The Survival Kit: software to analyze survival data including possibly correlated random effects

Gut microbiome and resistome characterization of pigs treated with commonly used post-weaning diarrhea treatments

BACKGROUND

The global burden of antimicrobial resistance demands additional measures to ensure the sustainable and conscious use of antimicrobials. For the swine industry, the post-weaning period is critical and for many years, antimicrobials have been the most effective strategy to control and treat post-weaning related infections. Among them, post-weaning diarrhea causes vast economic losses, as it severely compromises piglets' health and growth performance. In this study, 210 piglets were transferred from a farm with recurrent cases of post-weaning diarrhea to an experimental farm and divided into six different treatment groups to determine the effect of the different treatments on the growth performance and survival, the microbiome, and the resistome in a cross-sectional and longitudinal study. The different treatments included antimicrobials trimethoprim/sulfamethoxazole, colistin, and gentamicin, an oral commercial vaccine, a control with water acidification, and an untreated control. An extra group remained at the farm of origin following the implemented amoxicillin routine treatment. A total of 280 fecal samples from pigs at four different sampling times were selected for metagenomics: before weaning-treatment at the farm of origin, and three days, two weeks, and four weeks post-treatment.

RESULTS

The control group with water acidification showed a reduced death risk in the survival analyses and non-significant differences in average daily weight gain in comparison to the antibiotic-treated groups. However, the growth-promoting effect among antibiotic-treated groups was demonstrated when comparing against the untreated control group at the experimental farm. After four weeks of treatment, diversity indexes revealed significantly decreased diversity for the untreated control and the group that remained at the farm of origin treated with amoxicillin. For this last group, impaired microbial diversity could be related to the continuous amoxicillin treatment carried out at the farm. Analysis of the resistome showed that both gentamicin and amoxicillin treatments significantly contributed to the emergence of resistance, while trimethoprim/sulphonamide and colistin did not, suggesting that different treatments contribute differently to the emergence of resistance.

CONCLUSIONS

Overall, this shotgun longitudinal metagenomics analysis demonstrates that non-antibiotic alternatives, such as water acidification, can contribute to reducing the emergence of antimicrobial resistance without compromising pig growth performance and gut microbiome.

Longevity in South African Afrikaner cows as assessed through survival analysis

The Afrikaner breed of cattle is indigenous to South Africa and, due to their hardiness, was once the most popular breed amongst South African farmers, although in recent years their numbers have decreased. The goal of this study was to assess factors affecting length of productive life, defined as the interval between production of the first and last calf, in Afrikaner cattle using survival analysis. The data spanned 40 years with an observed measure of length of life for 29,379 cows from 374 herds. Relative to similar analyses, few (n = 2964; 8.4%) cows had records that were right censored. The median length of productive life of an Afrikaner cow was just less than 6 years. Cows that were younger at their first parturition had longer productive lives than those that were older at their first calving. Cows that were born in the period from December to February had shorter productive lives than those born between March and November. The estimated animal genetic variance of 0.266 resulted in a heritability estimate for length of productive life in Afrikaner cattle of 0.225. Thus, there appeared to be sufficient additive genetic variance in Afrikaner cattle to enable genetic improvement in their length of productive life.

Genetic evaluation for survival traits in Japanese quail line selected for fast growth rate

The main objectives of this study were to estimate genetic parameters for the survival, longevity and evaluate risk factors for the occurrence of mortality in a Japanese quail line selected for high growth rate during the period from hatch to 21 days of age (GR1-21) for eight generations and its control. Total number of 1095, 2289 and 16,506 for sires, dams and progeny, respectively, was used to estimate genetic parameters, a separate hatch of 687 chicks was used to examine the risk factors of quails in the selected (SL, 438) and control (CL, 249) lines. The proportion of censored quails until 42 days of age was 82.20 and 87.14 for SL and CL, respectively. The CL showed higher longevity than SL (38.42 vs. 36.86 days). In the two tested lines, mortality% significantly declined when body weight at death increased, however, the CL had a higher reduction of mortality% than the SL (50 vs. 42%). Survival and longevity had low heritability values, low genetic and phenotypic correlations between survival and longevity with GR1-21 and ranging from 0.025 to 0.208. The survival tended to be less correlated with GR1-21 and body weight at marketing age than the longevity.

