Estimate Co Variance Components Research Articles

Estimation of Genetic and Phenotypic Parameters for Growth Traits of Friesian Cattle Raised in Egypt.

Growth traits (GT) of 1691 Friesian calves by 74 sires and 789 dams over a 20 years (1997 to 2016) in Alkarda Farm, Egypt. Traits studied were weight at birth weight (BW), weaning weight (WW) and daily gain (DG). Records were analyzed Multiple Trait Likelihood (MTDFREML) to estimate covariance components and Heritability(h2), genetic correlations(rG) , maternal correlations (rm) and phenotypic correlations(rP), breeding values(BV), and Epigenetic trend (EGT)for growth traits (GT) of Friesian cattle raised in Egypt. Actual mean for BW,WW and DG were 28.6kg, 92.6kg and 0.60 gm , respectively. Direct heritability (h2a) estimates for BW, WW and DG were 0.32±0.06, 0.22±0.06 and 0.34±0.85, respectively; on the same time low maternal heritability (h2m) were 0.12±0.35, 0.08±0.49 and 0.18±0.71, respectively. The permanent environment (P2) was 0.021±0.70, 0.030±0.77 and 0.058±0.72 for BW, WW and DG, respectively. Phenotypic correlation (rP) were 0.99m while, direct genetic correlation (rg) are ranged from 0.56 to 0.96.While, maternal correlations (rm) ranged from were 0.48, to 0.93. Rang of breeding value (BV) estimated of calves for BW, WW and DG were 51.5kg, 10.1kg and 31.2 kg , the BV of sire for the same traits 17.7 kg, 101.0kg and 12.0g. While the range of dams BV were 11.4kg, 17.8kg and 17.7gm respectively. The results showed that it is better to choose on the basis of the BV of calves to obtain highly genetic improvement. Generally the direction was (EGT) positive in the autumn and summer 'while it was negative in the winter and spring of the studied traits. In addition, the estimated genetic trends of Epigenetics that the genetic performance of cows is affected by the exist environmental conditions, as the influence of the season, parity and year, which has shown an impact at some levels, so, sufficient care is necessary help them to rapid their full genetic possibility by improving environmental conditions Inappropriate. This results in animals showing their full genetic potential for GT, thus increasing the efficiency of selection. We conclude from this study: Improve the performance of the animal under study by estimating the environmental and genetic factors and knowing their impact on growth performance, which will allow them to set standards for assessing the performance of the animals. The traits under study are high to medium in the values ​​of genetic equivalence. The genetic correlations between the characteristics of the study are positive and high. The direct genetic and permanent effects are more effective in the selection process. The results show that all traits of growth have a clear potential for improved yield through direct genetic selection and more attention to environmental conditions through good care and selection based on breeding values. This results in animals showing their full genetic potential for growth traits, thus increasing the efficiency of selection.

Effects of Genotype by Environment Interaction on Genetic Gain and Genetic Parameter Estimates in Red Tilapia (Oreochromis spp.).

The extent to which genetic gain achieved from selection programs under strictly controlled environments in the nucleus that can be expressed in commercial production systems is not well-documented in aquaculture species. The main aim of this paper was to assess the effects of genotype by environment interaction on genetic response and genetic parameters for four body traits (harvest weight, standard length, body depth, body width) and survival in Red tilapia (Oreochromis spp.). The growth and survival data were recorded on 19,916 individual fish from a pedigreed population undergoing three generations of selection for increased harvest weight in earthen ponds from 2010 to 2012 at the Aquaculture Extension Center, Department of Fisheries, Jitra in Kedah, Malaysia. The pedigree comprised a total of 224 sires and 262 dams, tracing back to the base population in 2009. A multivariate animal model was used to measure genetic response and estimate variance and covariance components. When the homologous body traits in freshwater pond and cage were treated as genetically distinct traits, the genetic correlations between the two environments were high (0.85–0.90) for harvest weight and square root of harvest weight but the estimates were of lower magnitudes for length, width and depth (0.63–0.79). The heritabilities estimated for the five traits studied differed between pond (0.02 to 0.22) and cage (0.07 to 0.68). The common full-sib effects were large, ranging from 0.23 to 0.59 in pond and 0.11 to 0.31 in cage across all traits. The direct and correlated responses for four body traits were generally greater in pond than in cage environments (0.011–1.561 vs. −0.033–0.567 genetic standard deviation units, respectively). Selection for increased harvest body weight resulted in positive genetic changes in survival rate in both pond and cage culture. In conclusion, the reduced selection response and the magnitude of the genetic parameter estimates in the production environment (i.e., cage) relative to those achieved in the nucleus (pond) were a result of the genotype by environment interaction and this effect should be taken into consideration in the future breeding program for Red tilapia.

