scholarly journals Genetic analysis of clinical mastitis in different risk periods by linear and threshold models

2006 ◽  
pp. 1-7
Author(s):  
Enyew Negussie ◽  
Ismo Strandén ◽  
Esa Mäntysaari
Keyword(s):  
Genetic Analysis ◽  
Variance Components ◽  
Genetic Correlations ◽  
Heritability Estimate ◽  
Clinical Mastitis ◽  
Breeding Value ◽  
Threshold Models ◽  
Early Lactation ◽  
Data Set ◽  
Risk Period

Understanding the genetic basis of clinical mastitis (CM) during lactation is essential in deciding on the best measure of CM for breeding value evaluation. CM is one of the leading reasons for premature disposal of dairy cows. Culled cows have incomplete lactation records, and in statistical analysis this may cause sampling biases, because culled cows are seldom a random sample. It is, therefore, essential to study the effects of culling information on the genetic analysis of CM. The objectives of this study were first: to estimate heritability and genetic association between CM during the different stages of first lactation using linear and threshold models, second: to assess the effects culling information on the estimates of variance (co)variance components and associated genetic parameters. First lactation was divided into six lactation stages (risk periods) by days (d) after calving: CM1, (-7 to 150 d); CM2, (-30 to 30 d); CM3, (-30 to 150 d); CM4, (31 to 150 d); CM5, (150 to 300 d); CM6, (-30 to 300 d). To assess the effect of including or excluding records of cows that had been culled from the herd before the end of the risk period, two data sets were prepared. In the first data set (Data I), records of cows culled before the end of the risk period were not included. In the second data set (Data II), records of cows culled during the risk period were included; if the cow had been culled for mastitis reasons or had completed two-thirds of the opportunity period if culled for other reasons. Variance (co)variance components were estimated by linear and threshold-liability models employing Bayesian approach. Heritability estimates using the linear model ranged from 0.005 to 0.024 for Data I, and from 0.005 to 0.029 for Data II, depending on the stages of lactation or risk period defined. The corresponding estimates from the threshold-liability model ranged from 0.034 to 0.076, and from 0.043 to 0.083 for Data I and Data II, respectively. In general, increased sire variance and higher heritability were observed with the inclusion of culling information. Estimated genetic correlations between the CM traits were medium to high, and ranged from 0.42 to 0.99 in Data I, and from 0.61 to 0.99 in Data II. Thus CM cannot be regarded the same trait in the course of lactation. Results from the threshold analyses showed that the heritability of liability to CM was highest for CM2 and followed by CM6, CM3 and CM1with estimates of 0.083, 0.073, 0.073 and 0.072, respectively. Estimates for CM4 and CM 5 were the lowest with heritability of 0.043 and 0.047, respectively. The high heritability estimate for CM2 indicates that most genetic information is in early lactation. Thus, the best measure of CM would be to consider only cases in early lactation. However, as the genetic correlation between CM traits defined over the different risk periods were less than one, mastitis cannot be regarded as the same trait in the different parts of lactation. Thus, a multivariate model, treating mastitis in different stages of lactation as different traits, would be the best model for sire evaluation.

scholarly journals Genetic analysis of clinical mastitis during different risk periods in Finnish Ayrshire

2008 ◽  
Vol 16 (2) ◽  
pp. 115 ◽  
Author(s):  
E. NEGUSSIE ◽  
I. STRANDÉN ◽  
E. MÄNTYSAARI
Keyword(s):  
Genetic Variation ◽  
Genetic Information ◽  
Genetic Parameters ◽  
Genetic Correlations ◽  
Clinical Mastitis ◽  
Data Sets ◽  
Threshold Models ◽  
Early Lactation ◽  
Sire Evaluation ◽  
Using Data

Clinical mastitis (CM) records from first-lactation Finnish Ayrshire were analysed by linear and threshold models to assess the effects trait definition on estimates of genetic parameters and sire evaluation. The studied CM traits were defined by dividing lactation into six lactation stages (risk periods) by days (d) after calving: CM1 (-7 to 150 d), CM2 (-30 to 30 d), CM3 (-30 to 150 d), CM4 (31 to 150 d), CM5 (150 to 300 d), CM6 (-30 to 300 d). In addition, two data sets were prepared to assess the effect of excluding (Data I) or including (Data II) records of culled cows on estimates of genetic parameters. Sire variances and heritabilities were larger using Data II. When data from longer intervals was used heritabilities of CM were slightly higher than shorter intervals indicating that longer intervals tend to obscure genetic variation between animals. Of all CM traits, heritability of liability to CM with threshold-liability model was highest for CM2 (h2=0.083) implying that most of the genetic information on CM is in early lactation. In sire evaluation, a multitrait index calculated by combining CM2, CM4 and CM5 had the highest correlation with all other univariate CM trait evaluations. This and the magnitude (less than 1.0) of genetic correlations between CM traits suggest that a multitrait model considering CM from the different risk periods would be appropriate for CM sire evaluation.;