Combined single-step evaluation of functional longevity of dairy cows including correlated traits

BACKGROUND

For years, multiple trait genetic evaluations have been used to increase the accuracy of estimated breeding values (EBV) using information from correlated traits. In France, accurate approximations of multiple trait evaluations were implemented for traits that are described by different models by combining the results of univariate best linear unbiased prediction (BLUP) evaluations. Functional longevity (FL) is the trait that has most benefited from this approach. Currently, with many single-step (SS) evaluations, only univariate FL evaluations can be run. The aim of this study was to implement a "combined" SS (CSS) evaluation that extends the "combined" BLUP evaluation to obtain more accurate genomic (G) EBV for FL when information from five correlated traits (somatic cell score, clinical mastitis, conception rate for heifers and cows, and udder depth) is added.

RESULTS

GEBV obtained from univariate SS (USS) evaluations and from a CSS evaluation were compared. The correlations between these GEBV showed the benefits of including information from correlated traits. Indeed, a CSS evaluation run without any performances on FL showed that the indirect information from correlated traits to evaluate FL was substantial. USS and CSS evaluations that mimic SS evaluations with data available in 2016 were compared. For each evaluation separately, the GEBV were sorted and then split into 10 consecutive groups (deciles). Survival curves were calculated for each group, based on the observed productive life of these cows as known in 2021. Regardless of their genotyping status, the worst group of heifers based on their GEBV in 2016 was well identified in the CSS evaluation and they had a substantially shorter herd life, while those in the best heifer group had a longer herd life. The gaps between groups were more important for the genotyped than the ungenotyped heifers, which indicates better prediction of future survival.

CONCLUSIONS

A CSS evaluation is an efficient tool to improve FL. It allows a proper combination of information on functional traits that influence culling. In contrast, because of the strong selection intensity on young bulls for functional traits, the benefit of such a "combined" evaluation of functional traits is more modest for these males.

Analysis of Calving Ease and Stillbirth and Their Impact on the Length of Functional Productive Life in Slovak Holstein Cattle

The aim of the study was to determine the frequency of births according to the categories of calving difficulty and stillbirths and to evaluate the effect of these factors on the longevity of cows. Longevity is one of the traits that affect the overall profit in the dairy industry. A Weibull proportional hazard model was used to evaluate the influence of functional traits such as calving ease and stillbirth. Longevity was expressed as the length of a functional, productive life from the first calving to death or censoring, which was corrected for milk yield. The database included 918,568 calvings, where calving without assistance represented 83.34%, calving with the assistance of one person or the use of a slight mechanical pull represented 14.47%, difficult calving with the assistance of several people, the use of mechanical traction or the intervention of a veterinarian represented 2.16%, and cesarean section represented 0.03%. The mortality of calves, stillborn or dead within 48 h of birth, represented 1.07% and 6.59%, respectively. The frequency of alive female calves was higher (46.84%) than male calves (45.50%). Cows with higher lactations had almost half as many stillborn calves as heifers. The most stillborn calves were found in difficult births (59.48%). In easy calving, this proportion was 2.48%. Using survival analysis, we estimated the significant influence of the factors such as parity, milk production, herd size, age at first calving, herd × year × season, sex of calf, calving ease, and stillbirth on the length of the functional, productive life of cows. The risk of early culling of the cows with moderately difficult calving was 1.259 times higher than in the cows with easy calving. Difficult calving and cesarean section shorten the productive life, and the risk of culling reached 1.711 and 1.894, respectively. Cows that gave birth to a dead calf achieved a 2.939 times higher risk of culling compared to cows that gave birth to a live calf. In this study, a higher risk of early culling was found in cows that gave birth to a male calf. Evaluation of the calving ease and stillbirth can be used as indirect indicators at an earlier age of the animal in the selection process for long-lived animals with good productive and reproductive performance.

Survival analysis of productive life in Florida dairy goats using a Cox proportional hazards model

