Animal Genetics and Breeding Unit (AGBU)
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- PublicationRestricted Maximum Likelihood to estimate variance components for mixed models with two random factors
A Restricted Maximum Likelihood procedure is described to estimate variance components for a univariate mixed model with two random factors. An EM-type algorithm is presented with a reparameterisation to speed up the rate of convergence. Computing strategies are outlined for models common to the analysis of animal breeding data, allowing for both a nested and a crossclassified design of the 2 random factors. Two special cases are considered: firstly, the total number of levels of fixed effects is small compared to the number of levels of both random factors " secondly, one fixed effect with a large number of levels is to be fitted in addition to other fixed effects with few levels. A small numerical example is given to illustrate details.
- PublicationAdditive and Non-Additive Differences in the Postweaning Performance of Devon, Hereford and Reciprocal Cross Steers and Heifers(1990)
; - PublicationThe Effects of Population Structure on Responses to Artificial Selection: An Investigation of the Shifting Balance Theory(1990)
; Sewall Wright's Shifting Balance Theory, which postulates that evolution will be most rapid in populations subdivided into numerous small, semi-isolated demes, was evaluated by comparing responses to selection for increased adult bodyweight of 'D. melanoccaster' in three population models. Two were models previously evaluated (sub-lining with crossing of selected sub-lines at intervals, and a circular stepping-stone model), but which had not shown any advantage in subdivision. The third was a new model of Wright's recommended structure, and included excess diffusion from demes with higher phenotypic means to those with lower means every generation. Responses in these models were compared with those obtained by simple mass selection in a single large population. As reported in previous studies, no clear advantages in response were obtained in any of the subdivided models. In one replicate of the new "Wrightian" model however, the pattern of responses suggested the presence of a major non-additive effect producing extremely heavy flies. This effect spread throughout the system of semi-isolated demes comprising this treatment in a manner similar to that described by Wright for the operation of the Shifting Balance Process. The genetic basis of this effect was investigated by offspring-parent regressions with the effect present and absent, by crosses with unselected flies to produce F₁ and F₂ generations, and by attempting to map the gene(s) underlying the effect by chromosomal substitution techniques. However, no clear description of the effect was obtained. In addition to the selection programme, electrophoretic surveys of the experimental populations were conducted. These provided information on levels and partitioning of allozymic variation between and within demes/population units. The description of genetic structuring provided by this data was similar to that based on partitioning the phenotypic variance in bodyweight. Results obtained suggested that models used to evaluate subdivided populations both here and in previous studies, do not produce sufficient genetic differentiation to support inter-deme selection, at least on a simple additive basis. Finally, the relevance of these results to wider understanding of the Shifting Balance Theory is discussed. It is concluded that further evaluation of the Theory should be based upon computer simulation. This approach could be used to define necessary conditions for the operations of the Shifting Balance process, and thus provide a firmer basis for both experimental designs and recommendations regarding structuring of domestic and wild populations. - PublicationComparison of theoretical and simulated equilibrium genetic response rates with progeny testing in dairy cattle
The published theoretical estimates of equilibrium genetic change possible by progeny testing in dairy cattle are too high. Much of the overestimation is because no account has been taken of the temporary reduction in genetic variation due to selection of parents and ancestors. A particular efficient progeny testing scheme was modelled theoretically and simulated on computer using a continuous infinitesimal additive model. To make the simulation feasible an elite breeding herd of females was used, and progeny testing was done outside the herd. The proportional reduction in genetic variance due to previous selection was 0·25, 0·27 and 0·29 for original heritabilities of 0·05, 0·25 and 0·50, with the theoretical and simulated results being very similar. The theoretical and simulated proportional losses in equilibrium selection responses were 0·22 and 0·26, 0·21 and 0·22 and 0·21 and 0·25, respectively, for the three levels of heritability. Thus, most of the loss in response in the simulation results came from the reduction in genetic variance due to selection.
