Threshold Animal Model Research Articles

Genetic and genomic analyses of testicular hypoplasia in Nellore cattle.

Reproductive performance is a key indicator of the long-term sustainability of any livestock production system. Testicular hypoplasia (TH) is a morphological and functional reproductive disorder that affects bulls around the world and consequently causes major economic losses due to reduced fertility rates. Despite the improvements in management practices to enhance performance of affected animals, the use of hypoplastic animals for reproduction might contribute to expand the prevalence of this disorder. The aim of this study was to identify genomic regions that are associated with TH in Nellore cattle by performing a genome-wide association study (GWAS) and functional analyses. Phenotypic and pedigree data from 47,563 animals and genotypes (500,689 Single Nucleotide Polymorphism, SNPs) from 265 sires were used in this study. TH was evaluated as a binary trait measured at 18 months of age. The estimated breeding values (EBVs) were calculated by fitting a single-trait threshold animal model using a Bayesian approach. The SNP effects were estimated using the Bayes C method and de-regressed EBVs for TH as the response variable (pseudo-phenotype). The top-15 ranking windows (5-adjacent SNPs) that explained the highest proportion of variance were identified for further functional and biological network analyses. The posterior mean (95% highest posterior density) of the heritability for TH was 0.16 (0.08; 0.23). The most important genomic windows were located on BTA1, BTA3, BTA4, BTA5, BTA9, BTA22, BTA23, and BTA25. These windows explained together 22.69% of the total additive genetic variance for TH. Strong candidate genes associated with metabolism and synthesis of steroids, cell survival, spermatogenesis process and sperm motility were identified, which might play an important role in the expression of TH. Our findings contribute to a better biological understanding of TH and future characterization of causal variants might enable improved genomic prediction of this trait in beef cattle.

Genomic evaluation for calf wellness traits in Holstein cattle

Reducing calf morbidity and mortality is important for attaining financial sustainability and improving animal welfare on commercial dairy operations. Zoetis (Kalamazoo, MI) has developed genomic predictions for calf wellness traits in Holsteins that include calf respiratory disease (RESP; recorded between 0 and 365 d of age), calf scours (DIAR; recorded between 2 and 50 d of age), and calf livability (DEAD; recorded between 2 and 365 d of age). Phenotype and pedigree data were from commercial dairies and provided directly by producers upon obtaining their permission. The number of records ranged from 741,484 for DIAR to 1,926,261 for DEAD. The number of genotyped animals was 325,025. All traits were analyzed using a univariate threshold animal model including fixed effect of year of birth × calving season × region, and random effects of herd × year of birth and animal. A total of 45,425 SNP were used in genomic analyses. Animals genotyped with low-density chips were imputed to the required number of SNP. All analyses were conducted using single-step genomic BLUP implementing the "algorithm for proven and young" (APY) animals designed to accommodate very large numbers of genotypes. Estimated heritabilities were 0.042, 0.045, and 0.060 for RESP, DIAR, and DEAD, respectively. The genomic predicted transmitting abilities ranged between -8.0 and 24.0, -11.5 and 28.5, and -6.5 to 22.8 for RESP, DIAR, and DEAD, respectively. Reliabilities of breeding values were obtained by approximation based on partitioning of a function of reliability into contributions from records, pedigree, and genotypes, where the genotype contribution was approximated using the diagonal value of the genomic relationship matrix. The average reliabilities for the genotyped animals were 41.9, 42.6, and 47.3% for RESP, DIAR, and DEAD, respectively. Estimated genomic predicted transmitting abilities and reliabilities were approximately normally distributed for all analyzed traits. Approximated genetic correlations of calf wellness with Zoetis dairy wellness traits and traits included in the US national genetic evaluation were low to moderate. The results indicate that direct evaluation of calf wellness traits under a genomic threshold model is feasible and offers predictions with average reliabilities comparable to other lowly heritable traits. Genetic selection for calf wellness traits presents a compelling opportunity for dairy producers to help manage herd replacement costs and improve overall profitability.

Variance and covariance estimates for resistance to bacterial cold water disease and columnaris disease in two rainbow trout breeding populations1.

