Random regression models to estimate genetic parameters for test‐day milk yield in Brazilian Murrah buffaloes

The objective of this work was to estimate covariance functions for additive genetic and permanent environmental effects and, subsequently, to obtain genetic parameters for buffalo’s test‐day milk production using random regression models on Legendre polynomials (LPs). A total of 17 935 test‐day milk yield (TDMY) from 1433 first lactations of Murrah buffaloes, calving from 1985 to 2005 and belonging to 12 herds located in São Paulo state, Brazil, were analysed. Contemporary groups (CGs) were defined by herd, year and month of milk test. Residual variances were modelled through variance functions, from second to fourth order and also by a step function with 1, 4, 6, 22 and 42 classes. The model of analyses included the fixed effect of CGs, number of milking, age of cow at calving as a covariable (linear and quadratic) and the mean trend of the population. As random effects were included the additive genetic and permanent environmental effects. The additive genetic and permanent environmental random effects were modelled by LP of days in milk from quadratic to seventh degree polynomial functions. The model with additive genetic and animal permanent environmental effects adjusted by quintic and sixth order LP, respectively, and residual variance modelled through a step function with six classes was the most adequate model to describe the covariance structure of the data. Heritability estimates decreased from 0.44 (first week) to 0.18 (fourth week). Unexpected negative genetic correlation estimates were obtained between TDMY records at first weeks with records from middle to the end of lactation, being the values varied from ?0.07 (second with eighth week) to ?0.34 (1st with 42nd week). TDMY heritability estimates were moderate in the course of the lactation, suggesting that this trait could be applied as selection criteria in milking buffaloes.     

Random regression test day models to estimate genetic parameters for milk yield and milk components in Philippine dairy buffaloes

Heritabilities and genetic correlations for milk production traits were estimated from first‐parity test day records on 1022 Philippine dairy buffalo cows. Traits analysed included milk (MY), fat (FY) and protein (PY) yields, and fat (Fat%) and protein (Prot%) concentrations. Varying orders of Legendre polynomials (Leg_m) as well as the Wilmink function (Wil) were used in random regression models. These various models were compared based on log likelihood, Akaike's information criterion, Bayesian information criterion and genetic variance estimates. Six residual variance classes were sufficient for MY, FY, PY and Fat%, while seven residual classes for Prot%. Multivariate analysis gave higher estimates of genetic variance and heritability compared with univariate analysis for all traits. Heritability estimates ranged from 0.25 to 0.44, 0.13 to 0.31 and 0.21 to 0.36 for MY, FY and PY, respectively. Wilmink's function was the better fitting function for additive genetic effects for all traits. It was also the preferred function for permanent environment effects for Fat% and Prot%, but for MY, FY and PY, the Leg_m was the appropriate function. Genetic correlations of MY with FY and PY were high and they were moderately negative with Fat% and Prot%. To prevent deterioration in Fat% and Prot% and improve milk quality, more weight should be applied to milk component traits.     

Random regression models on Legendre polynomials to estimate genetic parameters for weights from birth to adult age in Canchim cattle*

The objective of this work was to estimate covariance functions for direct and maternal genetic effects, animal and maternal permanent environmental effects, and subsequently, to derive relevant genetic parameters for growth traits in Canchim cattle. Data comprised 49 011 weight records on 2435 females from birth to adult age. The model of analysis included fixed effects of contemporary groups (year and month of birth and at weighing) and age of dam as quadratic covariable. Mean trends were taken into account by a cubic regression on orthogonal polynomials of animal age. Residual variances were allowed to vary and were modelled by a step function with 1, 4 or 11 classes based on animal’s age. The model fitting four classes of residual variances was the best. A total of 12 random regression models from second to seventh order were used to model direct and maternal genetic effects, animal and maternal permanent environmental effects. The model with direct and maternal genetic effects, animal and maternal permanent environmental effects fitted by quadric, cubic, quintic and linear Legendre polynomials, respectively, was the most adequate to describe the covariance structure of the data. Estimates of direct and maternal heritability obtained by multi‐trait (seven traits) and random regression models were very similar. Selection for higher weight at any age, especially after weaning, will produce an increase in mature cow weight. The possibility to modify the growth curve in Canchim cattle to obtain animals with rapid growth at early ages and moderate to low mature cow weight is limited.     

