Lamb survival analysis from birth to weaning in Iranian Kermani sheep

Survival records from 1,763 Kermani lambs born between 1996 and 2004 from 294 ewes and 81 rams were used to determine genetic and non-genetic factors affecting lamb survival. Traits included were lamb survival across five periods from birth to 7, 14, 56, 70, and 90 days of age. Traits were analyzed under Weibull proportional hazard sire models. Several binary analyses were also conducted using animal models. Statistical models included the fixed class effects of sex of lamb, month and year of birth, a covariate effect of birth weight, and random genetic effects of both sire (in survival analyses) and animal (in binary analyses). The average survival to 90 days of age was 94.8%. Hazard rates ranged from 1.00 (birth to 90 days of age) to 1.73 (birth to 7 days of age) between the two sexes indicating that male lambs were at higher risk of mortality than females (P < 0.01). This study also revealed a curvilinear relationship between lamb survival and lamb birth weight, suggesting that viability and birth weight could be considered simultaneously in the selection programs to obtain optimal birth weight in Kermani lambs. Estimates of heritabilities from survival analyses were medium and ranged from 0.23 to 0.29. In addition, heritability estimates obtained from binary analyses were low and varied from 0.04 to 0.09. The results of this study suggest that progress in survival traits could be possible through managerial strategies and genetic selection.     

Estimates of genetic parameters for growth traits in Kermani sheep

Birth weight (BW), weaning weight (WW), 6-month weight (W6), 9-month weight (W9) and yearling weight (YW) of Kermani lambs were used to estimate genetic parameters. The data were collected from Shahrbabak Sheep Breeding Research Station in Iran during the period of 1993-1998. The fixed effects in the model were lambing year, sex, type of birth and age of dam. Number of days between birth date and the date of obtaining measurement of each record was used as a covariate. Estimates of (co)variance components and genetic parameters were obtained by restricted maximum likelihood, using single and two-trait animal models. Based on the most appropriate fitted model, direct and maternal heritabilities of BW, WW, W6, W9 and YW were estimated to be 0.10 +/- 0.06 and 0.27 +/- 0.04, 0.22 +/- 0.09 and 0.19 +/- 0.05, 0.09 +/- 0.06 and 0.25 +/- 0.04, 0.13 +/- 0.08 and 0.18 +/- 0.05, and 0.14 +/- 0.08 and 0.14 +/- 0.06 respectively. Direct and maternal genetic correlations between the lamb weights varied between 0.66 and 0.99, and 0.11 and 0.99. The results showed that the maternal influence on lamb weights decreased with age at measurement. Ignoring maternal effects in the model caused overestimation of direct heritability. Maternal effects are significant sources of variation for growth traits and ignoring maternal effects in the model would cause inaccurate genetic evaluation of lambs.     

Estimation of genetic parameters based on individual and group mean records in laying hens

(1) The study was conducted to estimate the heritability, genetic correlations and breeding values of laying hens based on individual records and group mean records. (2) Records of two pure lines from a commercial breeding programme of White Leghorns from three generations housed in single cages and in group cages were used. A total of 8483 and 8817 individual records of lines A and D, respectively, and a total of 1358 (line A) and 1161 (line D) group mean records were analysed. (3) An animal model using Restricted Maximum Likelihood (REML) was used to estimate variance components of individual records. Group mean records were analysed using the sire model, taking heterogeneity of error variance and correlated residual effects into account. Breeding values of sires were estimated based on the BLUP method using a multivariate sire model. Spearman Rank correlations were used to compare sire breeding values estimated from individual records and from group mean records. The traits studied were monthly egg production, cumulative production and egg weight. (4) Heritability estimates based on individual records were higher than from group mean records. Heritabilities for cumulative production records were higher than for monthly production, based on individual as well as group mean records. The estimates of genetic correlations between monthly egg production and cumulative production were moderate to high. Egg production and egg weight recorded individually were highly genetically correlated with those recorded on group means. Sire breeding values estimated from individual records showed high correlations with those from group mean records. (5) Differences in the ranking of sire breeding values estimated from individual vs group mean records were negligible, indicating that no genotype x environment interaction exists. Selection based on individual performance records of laying hens housed in single cages could give a good response on performance of laying hens housed in group cages. Cumulative egg production over periods 1 to 6 is the best trait for the selection programme.     