Family-based selective breeding can be an effective strategy for controlling diseases in aquaculture. This study aimed to estimate (co)variance components for resistance to bacterial cold water disease (BCWD) and columnaris disease (CD) in two unrelated rainbow trout nucleus breeding populations: the USDA, ARS, National Center for Cool and Cold Water Aquaculture odd-year line (ARS-Fp-R), which has been subjected to five generations of selection for improved resistance to BCWD, and the Troutlodge, Inc., May-spawning odd-year line (TLUM), which has been selected for improved growth performance but not for disease resistance. A total of 46,805 and 27,821 pedigree records were available from both populations, respectively. Between 44 and 138 families per generation and population were evaluated under controlled BCWD and CD challenges, providing 32,311 and 17,861 phenotypic records for BCWD resistance, and 13,603 and 9,413 for CD resistance, in the ARS-Fp-R and TLUM populations, respectively. A two-trait animal threshold model assuming an underlying normal distribution for the binary survival phenotypes was used to estimate (co)variance components separately for each population. Resistance to BCWD (h2 = 0.27 ± 0.04 and 0.43 ± 0.08) and CD (h2 = 0.23 ± 0.07 and 0.34 ± 0.09) was moderately heritable in the ARS-Fp-R and TLUM populations, respectively. The genetic correlation between the resistance to BCWD and CD was favorably positive in the ARS-Fp-R (0.40 ± 0.17) and TLUM (0.39 ± 0.18) populations. These findings suggest that both disease resistance traits can be improved simultaneously even if genetic selection pressure is applied to only one of the two traits.

Genetic Parameters for Resistance to Non-specific Diseases and Production Traits Measured in Challenging and Selection Environments; Application to a Rabbit Case.

Breeding for disease resistance is a challenging but increasingly necessary objective to overcome the issues with the reduced use of antibiotics and growing concern for animal welfare while limiting economic losses. However, implementing such strategies is a complex process because animals face numerous diseases, and the environments on selection farms differ from those on commercial farms. We evaluated whether selection for resistance to non-specific diseases based on a single visual record in selection (S) and challenging (Ch) environments is possible. Records from 23,773 purebred rabbits born between 2012 and 2016 were used in this study. After weaning (at 32 days of age), 17,712 rabbits were raised in the S environment and 6,061 sibs were raised in the Ch environment. Clinical signs of disease were recorded for all animals at the end of the test, at a single time point, at 70 or 80 days of age. The causes of mortality occurring before the end of the test were also recorded. Three disease traits were analyzed: signs of respiratory disease, signs of digestive disease, and a composite trait (Resist) taking into account signs of digestive, respiratory and various infectious diseases. This latter composite trait is proposed to capture the global resistance to disease. All disease traits were binary, with 0 being the absence of symptoms. Two production traits were also recorded: the number of kits born alive (4,121 litters) and the weaning weight (13,090 rabbits). Disease traits were analyzed with animal threshold models, assuming that traits are different in the two environments. Bivariate analyses were carried out using linear animal models. The heritabilities of the disease traits ranged from 0.04 ± 0.01 to 0.11 ± 0.03. The genetic correlations between disease traits in both environments were below unity (≤ 0.84), indicating genotype by environment interactions. Most of the genetic correlations between disease and production traits were not significantly different from zero, except between the weaning weight and Resist_S, with a favorable correlation of −0.34 ± 0.12. Given these genetic parameters, for the same level of exposure of rabbits to pathogens, the expected response to selection is a reduction of disease incidence of 4–6% per generation.

Genetic analysis of subclinical mastitis in early lactation of heifers using both linear and threshold models

