Genetic analyses of partial egg production in Japanese quail using multi-trait random regression models

1. The aim of the present study was to estimate genetic parameters for average egg weight (EW) and egg number (EN) at different ages in Japanese quail using multi-trait random regression (MTRR) models.

2. A total of 8534 records from 900 quail, hatched between 2014 and 2015, were used in the study. Average weekly egg weights and egg numbers were measured from second until sixth week of egg production.

3. Nine random regression models were compared to identify the best order of the Legendre polynomials (LP). The most optimal model was identified by the Bayesian Information Criterion. A model with second order of LP for fixed effects, second order of LP for additive genetic effects and third order of LP for permanent environmental effects (MTRR23) was found to be the best.

4. According to the MTRR23 model, direct heritability for EW increased from 0.26 in the second week to 0.53 in the sixth week of egg production, whereas the ratio of permanent environment to phenotypic variance decreased from 0.48 to 0.1. Direct heritability for EN was low, whereas the ratio of permanent environment to phenotypic variance decreased from 0.57 to 0.15 during the production period.

5. For each trait, estimated genetic correlations among weeks of egg production were high (from 0.85 to 0.98). Genetic correlations between EW and EN were low and negative for the first two weeks, but they were low and positive for the rest of the egg production period.

6. In conclusion, random regression models can be used effectively for analysing egg production traits in Japanese quail. Response to selection for increased egg weight would be higher at older ages because of its higher heritability and such a breeding program would have no negative genetic impact on egg production.     

Genetic analysis of production traits in turbot (Scophthalmus maximus) using random regression models based on molecular relatedness

Reliable estimates of genetic parameters for growth traits as a trajectory of age are needed to optimize existing turbot breeding programmes. To evaluate the potential of early selection strategies, the use of biometric body measurements, length (L), width (W) and area (A), at early ages as alternative indicators for the selection trait at harvest was explored. Random regression model (RRM) based on molecular relatedness (MR) was used to analyse the trajectory of genetic parameters for growth traits in turbot from 162 to 756 days posthatch (dph). Heritability estimates for body weight (BW) ranged from 0.34 to 0.54. Heritability estimates for W, A and L were also moderate to high ranging from 0.18 to 0.43. Estimates for L and W declined with age, while those for A increased towards harvest age. Genetic (r_G) and phenotypic (r_P) correlations between BW and the three morphometric traits L, A and W were estimated using simple bivariate animal models at young (AC1), medium (AC2) and old (AC3) age classes. Correlations between BW and morphometric body traits were high, ranging from 0.7 to 0.9 in all three age groups. Genetic correlations between traits were highest (>0.9) in AC3. To explore the potential for early selection, genetic correlations were derived from the RRM between all days of measurement for all traits separately. From dph 300 onwards, intratrait estimates of r_G were moderate to high (above 0.7 for dph 410 and higher ages for traits BW, L and A). Results showed that genetic selection for BW, L and A is promising and that A and L could be successfully used as alternative indicator traits if measurements of BW are not available. Large BW and A at harvest could be achieved as a correlated response to early selection for these traits at around 500 dph.     

Genetic correlations between body condition scores and fertility in dairy cattle using bivariate random regression models

Genetic correlations between body condition score (BCS) and fertility traits in dairy cattle were estimated using bivariate random regression models. BCS was recorded by the Swiss Holstein Association on 22,075 lactating heifers (primiparous cows) from 856 sires. Fertility data during first lactation were extracted for 40,736 cows. The fertility traits were days to first service (DFS), days between first and last insemination (DFLI), calving interval (CI), number of services per conception (NSPC) and conception rate to first insemination (CRFI). A bivariate model was used to estimate genetic correlations between BCS as a longitudinal trait by random regression components, and daughter's fertility at the sire level as a single lactation measurement. Heritability of BCS was 0.17, and heritabilities for fertility traits were low (0.01-0.08). Genetic correlations between BCS and fertility over the lactation varied from: -0.45 to -0.14 for DFS; -0.75 to 0.03 for DFLI; from -0.59 to -0.02 for CI; from -0.47 to 0.33 for NSPC and from 0.08 to 0.82 for CRFI. These results show (genetic) interactions between fat reserves and reproduction along the lactation trajectory of modern dairy cows, which can be useful in genetic selection as well as in management. Maximum genetic gain in fertility from indirect selection on BCS should be based on measurements taken in mid lactation when the genetic variance for BCS is largest, and the genetic correlations between BCS and fertility is strongest.     