Longevity is an economically important trait, since extending the functional life of a doe would allow us to keep the most productive females in the herd as long as possible, and this could result in the increased profitability of dairy farms. Thus, the objectives of this study were to determine the most important factors that influence the length of productive life (LPL) of female Florida goats and to estimate its genetic additive variance using a Cox proportional hazards model. The data consisted of 70,695 productive life records from 25,722 Florida females kidding between 2006 and 2020. A total of 19,495 does had completed their productive life while 6227 (24.2%) does had censored information. The pedigree contained information on 56,901 animals. The average censoring age and average failure age after first kidding for LPL were 36 and 47 months respectively. The model included, as time-independent effects, the age at first kidding and the interaction between herd, year and season of birth of the doe, and as time-dependent effects, the age at kidding, the interaction between herd, year and season of kidding, the within-herd class of milk production deviation, and the interaction between the lactation number and the stage of lactation. All fixed effects had a significant effect on LPL (p < 0.05). Does with older ages at the first kidding and an earlier age at kidding were at higher risk of being culled. A large difference among herds was observed in terms of culling risk, which highlighted the importance of adequate management practices. Also, high-producing does were less likely to be culled. The estimate of the additive genetic variance was 1.844 (in genetic standard deviation), with a heritability estimate of 0.58 ± 0.012. The results of this study are expected to contribute to the development of a genetic model for genetic evaluation of the length of the productive life of Spanish dairy goat breeds.

Combinations of Linear Type Traits Affecting the Longevity in Hungarian Holstein-Friesian Cows

Several research studies confirm the association of the linear type traits with longevity, but only with one trait at a time. The aim of our study was to analyse the influence of combinations for linear type traits on longevity in the Hungarian Holstein-Friesian cows. Data were provided by four herds; the filtered dataset consisted of 17,717 cows. From the 14 available linear type traits, the most important combinations were identified based on principal components and cluster analysis. From the six identified combinations, only three (chest width-body depth, fore udder attachment-udder depth, angularity-rear udder height) proved to have a significant effect on longevity. A wide chest and deep body caused a high-risk ratio of culling. The lowest risk ratio was observed with cows having intermediate chest width and intermediate body depth. Very angular cows having low rear udder height were at the highest risk of culling. The lowest culling risk was found in cows with a lack of angularity and high rear udder height. Weak and loose fore udder along with deep udder had increased culling risk. Strong and tight fore udder subclasses were the most favourable as their risk ratios decreased towards the shallowing of udder depth.

Influence of production, reproduction, morphology, and health traits on true and functional longevity in French Holstein cows

In the long term, resilient animals are able to maintain their normal biological processes when confronted with environmental perturbations, reducing their risk of being culled. Therefore, longevity can be proposed as an indicator of long-term resilience. Decisions to remove a given dairy cow from the herd are mainly related to low milk production (i.e., voluntary culling) or to reasons other than production (i.e., involuntary culling). The aptitude of animals to delay any culling is defined as true longevity (TL), whereas functional longevity (FL) is the ability to avoid involuntary culling. The aim of the study was to investigate the influence of production, reproduction, morphology, and health traits on TL and FL, to identify risk factors for culling. Data included 278,217 lactations from 122,461 Holstein Friesian cows reared in 640 herds. The length of productive life, calculated as the time between first calving and culling, or censoring, was used as the measure of longevity. Survival analysis was performed using proportional hazards models assuming a piecewise Weibull distribution of the baseline hazard function, with or without adjustment for milk production to evaluate FL and TL. Insemination status, calving ease, mastitis, somatic cell count, displaced abomasum, and udder depth had significant relationships with TL and FL. Differences in estimates of relative risk between TL and FL showed that milk production often influenced culling decisions: farmers are more prone to cull animals with low production even when they had good other characteristics. The culling risk factors identified in the present study can be used to study resilience in dairy cattle and to improve genetic evaluations of functional or total longevity.

Effect of Calving Difficulties and Calf Mortality on Functional Longevity in Polish Holstein-Friesian Cows

Simple Summary

Longevity, or the length of a cow’s productive life, is important in terms of profitability, animal welfare and environmental sustainability. In genetic evaluations, interest focuses on functional longevity, defined as a cow’s ability to avoid forced culling, an ability that increases the possibility of voluntary disposal based on economic criteria. Longevity is affected by several non-productive functional traits, among them those related to calving performance: calving ease (dystocia) and perinatal calf mortality (stillbirth). Parturition is a critical event in a cow’s life that has a number of different short- and long-term consequences. In the Polish Holstein-Friesian population, the incidence of dystocia and stillbirth is within the lower range of frequencies found in other dairy cattle populations. Our research showed that both traits affect functional longevity. Difficult calvings occur more frequently in heifers and increase the risk of involuntary culling more than in later parturitions. Additionally, a higher risk of culling is related to birth of a male calf. Moreover, the negative impact of calf mortality on longevity is also more pronounced in primiparous cows and in the case of delivery of male calves. Reducing the incidence of calving problems and perinatal mortality may improve the longevity of dairy cows.