Subclinical mastitis (SCM) causes economic losses for dairy producers by reducing milk production and leading to higher incidence of clinical mastitis and premature culling. The prevalence of SCM in first-lactation heifers is highest during early lactation. The objective of this study was to estimate genetic parameters for SCM in early lactation in first-parity Holsteins. Somatic cell count test-day records were collected monthly in 91 Canadian herds participating in the National Cohort of Dairy Farms of the Canadian Bovine Mastitis Research Network. Only the first test-day record available between 5 and 30 d in milk was considered for analysis. The final data set contained 8,518 records from first lactation Holstein heifers. Six alternative traits were defined as indicators of SCM, using various cutoff values of SCC, ranging from 150,000 to 400,000 cells/mL. Both linear and threshold animal models were used. Overall prevalence of SCM using the 6 traits ranged from 13 to 24%. Heritability estimates (standard error) from linear and threshold models ranged from 0.037 to 0.057 (0.015 to 0.018) and from 0.040 to 0.051 (0.017 to 0.020), respectively. We found strong genetic correlations (standard error) among alternative SCC traits, ranging from 0.90 to 0.99 (0.013 to 0.069), indicating that these 6 traits were genetically similar. Despite low heritability, based on estimated breeding values (EBV) predicted from both models, we noted exploitable genetic variation among sires. Higher EBV of SCM resistance corresponded to sires with a higher percentage of daughters without SCM. Based on a linear model (all 6 traits), percentage of daughters with SCM ranged from 5 to 13% and from 19 to 33% for the top 10% and worst 10% of 69 sires with minimum 20 daughters in at least 5 herds, respectively. Spearman's rank correlations among EBV of sires predicted from linear (from 0.75 to 0.95) and threshold (from 0.74 to 0.95) models were moderate to high, respectively. Very high rank correlations (0.98 to 0.99) between EBV predicted for the same trait from linear and threshold model indicated that reranking of sires based on model used was minimal. In conclusion, despite low heritability, we found utilizable genetic variation in early lactation of heifers. Hence, genetic selection to improve genetic resistance to SCM in early lactation of heifers was deemed possible.

Estimates of genetic parameters for growth, reproductive, and carcass traits in Nelore cattle using the single step genomic BLUP procedure

This study was carried out to estimate the heritability and genetic correlations between adjusted weights at 210 (W210) and 450 (W450) days of age, scrotal circumference adjusted at 365 (SC365) and 450 (SC450) days of age, age at first calving (AFC), probability of precocious calving (PPC), stayability (STAY), ribeye area (REA), subcutaneous backfat thickness (BF), and rump fat (RF) traits. The covariance components and genetic parameters for all traits but PPC and STAY were estimated considering a linear animal model, for the remaining traits a threshold animal model was used. The single-step genomic BLUP (ssGBLUP) procedure was used for all traits, and the correlation estimates were obtained by two-traits analysis. The heritability estimated by single-trait analysis were 0.21 ± 0.01, 0.43 ± 0.01, 0.47 ± 0.02, 0.52 ± 0.02, 0.11 ± 0.01, 0.12 (0.07–0.16), 0.37 (0.26–0.38), 0.33 ± 0.02, 0.17 ± 0.01 and 0.33 ± 0.02 for W210, W450, SC365, SC450, AFC, PPC, STAY, REA, BF and RF, respectively. Growth traits (W210 and W450) showed high (0.95) genetic correlation with one another, moderate (0.30 to 0.66) with REA and scrotal circumferences, and low (−0.07 to 0.20) with female reproductive traits (AFC, PPC, and STAY) and fat carcass indicator traits (BF and RF). Female reproductive traits displayed moderate (−0.29 to 0.52) genetic correlations with male reproductive traits, and varied from low to moderate (−0.02 to 0.35) with carcass traits. Additionally, carcass traits exhibited low to moderate (−0.02 to 0.48) genetic correlations with all traits, except for the genetic correlation between BF and RF (0.73). Hence, higher genetic gains by direct selection would be obtained for W450, SC365, SC450, STAY, REA, and RF. Selection to increase growth traits might increase carcass yield and scrotal circumference, and it would not affect carcass fat content, precocity, and cow longevity indicator traits. The results of this study encourage the use of PPC in Nelore cattle since the selection for such trait would improve the productivity and longevity of the cows. The inclusion of carcass quality indicator traits such as BF or RF in selection indices would increase the genetic gain for carcass grade, but it will require further studies to estimate the economic value of these traits.

