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The purpose of the study was to investigate a possible genotype by environment interaction in first calf South African Holstein cows for both production and reproduction traits. Data from 100 975 cows on a total mixed ration (TMR) and 22 083 pasture based cows were used. These cows were the progeny of 4 391 sires and 84 935 dams produced over a period of 11 generations. Traits analysed were milk production (corrected to a 305-day equivalent) and age at first calving (AFC). Both were recorded over a period of 30 years from 1980 - 2010. Production or AFC in each environment (TMR vs. pasture) was treated as a separate trait. Bivariate analyses, fitting an animal model using the ASREML software, were used to obtain genetic correlations between the traits measured in each environment. The fixed factors included were a concatenation of breeder-keeper-year for both milk production and AFC and age at first calving which was fitted as a linear regression for milk production. The random part consisted of the direct additive effects only. The genetic correlation for milk production measured in the two different environments was 0.90 (0.027) and that of age at first calving 0.28 (0.12). The heritability estimates for milk production were 0.23 (0.008) under the TMR system and 0.32 (0.015) for the pasture based system, while the estimates for AFC were 0.063 (0.005) and 0.055 (0.009), respectively. The rather large-scale effect in the heritability (0.23 → 0.32), as well as the correlation of less than one for milk production between the two environments, indicates that a G x E may exist. However, the low genetic correlation between the two environments for AFC is much more real and indicates that G x E should be taken into account when sire selection is performed.Keywords: Age at first calving, milk production, total mixed ration, pasture

The wildlife industry in South Africa has shown immense growth since the 1990s, which was brought about by the private game segment of the industry. In recent years, trophy quality Cape buffalo breeding animals have achieved extremely high prices. Much of the economic value of these animals can be attributed to horn size, which is important for breeding and hunting purposes. The main objective of the study was to estimate variance components for horn traits of economic importance as well as to develop guidelines for recording these traits. To date, no quantitative genetic analysis has been done for any traits in Cape buffalo. The total number of horn measurement records included in the evaluation was n = 945 for outer spread (BHSO), n = 470 for tip to tip (BHTSCI), n = 468 for left boss and n = 479 for right boss. For descriptive statistics, males and females were considered separately while age was divided into clusters of six months. A multi-trait animal model using Monte Carlo Markov Chains methods was used for the estimation of genetic parameters. Results suggest that it is not economically viable to measure horn spread and tip to tip of females after 48 months of age. Horns of the males continue to grow beyond 91 months of age. Boss records were unreliable owing to the applied measurement techniques for female and young animals. An inbreeding coefficient of 0.008 was calculated, suggesting adequate genetic diversity in the studied population. The heritability estimates of the horn traits were low, showing that extreme care has to be taken to develop effective selection programmes for the buffalo game industry using their horn genetic parameters. Further quantitative studies are required to support the results of the current study. Keywords: genetic correlation, genetic parameters, heritability, Monte Carlo Markov Chain

Much of the economic value of wildlife can be attributed to horn size, which is an important trait for trophy hunters. The main objective of the study was to estimate genetic parameters for the economically important horn traits of sable antelope that are currently being measured in the South African industry. To date, no quantitative genetic analysis has been done for any traits in sable antelope. The total number of records included in the evaluation were n = 1713 for horn length (SHL), n = 1503 for circumference (SHC), n = 1486 for tip to tip (SHTT), n = 1505 for tip length (SHT), and n = 1447 for rings (SHR). Males and females were considered separately in six-month age clusters. A Markov chain Monte Carlo (MCMC) multi-trait analysis was used to estimate (co)variance parameters for the horn traits. The results indicate a sex effect for all the traits and suggest that it is not economically viable to measure horn length of either sex after 54 months old. The horns of females are on average 40% shorter compared with bulls at maturity. Continuous horn growth throughout the lifetime of sable is suggested by the formation of ring posts, but is often masked by horn attrition and inadequate measuring techniques. An inbreeding coefficient of 0.0043 suggests adequate genetic diversity in the studied population. Heritability estimates of horn traits varied from 0.085 to 0.52, while genetic correlations ranged from 0.1 to 0.6 with the highest correlation being found between horn length and tip to tip. Further studies are recommended to confirm these results. Keywords: Game, genetic evaluation, heritability

