Genetic variation within and relationships among populations of Asian goats (Capra hircus)

Genetic variation at 59 protein coding loci (16 polymorphic) and 25 microsatellite loci was analysed for 11 indigenous south-east Asian goat populations, and the Australian feral population, to determine the magnitude of genetic differentiation and the genetic relationships among the populations. Significant deviations from Hardy–Weinberg equilibrium were detected in one or more populations for eight of the nine protein loci with codominant alleles, and for microsatellites for all except the two Sri Lankan populations and for all but four loci. For both marker types, average inbreeding coefficients ( F _IS) were exceptionally high. Heterogeneity of deviations from Hardy–Weinberg equilibrium for the microsatellites showed no differences for among loci within populations as compared with among populations within loci. For protein loci, however, the former was higher, indicating selection affecting allele frequencies at some loci. The variance among protein loci was significantly higher than among microsatellite loci, further indicating selection at some protein loci. There was significant differentiation among populations for both protein and microsatellite loci, most likely reflecting the geography of south-east Asia, and the presumed spread of goats throughout the region. Phylogenies derived from pair-wise genetic distance estimates show some similar clustering for the microsatellite and protein based trees, but bootstrap support was generally low for both. A phylogeny based on the combined set of 38 protein and microsatellite loci showed better consistency with geography and higher bootstrap values. The genetic distance phylogeny and the Weitzman diversity tree derived from microsatellite data showed some identical clusters, and both identified the Ujung Pandang and Australia populations as contributing most to overall genetic diversity.     

Estimation of (co)variance components and genetic parameters of greasy fleece weights in Muzaffarnagari sheep

Variance components and genetic parameters for greasy fleece weights of Muzaffarnagari sheep maintained at the Central Institute for Research on Goats, Makhdoom, Mathura, India, over a period of 29 years (1976 to 2004) were estimated by restricted maximum likelihood (REML), fitting six animal models including various combinations of maternal effects. Data on body weights at 6 (W6) and 12 months (W12) of age were also included in the study. Records of 2807 lambs descended from 160 rams and 1202 ewes were used for the study. Direct heritability estimates for fleece weight at 6 (FW6) and 12 months of age (FW12), and total fleece weights up to 1 year of age (TFW) were 0.14, 0.16 and 0.25, respectively. Maternal genetic and permanent environmental effects did not significantly influence any of the traits under study. Genetic correlations among fleece weights and body weights were obtained from multivariate analyses. Direct genetic correlations of FW6 with W6 and W12 were relatively large, ranging from 0.61 to 0.67, but only moderate genetic correlations existed between FW12 and W6 (0.39) and between FW12 and W12 (0.49). The genetic correlation between FW6 and FW12 was very high (0.95), but the corresponding phenotypic correlation was much lower (0.28). Heritability estimates for all traits were at least 0.15, indicating that there is potential for their improvement by selection. The moderate to high positive genetic correlations between fleece weights and body weights at 6 and 12 months of age suggest that some of the genetic factors that influence animal growth also influence wool growth. Thus selection to improve the body weights or fleece weights at 6 months of age will also result in genetic improvement of fleece weights at subsequent stages of growth.     

Application of robust procedures for estimation of breeding values in multiple-trait random regression test-day model