MODELOS DE REGRESSÃO ALEATÓRIA ATRAVÉS DO PESO CORPORAL EM CURVAS DE CRESCIMENTO DE AVES

In modern genetic evaluations, random regression models have been used as a custom tool in order to analyze longitudinal traits such as the ones involved in animal growth. Such traits as body weight have an easy mensuration and an excellent response to selection, which is a suitable and important feature for animal breeding programs. The purpose of this review is to discuss about different random regression models that are involved in farm bird growth. The random regression models are recommended as an alternative to genetic evaluation of traits that are regularly measured during the animal life. These models allow the prediction of regression coefficients that represent the behavior of the additive genetic value for each animal in the specific evaluated trait in relation to time (age). Thus, interminable values for the independent variable are considered 340 Colloquium Agrariae, vol. 13, n. Especial, Jan–Jun, 2017, p. 321-347 ISSN: 1809-8215. DOI: 10.5747/ca.2017.v13.nesp.000238 within a defined interval, through deviations of each animal in relation to an estimated and fixed curve. The covariance component estimates assigned to random regression coefficients allow the covariance estimation between any values of the independent variable for a modeled random effect, which is accomplished by the covariance function. Therefore, random regression models improve the use of the weight information, when covariance structures between the studied ages are taken into account during the evaluation. They also allow the description of the estimated variance components that are involved in growth, besides granting presumptions for others in the curve inside the interval estimation.

Covariance Genetic Estimates For Features Tabapuã Growth In Brazil

This review aimed to estimate covariance components for Tabapuã the growth characteristics in Brazil, using random regression models. The random regression models (MRA) make it possible to estimate coefficients of the covariance functions by the method of restricted maximum likelihood. These are suitable for longitudinal data analysis models, because of the deficiencies of conventional methods of quantitative genetic analysis, which are considered phenotypic values inherently continuous processes, as discrete processes. The covariance functions show the statistical correlation between two features of a trajectory at different points of same, ie that present in the arrangement have the same direction and magnitude. With the current concern of cutting bovinocultores regarding the growth of animals, the use of methods or techniques that provide increasingly accurate assessments of genetic parameters to be used in studying the development of animals for meat production is relevant

ESTIMATIVAS DE COVARIÂNCIA GENÉTICA PARA CARACTERÍSTICAS DE CRESCIMENTO DA RAÇA TABAPUÃ NO BRASIL

This review aimed to estimate covariance components for Tabapuã the growth characteristics in Brazil, using random regression models. The random regression models (MRA) make it possible to estimate coefficients of the covariance functions by the method of restricted maximum likelihood. These are suitable for longitudinal data analysis models, because of the deficiencies of conventional methods of quantitative genetic analysis, which are considered phenotypic values inherently continuous processes, as discrete processes. The covariance functions show the statistical correlation between two features of a trajectory at different points of same, ie that present in the arrangement have the same direction and magnitude. With the current concern of cutting bovinocultores regarding the growth of animals, the use of methods or techniques that provide increasingly accurate assessments of genetic parameters to be used in studying the development of animals for meat production is relevant

Genetic parameters for fatty acids in intramuscular fat from feedlot-finished Nelore carcasses