Subjectively assessed wool and conformation traits are widely used to select breeding ewes and rams in the sheep industry. Data from a Merino flock that is maintained at Elsenburg Research Farm were used to investigate animal model (co)variance components for ewe reproduction traits with subjectively assessed wool and conformation traits. Ewe reproduction traits were assessed at their first lambing opportunity at two years, or over a three-year period from their lambing opportunities at two to four years old. Relationships of ewe reproduction traits with subjectively measured wool and conformation traits were also investigated. All these traits were heritable, with a range from 0.16 ± 0.03 for topline (TOPL) to 0.64 ± 0.04 for woolly face score (WFS). Genetic correlations of number of lambs born (NLB1) with colour (COL), number of lambs weaned (NLW1) with COL and belly and points (BANDP) and total weight of lamb weaned (TWW1) with COL were negative and significant. Significant genetic correlations of ewe reproduction traits over three lambing opportunities were found between number of lambs born (NLB3) and WFS (0.23 ± 0.11) and between total weight weaned (TWW3) and face cover score (FCS) (-0.33 ± 0.16). Among these traits, the noteworthy favourable genetic correlation between total fold score (TOT) and NLB1 suggested that plainer ewes were more reproductive. This is important for the South African Merino industry as plainer sheep are more desirable because of their faster growth and higher lambing percentages and reduced chances of fly strike. Selection for improved ewe reproduction in Merino sheep thus would not result in marked unfavourable correlated responses in most of these subjective wool and conformation traits.Keywords: Correlations, heritability

The objective of this study was to investigate the effect of inbreeding depression on functional herd life in the South African Jersey population based on individual level and rate of inbreeding. A pedigree file of the South African Jersey breed (n = 912 638) was obtained from the Integrated Registration and Genetic Information System (INTERGIS). The data included registered, grade and imported animals. The percentages of animals in the pedigree file with two, one and zero parents unknown were 22%, 18% and 60%, respectively. The inbreeding coefficient for each animal (Fi) and the rate of individual inbreeding (ΔFi) as an alternative measure of inbreeding that is adjusted for the depth of known pedigree were calculated. The effect of inbreeding on functional herd life in each of the first three lactations was estimated, using a singletrait sire model on data collected from 1985 to 2003. Three analyses for survival in each of the first three lactations were conducted. In the first analysis, in addition to fixed and random effects, an individual inbreeding coefficient (Fi) was fitted as a linear covariate. In the second analysis, the inbreeding coefficient was included as a discrete variable with the following classes of inbreeding: 0 < F ≤ 3.125, 3.125 < F ≤ 6.25, 6.25 < F ≤ 12.5 and F > 12.5. In the third analysis, the individual rate of inbreeding (ΔFi) was included in the model as a linear covariate. The level of inbreeding in the SA Jersey population showed a gradual increase for the period 1985 to 1994, while the period 1995 to 2003 showed a rapid increase. The current mean level of inbreeding (for the year 2010) is 4.85% with a minimum and maximum of 0 and 31.34%, respectively. The rate of inbreeding showed a gradual increase from 0.36% to 0.43% between 1985 and 2003. The average rate of inbreeding is currently (for the year 2010) at 0.55%. There was a significant unfavourable relationship between inbreeding and functional herd life in the first and second lactations. The effect of inbreeding was more pronounced in the second lactation for both measures of inbreeding. Based on the current level of inbreeding, the reduction in functional herd life in the first lactation can be estimated as 0.68%. The corresponding estimate for the second lactation is 1.70%. The results from the current study indicate that the current level or rate of inbreeding has reached levels that are detrimental to functional herd life. Therefore, individual inbreeding coefficients should be considered in addition to genetic merit when breeding decisions are made by Jersey breeders.Keywords: Inbreeding, longevity, survival, dairy cattle

