Additive Genetic Random Effects Research Articles

Genetic analysis of ewe stayability and its association with lamb growth and adult production

Records from 2,525 adult Targhee ewes and 10,099 lambs were used to estimate genetic parameters in an animal model for ewe stayability (STAY), productive life (PL), adult BW (AW) and BCS, fleece characteristics, and number of lambs born (NLB) and for lamb BW at birth and approximately 45 d, 120 d (120W; weaning), 12 mo, and 18 mo of age. Stayabilities were analyzed as overall stayability (STAYn|2), which indicated presence or absence of a ewe at n yr of age, given that she was present at 2 yr of age, or marginal stayability (STAYn|n-1) recording the presence of a ewe at n yr of age, given that she was present in the previous year. Productive life was measured as the age of ewe in years at her last lambing. Lamb BW were corrected for age at weighing; BW taken at or before weaning were adjusted for effects of type of birth and rearing, age of dam, and sex using National Sheep Improvement Program methods. The NLB was likewise adjusted for effects of ewe age before analysis. Birth year was included as a fixed effect for all traits. Year of record and, for AW and CS, the number of lambs born or born and reared were also included in models for adult traits. Models for all traits included random additive genetic and residual effects. Random maternal genetic and dam permanent environmental effects were also included in the model for lamb (pre)weaning BW, and random permanent environmental effects of the ewe were included in models for adult traits. The heritability estimate for PL was 0.05 (P < 0.10). Additive variance in STAY was only present after 5 yr of age (P < 0.05), with estimated heritabilities ranging from 0.04 to 0.10. Phenotypic correlations between STAY and other traits were near zero, ranging from -0.07 to 0.14. Estimates of genetic correlations of STAY5|4 and STAY6|2 with maternal genetic effects on 120W were positive (both 0.46; P < 0.05), suggesting that STAY and maternal effects on 120W both reflect genetic variation in ewe fitness characteristics. Genetic correlations between STAY5|4 and 120W, AW, and NLB were not different from zero (0.06, 0.13, and -0.06, respectively; P > 0.10). However, genetic correlations between STAY6|2 and 120W, AW, and NLB were all negative, with values of -0.17, -0.32 (P < 0.05), and -0.03, respectively, indicating a possible small antagonism between STAY and genetic effects on body size.

Genetic effects on reproductive traits in Warmblood horses

Reproductive efficiency is an important issue in horse breeding. However, almost no estimates of genetic parameters of reproductive traits in horses can be found in the literature. The objective of the study was to estimate heritability and genetic trends of foaling rate and number of reproductive seasons in Warmblood horses. The records of 3965 mares from six studs were analyzed. Mares were on average kept for 7.3 reproductive seasons with a foaling rate of 66%. Models included fixed effects of stud, period of birth, breed and random additive genetic effect. Heritability estimates were 0.12 for foaling rate and 0.17 for number of reproductive seasons. Key words: Heritability, reproduction, horse

Effects of Composite β- and κ-Casein Genotypes on Milk Coagulation, Quality, and Yield Traits in Italian Holstein Cows

The aim of the study was to estimate the effect of the composite CSN2 and CSN3 genotypes on milk coagulation, quality, and yield traits in Italian Holstein cows. A total of 1,042 multiparous Holstein cows reared on 34 commercial dairy herds were sampled once, concurrently with monthly herd milk recording. The data included the following traits: milk coagulation time; curd firmness; pH and titratable acidity; fat, protein, and casein contents; somatic cell score; and daily milk, fat, and protein yields. A single-trait animal model was assumed with fixed effects of herd, days in milk, parity, composite casein genotype of CSN2 and CSN3 (CSN2-CSN3), and random additive genetic effect of an animal. The composite genotype of CSN2-CSN3 showed a strong effect on both milk coagulation traits and milk and protein yields, but not on fat and protein contents and other milk quality traits. For coagulation time, the best CSN2-CSN3 genotypes were those with at least one B allele in both the CSN2 and CSN3 loci. The CSN3 locus was associated more strongly with milk coagulation traits, whereas the CSN2 locus was associated more with milk and protein yields. However, because of the tight linkage between the 2 loci, the composite genotypes, or haplotypes, are more appropriate than the single-locus genotypes if they were considered for use in selection.