- PublicationVariance components due to direct and maternal effects for growth traits of Australian beef cattleVariance components for birth, weaning, yearling and final weight in Australian Hereford, Angus and Zebu Cross cattle were estimated by Restricted Maximum Likelihood. Six different animal models were fitted for each trait and breed, ranging from a simple model with animals as the only random effect to the most comprehensive model allowing for both genetic and environmental maternal effects and a genetic covariance between direct and maternal effects. The most detailed model generally provided the best fit to the data, though differences between models with at least one maternal effect (genetic or environmental) were often not significant. Ignoring maternal effects, direct heritability (h²) estimates were inflated substantially, in particular for growth till weaning. Significant maternal effects were found in all analyses except for final weight in Angus. There were marked differences between breeds in the relative magnitude of h² and the maternal heritability, and the direct-maternal genetic correlation (rAM). For Angus, rAM was low, positive and not significantly different from zero for all traits. For Hereford and Zebu Cross cattle, rAM was negative, moderate to large for weaning weight (-0.59 and -0.78) and somewhat smaller for yearling weight (-0.48 and -0.39). For Herefords, maternal environmental effects were consistently more important than maternal genetic effects.
- PublicationEstimation of genetic parameters for reproductive traits, production, carcase and meat quality traits in Australian pigs(Australian Association for Animal Breeding and Genetics (AAABG), 1995)
; - PublicationGenetic parameters for meat quality, carcase and production traits in Australian pigs(Australian Association for Animal Breeding and Genetics (AAABG), 1995)
; - PublicationThe Effect of Nitrogen and Protein Supplementation on Feed Intake, Growth and Digestive Function of Steers with Different Bos indicus, Bos taurus Genotypes when Fed a Low Quality Grass HayTwo studies were undertaken at Grafton, NSW, to determine the effects of supplementing a subtropical hay diet with a mixture of non-protein nitrogen (urea) and protein (protected casein), on the feed intake and growth of 20 steers of four genotypes (Study I), and on the digestive and metabolic functions of 16 of the steers that were fistulated in the rumen (Study 2). All steers were reared in the one subtropical environment. They consisted of backcross Hereford (H) (H × BH), backcross F1 (BH × BH) and backcross Brahman (B × BH), all of 50% heterosis, and a first-cross F1 of 100% heterosis (BxH). Steers in both studies were confined in pens and offered a basal diet of chaffed pasture hay (digestibility 52f 1.4% and nitrogen [N] content of 6.1 ± 0.2 g/kg dry matter [DM]) supplemented with minerals only (low N diet; 8 steers) or with urea or formaldehyde-treated casein and cottonseed meal (high N diet; 12 steers) for 49 days. There were eight steers, for each of the two diets in Study 2, which were fed for 30 days. There was a diet × genotype interaction (P < 0-05) in the daily DM intake (DMI) of hay by steers in Study 1. The mixed N supplement increased (P < 0.05) DM1 (per kg liveweight) by 14% in HxBH and by 13% in BxBH steers, but there was no significant effect of the supplement on the DM1 of BxH and BHxBH steers. Daily liveweight change was increased (P < 0.05) by the supplement from-30 to 250 (s.e.d ± 40) g/steer and there was no significant difference between genotypes. N supplementation increased (P < 0.05) rumen volume (63 to 87 ± 7.6 L) and fluid residence time (491 to 822 ± 76.9 min) (P < 0.05) in BHxBH steers, but the increases in other genotypes were not significant. Rumen ammonia concentration (30 to 61 ± 3 7 mg N/L) and plasma urea concentration (56 to 94 ± 6-0 g N/L) were increased (P < 0.05) by supplementation. Total protozoa density in rumen fluid was greater (P < 0.05) in BxBH than HxBH steers but did not differ significantly between supplemented and unsupplemented steers. The HxBH steers had the lowest density of small entodiniomorph protozoa when N-supplemented, which was less (P < 0.05) than that in BxBH steers which had the greatest density. Supplementation increased (P < 0.05) N retention but only B × BH steers had a positive N balance. These experiments indicated that there are some physiological differences between genotypes. The BxH genotype with the high hybrid vigour had a high DM1 on the low digestibility hay diet without the N supplements and it transferred more urea from the plasma pool to the gut. The backcross steers (HxBH and BxBH) had low DM1 which increased when supplemented. The high content B. indicus steers (BxBH) had positive net retentions of N, but the results indicated that rumen protected proteins may be more usefully fed to steers with a lower B. indicus content.