The aim of the present study was to estimate covariance components and genetic parameters for beef fatty acid (FA) composition of intramuscular fat in the longissimus thoracis muscle in Nelore bulls finished in feedlot. Twenty-two FAs were selected. The heritability estimates for individual FAs ranged from 0.01 to 0.35. The heritability estimates for myristic (0.25 ± 0.09), palmitic (0.18 ± 0.07), oleic (0.28 ± 0.09), linoleic (0.16 ± 0.06) and α-linolenic (0.35 ± 0.10) FAs were moderate. Stearic, elaidic, palmitoleic, vaccenic, conjugated linoleic acid, docosahexanoic, eicosatrienoic and arachidonic FAs had heritability estimates below 0.15. The genetic-correlation estimates between the individual saturated FAs (SFAs) were low and negative between myristic and stearic FAs (–0.22 ± 0.84), moderate between palmitic and myristic FAs (0.58 ± 0.56) and negative between palmitic and stearic FAs (–0.69 ± 0.45). The genetic correlations between the individual long-chain polyunsaturated FAs (PUFAs) were positive and moderate (>0.30). However, the genetic-correlation estimates between long-chain PUFAs and α-linolenic acid were low (<0.30), except for the correlation between arachidonic and α-linolenic acids. The genetic correlation estimates of the sums of SFAs with monounsaturated fatty acids and omega 6 FAs were low (0.25 ± 0.59 and –0.02 ± 0.51 respectively), high with PUFAs and omega 9 FAs (–0.85 ± 0.15 and 0.86 ± 0.17 respectively) and moderate with omega 3FAs (–0.67 ± 0.26). The present study demonstrated the existence of genetic variation and, hence, the possibility to increase the proportion of healthy and favourable beef FAs through selection. The results obtained in the study have provided knowledge to elucidate the additive genetic influence on FA composition of intramuscular fat. In addition, genetic-relationship estimates of intramuscular FA profile help seek strategies for genetic selection or genetic-based diet management to enhance the FA profile in Zebu cattle.

Joint estimation of (co) variance components and breeding values for mean and dispersion of days from calving to first service in Holstein cow

The present study explored the possibility of selection for uniformity of days from calving to first service (DFS) in dairy cattle. A double hierarchical generalised linear model with an iterative reweighted least-squares algorithm was used to estimate covariance components for the mean and dispersion of DFS. Data included the records of 27 113 Iranian Holstein cows (parity, 1–6) in 15 herds from 1981 to 2007. The estimated additive genetic variance for the mean and dispersion were 32.25 and 0.0139; both of these values had low standard errors. The genetic standard deviation for dispersion of DFS was 0.117, indicating that decreasing the estimated breeding value of dispersion by one genetic standard deviation can increase the uniformity by 12%. A strong positive genetic correlation (0.689) was obtained between the mean and dispersion of DFS. This genetic correlation is favourable since one of the aims of breeding is to simultaneously decrease the mean and increase the uniformity of DFS. The Spearman rank correlations between estimated breeding values in the mean and dispersion for sires with a different number of daughter observations were 0.907. In the studied population, the genetic trend in the mean of DFS was significant and favourable (–0.063 days/year), but the genetic trend in the dispersion of DFS was not significantly different from zero. The results obtained in the present study indicated that the mean and uniformity of DFS can simultaneously be improved in dairy cows.

A Comparison of Linear Models for Estimating Co-Variance Components and Genetic Parameters in Holstein Dairy Cattle

A Comparison of Linear Models for Estimating Co-Variance Components and Genetic Parameters in Holstein Dairy Cattle

<b>Effect of age of dam on weight of calf in the genetic assessment of Zebu cattle in random regression models

Current analysis estimated co-variance components and genetic parameters for growth traits by random regression models taking into consideration the cow's age on the weight of calves. Genealogical data and records on weights of male and female Zebu cattle, born between 1993 and 2011, were provided by the National Association of Breeders and Researchers (ANCP). Different models were compared by Akaike and Bayesian criteria. Legendre's orthogonal polynomials were used to model the direct and maternal genetic effects of maternal and animal permanent environmental effects. Joint modeling of cow age at the moment their progenies were weighed resulted in more accurate estimates of co-variance components and genetics parameters. Co-variance functions of the cow age retrieved the dam effect on real performance of the progenies, reduced biases, improved parameter estimates and predicted breeding rates.