Interação genótipo x ambiente e estimativas de parâmetros genéticos dos pesos aos 205 e 365 dias de idade de bovinos Nelore

Dados de pesos aos 205 (P205) e 365 (P365) dias de idade, de 46.408 animais Nelore, nascidos entre 1976 e 2000, provenientes de 530 rebanhos dos diversos estados brasileiros, foram utilizados para avaliar as interações genótipo x ambiente (IGA) e estimar herdabilidades direta e materna dos pesos pelo método da máxima verossimilhança restrita. O modelo estatístico utilizado incluiu efeitos fixos de grupo contemporâneo, idade da vaca ao parto (covariável) e efeitos aleatórios genéticos aditivo direto e materno. As correlações genéticas, estimadas para as características P205 e P365, cada uma considerada como característica distinta em cada uma das regiões Sul (S), Sudeste (SE), Centro-Oeste (CO), Norte (N) e Nordeste (NE), foram, respectivamente, 0,86 e 0,84, 0,64 e 0,35, 0,75 e 0,42, 0,79 e 0,86, 0,92 e 0,81, 0,95 e 0,83, 0,83 e 1,00, 0,88 e 0,81, 0,33 e 0,85, 0,63 e 0,99 para S e SE, S e CO, S e N, S e NE, SE e CO, SE e N, SE e NE, CO e N, CO e NE e N e NE. As baixas correlações genéticas indicaram que há efeito da interação genótipo x ambiente nas combinações que envolvem as regiões S/CO, S/N, S/NE, CO/NE e N/NE para P205 dias de idade e S/CO e S/N para P365 dias de idade, havendo, portanto, necessidade de avaliação genética regional quando se consideram regiões bastante distintas.

Avaliação genética multirracial para ganho de peso pré-desmama em bovinos de uma população composta

Objetivou-se neste trabalho estudar modelos com efeitos não-aditivos diretos e maternos em uma população composta em clima tropical, tentando minimizar esses efeitos para obtenção dos valores genéticos dos animais avaliados. Foram utilizados dados de animais de uma população composta, por meio da comparação de três modelos que incluíram os efeitos fixos de grupo contemporâneo, ordem de parto e heterose direta e materna e os efeitos aleatórios de efeito genético aditivo direto e materno. As análises foram realizadas em duas etapas; na primeira foram estudadas as estimativas dos efeitos raciais e de heterose individual e materna e na segunda etapa, calculadas as variâncias, herdabilidades e os valores genéticos dos animais. O efeito materno, quando não foi considerado no modelo, pareceu superestimar o efeito aditivo racial. Os efeitos aditivos raciais, racial materno e de heterose individual e materna influenciaram significativamente o ganho médio diário no pré-desmame, obtendo-se diferentes estimativas entre os tipos biológicos. Considerando o arquivo de dados corrigidos para os efeitos não-aditivos diretos e maternos, as herdabilidades direta e materna foram de 0,22 e 0,20, respectivamente. Os efeitos racial materno e de heterose individual e materna foram importantes fontes de variação para o ganho médio diário no pré-desmame e devem ser considerados durante a avaliação genética de uma população multirracial.

Genetic evaluation of performance traits in Brazilian Quarter Horse

The aim of this study was to estimate genetic parameters for racing performance traits in Quarter Horses in Brazil. The data (provided by the Sorocaba Jockey Club) came from 3 Brazilian hippodromes in 1994-2003, with 11 875 observations of race time and 7775 of the speed index (SI), distributed in 2403 and 2169 races, respectively. The variance components were estimated by the MTGSAM program, under animal models including the random additive genetic effect, random permanent environmental effect, and the fixed effects of sex, age and race. Heritabilities for race time and the SI, for the 3 distances studied (301, 365 and 402 m), varied from 0.26 to 0.41 and from 0.14 to 0.19, respectively, whereas repeatabilities varied from 0.36 to 0.68 (time) and from 0.27 to 0.42 (SI) and the genetic correlations from 0.90 to 0.97 (time) and from 0.67 to 0.73 (SI).