- PublicationGenetic relationships between carcase composition and meat quality in Australian pigsTo be successful in today's markets the meat quality and carcase composition of pork carcases must be of a high standard. Most selection programs consider leanness as the optimum characteristic of the carcase and neglect meat quality. In doing so this may lead to problems of poor pork quality. The inclusion of carcase composition and meat quality in a breeding program requires knowledge of the genetic correlations between these characteristics. The aim of this study was to estimate genetic parameters for carcase composition and meat quality in Australian Large White and Landrace pigs.
- PublicationGenetic relationships between litter size and meat quality traits in Australian PigsGenetic relationships between number born alive (NBA) and meat quality traits were studied in Australian pigs. Meat quality traits investigated were colour of the longissimus dorsi muscle, colour of the superior spiralis muscle, pH measured 45 minutes post mortem (pH-45), pH measured 24 hours post mortem (pH-24) and drip loss percentage. (Co)variances were estimated using a derivative-free Restricted Maximum Likelihood procedure fitting an animal model.
- PublicationGenetische Beziehungen zwischen Wurfgewichten und Productionsmerkmalen(Deutsche Gesellschaft fuer Zuechtungskunde E V, 1995)
; Eine gute Fruchtbarkeitsleistung der Sau ist gekennzeichnet durch eine hohe Anzahl gesunder abgesetzter Ferkel. Um dieses Ziel zu erreichen wurde bislang hauptsächlich die Anzahl lebend geborener Ferkel als Selektionskriterium herangezogen. Durch die positive Beziehung zur Überlebensrate von Ferkeln (Rydhmer, 1992) kommt dem durchschnittlichen Ferkelgewicht zum Zeitpunkt der Geburt ebenfalls eine Bedeutung zu. Eine gute Entwicklung der Ferkel ist weiterhin von einer hohen Milchleistung und guten Muttereigenschaften der Sau abhängig. Informationen über diese maternalen Komponenten können unter Produktionsbedingungen nur indirekt über das 21 Tage Wurfgewicht gewonnen werden.
Das Ziel dieser Arbeit war es, den Erblichkeitsgrad des durchschnittlichen Ferkelgewichts zum Zeitpunkt der Geburt und des 21 Tage Wurfgewichts zu schätzen und die genetischen Beziehungen zwischen diesen Fruchtbarkeitsmerkmalen und den Produktionsmerkmalen tägliche Zunahme und Rückenspeckdicke zu untersuchen.
- PublicationThe genetic foundation of fitness and reproduction traits in Australian pig populations. 1. Genetic parameters for weaning to conception interval, farrowing interval, and stayabilityData from 2 large Australian piggeries were used to estimate genetic parameters and to examine fixed effects for weaning to conception interval (WCI) and farrowing interval (FI) measured in the first 3 reproductive cycles, and sow stayability from the first to later i parities (STAY1i,). WCI and FI recorded following the first farrowing had low heritabilities (h2 = 0.08-0. l0), but estimates did not significantly differ from zero when these traits were recorded in later parities. Heritability estimates for STAY increased with parity of recording, ranging from 0.05 for STAY12 to 0.06 (STAYl3) and 0.09 (STAYl4). Genetic correlations between WCI12 or PI12 and stayability traits ranged from -0.22 to -0.54. Selecting for short WCI following the first farrowing should have favourable consequences for longevity of sows. Important fixed effects for WCI and FI were lactation length and the number of piglets nursed. Both short (<20 days) and long (>29 days) lactation periods led to an increase in WCI12 relative to the optimum lactation length of 21-23 days. WCI also increased with the number of piglets nursed by 1 day/additional piglet for litters ranging in size from <7 to >10 piglets. STAY was little affected by correcting for the average number of piglets born in previous litters.