Effect of missing data on the estimate of average daily feed intake of growing pigs.

The effect of missing records for feed intake per day (FID) on the estimate of average daily feed intake (DFI) during the test period of individual pigs was studied. Data from 192 growing pigs tested with single-space computerized feeding stations during an average of 93 d were used. True DFI was computed by averaging FID records per pig, individually. A first- and third-degree polynomial and a nonlinear function were fit to FID records per pig to estimate DFI by averaging estimated FID records per pig, individually. The three functions showed small differences for goodness of fit. Missing FID records were simulated by random as well as period-wise deletions of FID records. The effect of missing FID records was judged on the Pearson correlation between true and estimated DFI. Deleting randomly up to 70% of FID records per pig before fitting each function reduced this correlation only from 1.00 to .96 for each function. Deleting 25 successive FID records (approximately 27% of records) before fitting reduced the correlation to values ranging from .92 to .96 and from .59 to .96 for the first- and third-order degree polynomial function, respectively, and from .80 to .97 for the nonlinear function. Using iteratively reweighted least squares regression methods to exclude undesirable effects of outlier values gave similar results for the effect of missing FID records on estimated DFI. Results imply that considering incorrect FID records as missing is a good alternative for adjusting incorrect data in combination with using functions to estimate DFI of growing pigs. Use of a first-degree polynomial function is recommended. Moreover, use of functions enables a more efficient use of feeding stations by recording feed intake data during only parts of the test period.     

猪场生产记录的优化和利用

猪场在配种、分娩、断奶、免疫等生产过程中会产生各种记录，根据猪场的生产规律和各种记录之间的联系．对相关记录进行优化和处理，能够使其更好地服务于猪场的生产管理、规划及种猪的选育。阐述了猪场记录的分类、记录的处理更新和猪场信息的利用。     

Comparison of methods for handling censored records in beef fertility data: field data

The purpose of this study was to compare methods for handling censored days to calving records in beef cattle data, and verify results of an earlier simulation study. Data were records from natural service matings of 33,176 first-calf females in Australian Angus herds. Three methods for handling censored records were evaluated. Censored records (records on noncalving females) were assigned penalty values on a within-contemporary group basis under the first method (DCPEN). Under the second method (DCSIM), censored records were drawn from their respective predictive truncated normal distributions, whereas censored records were deleted under the third method (DCMISS). Data were analyzed using a mixed linear model that included the fixed effects of contemporary group and sex of calf, linear and quadratic covariates for age at mating, and random effects of animal and residual error. A Bayesian approach via Gibbs sampling was used to estimate variance components and predict breeding values. Posterior means (PM) (SD) of additive genetic variance for DCPEN, DCSIM, and DCMISS were 22.6d2 (4.2d2), 26.1d2 (3.6d2), and 13.5d2 (2.9d2), respectively. The PM (SD) of residual variance for DCPEN, DCSIM, and DCMISS were 431.4d2 (5.0d2), 371.4d2 (4.5d2), and 262.2d2 (3.4d2), respectively. The PM (SD) of heritability for DCPEN, DCSIM, and DCMISS were 0.05 (0.01), 0.07 (0.01), and 0.05 (0.01), respectively. Simulating trait records for noncalving females resulted in similar heritability to the penalty method but lower residual variance. Pearson correlations between posterior means of animal effects for sires with more than 20 daughters with records were 0.99 between DCPEN and DCSIM, 0.77 between DCPEN and DCMISS, and 0.81 between DCSIM and DCMISS. Of the 424 sires ranked in the top 10% and bottom 10% of sires in DCPEN, 91% and 89%, respectively, were also ranked in the top 10% and bottom 10% in DCSIM. Little difference was observed between DCPEN and DCSIM for correlations between posterior means of animal effects for sires, indicating that no major reranking of sires would be expected. This finding suggests little difference between these two censored data handling techniques for use in genetic evaluation of days to calving.     