INTERAÇÃO PAI-AVÔ-MATERNO NA ESTIMATIVA DE (CO)VARIÂNCIAS, E TENDÊNCIA GENÉTICA DO CRESCIMENTO PRÉ-DESMAMA EM GADO NELORE *

Adjusted weights at 120 (P120) and 240 (P240) days of age from 8,084 Nellore calves of both sexes were used to obtain estimate of (co)variance components and predictions of breeding values. Calves were born between 1987 and 1997 and raised on pasture in 31 herds. The complete mixed model for each trait included the fixed effects of contemporary group (herd-year-season-sex-management group) and six cow age at calving classes (2, 3, 4, 5, 6 to 9, and 10 years and older cows), and random additive genetic effects of animal (direct and maternal), maternal permanent environmental, sire x maternal grandsire interaction (PAM) and residual. Inclusion of PAM interaction explained between 2.8 and 3.1 % of the phenotypic variance, and caused a reduction in direct and maternal variances and an increase in direct-maternal covariances. Direct heritabilities diminished from 0.24 to 0.20 (P120), and from 0.24 to 0.19 (P240). Corresponding maternal heritabilities decreased from 0.17 to 0.13 and from 0.20 to 0.16. Direct-maternal genetic correlations increased from 0.05 to 0.29 (P120), and from -0.12 to 0.01 (P240), indicating no antagonism. Figures of annual breeding value means showed scarce or any progress during the analyzed period, particularly on maternal ability. Intensive use of few sires could be a major factor contributing to these results. The PAM interaction effect and the genetic trend must be investigated further on a database including recent information. KEY WORDS: (Co)variances, genetic trend, sire–maternal grandisre interaction.

Nonparametric Analysis of the Impact of Inbreeding on Production in Jersey Cows

Under dominance, the relationship between a quantitative trait and the inbreeding coefficient (F) is expected to be linear. Epistasis involving dominance effects or selection against inbred individuals can produce nonlinear patterns in the form of inbreeding depression. The form of the relationship between F and yield traits was explored via local regression (LOESS). First-lactation milk, fat, and protein records from 59,778 Jersey cows with at least 6 generations of known pedigree were used. The F ranged from 0.6 to 34% and median F was 6.3%. The LOESS regressions of predicted residuals from an animal model (empirical best linear unbiased predictions, EBLUP) on F were calculated for each trait; the EBLUP model included fixed herd-year-season, age at calving and DIM effects, and random additive genetic effects. The relationship between EBLUP residuals and inbreeding was complex and nonlinear. Yields were unaffected for F ≤7%, and inbreeding depression seemed to stabilize at F >20% for fat and protein yield. For SCS, both parametric and LOESS fits were consistent with the absence of sizable dominance effects. Effects of inbreeding on performance seemed to be more complex than suggested by previous studies based on linear regression. Results should be interpreted with caution because the data were scarce at high levels of F.

Herdabilidades para ganho de peso da desmama ao sobreano e perímetro escrotal ao sobreano e tendências genética e fenotípica para ganho de peso da desmama ao sobreano em bovinos Nelore-Angus

Com o objetivo de estimar herdabilidades para ganho de peso médio diário da desmama ao sobreano (GMDDS) e para perímetro escrotal ao sobreano (PES) e tendências genética e fenotípica para GMDDS, foram utilizados 47.668 registros de peso e de ganho de peso de uma população multirracial Nelore-Angus, coletados entre 1991 e 2001 em diversas regiões do Brasil. Os dados foram analisados pelo método REML e as estimativas das (co)variâncias foram obtidas por meio de um modelo animal, no qual foram considerados fixos os efeitos da composição racial do animal (obtida pela concatenação do percentual da raça Nelore do próprio animal, de seu pai e de sua mãe) e do grupo de contemporâneos pós-desmama (animais nascidos no mesmo rebanho, ano, época e pertencentes ao mesmo sexo e grupo de manejo) e, como aleatórios, os efeitos genético aditivo direto e residual. A herdabilidade para PES foi estimada utlizando-se o mesmo modelo, acrescido dos efeitos fixos do peso e da idade do animal ao sobreano (covariáveis). As médias para idade nas pesagens foram 215 e 528 dias para a desmama e o sobreano, respectivamente. A herdabilidade estimada para GMDDS foi 0,44 ± 0,02 e para PES, 0,22 ± 0,08. A tendência genética anual predita para GMDDS foi decrescente até 1996 e crescente a partir desse período. A tendência fenotípica anual foi de 9,4 g/dia/ano.