Robust procedures for estimation of breeding values were applied to multiple‐trait random regression test‐day (TD) model to reduce the influence of outliers on inferences. Robust estimation methods consisted of correcting selected observations (defined as outliers) in the process of solving mixed‐model equations in such a way that ‘new’ observations gave residuals (actual observation minus predicted) within k residual standard deviations for a given day in milk in 305‐day lactation. Data were 980 503 TD records on 63 346 Canadian Jersey cows. Milk, fat, protein and somatic cell score in the first three lactations were analysed jointly in the model that included fixed herd‐TD effect and regressions within region–age–season of calving, and regressions with random coefficients for animal genetic and permanent environmental effects. All regressions were orthogonal polynomials of order 4. Robust procedures for k = 1.5, 2.0, 2.5, 2.75 and 3.0 were contrasted with the regular best linear unbiased prediction (BLUP) method in terms of numbers and distributions of outliers, and estimated breeding values (EBV) of animals. Distributions of outliers were similar across traits and lactations. Early days in milk (from 5 to 15) were associated with larger frequency of outliers compared with the remaining part of lactation. Several, computationally simple, robust methods (for k > 2.0) reduced the influence of outlier observations in the model and improved the overall model performance. Differences in rankings of animals from robust evaluations were small compared with the regular BLUP method. No clear associations between changes in EBV (rankings) of top animals from different methods and the occurrence of outliers were detected.     

Genetic (co)variance components across age for Show Jumping performance as an estimation of phenotypic plasticity ability in Spanish horses

The purpose of this study was to study phenotypic plasticity ability for Show Jumping performance in horses according to age differences. For this study, 11 352 participations, belonging to 1085 horses grouped by age (4‐, 5‐ or 6‐year olds), were analysed. repeatability animal models (RAM) and multiple trait animal models (MTAM) were compared. RAM assumed the same covariance components for all age groups, whereas MTAM considered the results of every animal at every age group as different (but correlated) traits. The age, sex, starting order and training level were included as fixed effects. The random effects were the animal, the individual permanent environment, the competition and the rider. Six models were compared, and the rider–horse interaction was added as a random effect; furthermore, heterogeneous residual variance was taken into consideration only for MTAM. The study of the genetic correlations between age groups highlighted the presence of an age–genotype interaction and, therefore, an underlying environmental effect. This study may allow us to select horses with a plastic response, which show either a gradual response or a precocious response and thus gain or lose genetic potential with age, respectively.     

Estimates of (co)variance components for productive and composite reproductive traits in Iranian Cashmere goats

The objective of this study was to estimate variance and covariance components, in Iranian Cashmere goats, for birth weight (BWT) and weaning weight (WWT) performances of kids and total weight of kids weaned (TWW) per doe joined at first (TWW1), second (TWW2) and third (TWW3) parities by REML procedures using univariate and multivariate animal models. The analysis was based on 2313 records of kids and 940 records of does. Through ignoring or including maternal additive genetic or maternal permanent environmental effects, four different models were fitted for BWT and WWT performances. For TWW performances only two models (without or with service sire effect) were used. Models were compared using likelihood ratio test. Direct additive genetic and maternal permanent environmental effects had significant influence on BWT and WWT performances. These effects accounted for 9.4% and 15.6%, and 13.9% and 6.7% of phenotypic variation, respectively. No significant effect of service sire was observed on TWW. The estimates of heritabilities were 0.072, 0.109 and 0.082 for TWW1, TWW2 and TWW3, respectively. Direct genetic correlations among all performances were positive and low (for BWT with TWW) to high (for BWT with WWT and WWT with TWW). The corresponding estimates for phenotypic and residual correlations were moderate and lower than genetic correlations. The high genetic correlation among WWT and TWW suggests that direct selection on TWW1 or indirect selection on WWT would increase total weight of kids weaned per doe joined.     

Estimation of (co)variance components for birth weight in Nellore cattle using alternative data editing criteria

The aim of this study was to estimate the (co)variance components and breeding values for birthweight (BW) in Nellore cattle by considering or not identical weights that exhibit a high frequency within the contemporary group (CG). A total of 175,258 BW records of Nellore cattle born between 2002 and 2018 were used. The CG was formed by farm, year of birth, sex and feeding regime at birth. CGs with more than 16% of identical BW values were eliminated, generating a data file called BWd. Another file was created without removing these animals (BWt). A mixed linear model was used for statistical analysis, which included fixed and random effects. In both data files analysed, single-trait analysis was performed by Bayesian inference. The mean direct and maternal heritability for BW and the correlation between direct and maternal effects were 0.27, 0.07 and −0.07 for BWt, respectively, and 0.30, 0.093 and −0.07 for BWd. This method should affect the estimation of genetic merits of animals for BW, providing greater safety in the choice of sires.     