Monthly model for genetic evaluation of laying hens 1. Fixed regression.

1. This paper addresses the possibility of using a monthly model for the genetic evaluation of laying hens, based on the definition of a test day model with fixed regression as used in dairy cattle, in which monthly records were treated as repeated measurements of the same trait. 2. Production records of 6450 hens, daughters of 180 sires and 1335 dams were analysed using an animal model with restricted maximum likelihood (REML). The traits considered were individual monthly egg production and cumulative egg production in 11 months. Four different models were fitted to various combinations of monthly and cumulative records. The covariates were derived from the regression of Ali and Schaeffer (1987). 3. Spearman rank correlations were computed to compare breeding values from different models. Two types of correlations were computed: between individual breeding values and between sire breeding values based on subsets of full-sib records. 4. The results indicated that a monthly model with nested covariates produced higher heritability and permanent environmental variance than the models with non-nested or without covariates. The estimates of heritability obtained from monthly model were lower than the estimates from the cumulative model. The monthly model resulted in higher correlations of sire breeding values between two subsets of full-sib records than those from cumulative models. 5. In conclusion, the monthly model with nested covariates appears to be better than the model with non-nested covariates or without covariate. Although the heritability estimates obtained from the monthly model were lower, the monthly model with nested covariates could be better than the cumulative model for genetic evaluation of laying hens in the 1st cycle of laying period when using either full or part records. The use of information from odd months of production could be of interest for the evaluation of full records.     

Assessment of the quality of multi-institutional data for population-based epidemiological studies: a case study of atoxoplasmosis in Bali mynahs (Leucopsar rothschildi)

To evaluate the potential to conduct population-based epidemiologic studies using multi-institutional data, the quality of data extracted from the MedARKS system was evaluated with regard to atoxoplasmosis in Bali mynahs (Leucopsar rothschildi). Data extracted for 338 Bali mynahs from 34 institutions were analyzed for completeness, correctness, and consistency and subjectively analyzed for accessibility. Data completeness was ascertained by analysis of missing records, tests, and blank fields. Two hundred and sixty four records had animal enclosure information missing, nine records were missing from the parasitology module, and 85 records did not include tests or results. Data correctness was assessed by evaluation of unclear and inaccurate results. From 2,432 parasitology records, 81 tests (3.3%) were not definitive because of uninterpretable entries. Data consistency was assessed by comparing the problem list to positive tests in the parasitology module and listing of buffy coat smears in the clinical pathology module. Overall, six different terms with 28 values were used to denote "positive for Atoxoplasma sp.," and a substantial number of discrepancies were found between problem lists, parasitology modules, and test findings among these data records. In general, this study showed that the data contained in a computer patient record (CPR) system for zoos has great promise for population-level studies if specific areas are addressed, including 1) reduced reliance on free-text data entry, 2) universal use of a standardized vocabulary, 3) use of methods to identify and track individual animals accurately and easily, 4) integration of data checks and maintenance methods, and 5) concerted use of "centralized" animal medical record information.     

民国时期方志中的苜蓿考

方志是记载一个地区自然和社会各个方面历史和现状的综合性著作,苜蓿作为民国时期的重要物产资源被许多方志记录在册。本研究试图以植物考据学原理与方法,对华东、华北和西北等地诸省的56个方志中的苜蓿进行考查。结果表明,民国时期我国华东、华北和西北都有苜蓿种植,主要分布在安徽、江苏、山东、察哈尔、河北、山西、陕西、宁夏、甘肃、青海和新疆;许多方志还对苜蓿植物生态学特征进行了描述,对苜蓿种分的较为清晰,在民国时期河北种有紫花苜蓿(Medicago sativa)和黄花苜蓿(M. falcata),而山东既种有紫花苜蓿与黄花苜蓿,还种有南苜蓿(M.hispida);苜蓿常常被种于碱地进行肥田;苜蓿不仅是饲喂牛马的重要牧草资源,而且也是重要的蔬菜资源,还是很好的蜜源植物。     