The use of a random regression model to account for change in racing speed of German trotters with increasing age

In a genetic analysis of German trotters, the performance trait racing time per km was analysed by using a random regression model on six different age classes (2-, 3-, 4-, 5- and 6-year-old and older trotters; the age class of 3-year-old trotters was additionally divided by birth months of horses into two seasons). The best-fitting random regression model for the trait racing time per km on six age classes included as fixed effects sex, race track, condition of race track (fitted as second-order polynomial on age), distance of race and each driver (fitted as first-order polynomial on age) as well as the year-season (fitted independent of age). The random additive genetic and permanent environmental effects were fitted as second-order polynomials on age. Data consisted of 138,620 performance observations from 2,373 trotters and the pedigree data contained 9,952 horses from a four-generation pedigree. Heritabilities for racing time per km increased from 0.01 to 0.18 at age classes from 2- to 4-year-old trotters, then slightly decreased for 5 year and substantially decreased for 6-year-old horses. Genetic correlations of racing time per km among the six age classes were very high (rg = 0.82-0.99). Heritability was h2 = 0.13 when using a repeatability animal model for racing time per km considering the six age classes as fixed effect. Breeding values using repeatability analysis over all and within age classes resulted in slightly different ranking of trotters than those using random regression analysis. When using random regression analysis almost no reranking of trotters over time took place. Generally, the analyses showed that using a random regression model improved the accuracy of selection of trotters over age classes.

Between-founder heterogeneity in inbreeding depression for production in Jersey cows

Abstract Severity of inbreeding depression depends on the hidden (i.e., recessive) genetic load carried by a population. If the load is distributed unevenly among founder genomes, or founder-lines were exposed to variable amounts of selection, descendants from different founders may be differentially affected by inbreeding. Between-founder heterogeneity in inbreeding depression for production traits and somatic cell score in milk (SCS) was studied using records from 59,788 Jersey cows. Inbreeding coefficients ( F ) were partitioned into components due to four founders, plus a remainder. A two-stage statistical analysis was performed. First, empirical best linear unbiased predictions (EBLUP) of residuals for milk, fat and protein yield, and for SCS, were computed using linear models including fixed effects of herd–year–season, age at calving and days in milk, and random additive genetic effects of individual cows. Second, models with total and partial inbreeding coefficients as predictor variables were fitted to EBLUP residuals, for each trait. Tests of differences between slopes indicated that regressions of milk, fat and protein yield on partial inbreeding coefficients were heterogeneous; SCS did not exhibit inbreeding depression. Hence, alleles contributing to inbreeding depression for production in this Jersey population seem to be associated with specific founders. This indicates that a homogeneous effect of inbreeding on production may be an incorrect statistical specification in genetic evaluation models that attempt to account for inbreeding depression. Furthermore, the observed variability between effects of partial inbreeding due to different founders implies that inbreeding effects on yield traits may be due to alleles with major effects.

Short Communication: Genetic Correlation Between Test-Day Electrical Conductivity of Milk and Mastitis

Electrical conductivity (EC) of milk is an indicator of mastitis. If EC shows genetic variation and is genetically correlated to mastitis, it could be used in a breeding program that includes selection for improved mastitis resistance. In this study, daily records of EC and mastitis from about 1,500 Holstein cows were analyzed. A bivariate animal model was used for estimation of (co)variance components, including fixed effects of age of calving, herd-test-day, and days in milk, in addition to random additive genetic effects and permanent environmental effects. For EC, the estimated heritability was moderate (0.22 to 0.39), whereas for mastitis, the heritability was low (0.013). The genetic correlation between EC and mastitis was estimated to be 0.75, and genetic improvement of mastitis resistance should be feasible through selection for reduced EC.