Genetic parameters for sensory traits in longissimus muscle and their associations with tenderness, marbling score, and intramuscular fat in Angus cattle1

The objective of this study was to estimate heritabilities for sensory traits and genetic correlations among sensory traits and with marbling score (MS), Warner-Bratzler shear force (WBSF), and intramuscular fat content (IMFC). Samples of LM from 2,285 Angus cattle were obtained and fabricated into steaks for laboratory analysis and 1,720 steaks were analyzed by a trained sensory panel. Restricted maximum likelihood procedures were used to obtain estimates of variance and covariance components under a multitrait animal model. Estimates of heritability for MS, IMFC, WBSF, tenderness, juiciness, and connective tissue traits were 0.67, 0.38, 0.19, 0.18, 0.06, and 0.25, respectively. The genetic correlations of MS with tenderness, juiciness, and connective tissue were estimated to be 0.57 ± 0.14, 1.00 ± 0.17, and 0.49 ± 0.13, all positive and strong. Estimated genetic correlations of IMFC with tenderness, juiciness, and connective tissue were 0.56 ± 0.16, 1.00 ± 0.21, and 0.50 ± 0.15, respectively. The genetic correlations of WBSF with tenderness, juiciness, and connective tissue were all favorable and estimated to be -0.99 ± 0.08, -0.33 ± 0.30 and -0.99 ± 0.07, respectively. Strong and positive genetic correlations were estimated between tenderness and juiciness (0.54 ± 0.28) and between connective tissue and juiciness (0.58 ± 0.26). In general, genetic correlations were large and favorable, which indicated that strong relationships exist and similar gene and gene networks may control MS, IMFC, and juiciness or WBSF, panel tenderness, and connective tissue. The results from this study confirm that MS currently used in selection breeding programs has positive genetic correlations with tenderness and juiciness and, therefore, is an effective indicator trait for the improvement of tenderness and juiciness in beef. This study also indicated that a more objective measure, particularly WBSF, a trait not easy to improve through phenotypic selection, is an excellent candidate trait for genomic selection aimed at improving eating satisfaction.

Direct and social genetic effects on body weight at 270 days and carcass and ham quality traits in heavy pigs.

The aims of this study were to estimate covariance components for BW at 270 d (BW270) and carcass and ham quality traits in heavy pigs using models accounting for social effects and to compare the ability of such models to fit the data relative to models ignoring social interactions. Phenotypic records were from 9,871 pigs sired by 293 purebred boars mated to 456 crossbred sows. Piglets were born and reared at the same farm and randomly assigned at 60 d of age to groups (6.1 pigs per group on average) housed in finishing pens, each having an area of 6 m(2). The average additive genetic relationship among group mates was 0.11. Pigs were slaughtered at 277 ± 3 d of age and 169.7 ± 13.9 kg BW in groups of nearly 70 animals each. Four univariate animal models were compared: a basic model (M1) including only direct additive genetic effects, a model (M2) with nonheritable social group (pen) effects in addition to effects in M1, a model (M3) accounting for litter effects in addition to M2, and a model (M4) accounting for social genetic effects in addition to effects in M3. Restricted maximum likelihood estimates of covariance components were obtained for BW270; carcass backfat depth; carcass lean meat content (CLM); iodine number (IOD); and linoleic acid content (LIA) of raw ham subcutaneous fat; subcutaneous fat depth in the proximity of semimembranosus muscle (SFD1) and quadriceps femoris muscle (SFD2); and linear scores for ham round shape (RS), subcutaneous fat (SF), and marbling. Likelihood ratio tests indicated that, for all traits, M2 fit the data better than M1 and that M3 was superior to M2 except for SFD1 and SFD2. Model M4 was significantly better than M3 for BW270 (P < 0.001) and CLM, IOD, RS, and SF (P < 0.05). The contribution of social genetic effects to the total heritable variance was large for CLM and BW270, ranging from 33.2 to 35%, whereas the one for ham quality traits ranged from 6.8 (RS) to 11.2% (SF). Direct and social genetic effects on BW270 were uncorrelated, whereas there was a negative genetic covariance between direct and social effects on CLM, IOD, RS, and SF, which reduced the total heritable variance. This variance, measured relative to phenotypic variance, ranged from 21 (CLM) to 54% (BW270). Results indicate that social genetic effects affect variation in traits relevant for heavy pigs used in dry-cured hams manufacturing. Such effects should be exploited and taken into account in design of breeding programs for heavy pigs.