Genetic associations between mature size and condition score of Nelore cows, and weight, subjective scores and carcass traits as yearlings

The size and body condition of female livestock is critical for improving production efficiency. However, we know little about how height and body condition score in mature beef cattle are genetically related to traits observed when the animals are younger. In the present study, we used data from 321650 Nelore cattle, first, to compare genetic parameters and breeding values on the basis of different models employing weight (MW), height (MH) and body condition score (BCS) of mature cows (3–17 years old). Next, we estimated the genetic correlations between the three traits and assorted yearling traits (YW, weight; YC; conformation score; YP, precocity score; YM, muscling score; YN, navel score; LMA, longissimus muscle area; BF, back fat thickness). Finally, we obtained the expected direct responses to selection for MW, MH and BCS of cows and correlated responses for these traits when the selection was applied to yearling traits. For MW and MH, single-trait Bayesian analyses were used to evaluate the effects of including BCS when defining contemporary groups (BCS included, CG1; BCS not included, CG2). For BCS trait, linear and threshold animal models were compared. After, bi-trait analyses that included MW, MH or BCS with yearling traits were performed. The CG1 scenario resulted in a higher heritability for MW (0.45 ± 0.02) than did CG2 (0.39 ± 0.02). Both scenarios yielded the same heritability estimates for MH (0.35 ± 0.02). Sires’ rank correlations between predicted breeding values under CG1 and CG2 were 0.60–0.92 for MW and 0.90–0.98 for MH, considering different selection intensities. Thus, only for MW genetic evaluations, the incorporation of BCS in the definition of the contemporary groups is indicated. For BCS trait, the same sires were selected regardless of the model (linear or threshold). Genetic correlations between MW and five yearling traits (YW, YC, YP, YM and YN) ranged from 0.18 ± 0.03 to 0.84 ± 0.01. The MH had a higher and positive genetic association with YW (0.64 ± 0.02) and YC (0.54 ± 0.03), than with YN (0.18 ± 0.03). However, MH was negatively and lowly genetically correlated with YP (–0.08 ± 0.03) and YM (–0.14 ± 0.03). The BCS had positive genetic associations with all yearling traits, particularly with YP (0.61 ± 0.06) and YM (0.60 ± 0.07). Mature size and carcass traits exhibited a low to moderate negative genetic correlations. However, BCS had positive genetic associations with LMA (0.38 ± 0.12) and BF (0.32 ± 0.14). Despite a shorter generation interval, selection at the yearling stage will result in a slower genetic progress per generation than does direct selection for cow MW, MH or BCS. Moreover, using YW and YC as selection criteria will increase cattle size at maturity without altering BCS. Last, LMA or BF-based selection will reduce mature size, while improving BCS, as a correlated response.

Threshold and linear models for genetic evaluation of visual scores in Hereford and Braford cattle

Data from 127539 Hereford and Braford cattle were used to compare estimates of genetic parameters for navel, conformation, precocity, muscling and size visual scores at yearling, using linear and threshold animal models. In a second step, these models were cross-validated using a multinomial logistic regression in order to quantify the association between phenotype and genetic merit for each trait. For navel score, higher heritability was obtained with the threshold model (0.42 ± 0.02) in relation to the linear model (0.22 ± 0.02). However, similar heritability was estimated in both models for conformation, precocity, muscling and size, with values of 0.18 ± 0.01, 0.19 ± 0.01, 0.19 ± 0.01 and 0.26 ± 0.01, respectively, using linear model, and of 0.19 ± 0.01, 0.19 ± 0.01, 0.20 ± 0.01, and 0.29 ± 0.01, respectively, using threshold model. For navel score, Spearman correlations between sires’ breeding values predicted using linear and threshold models ranged from 0.60 (1% of the best sires are selected) to 0.96 (all sires are selected). For conformation, precocity, muscling and size scores, low changes in sires’ rank are expected using these models (Spearman correlations >0.86), regardless of the proportion of sires selected. Except for navel with the linear model, the direction of the associations between phenotype and genetic merit were in accordance with its expectation, as there were increases in the phenotype per unit of change in the breeding value. Thus, the threshold model would be recommended to perform genetic evaluation of navel score in this population. However, linear and threshold models showed similar predictive ability for conformation, precocity, muscling and size scores.

Genetic parameter estimation for long endurance trials in the Uruguayan Criollo horse.

The aim of this study was to estimate the genetic parameters of performance in a 750-km, 15-day ride in Criollo horses. Heritability (h2 ) and maternal lineage effects (mt2 ) were obtained for rank, a relative placing measure of performance. Additive genetic and maternal lineage (rmt) correlations among five medium-to-high intensity phase ranks (pRK) and final rank (RK) were also estimated. Individual records from 1,236 Criollo horses from 1979 to 2012 were used. A multivariate threshold animal model was applied to the pRK and RK. Heritability was moderate to low (0.156-0.275). Estimates of mt2 were consistently low (0.04-0.06). Additive genetic correlations between individual pRK and RK were high (0.801-0.924), and the genetic correlations between individual pRKs ranged from 0.763 to 0.847. The pRK heritabilities revealed that some phases were explained by a greater additive component, whereas others showed stronger genetic relationships with RK. Thus, not all pRK may be considered as similar measures of performance in competition.