EFEITOS GENÉTICOS DIRETOS E MATERNOS E SUAS TENDÊNCIAS EM PESOS À DESMAMA DE BOVINOS DA RAÇA NELORE MOCHA, NA REGIÃO PECUÁRIA DE GOIÁS

O objetivo do presente trabalho foi estimar os parâmetros genéticos e suas tendências de variação dos pesos à desmama de bovinos da raça nelore mocha nascidos na região pecuária Goiás entre 1977 e 2000. As estimativas dos parâmetros genéticos foram obtidas por meio de Modelo Animal. O modelo incluiu os efeitos fixos de grupo de contemporâneos, região, idade da vaca e os efeitos aleatórios do animal (direto, materno e de ambiente permanente da vaca). Tendências genéticas foram estimadas para os efeitos aditivos diretos e maternos, pela regressão ponderada das médias anuais dos valores genéticos diretos e maternos sobre o ano de nascimento dos animais. As estimativas de herdabilidade dos efeitos genéticos diretos e maternos foram 0,17 e 0,14, respectivamente. As tendências genéticas estimadas dos efeitos direto e materno foram de 0,56 kg/ano e 0,13 kg/ano, respectivamente. Os resultados indicam a existência de variabilidade genética suficiente para promover o ganho genético através da seleção e que os efeitos maternos devem ser considerados nos modelos de estimação.

Breeding value evaluation in Polish fur animals: Estimates of direct heritability and portion of litter variation of fur coat and reproduction traits

The study presents estimates of heritability for fur coat and reproduction traits in arctic and silver foxes kept on Polish farms. The estimates of variance components were calculated using the DFREML and single-trait animal models. Due to a discrete character of fur coat traits, they were analysed twice: (1) without normalisation of their scores distribution, (2) after the normal probability scale transformation of their scores. Linear models included random additive genetic and common litter environment effects, and fixed effects of farm &amp;times; year &amp;times; birth season in the silver fox or year &amp;times; birth season in the arctic fox as well as the fixed effect of female age when the reproduction traits were analysed. Moreover, the estimation of variance components for fur coat traits was done by a linear model with (Model 2) or without (Model 1) inbreeding coefficients included as linear covariable. In the arctic fox accounting for inbreeding and the data transformation did not markedly influence the estimates of heritability and the portion of litter variation calculated for the fur coat traits. An inbreeding effect was negligible (except for body size &amp;ndash; BS) likely due to the low inbred level of the arctic fox population. In the silver fox the comparison of estimates derived using 2 different linear models and 2 data sets revealed more differences than it was found in the arctic fox. Accounting for inbreeding usually led to lower estimates of heritability, mainly when heritabilities were derived from the normal probability scale-transformed data. Most of the estimates of heritability of reproduction traits were found within the range reported by other authors. However, somewhat higher heritabilities were found for litter size at birth &amp;ndash; LSB (0.205) and litter size at weaning &amp;ndash; LSW (0.250). &amp;nbsp; &amp;nbsp;

Associations between the prion protein genotype and performance traits of meat breeds of sheep

The prion protein (PrP) genotypes of four German meat breeds of sheep were examined in relation to their scores for muscle mass, conformation, wool quality, daily liveweight gain and ultrasonic...

Genetic Parameters for Test-Day Electrical Conductivity of Milk for First-Lactation Cows from Random Regression Models

Electrical conductivity (EC) of milk has been introduced as an indicator trait for mastitis during the last few decades. The correlation of EC to mastitis, easy access to EC data, and the low cost of recording are properties that make EC a good indicator trait for mastitis. In this study, EC was measured daily during the lactation and available from 2101 first-lactation Holstein cows in 8 herds in the United States. Data were analyzed with an animal model that included herd-test-day, age at calving and days in milk (DIM) as fixed effects, and random additive genetic and permanent environmental effects. A repeatability model and 5 random regression (RR) models with increasing order of Legendre polynomials were used. The goodness of fit for the different models was evaluated based on several tests. Our results indicate that the best model was a RR model with a fourth-order Legendre polynomial for both additive genetic and permanent environmental effects. Heritability estimates obtained with this model were from 0.26 to 0.36. Due to the relatively high heritability obtained for EC of milk, EC might be a potential indicator trait to use in a breeding program designed to reduce the incidence of mastitis.

An indication of major genes affecting hip and elbow dysplasia in four Finnish dog populations.