A selection and line x environment interaction study with grade Afrikaner cattle was established in 1956 at Matopos Research Station, Zimbabwe. Two selection lines of 100 cows each were reared in different management environments. The non-supplemented (NS) line relied on the range throughout the year and was mated to calve with the onset of the rains (December to February). The supplemented (S) line was offered protein-rich supplements during the dry season and mated to calve prior to the onset of the rains (October to December). In 1976, lines were sub-divided into 75 cows each, where one sub-line remained within each environment as a control; the remaining sub-lines were interchanged between environments. Bulls were selected on weaning weight within control lines, while replacement heifers were selected on weight at mating within sub-line. Data recorded over approximately six generations of selection (40 years) was analyzed. The direct heritability estimates were moderate for birth weight (0.4), but low (0.1 to 0.2) for the other traits, similarly maternal heritabilities were low (0.1 to 0.2). Permanent environmental effects due to dam were moderate (0.3) for weights at 205 days, weaning and at 12 months, and was still an important effect at 18 months. Relatively large negative (-0.4) direct-maternal genetic correlations were indicated for weaning and yearling weights. There were indications that all post-weaning weight traits evaluated were closely related giving rise to their joint inclusion in joint multivariate analysis. There were no indications of line x environment interactions, however, interaction of sire x year was important for all the traits highlighting the tremendous year to year variations experienced in the sub-tropics. There is a need to evaluate selection for genotypic stability, particularly for the more extensive farming environments.

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Genetic and environmental parameters were estimated for pre- and post-weaning average daily gain (ADG1, ADG2) and Kleiber ratio (KR1, KR2) using the ASREML program. Twelve models, formed with inclusion or exclusion of the maternal genetic, permanent environmental and common (litter) environmental variance components and the covariance between the direct and maternal additive effect on the basic direct additive genetic model, were used. The same models were applied to birth weight (BWT), weaning weight (WWT) and bi-monthly weights to 12 months of age (WT2 to WT12), and weight at 18 months of age (WT18). Two-trait analyses were done among all traits. Maternal genetic and common environmental components were found to be important for ADG1, KR1 and weights up to six-months of age, while the common environmental component was found to be important for ADG2 and KR2. The maternal permanent environmental component was important for WT2 and WWT. Total heritability estimates for ADG1, ADG2, KR1 and KR2 were 0.13, 0.04, 0.13, and 0.01, respectively. Direct genetic correlations of ADG1 with BWT, WWT and WT6 were 0.01, 0.96 and 0.84 while with KR1 they were -0.40, 0.75 and 0.66, respectively. The relatively higher heritability in weight traits and the presence of positive and high correlations of weight traits with daily gain and Kleiber ratio tend to suggest that it would be more practical to select on the weight traits to improve gain and efficiency.

Longevity is a major component of the breeding objective for dairy cattle in many countries because of its high economic value. The trait has been recommended for inclusion in the breeding objective for dairy cattle in South Africa. Linear models, random regression (RR) models, threshold models (TMs) and proportional hazard models (PH) have been used to evaluate longevity. This paper discusses these methodologies and their advantages and disadvantages. Heritability estimates obtained from these models are also reviewed. Linear methodologies can model binary and actual longevity, while RR and TM methodologies model binary survival. PH procedures model the hazard function of a cow at time t derived from survival from first calving to culling, death or censoring. It is difficult to compare methodologies for sire evaluation and ranking across countries because of the variation in the definition of longevity and the choice of model. Sire estimated breeding values (EBVs) are derived differently for the models. Sire EBVs from PH models are expressed as deviations of the culling risk from the mean of the base sires, expected percentage of daughters still alive after a given number of lactations, expected length of productive life in absolute terms or as standard deviation units. In linear, TM and RR modelling, sire EBVs for longevity have been expressed as deviations of survival from the mean estimated with Best Linear Unbiased Prediction (BLUP). Appropriate models should thus be developed to evaluate functional longevity for possible inclusion in the overall breeding objective for South African dairy cattle. Keywords: Dairy Cattle, Proportional Hazards, Random Regression, Survival Analysis