Aplicação de modelos de regressão aleatória utilizando diferentes estruturas de dados

Foram utilizadas 3.202 primeiras lactações de vacas da raça Holandesa de quatro fazendas da região Sudeste, para verificar a influência da estrutura de dados de produção de leite sobre os parâmetros genéticos. Foram testados quatro arquivos com diferentes estruturas: controles semanais (CS), arquivo mensal (CM), bimestral (CB) e trimestral (CT), com 122.842, 30.883, 15.837 e 12.702 controles, respectivamente. Um modelo de regressão aleatória foi empregado nas análises, considerando os efeitos genético aditivo e o de ambiente permanente de animal, como aleatórios. Os efeitos fixos, grupos de contemporâneos (GC) foram comuns para todos os arquivos de dados e foram compostos por fazenda, mês e ano do controle, além da co-variável idade da vaca ao parto (regressão linear e quadrática). As estimativas de herdabilidade apresentaram tendências mais semelhantes entre os arquivos de dados CS, CM e CB. O arquivo de dados CB apresentou estimativas de parâmetros genéticos com as mesmas tendências e magnitudes que os arquivos CS e CM, permitindo afirmar que não houve influência da estrutura dos dados sobre as estimativas dos componentes de (co)variância e que o controle leiteiro poderia ser realizado em uma estrutura CB

Genetic and environmental variance and covariance parameters for some reproductive traits of Holstein and Jersey cattle in Antioquia (Colombia)

The objective of this study was to estimate the genetic, phenotypic and environmental parameters for calving interval (CI), days open (DO), number of services per conception (NSC) and conception rate (CR) in Holstein and Jersey cattle in Antioquia (Colombia). Variance and covariance component estimates were obtained by an animal model that was solved using the derivative-free restricted maximum likelihood method. The means and standard deviations for CI, DO, NSC and CR were: 430.32±77.93 days, 127.15±76.96 days, 1.58±1.03 services per conception and 79.88±28.66% in Holstein cattle, and 409.33±86.48 days, 125.62±86.09 days, 1.48±0.98 services per conception and 84.08±27.23% in Jersey cattle, respectively. The heritability estimates (standard errors) were: 0.088(0.037), 0.082(0.037), 0.040(0.025) and 0.030(0.026) in Holstein cattle and 0.072(0.098), 0.090(0.104), 0.093(0.097) and 0.147(0.117) in Jersey cattle, respectively. The results show that the genetic, phenotypic and permanent environmental correlations in the two evaluated breeds were favorable for CI × DO, CI × NSC and DO × NSC, but not for CI × CR, DO × CR and NSC × CR. Genetic and permanent environmental correlations were high in most cases in Holstein cattle, whereas in Jersey cattle they were moderate. In contrast, phenotypic correlations were very low in both breeds, except for CI × DO and NSC × CR, which were high. Overall, the genetic component found was very low (<8%) in both evaluated breeds and this implies that their selection would take long time and that a good practical management of the herd will be essential in order to improve the reproductive performance.

