model (threshold or linear) and the linear animal model were slightly lower (0.96). The worst sires were ranked very similar across all models, whereas for the best sires some reranking occurred. Further, models were evaluated based on their ability to predict future data, which is one of the main concerns of animal breeders. The predictive ability of each model was determined by using 2 criteria: mean squared error and Pearson correlation between predicted and observed value. Overall, the 5 models did not differ in predictive ability. In contrast to expectations, sire models had the same predictive ability as animal models. Linear models were found to be robust toward departures from normality and performed equally well as threshold models.

Genetic architecture of rainbow trout survival from egg to adult

Survival from birth to a reproductive adult is a challenge that only robust individuals resistant to a variety of mortality factors will overcome. To assess whether survival traits share genetic architecture throughout the life cycle, we estimated genetic correlations for survival within fingerling stage, and across egg, fingerling and grow-out stages in farmed rainbow trout. Genetic parameters of survival at three life cycle stages were estimated for 249 166 individuals originating from ten year classes of a pedigreed population. Despite being an important fitness component, survival traits harboured significant but modest amount of genetic variation (h2=0.07-0.27). Weak associations between survival during egg-fry and fingerling periods, between early and late fingerling periods (rG=0.30) and generally low genetic correlations between fingerling and grow-out survival (mean rG=0.06) suggested that life-stage specific survival traits are best regarded as separate traits. However, in the sub-set of data with detailed time of death records, positive genetic correlations between early and late fingerling survival (rG=0.89) showed that during certain years the best genotypes in the early period were also among the best in the late period. That survival across fingerling period can be genetically the same, trait was indicated also by only slightly higher heritability (h2=0.15) estimated with the survival analysis of time to death during fingerling period compared to the analysis treating fingerling survival as a binary character (h2=0.11). The results imply that (1) inherited resistance against unknown mortality factors exists, but (2) ranking of genotypes changes across life stages.

Relationship between the lactation curve and udder disease incidence in different lactation stages in first-lactation Holstein cows

We examined the relationships between the shape of the first parity lactation curve and udder disease incidence at different stages of lactation in 538 Holstein cows. Data used were first-parity daily milk yields and treatment records. Each cow was classified according to whether or not it had had udder disease at least once over the whole lactation period or in one of three stages within the lactation period. We then examined the differences in the shapes of the lactation curves between the disease incidence and non-incidence group in each stage. Cows that had high rates of increase in milk yield and high milk yields in early lactation were predisposed to udder disease afterwards. Cows with high milk production over a long period but with low lactation persistency were predisposed to udder disease after the peak of lactation. There was no difference in total milk yield between incidence and non-incidence groups in all stages, suggesting that, for a comparable level of lactation, cows without udder diseases have flatter lactation curves.