Genetic analysis of docility score of Australian Angus and Limousin cattle

2018 ◽  
Vol 58 (2) ◽  
pp. 213 ◽  
Author(s):  
S. F. Walkom ◽  
M. G. Jeyaruban ◽  
B. Tier ◽  
D. J. Johnston
Keyword(s):  
Adverse Effect ◽  
Animal Model ◽  
Genetic Analysis ◽  
Genetic Parameters ◽  
Genetic Correlations ◽  
Production Costs ◽  
Breeding Value ◽  
Maternal Behaviour ◽  
Production Traits ◽  
Subjective Score

The temperament of cattle is believed to affect the profitability of the herd through impacting production costs, meat quality, reproduction, maternal behaviour and the welfare of the animals and their handlers. As part of the national beef cattle genetic evaluation in Australia by BREEDPLAN, 50 935 Angus and 50 930 Limousin calves were scored by seedstock producers for temperament using docility score. Docility score is a subjective score of the animal’s response to being restrained and isolated within a crush, at weaning, and is scored on a scale from 1 to 5 with 1 representing the quiet and 5 the extremely nervous or anxious calves. Genetic parameters for docility score were estimated using a threshold animal model with four thresholds (five categories) from a Bayesian analysis carried out using Gibbs sampling in THRGIBBS1F90 with post-Gibbs analysis in POSTGIBBSF90. The heritability of docility score on the observed scale was 0.21 and 0.39 in Angus and Limousin, respectively. Since the release of the docility breeding value to the Australian Limousin population there has been a favourable trend within the national herd towards more docile cattle. Weak but favourable genetic correlations between docility score and the production traits indicates that docility score is largely independent of these traits and that selection to improve temperament can occur without having an adverse effect on growth, fat, muscle and reproduction.

scholarly journals Genetic evaluations of traits recorded in British young horse tests

2011 ◽  
Vol 54 (5) ◽  
pp. 439-455
Author(s):  
I. D. Stewart ◽  
J. A. Woolliams ◽  
S. Brotherstone
Keyword(s):  
Variance Components ◽  
Genetic Correlations ◽  
Genetic Effect ◽  
Breeding Value ◽  
Value Prediction ◽  
Data Source ◽  
The Uk ◽  
Genetic Evaluations ◽  
Show Jumping ◽  
Prediction Evaluation

Abstract. Tests for young sport horses were recently introduced in Great Britain. This study characterises the young horse data, examines their suitability for genetic analysis and estimates the genetic parameters needed for breeding value prediction. Evaluation data from 2006–2009 were used. This included 1 887 evaluations of 1 323 horses, which were evaluated for competing in dressage, show jumping, eventing, endurance or as sport ponies. Traits assessed were conformation, correctness of paces, type and temperament, athleticism and veterinary. The distributions of traits were examined and correlations of traits between disciplines, for the effect of the horse, were estimated. These indicated that traits could be assumed to be genetically identical across disciplines. Variance components were estimated for each of the 5 traits, using an animal model, where random effects were the genetic effect of the horse and the permanent environment of the horse. Bivariate analyses were performed between pairs of traits. Mean scores for each trait in each discipline were between 8.02 and 8.24, and standard deviations were between 0.54 and 0.83. Heritabilities ranged between 20.3 % for athleticism and 42.2 % for type and temperament. The variance due to the horse’s permanent environment ranged from approximately 25 % for correctness of paces and athleticism to 51.6 % for veterinary. The genetic correlations between traits were generally high. The young horse tests (»Futurity«) recently introduced in the UK are a valuable data source for genetic evaluations. The most appropriate measure will be to combine young horse data with adult competition data to routinely estimate breeding values.

scholarly journals Impact of trainer and judges in the mare performance test of Warmblood Horses