Estimates of genetic parameters for stayability to consecutive calvings of Canadian Simmentals by random regression models1

Stayability to consecutive calvings was selected as a measure of cow longevity in the Canadian Simmental population. Calving performance data on 188,579 cows and culling information from the Total Herd Reporting System were used to determine whether a cow stayed in a herd for her second and later (up to the eighth) calvings, given that she had calved as 2 yr old. Binary records (n = 1,164,319) were analyzed with animal linear and threshold models including fixed effects of year of birth by season of birth by parity number and age of cow at first calving by parity number and random effects of contemporary group (CG) defined as herd of birth within year by season, animal additive genetic effect, and a cow permanent environmental (PE) effect. All random effects were Legendre polynomial regressions of the same order, defined on the scale from second to the eighth calving. Bayesian methods with Gibbs sampling were used to estimate covariance components and genetic parameters for random effects of models and selected variables on the longitudinal scale. Bayes factors and analyses of mean squared error and correlation between observed and predicted observations indicated that the linear model with regressions of order 3 was most plausible for generating the current data compared with a fixed regression and other random regression (both linear and threshold) models of order up to 4. Estimates of variances for all random effects from the best fitting model changed with the calving number. Estimates of heritability decreased in time: from 0.35 (SD = 0.006) for stayability to second calving to 0.13 (SD = 0.004) for stayability to the eighth calving. Variance due to PE effect constituted the largest part of the total variance of stayability for all longitudinal points followed by genetic and CG components. Genetic effects of stayability to different calvings were relatively highly correlated, from 0.62 (SD = 0.011) to 0.99 (SD = 0.001), and correlation decreased with the time span between calvings. Correlations for PE and CG effects showed similar trends. Animal genetic effect seemed to be less variable on the longitudinal scale compared with other random effects of the model. The first 2 principal components explained from 95% (PE effects) to 99% (genetic effect) of the total variance. The overall level of genetic stayability curve correlated well (from 0.87 to 0.99, with SD < 0.006) with genetic stayability to different calvings and therefore could be used as a single criterion in selection for stayability.

Parâmetros genéticos da curva de produção de ovos de uma linha fêmea de frango de corte

Objetivou-se com este trabalho estimar os parâmetros genéticos e fenotípicos dos parâmetros da curva de produção de ovos, pelo o modelo de polinômios segmentados ("x p"- idade das aves ao pico de postura, "P"- nível de produção no pico, "s" - taxa de decréscimo semanal na produção de ovos após o pico e "t" - tempo entre o início da postura e o pico de produção de ovos). Foram utilizados dados da produção de ovos semanal da 25ª até 64ª semanas de idade, provenientes de 2.398 matrizes de uma linhagem de frangos de corte. A estimação dos componentes de covariâncias, herdabilidade e correlações para esses parâmetros da curva de postura foram obtidas por máxima verossimilhança restrita. As tendências genéticas foram estimadas com as médias dos valores genéticos dos parâmetros da curva em função do ano de nascimento das matrizes. As médias das herdabilidades foram de baixa a média magnitudes, 0,25 (x p), 0,18 (P), 0,17 (s) e 0,10 (t). As correlações genéticas entre o parâmetro t e os demais parâmetros da curva foram positivas, variando de 0,21 até 1,00, sendo menor entre t e s e maior entre os parâmetros x p e t. Entre os parâmetros x p e P, a correlação também foi positiva, de magnitude média (0,39). As correlações foram negativas entre os parâmetros s e x p e s e P, apresentando-se menor entre s e x p (-0,17) e maior entre s e P (-0,91). As tendências genéticas encontradas para os parâmetros indicaram uma redução no tempo entre o início e pico de produção e idade ao pico de postura. O nível de produção apresentou uma queda no valor genético ao longo do período avaliado. Pode-se observar possível ganho genético para os parâmetros da curva de produção de ovos, contudo, deve-se atentar para as correlações genéticas positivas entre os parâmetro x p e P, o que pode levar a um aumento do nível de produção e a um aumento na idade ao pico de produção. O mesmo caso acontece com os parâmetros x p e s, indicando que as aves mais precoces ao pico poderão apresentar menor persistência.