Responses in residual feed intake in lines of Large White pigs selected for growth rate on restricted feeding (measured on ad libitum individual feeding)

Residual feed intake (RFI) represents the deviation of the actual ad libitum food consumption of each animal from that predicted from combination of growth rate, backfat and metabolic body weight measurements. After 4 years of divergent selection of pigs in lines for either high or low postweaning growth rate on restricted feeding, the high line exhibited a significant reduction in RFI relative to the low line. This indicated, to some extents, a lower energy requirement for maintenance in the high than in the low line, possibly because of reduced physical activity of the animals. Estimates of genetical parameters showed that RFI was moderately heritable and those genetic correlations of RFI with carcass backfat and food conversion ratio were moderate to highly positive.     

Estimates of (co)variance components and genetic parameters for body weights and first greasy fleece weight in Malpura sheep

Estimates of (co)variance components and genetic parameters were calculated for birth weight (BWT), weaning weight (WWT), 6 month weight (6WT), 9 month weight (9WT), 12 month weight (12WT) and greasy fleece weight at first clip (GFW) for Malpura sheep. Data were collected over a period of 23 years (1985–2007) for economic traits of Malpura sheep maintained at the Central Sheep & Wool Research Institute, Avikanagar, Rajasthan, India. Analyses were carried out by restricted maximum likelihood procedures (REML), fitting six animal models with various combinations of direct and maternal effects. Direct heritability estimates for BWT, WWT, 6WT, 9WT, 12WT and GFW from the best model (maternal permanent environmental effect in addition to direct additive effect) were 0.19 ± 0.04, 0.18 ± 0.04, 0.27, 0.15 ± 0.04, 0.11 ± 0.04 and 0.30 ± 0.00, respectively. Maternal effects declined as the age of the animal increased. Maternal permanent environmental effects contributed 20% of the total phenotypic variation for BWT, 5% for WWT and 4% for GFW. A moderate rate of genetic progress seems possible in Malpura sheep flock for body weight traits and fleece weight by mass selection. Direct genetic correlations between body weight traits were positive and ranged from 0.40 between BWT and 6WT to 0.96 between 9WT and 12WT. Genetic correlations of GFW with body weights were 0.06, 0.49, 0.41, 0.19 and 0.15 from birth to 12WT. The moderately positive genetic correlation between 6WT and GFW suggests that genetic gain in the first greasy fleece weight will occur if selection is carried out for higher 6WT.     

The impact of data structure on genetic (co)variance components of early growth in sheep,estimated using an animal model with maternal effects

Several studies have noted high negative correlations between maternal genetic and direct additive effects and their influence on additive and maternal heritability of early growth traits in sheep. Multigeneration data from the Suffolk Sire Reference Scheme (SSRS) were used to investigate the effect of data structure on estimates of direct and maternal (co)variances for lamb 8-wk weight. In all analyses the additive, maternal genetic, maternal environmental, and residual effects were fitted along with the covariance between direct and maternal additive effects. The contributions of particular genetic relationships to the estimates were studied by analyzing subsets of the SSRS data. A further eight subsets were formed having 10% or 50% of the dams with their own records and having one or two, three or four, five or six, and more than six offspring per dam. Analysis of data having only 10% of the dams with their own record and one or two offspring records yielded a high negative correlation (-0.99) between direct and maternal genetic effects. However, the seven other data sets with more records per dam or a higher proportion of dams with their own records produced values of -0.35 to -0.51. Data structure and the number of dams and granddams with records are important determinants of estimated direct and maternal effects in early growth traits.     