- PublicationThe genetic foundation of fitness and reproduction traits in Australian pig populations. 2. Relationships between weaning to conception interval, farrowing interval, stayability, and other common reproduction and production traitsData sets from 2 large Australian piggeries were used to estimate genetic parameters for the traits weaning to conception interval (WCIi-l,i) and farrowing interval (FIi-l,i), number born alive (NBAI), average piglet birthweight (BWi), 21-day litter weight (W21i), and sow stayability (STAYli) recorded for each ith parity, as well as sow average daily gain (ADG) and backfat (BF) recorded at the end of performance test. Over parities and herds, heritabilities for each trait were in the ranges: WCI/FI, 0.0-0.10; NBA, 0.09-0.16; BW, 0.11-0.35; W21, 0.12-0.23; STAYli, 0.02-0.09; ADG, 0.35-0.37; BF, 0.36-0.45. Genetic correlations between NBAl and NBA from later parities were significantly different from 1. In addition, in 1 herd negative genetic correlations (rg = -0.04 to -0.25) were found between sow stayability traits and NBA1, but not NBA recorded in later parities. Stayability was Unfavourably correlated with ADG and BF, and favourably correlated with WCI12. However, WCI12 was unfavourably correlated genetically with BF (rg = -0.24) but uncorrelated with ADG. Antagonistic relationships also existed between NBA and BW, NBA and W21, and BW and STAY. In addition to the traditional traits currently included in pig-breeding programs (e.g. ADG, BF, and NBA), traits such as WCI, BW, and STAY should also be considered as selection criteria to minimise the detrimental effects of antagonistic genetic relationships between traits.
- PublicationGenetic parameters for lean meat yield, meat quality, reproduction and feed efficiency traits for Australian pigs(1997)
; - PublicationSelection and mating strategies risks and rewards(1997)
; Best Linear Unbiassed Prediction provides a valuable mechanism through which effective selection practices can operate, potentially enhancing performance and producing significant increases in productivity and thus, frequently in profitability. However, current recognition of the potential risks associated with this enhanced performance through the impacts of risks such as inbreeding depression, offer a challenge to the effectiveness with which selection can operate. The broadening of the selection objective to address issues of risk in the selection process as described in this thesis integrates genetic objectives with economic perspectives. This is addressed through several areas. An initial consideration of this impact of accuracy in the selection process is undertaken from a single generational perspective. Longer term selection is addressed through the analysis of a range of selection and mating strategies including mate selection strategies that integrate increased genetic merit with the control of inbreeding (or similar risk factors). An assessment of long term strategies is undertaken through an adapted use of benefit cost methodology. ... The strategies were compared across a range of weightings on inbreeding (linked to decline in response). The results showed a preference for MS₀ (a mate selection option with no loss in response) over the selection and mating strategy (Pr) - however this preference was mediated when the additional cost of managing mate selection was taken into account and the weighting on inbreeding was low. Interestingly, the relative value of the MS₅ strategy was seen across all alternatives. This marked a reasonable point at which the benefits from reduced inbreeding might outweight the costs associated with some decline in potential response. While this analysis was undertaken for two levels of interest rate (0.6 and 1.0) and for two variations in the model, with one including an additional weighting on mate selection strategies to reflect the additional management costs they impose, the final results were not highly sensitive to these factors, indicating the strength of this approach for this assessment. - PublicationEstimates of genetic parameters for weaning weight of beef cattle accounting for direct-maternal environmental covariancesRestricted Maximum Likelihood algorithm estimates of (co)variance components due to maternal effects as well as a regression on maternal phenotype were obtained for seven weaning weight data sets of Australian and New Zealand beef cattle. Fitting such regression, analyses accounted for environmental covariances between dams and their offspring. Results show a substantial, negative regression on maternal phenotype (up to -0.2) for Hereford field data, accompanied by small, negative estimates of a direct-maternal genetic covariance. In contrast, for Angus and Limousins, the direct-maternal genetic covariance was clearly more important than its environmental counterpart, i.e., for these breeds an estimate of the direct-maternal genetic correlation of about -0.5 could not be attributed to a negative environmental relationship which previously had not been modeled correctly. Fitting a sire x herd-year interaction as an additional random effect increased the likelihood dramatically for all data sets. While estimates of the regression on maternal phenotype were little affected, fitting the interaction reduced estimates of the direct-maternal genetic covariance, substantially so for Angus and Limousin, reducing (absolute value) estimates of the corresponding correlations to -0.3 to -0.2.