Genetic parameters for concentrations of minerals in longissimus muscle and their associations with palatability traits in Angus cattle1

The objective of this study was to estimate genetic parameters for concentrations of minerals in LM and to evaluate their associations with beef palatability traits. Samples of LM from 2,285 Angus cattle were obtained and fabricated into steaks for analysis of mineral concentrations and for trained sensory panel assessments. Nine minerals, including calcium, copper, iron, magnesium, manganese, phosphorus, potassium, sodium, and zinc, were quantified. Restricted maximum likelihood procedures were used to obtain estimates of variance and covariance components under a multiple-trait animal model. Estimates of heritability for mineral concentrations in LM varied from 0.01 to 0.54. Iron and sodium were highly and moderately heritable, respectively, whereas the other minerals were lowly heritable except for calcium, copper, and manganese, which exhibited no genetic variation. Strong positive genetic correlations existed between iron and zinc (0.49, P < 0.05), between magnesium and phosphorus (0.88, P < 0.05), between magnesium and sodium (0.68, P < 0.05), and between phosphorus and potassium (0.69, P < 0.05). Overall tenderness assessed by trained sensory panelists was positively associated with manganese, potassium, and sodium and negatively associated with phosphorus and zinc concentrations (P < 0.05). Juiciness assessed by trained sensory panelists was negatively associated with magnesium and positively associated with manganese and sodium concentrations (P < 0.05). Livery or metallic flavor was not associated with any of the minerals (P > 0.05). Beefy flavor was positively associated with calcium, iron, and zinc and negatively associated with sodium concentration, whereas a painty or fishy flavor was positively associated with sodium and negatively associated with calcium and potassium concentrations (P < 0.05). Beef is a major contributor of iron and zinc in the human diet, and these results demonstrate sufficient genetic variation for these traits to be improved through marker-assisted selection programs without compromising beef palatability.

Genetic analysis of female fertility traits in Canadian Simmentals

Calving to first insemination (CFI) (probability that a cow will produce a calf from her first service) and days to calving (DC) (interval between the first exposure to the bull and calving) defined separately for heifers and multi-parity cows were analyzed with a 4-trait linear animal model. The data were 108,206 records on 56,879 Canadian Simmental females with artificial insemination (AI) and natural service (NS) breeding records from 1974 to 2010. The model included fixed effects of year-season of breeding, age of cow by season of breeding, and age of cow's dam. Random effects were: contemporary group defined as herd within breeding year-season by breeding status for the first insemination (AI or NS), service sire by year of breeding (for CFI only), animal genetic, and cow permanent environmental (PE) effects. Bayesian methods were used to estimate covariance components and genetic parameters. Three specific models with different levels of heterogeneity for covariances in NS and AI data were tested. Results are reported for the most plausible specification which was the model that assumed different residual covariances for NS and AI records. The data exhibited substantial heterogeneity of residual covariance components with respect to the type of first breeding, with AI records having larger residual variances for both traits. Pooled estimates (SD) of heritability ranged from 1.8% (0.33) for CFI in heifers to 3.5% (0.47) for DC in multi-parity cows. Interval trait (DC) had higher heritability compared with CFI; both traits expressed in older cows were more heritable than corresponding traits for heifers. Contemporary group contributed up to 58% (0.51) of the total variance for DC in heifers by NS breeding. Service sire and the PE were relatively larger (smaller) sources of variation compared with additive genetic (contemporary group) effects. All traits were highly genetically correlated: from 0.69 (0.06) for CFI in heifers and multi-parity cows to 0.92 (0.04) for DC in heifers and multi-parity cows. Environmental correlations ranged from −0.73 (0.01) between CFI in heifers and DC in older cows, to 0.91 (0.01) for DC in heifers and multi-parity cows. Results indicated that CFI and DC expressed different aspects of female fertility in beef cattle, and fertility of heifers and multi-parity cows seemed to be different traits genetically. All four traits could be used in a form of selection index in Canadian Simmentals to breed for better fertility. Genetic progress, however, would be challenging given low values of heritability.