Effects of correcting missing daily feed intake values on the genetic parameters and estimated breeding values for feeding traits in pigs

Daily feed intake (DFI) is an important consideration for improving feed efficiency, but measurements using electronic feeder systems contain many missing and incorrect values. Therefore, we evaluated three methods for correcting missing DFI data (quadratic, orthogonal polynomial, and locally weighted (Loess) regression equations) and assessed the effects of these missing values on the genetic parameters and the estimated breeding values (EBV) for feeding traits. DFI records were obtained from 1622 Duroc pigs, comprising 902 individuals without missing DFI and 720 individuals with missing DFI. The Loess equation was the most suitable method for correcting the missing DFI values in 5–50% randomly deleted datasets among the three equations. Both variance components and heritability for the average DFI (ADFI) did not change because of the missing DFI proportion and Loess correction. In terms of rank correlation and information criteria, Loess correction improved the accuracy of EBV for ADFI compared to randomly deleted cases. These findings indicate that the Loess equation is useful for correcting missing DFI values for individual pigs and that the correction of missing DFI values could be effective for the estimation of breeding values and genetic improvement using EBV for feeding traits.     

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.     

Efficacy of a genetically modified yeast phytase on phosphorus bioavailability in a corn-soybean meal based diet for growing pigs

We investigated the efficacy of genetically modified yeast (GMY) phytase on phosphorus (P) bioavailability in growing pigs fed a corn–soybean meal based diet. Crossbred barrows were fed a P-adequate, a low-P or a P-deficient diet containing 0.37, 0.27 and 0.14% non-phytate-P, respectively. The P-deficient diet was supplemented with wild-type yeast (WTY), Aspergillus (ASP) or GMY phytase at 750 PU per kilogram of food. Dietary ASP and GMY phytases increased plasma inorganic P (P_i) concentration and the apparent absorption of P, and decreased the concentration of a bone resorption marker, plasma type-I collagen C-terminal telopeptide (ICTP). Wild-type yeast phytase also increased the apparent absorption of P, but the changes in plasma P_i and ICTP concentrations were not significant. Although the dietary P_i-equivalencies based on plasma P_i and ICTP concentrations did not differ between WTY and ASP phytases, the equivalency of ASP phytase based on apparent absorption of P was higher than that of WTY phytase. The equivalency of GMY phytase calculated from each parameter was higher than that of WTY phytase, and did not differ from that of ASP phytase. These results suggest that efficacy of GMY phytase on P bioavailability was higher than WTY phytase, and as effective as ASP phytase in growing pigs.     

Comparison of plasma FSH concentration in boars and gilts from lines selected for ovulation rate and embryonal survival, and litter size and estimation of (co)variance components for FSH and ovulation rate

The objective of this research was to determine whether plasma concentration of FSH was genetically correlated with ovulation rate and thus was a useful trait for indirect selection. Blood samples were collected from 619 animals from five lines of pigs. Line I was selected for increased index of ovulation rate and embryonal survival, and Line C was its randomly selected control. Pigs sampled from Lines I and C were from generations 12 and 13. Pigs from three additional lines that were derived from eighth-generation pigs of Lines I and C also were used. These lines were Line C2, a randomly selected control derived from Line C, Line COL, derived from Line C, and Line IOL, derived from Line I; each of these lines was selected an additional five generations for increased ovulation rate and increased litter size. A single blood sample was collected from each pig between 46 to 63 (d 58), 86 to 98 (d 90), 110 to 133 (d 124), and 147 to 153 (d 150) d of age. The heritability of ovulation rate was .28 and heritabilities of plasma concentration of FSH at d 58, 90, 124, and 150 were .41, .25, .12, and 0, respectively. Genetic correlations between ovulation rate and d-58, d-90, and d-124 plasma concentration of FSH were .31, .23, and 0, respectively. Line I gilts had greater estimated breeding values for plasma concentration of FSH at d 58 and 90 than Line C gilts (P < .01). Line COL gilts had greater estimated breeding values for plasma concentration of FSH at d 58 than Line C2 gilts (P < .01). Line I boars had greater estimated breeding values for plasma concentration of FSH at d 90 than Line C boars (P < .05). Even though genetic correlations were low, selection for increased plasma concentration of FSH was estimated to be 93% as effective in changing ovulation rate as direct selection because selection for FSH can be practiced in both sexes. Thus, selection for increased plasma concentration of FSH seems to be a practical method for increasing ovulation rate in pig breeding programs without using laparoscopy.     