The aim of the study was to assess the possible existence of major genes influencing hip and elbow dysplasia in four dog populations. A Bayesian segregation analysis was performed separately on each population. In total, 34 140 dogs were included in the data set. Data were analysed with both a polygenic and a mixed inheritance model. Polygenic models included fixed and random environmental effects and additive genetic effects. To apply mixed inheritance models, the effect of a major gene was added to the polygenic models. The major gene was modelled as an autosomal biallelic locus with Mendelian transmission probabilities. Gibbs sampling and a Monte Carlo Markov Chain algorithm were used. The goodness-of-fit of the different models were compared using the residual sum-of-squares. The existence of a major gene was considered likely for hip dysplasia in all the breeds and for elbow dysplasia in one breed. Several procedures were followed to exclude the possible false detection of major genes based on non-normality of data: permuted datasets were analysed, data-transformations were applied, and residuals were judged for normality. Allelic effects at the major gene locus showed nearly to complete dominance, with a recessive, unfavourable allele in both traits. Relatively high estimates of the frequencies of unfavourable alleles in each breed suggest that considerable genetic progress would be possible by selection against major genes. However, the major genes that are possibly affecting hip and elbow dysplasia in these populations will require further study.

Breed Comparisons of Weight, Weight Adjusted for Condition Score, Height, and Condition Score of Beef Cows

Breeds were compared for differences in BW (n = 56,731), heights (n = 51,407) and body condition scores (BCS, n = 56,371) of 2- to 8-yr-old cows from four cycles of the Germplasm Evaluation (GPE) Program at the U. S. Meat Animal Research Center (MARC). Angus, Hereford, and topcross cows from 22 breeds of sires were produced. The mixed model for repeated measures of BW, height, and BCS included random additive genetic and permanent environmental effects of the cow. Differences among crosses were significant for all traits. In general, BW, within cycle, was greater for cows sired by breeds of large size and low milk production (Chianina and Charolais) than for those of large size and moderate milk production (Maine Anjou, Salers, and Shorthorn), moderate size and moderate milk production (Angus and South Devon), moderate size and low milk production (Hereford), and small size and low milk production (Galloway and Longhorn). Breeds of moderate size and moderately high milk production (Pinzgauer, Red Poll, and Tarentaise) were even lighter. Cows with Jersey sires were separated from all other breed groups because of light BW. Cows with sires of British origin tended to be lighter than those of continental European origin. Cows with Bos indicus sires (Brahman and Nellore) ranked between other breeds of large and moderate size for BW or for BW adjusted for BCS. In general, adjustment for BCS did not alter rankings of breed groups for differences in cow BW. Differences among breed groups for height closely followed differences for BW.

Random regression analyses of feed intake of individually tested beef steers

Objective of the study was to apply random regression models to daily dry matter intakes (DMI) of 376 beef steers fed for up to 168 days for evaluating genetic parameters and the optimum period of test. Steers were tested in a research station in Canada from 1997 to 2001. Models included fixed effects of biological breed type, test group, herd of origin and starting age and random additive genetic and permanent environmental effects of animal. Legendre polynomials on days of test were fitted for all fixed and random effects, except for biological types, which were estimated as linear regression on biological type composition. Heritability substantially improved from the first week up to 84 days on test (0.23 to 0.49), when it reduced the rate of increase. Genetic correlation between cumulative feed intake in the entire period of test and the intake up to 84 days was high (0.93). Results indicated that a test period of 84 days could be used for evaluating cumulative feed intake of steers for a 168 days growth period. Genetic eigenfunctions revealed that changes to the shape of the feed intake curve seem to be more difficult than changes to the overall level of intake of steers.

Herd of origin effect on weight gain of station-tested beef bulls

The effect of herd of origin on genetic evaluation of weight gain of beef bulls in central test stations was examined by univariate and bivariate analyses, which included bull’s estimated weight gain on test (BEG) and pre-weaning gain (WG) of bulls and their contemporaries in the herd of origin. Bulls were weighed every 28 days on 112 or 140-day station test. BEG was estimated fitting fixed linear regressions to the weights on test of each bull. The bivariate model included random direct additive genetic and dam effects and fixed breed effects for both traits, fixed management group and sex of calf by age of cow effects for WG and fixed test group and random herd of origin by year (HY) effects for BEG. Variance components and EBV were estimated applying models with or without HY effect, which were compared using likelihood ratio test and two information criteria. The effect of HY was significant on BEG, contributing around 8% to total phenotypic variation. Inclusion of HY effect caused EBV to re-rank among top bulls (rank correlation of 0.85 and 0.75 among 5% and 1% best bulls, respectively). Interaction of HY by sire was shown not to be of concern.