Haematological profile on non-lactating Mediterranean buffaloes (Bubalus bubalis) ranging in age from 24 months to 14 years

Haematological studies were performed on 100 clinically normal non-lactating Mediterranean buffalo species ranging in age from 24 months to 14 years, to determinate the range of normal haematological values for this ruminant species. The animals were divided in 5 groups according to age: Group I, 2-3 years old which had never calved, Group II, 3-4 years old (primipara buffaloes), Group III, 5-7 years old, Group IV 8-10 years old and Group V over 10 years of age. All the haematological values obtained were comparable with the normal values found in adult cattle, and similar to those reported in Indian water buffalo species. The heifer buffalo showed an higher values for packed cell volume (PCV) compared with the older animals, but lower values for mean corpuscular haemoglobin concentration (MCHC) and mean corpuscular haemoglobin (MCH) (P 0.01). In animals above 8 years of age, the white cell count was lower with a significant reduction in absolute values of lymphocytes (P 0.01). Higher absolute values of eosinophils levels was found in the group V (P 0.01).     

Topographic laparoscopy for buffaloes in the quadruped position

This study aimed to describe the anatomical topography of the abdominal cavity of buffaloes in the quadruped position to establish the best endosurgical access and vantage points and identify possible limitations. Laparoscopies were performed on 10 healthy female buffaloes obtained from the Universidade Federal Rural da Amazônia to explore possible access points to the abdomen. Techniques for assessing and possibly observing certain organs and structures through the left and right flanks of 10 animals have been described. In five animals, access was created through the right side of the last intercostal space to allow more cranial access to the abdominal cavity. Despite the presence of the rumen, access through the left flank allowed the visualization of the structures of the gastrointestinal tract and the genitourinary system. With access through the right flank, however, imaging was hampered by the presence of the greater omentum and its deep and superficial walls, which prevented the progression of the endoscope. Access through the last right intercostal space allowed the visualization of the cranial structures of the abdominal cavity, such as the caudate process, right lobe of the liver, right kidney, and pancreas. Laparoscopic access through the left flank and the last intercostal space in healthy buffaloes in the quadruped position is feasible, and it is promising for the exploration, diagnosis, and treatment of various disorders in buffaloes.     

Comparative studies on temperature threshold for heat shock protein 70 induction in young and adult Murrah buffaloes

To know the temperature threshold for heat shock protein 70 (HSP70) induction in lymphocytes and to assess physiological changes, if any, in relation to HSP70 induction in young and adult Murrah buffaloes, this study was divided into two parts: I. In vivo study: where assay of HSP70 was performed in blood samples collected from acutely exposed young and adult Murrah buffaloes (n = 6) inside a climatic chamber at 40, 42 and 45 °C for 4 h and thermoneutral temperature (22 °C). Physiological parameters viz., rectal temperature, respiratory rate, pulse rate and skin temperature of different body parts were monitored to assess magnitude of stress in the animals owing to thermal exposure II. For in vitro study, equal numbers of lymphocyte cells were separated from blood collected from young and adult buffaloes and were subjected to four temperature treatments (38, 40, 42 and 45 °C) for 4 h. A significant increase (p < 0.05) in all the physiological parameters in both young and adult buffaloes was observed after exposure to 40, 42 and 45 °C for 4 h as compared to 38 °C. The average plasma HSP70 concentrations (ng/ml) were significantly higher (p < 0.05) at 40, 42 and 45 °C as compared to 38 °C in both young and adult and were higher in young than adult buffaloes at 38 and 45 °C. Heat shock protein 70 level in lymphocyte lysate showed highest concentration after 3-h exposure to all temperatures (40, 42 and 45 °C) in both young and adult buffaloes. The intensity of changes of all physiological parameters was more in young animals than in the adults indicating the greater susceptibility of younger animals to heat stress and was found to be changed at around 40 °C when animals were exposed to different temperatures, indicating the possibility that HSP70 production may be initiated at this temperature which is 2 or 3 °C higher than core body temperature.     