Genetic parameters and accuracy of traditional and genomic breeding values for eye pigmentation, hair coat and breed standard in Hereford and Braford cattle

The objectives of this research were to estimate genetic parameters using a threshold animal model by traditional (pedigree and phenotype) and single-step genomic BLUP methodologies, and assess breeding value accuracy gains with the inclusion of genomic information for eye pigmentation (EP), hair coat at weaning (HW) and yearling (HY) and breed standard (BS) in Hereford and Braford cattle. The relationship of these traits with tick resistance was also evaluated. The data used in this study were obtained from Conexão Delta G breeding program and belong to animals born between 1991 and 2014, totaling 169,839 individuals in the pedigree data, 73,615 phenotypes for EP, 81,043 for HW, 41,390 for HY, 28,186 for BS and 16,621 for tick count (TC). The genotypic data, after quality control, retained 41,011 SNP markers and 3,954 samples, including 2841 Braford and 909 Hereford animals with phenotypic records for at least one of the considered traits. Estimated heritabilities through traditional and genomic methods ranged from high to medium magnitude, being, respectively 0.46 ± 0.02 and 0.46 ± 0.02 for EP, 0.44 ± 0.03 and 0.44 ± 0.03 for HW, 0.42 ± 0.02 and 0.41 ± 0.02 for HY and 0.33 ± 0.02 and 0.32 ± 0.02 for BS. Genetic correlations among all traits were of low magnitude (-0.23 < rg < 0.29), except between HW and HY (0.62). The use of genomic information provided higher accuracy levels with gains of 0.28 and 0.14 for EP, 0.13 and 0.07 for HW, 0.16 and 0.30 for HY and 0.10 and 0.04 for BS traits, respectively considering k-means and random grouping cross-validation strategies. Thus, it is possible to obtain genetic gains in adaptation through selection for the studied traits. High genetic correlation between the hair coat evaluated at weaning and yearling indicates that selection for these traits can be performed in advance at weaning. Although low, the favorable correlations between adaptation traits favors the selection of animals that are more adapted to the tropical environmental conditions, using correlated responses to increased eye pigmentation and reduced hair coat and tick count simultaneously. The prediction of breeding values using genomic information by the single-step method should result in more accurate predictions compared to traditional pedigree evaluations.

Genetic evaluation of reproductive potential in the Zatorska goose under a conservation program.

The aim of this study was to estimate the genetic parameters and inbreeding effect on the fertility, embryo mortality and hatchability traits in the Zatorska goose covered by the animal genetic resources conservation program. The material for this study contains information about results of hatching of 18863 eggs from 721 dams and 168 sires, laid between 1998-2015. Genetic parameters were estimated based on the threshold animal model by the use of Restricted Maximum Likelihood and Gibbs sampling. The percentage of fertilized eggs ranged yearly between 37-80%. The percentage of embryo mortality was very low, ranging between 4.63-23.73%. The percentage of the hatched goslings from the total number of analyzed eggs was on average 33.18%, and 53.72% from fertilized eggs. On average based on both methods, the heritability estimates of the fertility, embryo mortality and hatchability reached 0.36, 0.07, 0.24 for males and 0.44, 0.11, 0.32 for females. The genetic trend had increasing tendency for fertility and hatchability and was stable for embryo mortality for both sexes. The obtained result shows that the Zatorska goose can be still maintained in the reserves of the local gene pool according to current rules and use in the local market as a breed with good reproductive potential.

Genetic parameters for marbling and body score in Anglonubian goats using Bayesian inference via threshold and linear models.