Abstract

Longevity is one of the functional traits that considerably affect dairy herd profitability. A Weibull proportional hazards model was used to evaluate the impact of difficult calvings and calf stillbirths on cow functional longevity, defined as length of productive life corrected for milk production. The data for analysis comprised calving ease and calf mortality scores of 2,163,426 calvings, 34.4% of which came from primiparous cows. The percentage of male calves was 53.4%. Calving ease was scored as “without assistance” (34.44%), “with assistance” (62.03%), “difficult—hard pull” (3.39%), and “very difficult, including caesarean section” (0.14%). Calf mortality scores were “live born” (94.21%) and “stillborn or died within 24 h” (5.79%). The Weibull proportional hazards model included classes of calving ease or calf mortality scores × parity (1, ≥2) × sex of calf as time-dependent fixed effect. The model also included time-dependent fixed effects of year × season, parity × stage of lactation, annual change in herd size, fat yield and protein yield, time-independent fixed effect of age at first calving, and time dependent random herd × year × season. In first-parity cows, very difficult birth of a bull or heifer increased the relative risk of culling, respectively, 2.18 or 1.26 times as compared with calving without assistance. In later parities, the relative risk of culling related to very difficult calving was 2.0 times (for male calves) and 1.33 times (for female calves) higher than the relative risk of culling associated with calving without assistance. Calf mortality showed a negative impact on longevity in both heifers and cows. First-parity stillbirth increased the relative risk of culling depending on sex of calf by 18% in females and by 15% in males; in later parities the increase of the relative risk of culling was lower (by 7% for females, 9% for males). Difficult calvings and their consequences, especially in primiparous cows, may negatively influence dairy herd profitability by reducing the length of cows’ productive life.

Genomic Correlations Between the Gaits of Young Horses Measured by Accelerometry and Functional Longevity in Jumping Competition

Functional longevity is essential for the well-being of horses and the satisfaction of riders. Conventional selection using longevity breeding values calculated from competition results is not efficient because it takes too long to obtain reliable information. Therefore, the objective was to identify early criteria for selection. We assessed two types of early criteria: gait traits of young horses and QTLs. Thus, our aim was to estimate the genetic correlation between gait traits and longevity and to perform a genome-wide association study (GWAS) for longevity. Measurements of gaits by accelerometry were recorded on 1,477 show jumping horses that were 4 to 5 years old. Gait analysis provided 9 principal components describing trot, canter, and walk. Longevity estimated breeding values (EBVs) for stallions were calculated using a survival analysis of more than 900,000 years of performances by 179,448 show jumping horses born from 1981 onwards. Longevity was measured as the number of years spent in competition. Model included region and month of birth, age at first competition, year, and performance level. Longevity EBVs were deregressed to obtain weighted pseudo-performances for 1,968 stallions. Genomic data were available for 3,658 jumping horses. Seventy-eight percent of the horses measured for gaits and twenty-five percent of those measured for longevity were genotyped. A GWAS of longevity revealed no significant QTLs. Genetic parameters between each of the 9 principal components of the gait variables and longevity were evaluated with a bi-trait animal linear mixed model using single-step GBLUP analysis with the relationship matrix constructed from genomic data and genealogy (24,448 ancestors over four generations). The heritability of the gait traits varied from 0.11 to 0.44. The third principal component for trot (high lateral activity) and the first principal component for canter (high dorsoventral activity and low stride frequency) were moderately genetically correlated with higher longevity: r_g = 0.38 (0.15) and 0.28 (0.13), respectively. Our study revealed that functional longevity is a polygenic trait with no major genes. We found new correlations between longevity and gait traits. Before using gait characteristics in a selection plan, these correlations need to be understood better at the biomechanical level.