Comparison of two models to estimate genetic parameters for number of born alive in pigs

The performance of the two‐trait animal model that regards the first parity and later parities as two different traits in estimating genetic parameters for number of born alive (NBA) was examined using real and simulated data. Genetic parameters for NBA were estimated in purebred Landrace and Large White pigs using a single‐trait repeatability model (Model 1) that regards all parities as the same trait and a two‐trait animal model (Model 2) that regards the first and the later parities as different traits. For Model 2, the permanent environmental effect was fitted to only the records of the later parities. Heritability for NBA estimated using Model 1 was 0.12 for Landrace and 0.11 for Large White. Estimated heritability for NBA of the first parity and the later parities was 0.21 and 0.16, respectively, for Landrace; 0.18 and 0.16, respectively, for Large White obtained using Model 2, and higher than those in both breeds obtained using Model 1. Further results based on data simulated using the Monte Carlo method suggest that estimated additive genetic variance could be more biased using Model 2 than Model 1.     

Teat characteristics in relation to animal temperament during milking in buffaloes,and comparison of buffalo and cow teat morphology

This study aimed to examine the teat characteristics in relation to the animal temperament during milking in the Anatolian buffaloes using ultrasonographic, histomorphological and immunohistochemical methods. The teat canal length (TCL), teat wall thickness (TWT), teat cisternal diameter (TCD), teat diameter (TD), teat length (TL), and teat circumference (TC) values in docile (n = 5) and nervous (n = 7) buffaloes were measured at the 0th, 3rd and 6th minute of stimulation. In additional experiments, comparative histomorphology and immunohistochemical examinations of buffalo (n = 7) and cow teats (n = 8) were performed. It was determined that post-stimulation mean TCL values were significantly higher in nervous buffaloes than those of teats in docile buffaloes (p < .05). A significant positive correlation between TCD and TD, TL and TC in both docile and nervous buffaloes was noted (p < .05). Unlike nervous buffaloes where only 3/14 teat canals were open by 3rd minute of milking stimulation, almost all (9/10) teat canals were observed opened in docile buffaloes. There were fewer muscle but more collagen bundles in buffalo teats compared with cow teats. It seems that temperament of animal during milking effects the milking efficiency, and in nervous buffaloes, probably the stimulation alone may not be sufficient for opening of the teat canal and hence achieve complete milking.     

Random regression model estimation of genetic parameters for show‐jumping results of Hungarian Sporthorses

The aim of this study was to estimate the genetic parameters for show‐jumping competition performance of Hungarian Sporthorses using a random regression model. There were 21 210 records from 739 horses collected in Hungary between 1996 and 2004. Performance was expressed as shifted Blom normalized ranks and as the difference between fence height and fault points. The random regression model (RRM) included fixed effects for sex, year, location, and obstacle height and random effects for animal, rider and permanent environment. Regressions for the random effects in the RRM were modelled with Legendre polynomials from first to fifth order of fit. The model focused on performance of horses from 4 to 11 years of age, with heterogeneous residual variances considered. The heritabilities were low to moderate for both variables. Genetic and phenotypic correlations between different ages decreased with increasing distance between the ages.     

Modeling lactation curves and estimation of genetic parameters in Holstein cows using multiple‐trait random regression models

We compared the goodness of fit of three mathematical functions (including: Legendre polynomials, Lidauer‐Mäntysaari function and Wilmink function) for describing the lactation curve of primiparous Iranian Holstein cows by using multiple‐trait random regression models (MT‐RRM). Lactational submodels provided the largest daily additive genetic (AG) and permanent environmental (PE) variance estimates at the end and at the onset of lactation, respectively, as well as low genetic correlations between peripheral test‐day records. For all models, heritability estimates were highest at the end of lactation (245 to 305 days) and ranged from 0.05 to 0.26, 0.03 to 0.12 and 0.04 to 0.24 for milk, fat and protein yields, respectively. Generally, the genetic correlations between traits depend on how far apart they are or whether they are on the same day in any two traits. On average, genetic correlations between milk and fat were the lowest and those between fat and protein were intermediate, while those between milk and protein were the highest. Results from all criteria (Akaike's and Schwarz's Bayesian information criterion, and ?2*logarithm of the likelihood function) suggested that a model with 2 and 5 coefficients of Legendre polynomials for AG and PE effects, respectively, was the most adequate for fitting the data.     