- PublicationPhenotypic performance of gilts and young boars can be predicted from their estimated breeding values for growth rate and backfatEstimated Brooding Values (EBVs) obtained from genetic evaluation programs such as PIGBLUP (Henzell, 1995) are used by breeders to select genetically superior animals. The PIGBLUP program uses information from all relatives, therefore an animal without records can obtain an EBV for a trait using information from relatives. Differences in EBVs represent the expected differnce in phenotypic performance of these animals. The aim of this study was to obtain EBVs for average daily gain and backfat of gilts and young boars and to compare ranking on these EBVs with mean phenotypic performances.
- PublicationEstimation of genetic and phenotypic covariance functions for longitudinal or 'repeated' records by restricted maximum likelihoodCovariance functions are the equivalent of covariance matrices for traits with many, potentially infinitely many, records in which the covariances are defined as a function of age or time. They can be fitted for any source of variation, e.g. genetic, permanent environment or phenotypic. A suitable family of functions for covariance functions are orthogonal polynomials. These give the covariance between measurements at any two ages as a higher order polynomial of the ages at recording. Polynomials can be fitted to full or reduced order. The former is equivalent to a multivariate analysis estimating covariance components. A reduced order fit involves less parameters and smoothes out differences in estimates of covariances. It gives predicted covariance matrices of rank equal to the order of fit. The coefficients of covariance functions can be estimated by restricted maximum likelihood through a reparameterisation of existing algorithms to estimate covariance components. For a simple animal model with equal design matrices for all traits, computational requirements to estimate covariance functions are proportional to the order of fit for the genetic covariance function. Applications to simulated data and a set of beef cattle data are shown.
- PublicationGenetic parameters for ham yield and bacon yield after processing and their genetic relationship to meat quality traits in Australian pigs(Association for the Advancement of Animal Breeding and Genetics (AAABG), 1997)
; From a data set including Large White and Landrace pigs with 3000 records on meat quality traits a subset of 1000 animals had information available on ham and bacon yield after processing. Genetic parameters were estimated for these manufacturing traits. Heritability estimates were 0.11 and 0.06 for ham and bacon yield. A high ham yield was genetically associated with a higher pH at 45 minutes and 24 hours after slaughter, a darker colour of the m. longissimus dorsi and a reduced drip loss percentage. In contrast, genetic correlation between bacon yield and meat quality traits were of opposite sign which might have been due to differences in the processing procedures. Middles from animals developing pale, soft and exudative (PSE) meat had a higher uptake of brine which was better retained in comparison to hams.
- PublicationGenetic influences on pork qualityThe genetic influences on pork quality including that of the major genes, the halothane gene and the RN gene, are discussed in this paper. Breed differences and genetic parameters for meat quality traits are summarise. In addition, genetic influences on boar taint and further developments in genetic improvement of meat quality are discussed. The effect of the halothane gene on meat quality traits and the relationship between this gene and muscle morphology is discussed. In addition, the RN gene is described which has a high frequency in Hampshire and marker information to this gene is presented. lndications for further major genes influencing meat quality traits are summarised. Breed differences in meat quality are due to different levels of the halothane gene as well as different levels of leanness. Special reference is given to Durocs, the breed with a higher intramuscular fat content. The summary of genetic parameters shows moderate heritabilitics for meat quality traits pertaining to PSE and dark, firm, dry (DFD) while intramuscular fat content is highly heritable. Genetic correlations between meat quality traits reflect characteristics of PSE and DFD meat. Components of boar taint differ between breeds. In addition, these components are highly heritable and might be influenced by major genes. Currently, DNA tests exist for the halothane and RN gent. It is most likely that further major genes or marker related to quantitative trait loci (QTL) will be detected. Meat quality traits should be incorporated into selection decisions in order to prevent further deterioration in these traits as a consequence of selection for higher lean meat growth.