Effect of housing conditions (clean vs. dirty) on growth performance and feeding behavior in growing pigs in a tropical climate

The effect of bad sanitary conditions on growth performance and feeding behaviour were studied on a total of 48 Large White pigs between 95 and 130 d of age. This experiment carried out during the hot season in a tropical humid climate. Two groups of 12 pigs each were housed in a clean environment in which the pens were disinfected thoroughly prior to stocking and maintained in a clean state by daily washing the pens and by weekly emptying the manure stored beneath the partial concrete floor. The dirty environment was achieved by not cleaning the pens prior to stocking or throughout the experiment and by storing the manure beneath the floor slats throughout the experimental period. The microbial pressure was increased by introducing 5 additional non experimental pigs near each experimental dirty pen. Feeding behaviour parameters were measured using automatic feed dispensers. Pigs housed in a clean environment consumed more feed (2.283 vs. 1.953 kg/d; P < 0.001) and grew faster (871 vs. 780 g/d; P < 0.05) than those housed in the dirty environment. No significant effect on treatment was reported for the feed conversion efficiency (2.70 kg/kg on average). The reduced average daily feed intake in dirty pens was associated with a reduction of the meal size (334 vs. 282 g/meal; P = 0.10) whereas the meal frequency was not affected by treatment (7.5 meals/d on average). The rate of feed intake was significantly higher in the clean than in the dirty environment (34.0 vs. 29.9 g/min; P < 0.05).     

Impact of two types of complete pelleted,wild ungulate feeds and two pelleted feed to hay ratios on the development of urolithogenic compounds in meat goats as a model for giraffes

Urolith formation has been documented in giraffes and goats. As research in giraffes poses logistical challenges, 16 buck goats were used as a model. The impact of two commercially available, pelleted feeds used for giraffes, ADF‐16 and Wild Herbivore (WH), as well as the impact of alfalfa hay and pellet proportions (20% hay:80% pellets, 80P or 80% hay:20% pellet, 20P) on the formation of urolithogenic precursors in goat urine was accomplished in a 2 × 2 factorial balance study. Complete diets contained 0.60, 0.32, 0.35 and 0.26% phosphorus (P) with calcium:P ratios of 1.60, 4.16, 3.06 and 5.23, for 80P‐ADF‐16, 20P‐ADF‐16, 80P‐WH and 20P‐WH respectively. Total faeces and urine were collected over two 5‐day periods to assess N and mineral balance. Fresh urine samples were collected and evaluated microscopically for urolithic crystal content. Urinary nitrogen (N) was lower and N retention was higher in goats fed 80P diets (p < 0.05). Intake of P was greatest for goats fed 80P‐ADF‐16; however, urinary P excretion and P retention were not affected by treatment. Crystal scores were higher in animals receiving 80P diets (p = 0.08), with crystals being composed predominantly of calcium phosphate. Urine pH was alkaline (>8) for all treatments. Urinary P concentration, a risk factor for urolithiasis, was highest (p ≤ 0.06) in the 80P‐ADF‐16 treatment (0.38 vs. 0.01, 0.02 and 0.04 mg/dl for 20P‐ADF‐16, 80P‐WH and 20P‐WH respectively), reflecting its highest dietary P level. Further investigation is recommended to determine the long‐term effects of these diets on urolithogenic compound formation.