Estimation of genetic parameters for ultrasound-predicted percentage of intramuscular fat in Angus cattle using random regression models

The present study included 3,358 observations of 675 bulls and heifers from the Iowa State University beef cattle breeding project. Data were collected over a 3-yr period between 1998 and 2000. Each year, cattle were scanned four to six times for ultrasound-predicted percentage of intramuscular fat (UPFAT) and other ultrasound traits, starting at a minimum age of 28 wk. The objective of the current study was to estimate variance components, heritability, and repeatability of UPFAT in young bulls and heifers. Data were subjected to random-regression animal models that included fixed effects of contemporary group, fixed Legendre polynomial of age at measurement, and random regression coefficients on Legendre polynomial of age at measurement for animals' direct genetic and direct permanent environmental effects. Phenotypic and genetic models involving different levels of polynomial fit for the animal component were considered. A model fitting a linear effect of Legendre polynomial of age at a measurement for animal direct genetic and direct permanent environmental effects and a homogeneous error variance described the present data adequately. Heritability of UPFAT ranged from 0.32 at 28 wk of age to a maximum of 0.53 at 63 wk. Repeatability of UPFAT increased from a minimum of 0.60 at ages of 28 to 39 wk to a maximum of 0.80 at ages 61 to 63 wk. Heritability and repeatability of yearling UPFAT were 0.50 and 0.71, respectively. With the exception of minor differences at earlier ages, fitting heterogeneous error variances did not have an effect on genetic parameter estimates for most ages of measurement. The present results showed an optimal heritability and repeatability of UPFAT measures around 52 wk and through at least 63 wk of age. This suggested that differences in UPFAT measures during this period also are good measures of differences in marbling genetic potential of Angus cattle.     

Estimation of genetic parameters for farrowing traits in purebred Landrace and Large White pigs

Genetic parameters were estimated for six reproductive traits related to farrowing events in Landrace and Large White pigs; total number born (TNB), number born alive (NBA), number stillborn (NSB), total litter weight at birth (LWB), mean litter weight at birth (MWB), and gestation length (GL). We analyzed 62,534 farrowing records for 10,637 Landrace dams and 49,817 farrowing records for 8,649 Large White dams. Estimated heritabilities of TNB, NBA, NSB, LWB, MWB, and GL by single‐trait repeatability model analyses were 0.12, 0.12, 0.08, 0.18, 0.19, and 0.29, respectively, in Landrace, and 0.12, 0.10, 0.08, 0.18, 0.16, and 0.34, respectively, in Large White. Genetic correlation between NBA and NSB was unfavorable: 0.20 in Landrace and 0.33 in Large White. Genetic correlations of GL with the other five traits were weak: from ?0.18 with NSB to ?0.03 with NBA in Landrace, and from ?0.22 with NSB to ?0.07 with NBA in Large White. LWB had a highly favorable genetic correlation with NBA (0.74 in both breeds), indicating the possibility of using LWB for the genetic improvement of NBA.     