Comparison of homogeneity and heterogeneity of residual variance using random regression test-day models for first lactation Japanese Holstein cows

Using a large‐scale data set that included first lactation test day records from 1975 to 2000 for Japanese Holsteins, genetic parameters for milk yield were estimated by using random regression (RR) test‐day models (TDM) with heterogeneous and homogeneous residual variances. It is necessary for the RR‐TDM to include a function that explains the shape of the lactation curve. The RR‐TDM with the LW curve, which combined Wilmink's curve and a Legendre polynomial, was used for fitting the model for milk yield. In recent years, increases in residual variance have been noted for Japanese dairy cattle. Thus, three kinds of heterogeneous residual variance over the calving year were considered: H1, H2 and HG. Linear and quadratic exponential functions for the calving year were used in H1 and H2, respectively. Residual variance of HG was divided into five groups according to calving year. Homogeneous residual variance was HO. All heterogeneous residual variances increased with calving year in an almost linear fashion. Residual variance increased over the study period. However, there is no need to consider heterogeneous residual variances in genetic evaluations, because the heterogeneity of residual variance over the years did not affect the ranking of top sires and cows.     

Genetic evaluation of growth of Kenya Boran cattle using random regression models

Data consisting of 18 884 weight records collected from 1273 Boran cattle from birth to 24 months of age were used to estimate covariance functions and genetic parameters for growth of Boran cattle using random regression (RR) models under a situation of small herd size and inconsistent recording. The RR model fitted quadratic Legendre polynomials of age at recording for additive genetic and permanent environmental effects. Genetic variance increased from birth, reaching an asymptotic value at 455 days and was maximum at 525 days of age after which it gradually dropped. Permanent environmental variance increased throughout the trajectory. Estimates of temporary environmental variance were heterogeneous across ages. Direct heritability and permanent environmental variance as a proportion of phenotypic variance fluctuated greatly during the early ages but later stabilized at intermediate to later ages; the estimates ranged from 0.11 to 0.33 and from 0.18 to 0.83, respectively. Genetic correlation estimates were positive, ranging from 0.10 to unity. The estimates declined with increasing in lag between the age points. Phenotypic correlation pattern was erratic between early ages, negatively low (-0.02) between the extreme data points and moderate to highly positive (>0.50) between intermediate and later points, with prominent spikes along the diagonal. It is concluded that RR models have potential for modelling growth of Boran cattle, notwithstanding conditions of small herd sizes and inconsistent recording.     

Accessing genotype by environment interaction using within- and across-country test-day random regression sire models

First-lactation test-day (TD) milk records of Luxembourg and Tunisian Holsteins were analysed for evidence of genotype by environment interaction (G × E). The joint data included 730 810 TD records of 87 734 cows and 231 common sires. Random regression TD sire models with fourth-order Legendre polynomials were used to estimate genetic parameters via within- and across-country analyses. Daily heritability estimates of milk yield from within-country analysis were between 0.11 and 0.32, and 0.03 and 0.13 in Luxembourg and Tunisia, respectively. Heritability estimates for 305-day milk yield and persistency (defined as the breeding value for milk yield on DIM 280 minus the breeding value on DIM 80) were lower for Tunisian Holsteins compared with the Luxembourg population. Specifically, heritability for 305-day milk yield was 0.16 for within- and 0.11 for across-country analyses for Tunisian Holsteins and 0.38 for within- and 0.40 for across-country analyses for Luxembourg Holsteins. Heritability for apparent persistency was 0.02 for both within- and across-country analyses for Tunisian Holsteins and 0.08 for within- and 0.09 for across-country analyses for Luxembourg Holsteins. Genetic correlations between the two countries were 0.50 for 305-day milk yield and 0.43 for apparent persistency. Moreover, rank correlations between the estimated breeding values of common sires for 305-day milk yield and persistency, estimated separately in each country, were low. Low genetic correlations are evidence for G × E for milk yield production while low rank correlations suggest different rankings of sires in both environments. Results from this study indicate that milk production of daughters of the same sires depends greatly on the production environment and that importing high merit semen for limited input systems might not be an effective strategy to improve milk production.     