Use of serial pig body weights for genetic evaluation of daily gain

This study examined the utility of serial weights from FIRE (Feed Intake Recording Equipment, Osborne Industries, Inc., Osborne, KS, USA) stations for an analysis of daily gain. Data included 884 132 body weight records from 3888 purebred Duroc pigs. Pigs entered the feeder station at age 77–149 days and left at age 95–184 days. A substantial number of records were abnormal, showing body weight close to 0 or up to twice the average weight. Plots of body weights for some animals indicated two parallel growth curves. Initial editing used a robust regression, which was a two‐step procedure. In the first step, a quadratic growth curve was estimated assuming small or 0 weights for points far away from the curve; the process is iterative. In the second step, weights more than 1.5 SD from the estimated growth curve were treated as outliers. The retained body weight records (607 597) were averaged to create average daily weight (170 443) and then used to calculate daily gains (152 636). Additional editing steps included retaining only animals with ≥50 body weight records and SD of the daily gain ≤2 kg, followed by removing records outside 3 SD from the mean for given age, across all the animals – the resulting data set included 69 068 records of daily gain from 1921 animals. Daily gain based on daily, weekly and bi‐weekly intervals was analysed using repeatability models. Heritability estimates were 0.04, 6 and 9%, respectively. The last two estimates correspond to heritability of 28% for a 12 week interval. For daily gain averaged weekly, the estimate of heritability obtained with a random regression model varied from 0.07 to 0.10. After extensive editing, body weight records from automatic feeding stations are useful for genetic analyses of daily gain from weekly or bi‐weekly but not daily intervals.     

The impact of data structure on genetic (co)variance components of early growth in sheep,estimated using an animal model with maternal effects

Several studies have noted high negative correlations between maternal genetic and direct additive effects and their influence on additive and maternal heritability of early growth traits in sheep. Multigeneration data from the Suffolk Sire Reference Scheme (SSRS) were used to investigate the effect of data structure on estimates of direct and maternal (co)variances for lamb 8-wk weight. In all analyses the additive, maternal genetic, maternal environmental, and residual effects were fitted along with the covariance between direct and maternal additive effects. The contributions of particular genetic relationships to the estimates were studied by analyzing subsets of the SSRS data. A further eight subsets were formed having 10% or 50% of the dams with their own records and having one or two, three or four, five or six, and more than six offspring per dam. Analysis of data having only 10% of the dams with their own record and one or two offspring records yielded a high negative correlation (-0.99) between direct and maternal genetic effects. However, the seven other data sets with more records per dam or a higher proportion of dams with their own records produced values of -0.35 to -0.51. Data structure and the number of dams and granddams with records are important determinants of estimated direct and maternal effects in early growth traits.     

Genetic evaluation of heat tolerance in Holstein cows in Japan

We used test‐day records and daily records from provincial weather stations in Japan to evaluate heat tolerance (HT) in Holstein cows according to a random regression test‐day model. Data were a total of 1,641,952 test‐day records for heritability estimates and 17,245,694 test‐day records for genetic evaluation of HT by using milk yield and somatic cell score (SCS) in Holstein cows that had calved for the first time in 2000 through 2015. Temperature–humidity index (THI) values were estimated by using average daily temperature and average daily relative humidity records from 60 provincial Japanese weather stations. The model contained herd–test‐day, with lactation curves on days in milk within month–age group as a fixed effect. General additive genetic effect and HT of additive genetic effect were included as random effects. The threshold value of THI was set to 60. For milk yield, estimated mean heritabilities were lower during heat stress (THI = 78; 0.20 and 0.28) than when below the heat stress threshold (THI ≤ 60; 0.26 and 0.31). For SCS, heritability estimates (range 0.08–0.10) were similar under all heat stress conditions. Genetic trends of HT indicated that EBVs of HT are changing in an undesirable direction.     