Polynomial order selection in random regression models via penalizing adaptively the likelihood

Orthogonal Legendre polynomials ( LP ) are used to model the shape of additive genetic and permanent environmental effects in random regression models ( RRM ). Frequently, the Akaike ( AIC ) and the Bayesian ( BIC ) information criteria are employed to select LP order. However, it has been theoretically shown that neither AIC nor BIC is simultaneously optimal in terms of consistency and efficiency. Thus, the goal was to introduce a method, ‘penalizing adaptively the likelihood’ ( PAL ), as a criterion to select LP order in RRM. Four simulated data sets and real data (60 513 records, 6675 Colombian Holstein cows) were employed. Nested models were fitted to the data, and AIC, BIC and PAL were calculated for all of them. Results showed that PAL and BIC identified with probability of one the true LP order for the additive genetic and permanent environmental effects, but AIC tended to favour over parameterized models. Conversely, when the true model was unknown, PAL selected the best model with higher probability than AIC. In the latter case, BIC never favoured the best model. To summarize, PAL selected a correct model order regardless of whether the ‘true’ model was within the set of candidates.     

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.     

Estimates of genetic parameters for worm resistance,wool and growth traits in Merino sheep of Uruguay

The genotype of an individual and the environment as the maternal ability of its dam have substantial effects on the phenotype expression of many production traits. The aim of the present study was to estimate the (co)variance components for worm resistance, wool and growth traits in Merino sheep, testing the importance of maternal effects and to determine the most appropriate model for each trait. The traits analyzed were Greasy Fleece Weight (GFW), Clean Fleece Weight (CFW), average Fibre Diameter (FD), Coefficient of Variation of FD (CVFD), Staple Length (SL), Comfort Factor (CF30), Weaning Weight (WWT), Yearling Body Weight (YWT) and Faecal worm Egg Count (FEC). The data were recorded during a 15-year period from 1995 to 2010, from Uruguayan Merino stud flocks. A Bayesian analysis was performed to estimate (co)variance components and genetic parameters. By ignoring or including maternal genetic or environmental effects, five different univariate models were fitted in order to determine the most effective for each trait. For CVFD and YWT, the model fitting the data best included direct additive effects as the only significant random source of variation. For GFW, CFW, FD, SL and CF30 the most appropriate model included direct-maternal covariance; while for FEC included maternal genetics effects with a zero direct-maternal covariance. The most suitable model for WWT included correlated maternal genetic plus maternal permanent environmental effects. The estimates of direct heritability were moderate to high and ranged from 0.15 for log transformed FEC to 0.74 for FD. Most of the direct additive genetic correlation (rg) estimations were in the expected range for Merino breed. However, the estimate of rg between FEC and FD was unfavourable (−0.18±0.03). In conclusion, there is considerable genetic variation in the traits analyzed, indicating the potential to make genetic progress on these traits. This study showed that maternal effects are influencing most of traits analyzed, thus these effects should be considered in Uruguayan Merino breeding programs; since the implementation of an appropriate model of analysis is critical to obtain accurate estimates.     

Variance components and genetic parameters for weight and size at birth in the Boer goat

Variance components, heritability (direct additive and maternal) and correlations (additive genetic, phenotypic, maternal genetic and environmental) of body weight (BW) and body size including length (BL), height (BH) and chest girth (BCG) at birth in Boer goats were estimated on the basis of 5096 records obtained from a Boer Goat Breeding Station in Yidu, China, during 2001–2005. The parameters were estimated using a DFREML procedure by excluding or including maternal genetic or permanent maternal environmental effects, four different analysis models were fitted in order to determine the optimum model for each trait. The environmental factors such as year, season, sex and litter size (LS, number of kids) were investigated as the fixed effects. The results showed that the maternal effects were important determinants of estimated the genetic parameters for birth traits. Year and season had significant effect on birth traits. Single births and male kids had the heaviest live weight and the largest body size at birth. The mean values and standard deviation (SD) of BW, BL, BH and BCG were 3.87 ± 0.85 kg, 31.67 ± 2.87 cm, 32.92 ± 2.80 cm, 33.46 ± 3.21 cm. The mean values and standard error (SE) of direct additive heritability estimates for BW, BL, BH and BCG calculated with the optimum model were 0.19 ± 0.08, 0.14 ± 0.07, 0.24 ± 0.09 and 0.25 ± 0.10, respectively. For all the birth traits, estimates of the correlations between direct additive and maternal genetic (r_a–m) were negative. The estimates of additive genetic and phenotypic correlations among the birth traits were high and positive, and implied no genetic antagonisms among these traits analyzed. The estimates of maternal genetic correlations also were high and positive. Medium and positive environmental correlations indicated the important effects of environmental factors on early growth traits.     