ObjectiveThe aim of this study was to estimate (co) variance components and genetic parameters for categorical carcass traits using Bayesian inference via mixed linear and threshold animal models in Anglonubian goats.MethodsData were obtained from Anglonubian goats reared in the Brazilian Mid-North region. The traits in study were body condition score, marbling in the rib eye, ribeye area, fat thickness of the sternum, hip height, leg perimeter, and body weight. The numerator relationship matrix contained information from 793 animals. The single- and two-trait analyses were performed to estimate (co) variance components and genetic parameters via linear and threshold animal models. For estimation of genetic parameters, chains with 2 and 4 million cycles were tested. An 1,000,000-cycle initial burn-in was considered with values taken every 250 cycles, in a total of 4,000 samples. Convergence was monitored by Geweke criteria and Monte Carlo error chain.ResultsThreshold model best fits categorical data since it is more efficient to detect genetic variability. In two-trait analysis the contribution of the increase in information and the correlations between traits contributed to increase the estimated values for (co) variance components and heritability, in comparison to single-trait analysis. Heritability estimates for the study traits were from low to moderate magnitude.ConclusionDirect selection of the continuous distribution of traits such as thickness sternal fat and hip height allows obtaining the indirect selection for marbling of ribeye.

Evaluation of genetic resistance to Salmonella Pullorum in three chicken lines

Resistance to diseases varies considerably among populations of the same species and can be ascribed to both genetic and environmental factors. Salmonella Pullorum (SP) is responsible for significant losses in the poultry industry, especially in developing countries. To better understand SP resistance in chicken populations with different genetic backgrounds, we orally challenged 3 chicken lines with SP-a highly selected commercial breed (Rhode Island Red, RIR), a local Chinese chicken (Beijing You, BY), and a synthetic layer line (dwarf, DW)-at 4 d of age. Two traits related to SP resistance, survival, and bacterial carriage in the spleen were evaluated after infection. Survival rates were recorded up to 40 d of age when all chickens still alive were killed to verify the presence of SP in the spleen to determine carrier state. Mortalities for RIR, BY, and DW chicks were 25.1%, 8.3%, and 22.7%, respectively, and the corresponding carrier-states in the spleens were 17.9%, 0.6%, and 15.8%. Survival and carrier-state heritabilities were estimated using an animal threshold model. Survival heritability was 0.197, 0.091, and 0.167 in RIR, BY, and DW populations, respectively, and the heritabilities of carrier state for DW and RIR were 0.32 and 0.16, respectively. This is the first time that the heritability of the SP carrier state has been evaluated in chickens. Our study provides experimental evidence that chickens with various genetic background exhibited significantly different SP-resistant activities and heritabilities. These results may be useful for selecting lines with better disease resistance.

Heritability of patellar luxation in the Chihuahua and Bichon Frise breeds of dogs and effectiveness of a Swedish screening programme

Patellar luxation is one of the more common orthopaedic diseases of dogs and is relatively frequent in some toy breeds, including the Chihuahua and Bichon Frise. Using data provided by the Swedish Kennel Club, genetic parameters, including heritability, were estimated for patellar luxation in the Chihuahua from 1999 to 2014 and in the Bichon Frise from 1997 to 2014. The effects of the current screening programmes for patellar luxation in these breeds were evaluated. Patellar luxation was defined as a binary trait, treating dogs as affected or unaffected. The edited data included 7024 records for the Chihuahua and 1071 records for the Bichon Frise. Patellar luxation was analysed using mixed linear and threshold animal models, including fixed effects of sex, birth month, birth year, age at veterinary examination, random effects of the examining veterinary surgeon, genetic effect of the individual and residual. The prevalence of patellar luxation was 23% in the Chihuahua and 12% in the Bichon Frise. Using threshold analysis, estimated heritabilities were 0.25 for the Chihuahua and 0.21 for the Bichon Frise on the observable scale, and 0.46 for the Chihuahua on the underlying scale. It was concluded that there is genetic variation in patellar luxation and that there has been a slight genetic improvement over the study period in the Chihuahua. Further genetic progress would be facilitated by selection using estimated breeding values based on veterinary screening records.