Genetic evaluation using random regression models with different covariance functions for test‐day milk yield in an admixture population of Thailand goats

The objectives of this study were to compare covariance functions (CF) and estimate the heritability of milk yield from test‐day records among exotic (Saanen, Anglo‐Nubian, Toggenburg and Alpine) and crossbred goats (Thai native and exotic breed), using a random regression model. A total of 1472 records of test‐day milk yield were used, collected from 112 does between 2003 and 2006. CF of the study were Wilmink function, second‐ and third‐order Legendre polynomials, and linear splines 4 knots located at 5, 25, 90 and 155 days in milk (SP25–90) and 5, 35, 95 and 155 of days in milk (SP35–95). Variance components were estimated by restricted maximum likelihood method (REML). Goodness of fit, Akaike information criterion (AIC), percentage of squared bias (PSB), mean square error (MSE), and empirical correlation (RHO) between the observed and predicted values were used to compare models. The results showed that CF had an impact on (co)variance estimation in random regression models (RRM). The RRM with splines 4 knots located at 5, 25, 90 and 155 of days in milk had the lowest AIC, PSB and MSE, and the highest RHO. The heritability estimated throughout lactation obtained with this model ranged from 0.13 to 0.23.     

Genetic evaluation of growth in Barki sheep using random regression models

The objective of the current study was to estimate covariance components of growth at different ages from birth to yearling in Barki lambs. A total of 16,496 records for body weights at birth (W0), 3 (W3), 6 (W6), 9 (W9), and 12 (12) months of age for Barki lambs were available. Two statistical approaches were used; multi-trait (MT) and random regression (RR) animal models assuming two random effects only, additive genetic effect (σ²_a) and permanent environmental effect (σ²_pe) of the animal. Regarding the RR model, Legendre polynomials (LP) of different orders for the random parts were compared in order to evaluate the most appropriate model. Bayesian information and Akaike information criteria suggested that the optimal RR model included the third order for fixed effect of lamb age and σ²_pe, and fourth order of LP for σ²_a (LP₃₄₃). Estimates of direct heritability (h²_a) from LP₃₄₃ showed an ascending pattern, as it was 0.06 ± 0.03 for birth weight and reached to the peak at 9 months (0.42 ± 0.02). Thereafter, it declined again at the end of trajectory (12 months of age; 0.27 ± 0.03). The MT model showed a fluctuated pattern and lower estimates of h²_a (0.19 ± 0.03, 0.11 ± 0.02, 0.12 ± 0.02, 0.11 ± 0.03, and 0.16 ± 0.04 for W0, W3, W6, W9, and W12, respectively). Considerably, similar ascending patterns of the ratio of σ²_pe to phenotypic variance were reported from both RR (from 3 to 50%) and MT models (from 5 to 20%). Of interest, the RR model showed higher predicting ability of the breeding values compared with the MT model, which is an indicator for the suitability of RR models for analyzing the consecutive growth traits in sheep. Results suggested that the Barki sheep has a potential for genetic selection based on weight at different ages with selection likely to be more efficient at 9 months of age.