2005 ◽  
Vol 48 (2) ◽  
pp. 113-120 ◽  
Author(s):  
G. Dietl ◽  
S. Hoffmann ◽  
N. Reinsch
Keyword(s):  
Breeding Success ◽  
Variance Components ◽  
Performance Test ◽  
Observation Time ◽  
Breeding Value ◽  
Data Set ◽  
Phenotypic Correlations ◽  
Genetic And Phenotypic Correlations ◽  
Abstract Data ◽  
Estimated Heritability

Abstract. Data of the mare performance test of the Mecklenburger Warmblood Horses were used to estimate genetic and phenotypic (co-)variance components. The data set included the records of 1628 mares tested on station in the years 1993 to 2004. The pedigree contained information of 9560 horses. The investigated traits were trot, canter, walk, manner, ability and ride ability, according to trainer, judges and foreign riders. The estimated heritability coefficients, genetic and phenotypic correlations are in the range of the results report by other authors. The ride ability earns an exception position because a very low heritability was found. A comparison of the heritability coefficients between the trainers' scores and judges' scores makes very evident that the trainers are more able to evaluate the breeding value of the mare. This can probably be caused by the longer observation time of trainers during the stay of the mare on station lasting 14 days in comparison to the judges having only approximately 10 minutes. The current weights of trainers' scores and of judges' scores with 0.5 to 0.5 to generate the total score is not optimal. A stronger emphasis on the scores of the trainers promises an increasing breeding success of approximately 5 to 7 percent.

scholarly journals Genetic analysis and clonal stability of two yellow cypress clonal populations in British Columbia

2013 ◽  
Vol 62 (1-6) ◽  
pp. 173-186 ◽  
Author(s):  
B. S. Baltunis ◽  
J. H. Russell ◽  
A.Van Niejenhuis ◽  
J. Barker ◽  
Y. A. El-Kassaby
Keyword(s):  
British Columbia ◽  
Genetic Analysis ◽  
Combining Ability ◽  
Variance Components ◽  
Genetic Variance ◽  
Genetic Correlations ◽  
Specific Combining Ability ◽  
Type B ◽  
Height Range ◽  
Coastal British Columbia

AbstractGenetic analysis of height and form at age 12 years of 697 yellow cypress (Callitropsis nootkatensis [D. Don] Oerst.) clones tested across seven sites in coastal British Columbia (BC) were explored in populations: Population 1 - No Pedigree and Population 2 - Reconstructed Pedigree. Genetic variances were statistically significant but generally higher σ̂g2was observed for Population 2. Height and form were under low to moderate genetic control as indicated by clonal repeatability and estimates were relatively similar between populations. For example, average Ĥ2in Population 2 was 0.31 for height (range: 0.18-0.45) and 0.22 for form (range: 0.06-0.32). While average Ĥ2in Population 1 was 0.25 for height (range: 0.19-0.35) and 0.18 for form (range: 0.09-0.27). The reconstructed pedigree in Population 2 allowed partitioning the genetic variance (σ̂g2) into component parts of additive (σ̂a2), specific combining ability (σ̂s2), and clone (σ̂c2); however, general lack of structure within the population resulted in variance components to be estimated with little precision for additive and specific combining ability. The majority of genetic variation was associated with clone for both traits. For example, σ̂c2accounted for 57.6% and 62.5% of the total genetic variance for height and form, respectively. Growth and form responses of clones across test environments were relatively stable and overall type-B genetic correlations were in excess of 0.8 for both traits implying clones selected for production populations should respond favorably across the seed planning zone for yellow cypress in coastal BC.

scholarly journals Genetic and nongenetic factors associated with the fate of maiden ewe lambs: slaughtered without ever lambing versus retained for breeding1

2019 ◽  
Vol 4 (1) ◽  
pp. 242-249 ◽  
Author(s):  
Noirin McHugh ◽  
Thierry Pabiou ◽  
Kevin McDermott ◽  
Eamon Wall ◽  
Donagh P Berry
Keyword(s):  
Mixed Models ◽  
Variance Components ◽  
Threshold Model ◽  
Genetic Correlations ◽  
Decision Support Tool ◽  
Data Set ◽  
Support Tool ◽  
Ewe Lambs ◽  
Ewe Lamb ◽  
First Time