Estimation of genetic parameters for longevity traits in dairy cattle: A review with focus on the characteristics of analytical models

Longevity is an economically important trait of dairy cattle for increasing the profitability of dairy management. The reasons for culling can be either voluntary (primarily productivity) or involuntary (primarily health and fertility). Longevity characteristics include: (i) true longevity (all culling reasons, including productivity); and (ii) functional longevity (all culling reasons, except productivity). Improvements to longevity are made to decrease the rate of involuntary culling rather than extend the herd life (HL). The proportional hazard model is useful for evaluating genetic ability for HL. However, the differences between estimates made using the proportional hazard model and those made using linear single or multiple‐trait animal models are not clear. The model commonly used for evaluation differs among countries. Productive traits, udder traits, and feet and legs traits are genetically correlated with longevity, and consequently these traits are used to indirectly evaluate longevity. The reliability of estimates of genetic ability for longevity is increased by combining direct and indirect estimates. In Japan, HL is evaluated using the multiple‐traits model. The genetic correlations between HL and other traits vary with the birth year. Therefore, these genetic correlations need to be reviewed regularly.     

Direct and maternal (co)variance components and genetic parameters for growth and reproductive traits in the Boran cattle in Kenya

Direct and maternal (co)variance components and genetic parameters were estimated for growth and reproductive traits in the Kenya Boran cattle fitting univariate animal models. Data consisted of records on 4502 animals from 81 sires and 1010 dams collected between 1989 and 2004. The average number of progeny per sire was 56. Direct heritability estimates for growth traits were 0.34, 0.12, 0.19, 0.08 and 0.14 for birth weight (BW), weaning weight (WW), 12-month weight (12W), 18-month weight (18W) and 24-month weight (24W), respectively. Maternal heritability increased from 0.14 at weaning to 0.34 at 12 months of age but reduced to 0.11 at 24 months of age. The maternal permanent environmental effect contributed 16%, 4% and 10% of the total phenotypic variance for WW, 12W and 18W, respectively. Direct-maternal genetic correlations were negative ranging from −0.14 to −0.58. The heritability estimates for reproductive traits were 0.04, 0.00, 0.15, 0.00 and 0.00 for age at first calving (AFC), calving interval in the first, second, and third parity, and pooled calving interval. Selection for growth traits should be practiced with caution since this may lead to a reduction in reproduction efficiency, and direct selection for reproductive traits may be hampered by their low heritability.     

Estimation of genetic parameters for hip dysplasia in Czech Labrador Retrievers

The objective of this study was to estimate the genetic parameters, genetic trends and breeding values using linear model (LM) and threshold model (TM) for the development of hip dysplasia (HD) in Labrador Retrievers in the Czech Republic (n = 3151). The right and left hip joints were evaluated separately using the Fédération Cynologique Internationale scoring system. Four linear and four TMs were tested for the correct estimation of genetic parameters. All the tested models utilized fixed effects of sex, assessor, year of birth, regression of age at evaluation, random direct genetic effects and the effect of the animals' permanent environments. The models differed in the inclusion of the following effects: fixed effects of regression of inbreeding coefficient, random maternal effect and random effect of the maternal permanent environment. Compared to the TM, the LM provided lower coefficients of direct (0.25-0.29 versus 0.26-0.35) and maternal heritability (0.01-0.02 versus 0.03-0.05), repeatability (0.76-0.77 versus 0.78-0.83) and of the correlation between direct and maternal effects (-0.55 to -0.21 versus -0.80 to -0.27). In the tested models, no statistical significance was found for fixed regression of inbreeding coefficients or for the random effect of the permanent maternal environment. In spite of the similarity of the LM and TM results, the TM is recommended as the more suitable model for estimating genetic parameters and subsequent breeding values for HD in Labrador Retrievers in the Czech Republic.