Survival analysis and reproductive performance of Dorper x Tumele sheep

Productivity and profitability of sheep farming are highly influenced by lamb survival and ewe reproductive performance. Thus, this study was conducted to evaluate the survival and reproductive performance of crossbred sheep. Data collected from 2009 to 2018 from Sirinka sheep breeding stations were utilized for this study. Survival analysis was conducted by using Survival Kit 6.12 software with the Weibull model and the general linear model of SAS 9.0 was used to analyze reproductive traits. The overall mean survival rate of Dorper x Tumele crossbred lambs at 3, 6 and 12 months of age were 86.0, 76.6, and 67.9%, respectively. About 46.8% of mortality from the total death was observed during the first 120 days of life. Gastrointestinal parasites, pneumonia and septicemia were the major causes of lamb mortality. Birth weight, birth type, sex and year of lambing were the most important risk factors for survival of crossbred lambs. The overall least-squares means for litter size at birth, litter size at weaning, total litter weight at birth and total litter weight at weaning were 1.10 lambs, 0.94 lambs, 3.28 kg and 15.5 kg, respectively. Birth type, sex and year of lambing were the most determinants of ewe productive traits. Tumele and their crossbred sheep had good mothering ability necessary to successfully raise lambs to weaning. The current crossbreeding program which aims to improving growth performance had a positive influence on the survival rate of lambs. Improvement of environmental in the flock, special care for small lambs and indirect selection based on birth weight would lead to further survival improvement.

Selection response for Streptococcus agalactiae resistance in Nile tilapia Oreochromis niloticus

The potential of selection to improve resistance to streptococcosis was evaluated in a commercial population of Nile tilapia in Thailand. The base generation (G0) consisted of offspring from 98 sires and 149 dams using a partly nested design. At 60 days post-hatch, 30 fish from each family were injected intraperitoneally with a Streptococcosis agalactiae solution (1 × 10⁹  CFU/ml) and evaluated for 14 days. Disease resistance was recorded as the number of days from challenge until death (DD) and as a binary (BIN) trait (dead/alive) on day 14. Three models were used for genetic analyses: Cox frailty model for DD; animal model for DD; and animal model for BIN. Age at challenge was fitted as a covariate and contemporary group as fixed or random effect, depending on the model. Fish from the 18 most resistant families were selected to produce the first generation (G1). Heritability estimates for G0 were 0.22, 0.14 ± 0.02 and 0.11 ± 0.02 for the Cox, linear DD and linear BIN models, respectively. Selection response indicated that the risk of death decreased to 54%, survival time increased to 3.4 days and survival rate increased to 21%. These results suggest that genetic improvement is possible for this population.

Relationship between somatic cell score and longevity of Holstein cows in Brazil using a piecewise Weibull proportional-hazard model

The objective of the present work was to evaluate the effect of somatic cell score on the longevity of Holstein cows raised all over Brazil, using a piecewise Weibull proportional-hazard model. The following two longevity traits were defined: true longevity, number of days from first calving to culling; and functional longevity, approximated by correcting true longevity to within-herd-year production. Records on productive life of 131330 cows were used. The model included the time-independent effect of age at first calving. The other effects were time-dependent, and included the following: region by year of calving, variation in herd-size class, milk-production class by year of calving within herd, within-herd milk-production class by number of lactations, within-herd fat content, within-herd protein content, and somatic cell score (SCS). The overall mean of the somatic cell counts (SCC) was 322000 cells/mL. The highest SCC mean was found between 130 to 290 days of lactation. The SCC mean decreased over the years. Cows from Region 5 (Rio Grande do Sul) showed higher SCC means. The risk of culling was slightly higher for functional longevity than for true longevity. The impact of longevity was high in cows from first to fourth lactation with a high SCS, with the risk of culling varying from 0.90 (true longevity: second lactation and Class 2) to 1.2 (functional longevity: fourth lactation and Class 5). Cows at the fifth lactation with a lower SCS had a higher risk of culling (1.4). Including the effect of SCS class by stage of lactation in the models was not beneficial. The decrease in SCS, especially from the first to fourth lactation, can be used for indirect selection to improve the longevity of Holstein cows in Brazil.

Disentangling Genetic Variation for Resistance and Endurance to Scuticociliatosis in Turbot Using Pedigree and Genomic Information