     

Autoregressive and random regression test-day models for multiple lactations in genetic evaluation of Brazilian Holstein cattle

Autoregressive (AR) and random regression (RR) models were fitted to test-day records from the first three lactations of Brazilian Holstein cattle with the objective of comparing their efficiency for national genetic evaluations. The data comprised 4,142,740 records of milk yield (MY) and somatic cell score (SCS) from 274,335 cows belonging to 2,322 herds. Although heritabilities were similar between models and traits, additive genetic variance estimates using AR were 7.0 (MY) and 22.2% (SCS) higher than those obtained from RR model. On the other hand, residual variances were lower in both traits when estimated through AR model. The rank correlation between EBV obtained from AR and RR models was 0.96 and 0.94 (MY) and 0.97 and 0.95 (SCS), respectively, for bulls (with 10 or more daughters) and cows. Estimated annual genetic gains for bulls (cows) obtained using AR were 46.11 (49.50) kg for MY and −0.019 (−0.025) score for SCS; whereas using RR these values were 47.70 (55.56) kg and −0.022 (−0.028) score. Akaike information criterion was lower for AR in both traits. Although AR model is more parsimonious, RR model assumes genetic correlations different from the unity within and across lactations. Thus, when these correlations are relatively high, these models tend to yield to similar predictions; otherwise, they will differ more and RR model would be theoretically sounder.     

Oral thyroxine administration mimics photoperiodically induced gonadal growth in Japanese quail

Most temperate‐zone animals are seasonal breeders. In a previous study, it was found that light‐induced hormone conversion of thyroxine (T₄) prohormone to active 3,5,3′‐triiodothyronine (T₃) in the mediobasal hypothalamus regulates photoperiodic response of gonads in Japanese quail. Here the effect of T₄ or T₃, administered in drinking water, on testicular growth in the Japanese quail kept under short days is shown. Testicular length was significantly increased in birds given T₄ at doses of 4, 8 and 10 mg/L, while any dose of T₃ had little effect on testicular growth. High doses (8 and 10 mg/L) of T₄ and T₃ resulted in high mortality and/or reduction of bodyweight. Among all of the treatment, 4 mg/L of T₄ was the most effective on photoperiodic testicular growth, which caused little reduction in bodyweight. These data provide a new conventional method for promoting gonadal growth under short days.     

Genetic evaluation of dairy cattle for conformation traits using random regression models

Random regression models were applied to eight conformation traits (i.e. stature, rump angle, thurl width, rear leg set, rear udder width, rear udder height, udder depth, and fore udder attachment) of Holstein cows from the northeastern United States. Covariates for fixed and random regressions included age and age‐squared for six of the traits, and two additional covariates were included for rear udder width and rear udder height. Other effects in the model were herd—year‐classifier and months in milk. Fixed covariates were nested within year of birth of the cow. Variance components were estimated using Bayesian theory and Gibbs sampling procedure. Estimated breeding values from the random regression models were compared to two single trait models. The first model utilized only the first classification record of the cow in first lactation, and the second model utilized all classifications of the cow in a simple repeatability model. Additive genetic merit for conformation traits changed with the age of the animal. Some traits were affected by age more than others. The single trait, single record model and the simple repeatability model were not appropriate in predicting breeding values at mature ages for rear udder width and rear udder height.     

Genetic parameters for feed efficiency and body weight traits in Japanese quail

1. The objectives of the present study were to estimate heritability and genetic correlations for feed efficiency and body weight (BW) in Japanese quail.

2. Recorded traits during different weeks of the growing period were BW from hatch to 35 d, feed intake (FI), feed conversion ratio (FCR) and residual feed intake (RFI) from hatch to 28 d of age.

3. Genetic parameters were estimated by restricted maximum likelihood method using ASREML software. The results showed that heritability estimates for BW ranged from 0.11 to 0.22, and maternal permanent environmental effect was the highest at hatch (0.45). FCR, RFI and FI showed moderate heritabilities ranging from 0.13 to 0.40.