Abstract The decision on which ewe lamb to retain versus which to sell is likely to vary by producer based on personal preference. What is not known, however, is if any commonality exists among producers in the characteristics of ewe lambs that influence their eventual fate. The objective of the present study was to determine what genetic and nongenetic factors associate with the fate of maiden ewe lambs. The fate of each ewe lamb born in the present study was defined as either subsequently: 1) having lambed in the flock, or 2) was slaughtered without any recorded lambing event. A total of 9,705 ewe lamb records from 41 crossbred flocks were used. The logit of the odds of the ewe lamb being retained for lambing was modeled using logistic regression. Variance components were then estimated for the binary trait representing the fate of the ewe lamb using animal linear and threshold mixed models. The genetic correlations between fate of the ewe lamb and preweaning, weaning, or postweaning liveweight were also estimated. From the edited data set, 45% of ewe lambs born entered the mature flock as ewes. Ewe lambs reared as singles, with greater levels of heterosis but lower levels of recombination loss, born to dams that lambed for the first time as hoggets, with greater breed proportion of the Belclare, Suffolk, Texel, and Llyen breeds were more likely (P < 0.001) to eventually lamb in the flock than be slaughtered without ever lambing. Irrespective of the age of the animal when weighed, heavier ewe lambs were more likely to eventually lamb (P < 0.001). The genetic SD and direct heritability of fate of the ewe lamb estimated in the univariate linear model was 26.58 percentage units and 0.31 (SE = 0.03), respectively; the heritability was 0.30 when estimated using the threshold model. The corresponding direct heritability of fate of the ewe lamb estimated in the bivariate analyses with liveweight ranged from 0.29 (SE = 0.03; preweaning weight) to 0.35 (SE = 0.04; postweaning weight). The genetic correlations estimated between fate of the ewe lamb and the liveweight traits were weak to moderate but strengthened as the age of the ewe lamb at weighing increased. Results from this study provide an understanding of the factors producers consider when selecting females for retention versus slaughter which may form useful parameters in the development of a decision support tool to identify suitable ewe lambs for retention.

Genetic parameters of pathogen-specific incidence of clinical mastitis in dairy cows

2002 ◽  
Vol 74 (2) ◽  
pp. 233-242 ◽  
Author(s):  
Y. de Haas ◽  
H. W. Barkema ◽  
R. F. Veerkamp
Keyword(s):  
Milk Yield ◽  
Selection Index ◽  
Genetic Correlations ◽  
Relative Weight ◽  
Clinical Mastitis ◽  
Coagulase Negative Staphylococci ◽  
Data Set ◽  
E Coli ◽  
Streptococcus Uberis ◽  
Current Selection

AbstractData from 274 Dutch herds recording clinical mastitis (CM) over an 18-month period were used to quantify the genetic variation for overall and pathogen-specific CM. Analysed pathogens were Staphylococcus aureus, coagulase negative staphylococci (CNS), Escherichia coli, Streptococcus dysgalactiae, Streptococcus uberis and other streptococci. The data set contained 47 563 lactations of 28 695 cows of different parities. Cases of overall and pathogen-specific CM were treated as all-or-none traits. Variance components for the sire, maternal grandsire and permanent environmental effect were estimated using generalized linear mixed models with a logit link function for the binary traits. Average number of days at risk and in milk on trial was 198 days. The estimated heritability for overall CM was 0·04, and similar heritabilities for the pathogen-specific CM were estimated. Repeatability across lactations was low for overall and pathogen-specific CM (0·10 to 0·14). Genetic correlations with milk yield and somatic cell score (SCS) differed according to pathogen. For instance, the incidence rate of clinical E. coli mastitis was slightly unfavourably correlated with milk yield at 150 days (0·13) but stronger with SCS (0·74). Whereas, the genetic correlations with clinical Str. dysgalactiae mastitis were 0·70 and 0·16, respectively. The expected correlated responses showed that current selection practices (using milk yield and SCS) will be effective in reducing the incidence of E. coli and CNS but less effective in reducing the incidence of S. aureus and Str. dysgalactiae, even with a large relative weight for SCS in the selection index.

scholarly journals Poisson versus threshold models for genetic analysis of clinical mastitis in US Holsteins

2009 ◽  
Vol 92 (10) ◽  
pp. 5239-5247 ◽  
Author(s):  
A.I. Vazquez ◽  
K.A. Weigel ◽  
D. Gianola ◽  
D.M. Bates ◽  
M.A. Perez-Cabal ◽  
...  
Keyword(s):  
Genetic Analysis ◽  
Clinical Mastitis ◽  
Threshold Models

scholarly journals Breeding value evaluation in Polish fur animals: Estimates of (co)variances due to direct and litter effects for fur coat and reproduction traits