Genetic analysis of longevity and lamb survival from birth to yearling in Moghani sheep

ABSTRACTThe objective of this study was to estimate genetic parameters for longevity and survival traits from birth to yearling in Moghani breed of sheep. The data set comprised of 4580 lamb survival records collected during 1994 to 2012 in the breeding station of Moghani sheep. Traits studied were cumulative lamb survival from birth up to 3 (S1), 6 (S2), 9 (S3) and 12 (S4) months of age, and corresponding longevity of lambs (L1, L2, L3 and L4, respectively). The linear and threshold animal model analyses were run using a restricted maximum likelihood method and average information algorithm (AIREML) of the WOMBAT software and MATVEC program, respectively. Also, cumulative survival traits were analysed using the sire model through the Weibull proportional hazard function of the MATVEC program. Direct heritability estimates obtained from different linear models varied from 0.004–0.021, 0.014–0.023, 0.058–0.069 and 0.006–0.061 for L1, L2, L3 and L4, respectively. Also, heritability estimates on the logarithmic scale for S1, S2, S3 and S4 obtained from the Weibull sire model were 0.57, 0.40, 0.08 and 0.03, respectively. Medium to high estimates of heritability for survival traits, employing proportional hazard models, suggest that lamb survival could be improved through direct selection within the flock.

Genetic analysis of age at first calving, accumulated productivity, stayability and mature weight of Nellore females

The female reproductive performance, productivity and size are strongly associated with production efficiency of herds raised in a tropical environment. The age at first calving (AFC), accumulated productivity (AP), stayability (STAY) and mature weight (MW) could be used as indicators of these traits. In this study, the genetic parameters and correlations between AFC, AP, STAY and MW measured in Nellore females were estimated, in order to provide support for the beef cattle evaluation programs. In addition, the genetic changes for these traits were obtained. The (co)variance components were estimated by Gibbs sampling by four-trait multivariate analysis, using a threshold animal model for STAY and linear animal model for the other traits (AFC, AP and MW). Heritability of AFC, AP and STAY showed low values, with posterior means of 0.13 ± 0.02, 0.14 ± 0.01 and 0.19 ± 0.03, respectively. On the other hand, for MW were estimated mean heritability of 0.44 ± 0.03 and repeatability of 0.77 ± 0.03, demonstrating the importance of genetic and permanent environmental effects for the expression of beef cows' size. The AFC showed null genetic correlation with AP (−0.06 ± 0.12) and MW (0.01 ± 0.09) and low and negative with STAY (−0.15 ± 0.11). The AP showed high genetic correlation with STAY (0.86 ± 0.03) and weak with MW (0.23 ± 0.09). Positive and moderate genetic association was estimated between STAY and MW (0.66 ± 0.05). Annual direct genetic trends of 0.19 kg, 0.30 units and 0.10 kg were estimated for AP, STAY and MW, respectively, and were significant (P < 0.05) for STAY and MW. For AFC, negative and favorable annual genetic change was estimated (−0.08 months, P < 0.05). In this population, the selection of heifers for an early reproductive age should have little influence, however favorable, in the time that the cows remain in the herd. The use of AP as a selection criterion should result in smaller changes in the females' mature weight when compared to selection based on STAY.

Genome-wide association study for ketosis in US Jerseys using producer-recorded data

Ketosis is one of the most frequently reported metabolic health events in dairy herds. Several genetic analyses of ketosis in dairy cattle have been conducted; however, few have focused specifically on Jersey cattle. The objectives of this research included estimating variance components for susceptibility to ketosis and identification of genomic regions associated with ketosis in Jersey cattle. Voluntary producer-recorded health event data related to ketosis were available from Dairy Records Management Systems (Raleigh, NC). Standardization was implemented to account for the various acronyms used by producers to designate an incidence of ketosis. Events were restricted to the first reported incidence within 60 d after calving in first through fifth parities. After editing, there were a total of 42,233 records from 23,865 cows. A total of 1,750 genotyped animals were used for genomic analyses using 60,671 markers. Because of the binary nature of the trait, a threshold animal model was fitted using THRGIBBS1F90 (version 2.110) using only pedigree information, and genomic information was incorporated using a single-step genomic BLUP approach. Individual single nucleotide polymorphism (SNP) effects and the proportion of variance explained by 10-SNP windows were calculated using postGSf90 (version 1.38). Heritability of susceptibility to ketosis was 0.083 [standard deviation (SD) = 0.021] and 0.078 (SD = 0.018) in pedigree-based and genomic analyses, respectively. The marker with the largest associated effect was located on chromosome 10 at 66.3 Mbp. The 10-SNP window explaining the largest proportion of variance (0.70%) was located on chromosome 6 beginning at 56.1 Mbp. Gene Ontology (GO) and Medical Subject Heading (MeSH) enrichment analyses identified several overrepresented processes and terms related to immune function. Our results indicate that there is a genetic component related to ketosis susceptibility in Jersey cattle and, as such, genetic selection for improved resistance to ketosis is feasible.