Selective breeding for improving host responses to infectious pathogens is a promising option for disease control. In fact, disease resilience, the ability of a host to survive or cope with infectious challenge, has become a highly desirable breeding goal. However, resilience is a complex trait composed of two different host defence mechanisms, namely resistance (the ability of a host to avoid becoming infected or diseased) and endurance (the ability of an infected host to survive the infection). While both could be targeted for genetic improvement, it is currently unknown how they contribute to survival, as reliable estimates of genetic parameters for both traits obtained simultaneously are scarce. A difficulty lies in obtaining endurance phenotypes for genetic analyses. In this study, we present the results from an innovative challenge test carried out in turbot whose design allowed disentangling the genetic basis of resistance and endurance to Philasterides dicentrarchi, a parasite causing scuticociliatosis that leads to substantial economic losses in the aquaculture industry. A noticeable characteristic of the parasite is that it causes visual signs that can be used for disentangling resistance and endurance. Our results showed the existence of genetic variation for both traits (heritability = 0.26 and 0.12 for resistance and endurance, respectively) and for the composite trait resilience (heritability = 0.15). The genetic correlation between resistance and resilience was very high (0.90) indicating that both are at a large extent the same trait, but no significant genetic correlation was found between resistance and endurance. A total of 18,125 SNPs obtained from 2b-RAD sequencing enabled genome-wide association analyses for detecting QTLs controlling the three traits. A candidate QTL region on linkage group 19 that explains 33% of the additive genetic variance was identified for resilience. The region contains relevant genes related to immune response and defence mechanisms. Although no significant associations were found for resistance, the pattern of association was the same as for resilience. For endurance, one significant association was found on linkage group 2. The accuracy of genomic breeding values was also explored for resilience, showing that it increased by 12% when compared with the accuracy of pedigree-based breeding values. To our knowledge, this is the first study in turbot disentangling the genetic basis of resistance and endurance to scuticociliatosis.

Mountain pasturing of rearing stock reduces the culling risk as dairy cows

Alpine transhumance or droving livestock to mountainous areas during summer months is highly relevant for Austrian agriculture but also for other countries in Alpine regions. Access of rearing stock to mountain pastures is often claimed to be beneficial with respect to health and longevity, but the robust evidence is scarce. Therefore, its effect was tested by including it in the routine genetic evaluation data set for longevity. Alpine transhumance records from 2004 to 2013 were used. After several plausibility checks and restriction to animals with sire and dam known, records of 871 287 dual-purpose Fleckvieh cows sired by 9953 bulls were available. Data were analysed by means of survival analysis accounting for the time-dependent fixed effects of region-year-season, relative performance within herd, change of herd size, and Alpine pasturing of cows, the fixed effects age at first calving and Alpine pasturing of rearing stock, the random time-dependent effect of herd-year and the random genetic effects of sire and maternal grandsire. Fleckvieh cows that had access to Alpine pasture during their rearing period at least once for a minimum of 60 days had functional longevity that was nearly 2 months prolonged compared with cows that had always stayed on the farms as calves or heifers. In a more detailed analysis, the lowest relative culling risk among the significant estimates was observed for cows that had been Alpine pastured in years 1 and 3; it was about 15% below that of cows that never had access to mountain grazing. Evidence for the beneficial effect of Alpine pasturing of rearing stock on the animals' later fitness, indicated by longevity, could thus be provided.

Impact of conformation traits on functional longevity in South African Holstein cattle

A proportional hazards model with a piecewise Weibull baseline hazard was used to determine the impact of observed scores for rump, udder, feet and leg traits on longevity. Conformation data of a total of 15 704 cows with either of or all 13 type traits for the period 1995–2013 were obtained from the Holstein Society of South Africa. Functional longevity was defined as the number of days from first calving to culling or censoring, adjusted for production. Type traits were fitted to the reference model one at a time. The model included the fixed time-dependent effect of region by year of calving, within-herd milk production class by year-season, number of lactations by stage of lactation by within-herd milk production class, protein and fat percent production class by year of calving, herd size by annual herd size change, fixed time-independent effect of age at first calving and presence of type record. Cows without type scores were 7–26% more likely to be culled than those with scores. Udder traits had the greatest impact on functional longevity. Fore teat placement had the strongest influence on functional longevity followed by udder depth, fore udder attachment, median ligament and rear treat placement. Rump and udder width had the least Chi-square contributions. Risk of culling was significantly higher for cows with very narrow chest, weak median ligament, extremely towed out teats and short rump height. There is potential for indirectly selecting animals for longevity based on udder type trait information.