2011 ◽  
Vol 51 (No. 1) ◽  
pp. 39-46 ◽  
Author(s):  
H. Wierzbicki ◽  
W. Jagusiak
Keyword(s):  
Litter Size ◽  
Genetic Correlations ◽  
Reproductive Traits ◽  
Original Data ◽  
Breeding Value ◽  
The Arctic ◽  
Data Set ◽  
Value Evaluation ◽  
Reproduction Traits ◽  
Fur Animals

5 540 records of the arctic fox fur coat and reproductive traits collected in 1983–1999 were studied. The analyzed traits were: body size (BS), colour type (CT), colour purity (CP), coat density (CD), hair length (HL), general appearance (GA), total score (TS), skin length (SL), litter size at birth (LSB), litter size at weaning (LSW), number of dead pups (NPD), pup weight at weaning (PW), and pregnancy length (PL). (Co)variance components were estimated using a derivative-free algorithm of REML and a multi-trait animal model. Random effects were direct additive, common litter environment and residual. The genetic parameters for the fur coat traits (discrete characters) were estimated twice: using the original data set, and the data set in which the distribution of fur coat scores was normalised using a probit link function. Direct heritability estimates obtained from the original data set ranged from 0.108 for SL to 0.276 for HL, and were somewhat lower than those estimated using the transformed data set (they ranged from 0.109 for GA to 0.315 for CT). Reproductive traits were lowly heritable with direct heritabilities ranging from 0.060 for PW to 0.174 for LSB. Estimates of the portion of litter variation calculated from the original and transformed data set were comparable ranging from 0.045 for GA to 0.156 for CP, and from 0.059 for GA to 0.185 for TS, respectively. Genetic correlations between fur coat traits ranged from high favourable (0.948 between SL and BS, original data) to strong negative ones between CP and GA (–0.405, transformed data). High positive genetic correlations were found between LSB and LSW (0.954), and between LSB and NPD (0.783), whereas PL was negatively correlated with all other reproductive traits.  

scholarly journals 211 Changes in genetic parameters of fitness and growth traits under genomic selection in pigs

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 41-41
Author(s):  
Jorge Hidalgo ◽  
Shogo Tsuruta ◽  
Daniela Lourenco ◽  
Yijian Huang ◽  
Kent Gray ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Genomic Selection ◽  
Variance Components ◽  
Genetic Parameters ◽  
Growth Traits ◽  
Average Daily Gain ◽  
Genetic Correlations ◽  
Data Set ◽  
Daily Gain ◽  
Over Time

Abstract Genomic selection increases intensity of selection and decreases generation interval. However, intensive selection reduces genetic variation and can strengthen undesirable genetic correlations. The purpose of this study was to investigate changes in genetic parameters of litter size (LS), number born alive (NBA), number born dead (NBD) and average daily gain (ADG) and weight at off-test (WT) in pigs over time. The data set contained 20,086 (LS), 21,230 (NBA), 21,230 (NBD), 144,717 (ADG) and 144,718 (WT) phenotypic records. Pedigree file included 369,776 animals born between 2001 and 2018, of which 39,038 were genotyped. Two trait models were evaluated (LS-ADG, LS-WT, NBA-ADG, NBA-WT, NBD-ADG and NBD-WT) using 3-year sliding subsets starting from 2010. Variance components and genetic parameters were estimated using GIBBS2F90 program. Computations were performed with (BLUP) or without (ssGBLUP) genotypes. For BLUP (ssGBLUP), the changes in heritability from 2010–2012 to 2015–2018 were 0.08 to 0.09 (0.08 to 0.06) for LS, 0.33 to 0.24 (0.37 to 0.16) for ADG, 0.11 to 0.07 (0.10 to 0.07) for NBD, and 0.32 to 0.24 (0.38 to 0.17) for WT. Differences were also observed for genetic correlations as they were -0.23 to -0.73 (-0.31 to -0.58) for LS-ADG, -0.24 to -0.74 (-0.31 to -0.50) for LS-WT, -0.33 to -0.65 (-0.41 to -0.53) for NBA-ADG, -0.35 to -0.66 (-0.42 to -0.45) for NBA-WT, 0.12 to 0.04 (0.12 to 0.16) for NBD-ADG, and 0.11 to 0.05 (0.11 to 0.22) for NBD-WT. Genomic selection in pigs reduced heritabilities and emphasized the antagonistic relationship that are under strong selection. Heritabilities estimated from ssGBLUP declined more than those by BLUP while changes in the genetic correlations were smaller and more gradual by ssGBLUP. Differences between ssGBLUP and BLUP could be caused by genomic pre-selection unaccounted for by BLUP.

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