4.Genetic correlations of BW₂₈ with FI_0–28 (0.88) and RFI_0–28 (0.1) and genetic correlation of FI_0–28 with FCR_0–28 (0.13) and RFI_0–28 (0.52) were positive. A negative genetic correlation was found between BW₂₈ and FCR_0–28 (?0.49). There was a high positive genetic correlation (0.67) between RFI_0–28 and FCR_0–28.

5. In conclusion, selection for increased BW and reduced FI in a selection index could be recommended to improve feed efficiency traits including FCR and RFI in Japanese quail.     

Characterization of the cathelicidin cluster in the Japanese quail (Coturnix japonica)

The Japanese quail has several advantages as a low‐fat meat bird with high immunity against diseases. Cathelicidins (CATHs) are antimicrobial peptides that play an important role in innate immunity. The aim of this study was to characterize the CATH cluster in the Japanese quail (Coturnix japonica). The Japanese quail CATH (CjCATH) cluster, contains four CATH genes, as in the chicken. The coding sequences of CjCATHs exhibited >85.3% identity to chicken CATHs. The predicted amino acid sequences of the four CjCATH genes contained the cathelin‐like domain characteristic of CATH proteins. Polymorphisms were detected in the open reading frames (ORFs) of all CjCATH sequences. Two amino acid substitutions were observed in the antimicrobial region of the mature peptide of CjCATH2, and predicted to influence peptide function. CjCATH1 is expressed in lung, heart, bone marrow and bursa of Fabricius (BF). CjCATH2 is expressed in bone marrow. CjCATH3 is expressed in lung, heart, bone marrow, BF, tongue and duodenum. CjCATHB1 is expressed in bone marrow and BF. This study is the first to characterize CATH genes in the Japanese quail, and identifies novel antimicrobial peptide sequences belonging to the cathelicidin family, which may play a role in immunity in this species.     

Immunohistochemical and ultrastructural characterization of the ovarian surface epithelium of Japanese quail (Coturnix japonica)

Contrary to humans, most ovarian tumors in other species do not arise from the ovarian surface epithelium but are of follicular‐, stromal‐ or germ‐cell origin. One of the few species where ovarian cancer arises from the ovarian surface epithelium (OSE) is chicken (Gallus domesticus). Little is known about the morphology of the OSE in other avian species. In our study we analyzed the OSE morphology of Japanese quail (Coturnix japonica) using ultrastructural and histochemical techniques. Carbohydrate residues have been studied by using a panel of fluorescein isothiocyanate labeled lectins. Japanese quails are commonly used animal models in biomedical research as their housing is comparatively inexpensive and they show a short generation interval. Our ultrastructural and histochemical results demonstrate that the quail ovarian surface epithelium shows characteristic features which resemble the epithelia of both chicken and human. Additionally, the ovarian surface epithelium of the Japanese quail contains cytokeratin as well as vimentin intermediate filaments in their cytoplasm. Therewith and among other parts the quail OSE shows many characteristic features also seen in those of humans, which may qualify quail's ovary as a potential animal model for human ovarian carcinomas.     

Variance component estimations for race performance of thoroughbred horses in Brazil by random regression model

A total of 306,698 racing performance data recorded between 1992 and 2002 from 25495 Brazilian Thoroughbred horses was analyzed to estimate the variance components using the Random Regression Model (RRM) compared to the Classical Repeatability Animal Model (CRAM). The performance was evaluated using the race time (in seconds) to run distances of 1000, 1100, 1200, 1300, 1400, 1500 or 1600 meters. The pedigree of each horse was extended as far as possible, with a total of 36,659 animals. The simple correlation between Breeding Value (BV) for the race time estimated by both procedures was high (r = 0.963) when the data were expressed at the mean level of all distances. However, with the RRM it was possible to estimate the genetic parameters and the BV of all animals at the trajectory of each one of the seven distances. Also, results clearly showed that a single BV estimated by CRAM, is neither an adequate nor a sufficient indicator for the selection of the best horses throughout the trajectory of distance performance. We concluded that the RRM procedure is highly recommended for the evaluation of racehorse performance.     