Technical note: PaGELL v.1.5: A flexible parametric program for the Bayesian analysis of longevity data within the context of animal breeding

This technical note presents the program PaGELL v.1.5 (Parametric Genetic Evaluation of Lifespan in Livestock), a flexible software program to analyze (right-censored) longevity data in livestock populations, with a special emphasis on the genetic evaluation of the breeding stock. This software relies on a parametric generalization of the proportional hazard model; more specifically, the baseline hazard function follows a Weibull process and flexibility is gained by including an additional time-dependent effect with the number of change points defined by the user. The program can accommodate 3 different sources of variation (i.e., systematic, permanent environmental, and additive genetic effects) and both fixed and time-dependent patterns (only for systematic and permanent environmental effects). Analyses are performed within a Bayesian context by sampling from the joint posterior distribution of the model, and model fit can be easily determined by the calculation of the deviance information criterion. Although this software has already been used on field data sets, its performance has been double-checked on simulated data set, and results are presented in this technical note. PaGELL v.1.5 was written in Fortran 95 language and, after compiling with the GNU Fortran Compiler v.4.7 and later, it has been tested in Windows, Linux, and MacOS operating systems (both 32- and 64-bit platforms). This program is available at http://www.casellas.info/files/pageII.zip.

Estimation of genetic parameters for functional longevity in the South African Holstein cattle using a piecewise Weibull proportional hazards model

Non-genetic factors influencing functional longevity and the heritability of the trait were estimated in South African Holsteins using a piecewise Weibull proportional hazards model. Data consisted of records of 161,222 of daughters of 2,051 sires calving between 1995 and 2013. The reference model included fixed time-independent age at first calving and time-dependent interactions involving lactation number, region, season and age of calving, within-herd class of milk production, fat and protein content, class of annual variation in herd size and the random herd-year effect. Random sire and maternal grandsire effects were added to the model to estimate genetic parameters. The within-lactation Weibull baseline hazards were assumed to change at 0, 270, 380 days and at drying date. Within-herd milk production class had the largest contribution to the relative risk of culling. Relative culling risk increased with lower protein and fat per cent production classes and late age at first calving. Cows in large shrinking herds also had high relative risk of culling. The estimate of the sire genetic variance was 0.0472 ± 0.0017 giving a theoretical heritability estimate of 0.11 in the complete absence of censoring. Genetic trends indicated an overall decrease in functional longevity of 0.014 standard deviation from 1995 to 2007. There are opportunities for including the trait in the breeding objective for South African Holstein cattle.

Genetic analysis and genomic selection of stayability and productive life in New Zealand ewes

Genetic parameters for ewes were estimated for stayability (STAY) and productive life (Prodlife). Records from 658,871 animals from 241 seed stock or ram breeder flocks and one research flock were used to estimate parameters for ram breeder flock STAY and Prodlife. These flocks would have a culling policy based on criteria typical of a commercial enterprise, but including culls based on knowledge such as estimated breeding values. A subset of 35,688 of these animals from 4 ram breeder and one research flock was used to infer the animals that might be culled based on the perspective of a commercial flock as these flocks recorded reasons for culling. These data were used to estimate parameters for commercial flock STAY and Prodlife. Heritability for ram breeder flock STAY until age 3 to 6 yr ranged from 0.07 to 0.09. The heritability of commercial flock STAY was similar in yr 5 and 6, but lower at 0.05 (age 3) and 0.07 (age 4). Heritability of Prodlife for ram breeder flock and commercial flock was respectively 0.10 and 0.13. The genetic correlations between ram breeder flock STAY and commercial flock STAY ranged from 0.20 to 0.99. Both STAY and Prodlife were most correlated genetically with the trait number of lambs born, at about 0.4, and to a lesser degree, live weight up to the age of 12 mo for the traits analyzed with lower genetic correlations estimated for the commercial flocks. Live weight at 18 mo and fleece weight had little or no correlation with STAY and Prodlife. From the data set used to estimate genetic parameters from a ram breeder flock, 4,330 animals were genotyped with the Illumina OvineSNP50 BeadChip and the genotypes used to develop genomic predictions via genomic best linear unbiased prediction. The animals used in the training data set were multibreed, but were heavily Romney breed based. The genomic prediction accuracy for ram breeder flock STAY, according to breed, was dependent on sample size and ranged from 0.4 to 0.44 for Romney and 0.26 to 0.4 for Coopworth. Accuracies for Perendale and Composites, for which sample sizes were less, were more variable. This study has derived genetic parameters for STAY and Prodlife and investigated genomic predictions for these traits. As these traits are of low heritability, sex limited and expressed late in life genomic selection will be useful.

A MapReduce approach to diminish imbalance parameters for big deoxyribonucleic acid dataset

BACKGROUND

In the age of information superhighway, big data play a significant role in information processing, extractions, retrieving and management. In computational biology, the continuous challenge is to manage the biological data. Data mining techniques are sometimes imperfect for new space and time requirements. Thus, it is critical to process massive amounts of data to retrieve knowledge. The existing software and automated tools to handle big data sets are not sufficient. As a result, an expandable mining technique that enfolds the large storage and processing capability of distributed or parallel processing platforms is essential.