A penalized likelihood approach to pooling estimates of covariance components from analyses by parts

Estimates of covariance matrices for numerous traits are commonly obtained by pooling results from a series of analyses of subsets of traits. A penalized maximum-likelihood approach is proposed to combine estimates from part analyses while constraining the resulting overall matrices to be positive definite. In addition, this provides the scope for 'improving' estimates of individual matrices by applying a penalty to the likelihood aimed at borrowing strength from their phenotypic counterpart. A simulation study is presented showing that the new method performs well, yielding unpenalized estimates closer to results from multivariate analyses considering all traits, than various other techniques used. In particular, combining results for all sources of variation simultaneously minimizes deviations in phenotypic estimates if sampling covariances can be approximated. A mild penalty shrinking estimates of individual covariance matrices towards their sum or estimates of canonical eigenvalues towards their mean proved advantageous in most cases. The method proposed is flexible, computationally undemanding and provides combined estimates with good sampling properties and is thus recommended as alternative to current methods for pooling.

Genetic parameters for carnitine, creatine, creatinine, carnosine, and anserine concentration in longissimus muscle and their association with palatability traits in Angus cattle1

The objective of this study was to estimate genetic parameters for carnitine, creatine, creatinine, carnosine, and anserine concentration in LM and to evaluate their associations with Warner-Bratzler shear force (WBSF) and beef palatability traits. Longissimus muscle samples from 2,285 Angus cattle were obtained and fabricated into steaks for analysis of carnitine, creatine, creatinine, carnosine, anserine, and other nutrients, and for trained sensory panel and WBSF assessments. Restricted maximum likelihood procedures were used to obtain estimates of variance and covariance components under a multiple-trait animal model. Estimates of heritability for carnitine, creatine, creatinine, carnosine, and anserine concentrations in LM from Angus cattle were 0.015, 0.434, 0.070, 0.383, and 0.531, respectively. Creatine, carnosine, and anserine were found to be moderately heritable, whereas almost no genetic variation was observed in carnitine and creatinine. Moderate positive genetic (0.25, P < 0.05) and phenotypic correlations (0.25, P < 0.05) were identified between carnosine and anserine. Medium negative genetic correlations were identified between creatine and both carnosine (-0.53, P < 0.05) and anserine (-0.46, P < 0.05). Beef and livery/metallic flavor were not associated with any of the 5 compounds analyzed (P > 0.10), and carnitine concentrations were not associated (P > 0.10) with any of the meat palatability traits analyzed. Carnosine was negatively associated with overall tenderness as assessed by trained sensory panelists. Similar negative associations with overall tenderness were identified for creatinine and anserine. Painty/fishy was the only flavor significantly and negatively associated with creatinine and carnosine. These results provide information regarding the concentration of these compounds, the amount of genetic variation, and evidence for negligible associations with beef palatability traits in LM of beef cattle.

Multivariate statistical analysis of deformation tensors: independent vs. correlated tensor observations

In the presence of errors in measuring a random displacement field (under the normal distribution assumption of displacement field), stochastic behaviors of principal components of deformation tensors (strain tensor and tensor of change of curvature (TCC)), based on the intrinsic assumption of geometrical modeling of surface deformation analysis, are discussed. We divided the contents into two parts: In the first, we considered independent random vectors of repeated tensor measurements. In the second step, we considered correlations among repeated measurements. Then, covariance components between tensor elements by Helmert estimator, based on prior information of variance components, are estimated. As a case study, both assumptions are applied to the estimation of principal components of deformation rate tensor observations in Zagros region (Western Iran). The results of numerical analysis showed that greatest shortening is accommodated in oblique orientation (NS) with respect to the Main Recent Fault (MRF), northwest part of North Zagros, Central Iran block and MRF, respectively. Most of the extensions occurred in the east part of the belt. The pattern of eigenspace components of TCC shows highest positive values across the NW region, nearly in orthogonal direction to the MRF and Main Zagros Fault (MZF). The pattern has insignificant values in the Central Zagros. It takes the significant negative values across the SW part, especially along the SPF and Persian Gulf shore. The effect of non-independent observations on the estimation of eigenspace components of deformation tensors (strain tensor and TCC) shows that the estimation of covariance components has influence on the confidence intervals of eigenspace components, especially in seismically active regions of the belt (along the Persian Gulf shore, NW of the belt and region between the Central Iran block and MRF). The results demonstrate the importance of considering the correlation structure among the observations on statistical behavior of principal components of deformation tensors in seismically active regions.