Effects of probiotic Bacillus cereus toyoi on abdominal fat accumulation in the Japanese quail (Coturnix japonica)

Effects of a commercial probiotic, Bacillus cereus toyoi on abdominal fat accumulation in the Japanese quail fed either a commercial control diet (crude protein (CP), 23.5%; metabolizable energy (ME), 11.7MJ/kg) or a high‐energy diet (CP, 23.0%; ME, 13.8MJ/kg) were investigated. Four‐week‐old male birds (n = 108) were divided into four diet groups: control diet, control with probiotic, high‐energy diet and high‐energy diet with probiotic. At 8 weeks and 12 weeks of age (4 and 8 weeks of probiotic supplementation period, respectively), abdominal fat, muscles and the liver were weighed. The weight of total fat and protein in the muscles and liver were also determined. A rectal temperature was recorded weekly. Bodyweight and feed intake in both diets were not affected by probiotic supplementation. At 8 weeks of age, birds fed the control diet with probiotic had significantly less abdominal fat than those fed without the probiotic, and a similar tendency was seen for both diet groups at 12 weeks of age. The decrease in abdominal fat coincided with an increase in rectal temperature. These results suggest that greater metabolizable energy was consumed through elevation of heat production by supplementation of B. cereus toyoi, with hardly any energy stored as body fat. Probiotic supplementation appears to induce greater muscle weight, higher protein and lower lipid content in muscles by 8 weeks of age, and lower lipid content in muscles and greater liver weight by 12 weeks of age, in the Japanese quail.     

Mapping of expressed sequence tag markers with a cDNA-amplified fragment length polymorphism method in Japanese quail (Coturnix japonica)

In our previous study, a Kobe‐NIBS Japanese quail (KNQ) linkage map was constructed mainly using amplified fragment length polymorphism (AFLP) markers. In order to compare chicken and quail chromosomes, we developed expressed sequence tag (EST) markers derived from cDNA‐AFLP fragments and localized these markers on the linkage map. Using a total of 128 AFLP primer combinations, 24 polymorphic bands were obtained between a neurofilament‐deficient mutant quail line male and a muscular disorder quail line female, which were the parents of the KNQ resource family. Nine of the 24 markers were mapped by linkage analysis. These markers were mapped to seven linkage groups, namely 1, 2, 3, 6, 8, 15 and 42. A subsequent homology search using chicken genome sequences strongly suggests that these linkage groups correspond with chicken chromosomes 1, 2, 3, 5, 15, 23 and 26.     

Influence of animal age on body concentrations of minerals in Japanese quail (Coturnix japonica)

Mathematical modelling of the relationships between mineral inputs and outputs would enable the prediction of mineral requirements of poultry under a wide range of conditions. To establish the feasibility of possible modelling of mineral requirements, the current study aimed to describe the individual mineral concentrations of whole bodies of quail over the life cycle from hatching to 70 days of age. Quail were reared indoors without any restrictions that could limit growth. Sampling of birds (n = 6–18) was carried out at 0, 3, 7, 14, 21, 35, 49 and 70 days after hatching. Freeze‐dried samples of whole bodies (digestive contents removed) were analysed for ash, and macrominerals (calcium, magnesium, phosphorus, potassium, sodium) and microminerals (copper, iron, manganese, nickel, selenium, zinc). Ash concentration followed a curvilinear trend, with a maximum of 101.7 g/kg dry matter at 32.77 days. Individual mineral concentrations, expressed as a proportion of ash, were fluctuating over time, with the most prominent changes at 3 days and again at either 14 or 21 days. Dissimilar patterns in individual mineral concentrations resulted that ratios between minerals followed inconsistent patterns over time. Although mineral contents in absolute quantities can be described through modelling over the entire life cycle of the bird, it can be concluded that variable concentrations of individual minerals could complicate further model development.