METHOD

In this analysis, a contemporary distributed clustering methodology for imbalance data reduction using k-nearest neighbor (K-NN) classification approach has been introduced. The pivotal objective of this work is to illustrate real training data sets with reduced amount of elements or instances. These reduced amounts of data sets will ensure faster data classification and standard storage management with less sensitivity. However, general data reduction methods cannot manage very big data sets. To minimize these difficulties, a MapReduce-oriented framework is designed using various clusters of automated contents, comprising multiple algorithmic approaches.

RESULTS

To test the proposed approach, a real DNA (deoxyribonucleic acid) dataset that consists of 90 million pairs has been used. The proposed model reduces the imbalance data sets from large-scale data sets without loss of its accuracy.

CONCLUSIONS

The obtained results depict that MapReduce based K-NN classifier provided accurate results for big data of DNA.

Evaluation of the length of competitive life in Hungarian sport horses

The aim of this study was to analyse the duration of the competitive life of jumping horses in Hungary to assess the potential for genetic evaluation and to get information about the risk factors affecting jumping performance of sport horses. The data set included lifetime performance in jumping competitions for 8475 horses born from 1992 onwards with records between 1996 and 2011 (32.7% were right-censored). Longevity was measured as the number of years spent in the competition. Discrete time survival model included fixed effects of gender, age at first competition, and the time-dependent effect of competition level. All fixed effects were highly significant (p < 0.001). The highest risk of ending the race career was estimated for horses competing in the lowest level (category 1) events. The smallest risk was found in horses competing in the highest category. The culling risk for stallions was 15% higher, for geldings 20% lower when compared to mares. As the age at the first competition result increased, the risk ratio also increased. Risk ratios of horses starting as 8 years old or older were 56% higher than those of 5-year-old horses. The longest time in sport tracks belonged to horses starting their career as 4 years old. Their culling risk was 20% lower than those of 5-year-old horses. The heritability of the length of competitive life was 0.17. Breeding values were predicted for each animals, and 47 showed an accuracy greater than 0.60. The clear benefit of the analysis was shown by comparison of offspring to extreme stallion groups.

Comparison between sire-maternal grandsire and animal models for genetic evaluation of longevity in a dairy cattle population with small herds

Survival analysis techniques for sire-maternal grandsire (MGS) and animal models were used to test the genetic evaluation of longevity in a Slovenian Brown cattle population characterized by small herds. Three genetic models were compared: a sire-MGS model for bulls and an approximate animal model based on estimated breeding values (EBV) from the sire-MGS model for cows, an animal model, and an animal model based on the estimated variance components from the sire-MGS model. In addition, modeling the contemporary group effect was defined as either a herd or a herd-year (HY) effect. With various restrictions on the minimum HY group size (from 1 to 10 cows per HY), changes in estimates of variance components, and consequently also in EBV, were observed for the sire-MGS and animal models. Variance of contemporary group effects decreased when an HY effect was fitted instead of a herd effect. In the case of a sire-MGS model, estimates of additive genetic variance were mostly robust to changes in minimum HY group size or fitting herd or HY effect, whereas they increased in the animal model when HY instead of herd effects was fitted, possibly revealing some confounding between cow EBV and contemporary group effect. Estimated heritabilities from sire-MGS models were between 0.091 and 0.119 and were mainly influenced by the restriction on the HY group size. Estimated heritabilities from animal models were higher: between 0.125 and 0.160 when herd effect was fitted and between 0.171 and 0.210 when HY effect was fitted. Rank correlations between the animal model and the approximate animal model based on EBV from the sire-MGS model were high: 0.94 for cows and 0.93 for sires when a herd effect was fitted and 0.90 for cows and 0.93 for sires when an HY effect was fitted. Validation performed on the independent validation data set revealed that the correlation between sire EBV and daughter survival were slightly higher with the approximate animal model based on EBV from the sire-MGS model compared with the animal model. The correlations between the sire EBV and daughter survival were higher when the model included an HY effect instead of a herd effect. To avoid confounding and reduce computational requirements, it is suggested that the approximate animal model based on EBV from the sire-MGS model and HY as a contemporary group effect is an interesting compromise for practical applications of genetic evaluation of longevity in cattle populations.