Antimicrobial use through feed, water, and injection in 20 swine farms in Alberta and Saskatchewan

Antimicrobial resistance (AMR) is an emerging animal welfare and public health issue linked to antimicrobial use (AMU) in livestock. This study was conducted in 2004 on 20 swine farms in Alberta and Saskatchewan. On-farm records and questionnaires were used to retrospectively describe the antimicrobial exposures of pigs through feed, water, and injection. Antimicrobial use in all production categories was described over 12 months. On-farm records and questionnaires provided sufficient data to describe antimicrobial exposure rates through feed and water. In contrast, on-farm records did not supply sufficient data to describe parenteral antimicrobial exposure rates. Records lacked data on the number of exposures per treatment, therefore parenteral AMU was described as an exposure incidence. Parenteral exposure records were often unavailable for pigs less than 22 kg, in which case questionnaires were used. The incidence of parenteral AMU was significantly higher in herds reporting exposure by questionnaire compared with existing records, suggesting that on-farm records did not reliably describe parenteral AMU. However, because antimicrobial exposures in feed and water were markedly more common than through injection, it was concluded that existing on-farm data would be a valuable resource for investigating AMU and AMR in pigs.     

Quantitative analysis of production traits in saltwater crocodiles (Crocodylus porosus): III. juvenile survival

Mortality records of 1302 juvenile crocodiles were available for analysis. Crocodiles that were slaughtered during this study were treated as censored (n = 2151). Additionally, records from animals that had neither died nor been slaughtered, i.e. were still alive in the production system (n = 1582), were censored at the last date of data collection. There were a total of 3733 censored records. The data were all full‐sib records from 29 parental pairs from Janamba Croc Farm (Northern Territory, Australia), collected over nine consecutive years. Data were analysed using an extension of Cox's proportional hazards model to include frailty (random) terms to account for genetic effects. Heritability of log survival time for juvenile crocodile survival was 0.15 (SE 0.04). The probability of a juvenile crocodile surviving to day 400 was estimated to be only 51%. These results are the first to quantify juvenile survival in a captive breeding situation. Also, this is the first heritability estimate of crocodile survival and is a fundamental element in the development of a genetic improvement programme.     

Effects of selection of data on estimates of breeding values by three methods for litter size, backfat, and average daily gain in swine

Estimated breeding value was calculated based on individual phenotype (SP), an index of individual phenotype and full- and half-sib family averages (SI), or Best Linear Unbiased Prediction (BLUP). Traits considered were litter size (LS), backfat (BF), and ADG. Estimated breeding values were calculated using all data and after deletion of the poorest 5, 10, 15, or 20% of the records for BF and ADG, or 4.8, 8, 13, or 21% of the records for LS. When all data were used, expected genetic gain from BLUP was greater than for SP by 22, 7, and 31% and greater than for SI by 10, 4, and 21% for LS, BF, and ADG, respectively. Expected genetic gain was 4, 0, and 3% lower for LS, BF, and ADG, respectively, for selection on breeding values estimated by SI after the poorest 20% of the records were deleted compared with selection on estimates by SI using all the data. Genetic gain using BLUP on data with the poorest 20% of the records deleted was reduced by 5, 2, and 8% for LS, BF, and ADG, respectively, compared with genetic gain using BLUP on all the data. The advantage in genetic gain of BLUP, with 20% of the poorest records deleted, over SP was 15, 5, and 21% for LS, BF, and ADG, respectively. Although BLUP is affected to a greater degree by deletion of records than is SP or SI, selection of swine using BLUP on field data would improve response to selection over the use of SP or SI.     

Selecting for efficiency of egg production using food-consumption records in layer-type chickens

1. The purpose of the experiment was to evaluate the use of food consumption records in selection to improve layer-type chickens. 2. Twelve subpopulations of Leghorns, including 5878 tested birds, were used in a selection experiment which lasted 5 generations. Four were selected using an index (I1) that combined information on body weight (BW), egg-mass output (EM), and individual food-consumption records (FC). Four were selected using an index (I2) that combined information just on BW and EM. The remaining 4 served as controls, with selection differentials set to zero in each generation. 3. Differences between the selected groups, control-corrected each generation, measured the "food-record effect". 4. Including food-consumption records in the selection criterion resulted in increased body weight (7%), reduction in food consumption (6 to 9%), increase in food efficiency (egg mass/food consumption) (2 to 5%), and increase in income over food costs (10%), relative to selection not involving food records.     