Direct and maternal additive effects are not the main determinants of Iberian piglet perinatal mortality.

Data of 127,800 Iberian piglets were used to study genetic parameters of mortality at birth at the piglet level. These records proceed from three data sets: 4,987litter of 2,156 sows of a dam line, 2,768litter of 817 sows of a complete diallel cross between four Iberian strains and 7,153litter of 2,113 sows of the Torbiscal composite line. Perinatal mortality was considered as a binary trait, and Bayesian threshold animal models were fitted to separately analyse the three data sets. The posterior means of direct heritability were 0.010, 0.004 and 0.003, and those of maternal heritability were 0.034, 0.011 and 0.014 for dam line, diallel cross and Torbiscal line, respectively. Important effects of litter size and parity order were inferred in the three data sets, of within-breed cross-breeding parameters in the diallel cross and of sex and sow handling in the Torbiscal line Therefore, the inclusion of perinatal mortality in the objective of selection is questionable in this breed and strategies for reducing piglet mortality successful in other breeds should be considered.

Genetic analysis for quality of frozen embryos produced by Holstein cattle donors in Canada

The number of embryos produced by Holstein donors has been shown to be heritable, so it could be possible to genetically select for this trait to improve the efficiency of the assisted reproductive technology (ART) in dairy cattle. Another important parameter to consider for achieving good results from ART is embryo quality because embryos of good quality have more chance of producing live offspring. The possibility of using genetic selection for increasing the quality of embryo produced from ART has yet to be assessed. The objective of this study was, therefore, to perform a genetic analysis of embryo quality of Holstein donors in Canada using data recorded by Holstein Canada. The data set used was missing quality score data for embryos transferred fresh into a recipient, so the analyses were only performed for frozen embryos. With most traits in the Canadian dairy industry being evaluated with linear models, embryo quality was also evaluated with this class of models. However, considering the categorical nature of embryo quality, a threshold model was also evaluated. Embryo quality data were analyzed with either a univariate linear animal model or a univariate binomial threshold animal model. Genetic parameters estimated from the different models were comparable. A low heritability was found for the donor (0.04 ± <0.01) and the service sire (0.02 ± <0.01), but the repeatability estimate for the donor was higher (0.17), indicating that it was worthwhile to use a repeated records model. Overall, considering the low genetic parameters estimated, slow genetic progress is expected for the quality of frozen embryos produced by Canadian Holstein donors. Rank correlations were calculated between breeding values estimated from different models. High correlations were found between all models, indicating that no substantial re-ranking of the animals is expected from the different models. So, even though a threshold model is better suited for the analysis of categorical data, a linear model could be used for the analysis of embryo quality because it is less computationally demanding.

Genomic analysis of stayability in Nellore cattle.

Stayability, which can be defined as the probability of a cow calving at a certain age when given the opportunity, is an important reproductive trait in beef cattle because it is directly related to herd profitability. The objective of this study was to estimate genetic parameters and to identify possible genomic regions associated with the phenotypic expression of stayability in Nellore cows. The variance components were estimated by Bayesian inference using a threshold animal model that included the systematic effects of contemporary group and sexual precocity and the random effects of animal and residual. The SNP effects were estimated by the single-step genomic BLUP method using information of 2,838 animals (2,020 females and 930 sires) genotyped with the Illumina High-Density BeadChip Array (San Diego, CA, USA). The variance explained by windows formed by 200 consecutive SNPs was used to identify genomic regions of largest effect on the expression of stayability. The heritability was 0.11 ± 0.01 when A matrix (pedigree) was used and 0.14 ± 0.01 when H matrix (relationship matrix that combines pedigree information and SNP data) was used. A total of 147 candidate genes for stayability were identified on chromosomes 1, 2, 5, 6, 9 and 20 and on the X chromosome. New candidate regions for stayability were detected, most of them related to reproductive, immunological and central nervous system functions.