Completeness of handwritten preanaesthetic records at two veterinary referral institutions

Objective

To retrospectively analyse handwritten preanaesthetic records for completeness at two veterinary referral institutions: a university veterinary teaching hospital and a private veterinary referral hospital. To evaluate if emergency records were less complete compared with non-emergency records. Animal or Animal Population Two hundred and fifty preanaesthetic records at each referral institution.

Estimation of genetic parameters for superovulatory response traits in Japanese Black cows

The aim of this study was to estimate genetic parameters for superovulatory response traits in order to explore the possibility of genetic improvement in Japanese Black cows. We analyzed 19 155 records of the total number of embryos and oocytes (TNE) and the number of good embryos (NGE) collected from 1532 donor cows between 2008 and 2018. A two-trait repeatability animal model analysis was performed for both. Because records of TNE and NGE did not follow a normal distribution, the records were analyzed following no, logarithmic, or Anscombe transformation. Without transformation, the heritability estimates were 0.26 for TNE and 0.17 for NGE. With logarithmic transformation, they were 0.22 for TNE and 0.18 for NGE. With Anscombe transformation, they were 0.26 for TNE and 0.18 for NGE. All analyses gave similar genetic correlations between TNE and NGE, ranging from 0.60 to 0.71. Spearman’s rank correlation coefficient between breeding values of cows with more than 10 records was ≥0.95 with both transformations. Thus, the genetic improvement of TNE and NGE of donor cows could be possible in Japanese Black cattle.     

Use of free text clinical records in identifying syndromes and analysing health data

The analysis of data in clinical records could be useful to epidemiologists in planning analytical studies and identifying new research initiatives. This paper describes the method used to develop a systematic, replicable technique for compressing many words of text into fewer content categories on the basis of explicit rules of user-defined coding, and systematically sorting a large volume of records accurately and reliably. The method was used to categorise the reasons for retirement from racing in Hong Kong of 3727 thoroughbred racehorses between the 1992/93 and 2003/04 racing seasons into a user-defined dictionary. An automated process successfully categorised 95 per cent of the records. The other 5 per cent were assigned manually to one of the dictionary categories. The whole process from initial screening to the categorisation of all the records took approximately 100 man-hours to complete.     

Evaluation of Breeding Value and Selection of Bull Dams in the Danish Dairy Breeds: I. Studies on Realized Efficiency of Bull Dam and Bull Sire Selection

Abstract

The relationship between twice the adjusted daughter yield deviation (DYD) of the son and the average of the estimated breeding values (EBV) of his parents was investigated for milk and fat yield. Deviations from expectations of DYD minus the pedigree index and the regression of DYD on the EBV for each of the parents were estimated. The EBV of each bull dam was calculated in several ways using different combinations of pedigree information and their own records. In all, 1693 bulls (880 Black and White (BW), 418 Red Danish (RD) and 395 Danish Jersey (DJ)) with Direct Updating indices for milk and fat yield were included in the investigation. Mean discrepancies between estimated and observed genetic merit for kg of milk yield were ?348 for BW, ?213 for RD and ?228 for DJ, when all of the bull dams' individual records were utilized in breeding value estimation. The corresponding mean discrepancies for kg of fat yield were ?14.7, ?11.5 and ?11.9, respectively. The discrepancies were positively correlated with the number of lactation records included in the dams' EBVs. Regression coefficients of bull DYDs on bull dam breeding values were significantly lower than expected for RD and BW regardless of the number of individual lactation records included in the dams' indexes for milk and fat yield. For all three breeds, the regression coefficients were lowest for fat yield. The most probable cause of overestimation in bull dam EBVs is preferential treatment, particularly in second and later lactations. To avoid this bias, estimation of a bull dam's breeding value should be based on pedigree information and on records from only her first lactation.