Yearling live weight and fleece trait data were obtained from between 2214 and 2270 yearling SA Mutton Merino progeny of the Elsenburg flock during a 20-year period from 1983 to 2002. Information of (co)variances for these traits in SA Mutton Merinos is exceedingly scarce in the literature. Estimates of (co)variance components and ratios were thus obtained from these data, using an Animal Model. Coefficients of variation, for live weight as well as greasy and clean fleece weight were above 18%. Corresponding values for clean yield and fibre diameter were below 9%. Estimates of heritability were 0.23 for yearling live weight, 0.38 for greasy fleece weight, 0.39 for clean fleece weight, 0.59 for clean yield and 0.67 for fibre diameter. Maternal permanent environmental variance ratios were only significant for live weight, greasy fleece weight and clean fleece weight, amounting to 0.09, 0.06 and 0.06, respectively. Genetic correlations between yearling live weight and wool weight were positive but low (0.14 for greasy fleece weight and 0.13 for clean fleece weight). Those of live weight with clean yield and fibre diameter were zero and 0.22, respectively. The genetic correlation between greasy fleece weight and clean fleece weight was 0.87. The genetic correlations of greasy fleece weight with clean yield and fibre diameter were –0.07 and 0.21, respectively. Corresponding correlations with clean fleece weight were 0.43 and 0.38, respectively. The genetic correlation of clean yield with fibre diameter amounted to 0.33. In most cases, the derived values were in agreement with those derived from Merino data sets.

Data were recorded for birth weight, birth coat score and weaning weight of between 2018 and 4235 Merino lambs born over a 17-year interval from 1986 to 2002. The resource population was divergently selected from the same base population since 1986, either for (H line) or against (L line) maternal multiple rearing ability. Direct additive genetic variances - expressed as a ratio of the total phenotypic variance (h2, direct heritability) - were estimated at 0.12 + 0.03 for birth weight, 0.70 + 0.05 for birth coat score and 0.13 + 0.04 for weaning weight. Maternal genetic variance ratios (m2) were estimated at 0.23 + 0.04 for birth weight and 0.10 + 0.04 for weaning weight. It was not significant for birth coat score. Maternal permanent environmental variance ratios (c2) for the respective traits amounted to 0.08 + 0.03 for birth weight, 0.04 + 0.02 for birth coat score and 0.08 + 0.03 for weaning weight. No consistent phenotypic or genetic differences in favour of either line were found for birth weight or birth coat score. Compared to L line lambs, phenotypic means for weaning weight were heavier in favour of H line lambs from 1995. This trend was confirmed by divergence in yearly averaged direct breeding values in the H and L lines. Expressed as percentage of the overall phenotypic mean for weaning weight, genetic changes amounted to +0.23% in the H line and -0.26% in the L line. A corresponding maternal genetic trend amounting to -0.19% of the overall phenotypic mean for weaning weight was found in the L line, while no maternal genetic change could be discerned in the H line. Divergent selection for multiple rearing ability thus did not influence birth weight and birth coat score, while the correlated response in weaning weight was favourable. Keywords: Direct heritability, Genetic trends, Maternal heritability, Parameter estimation, Smoothing splines South African Journal of Animal Science Vol.33(4) 2003: 248-256

Ninety bull calves of five Bonsmara strains, viz. Edelheer (E), T-49 (T), Wesselsvlei (W), Roodebos (R) and Belmont Red (BR), and two Nguni sub-populations, viz. Bartlow (B) and non-Bartlow (NB), were fattened under intensive feeding conditions and serially slaughtered at four different slaughter weights. Phylogenetic relationships between the five Bonsmara strains and between the two Nguni subpopulations were determined by means of blood typing. Growth performance, carcass characteristics and meat quality characteristics were compared between the sub-populations of each breed. Genetic distances between the Bonsmara animals confirmed the existence of five genetic subpopulations with variation in genetic distances between them. The genetic distance between the two Nguni subpopulations was very small, indicating genetic similarity. Means for production and product characteristics were adjusted for mean subcutaneous fat percentage by means of analysis of covariance. T gained weight faster and more efficiently on a live and carcass weight basis than the other Bonsmara groups, while B gained carcass and muscle weight more efficiently than NB. T had proportionally more meat in the high-priced cuts of the carcass than W. Muscle of the W line had a higher ageing potential (measured as myofibrillar fragmentation; MFI) than T, resulting in higher tenderness scores for W. Similarly, B had higher MFI for muscle aged for one or seven days, coupled with more tender meat than NB. Pairwise correlations between growth and muscle characteristics indicated that fast growing animals tend to produce less tender meat. South African Journal of Animal Science, Vol 31, Issue 3, Oct – Dec (2001): pp.181-194

The object of this study was to estimate heritabilities and genetic correlations for reproductive traits in a composite multibreed beef cattle herd using multitrait analysis. A REML procedure fitting a multitrait animal model was used to analyse data. Heritabilities and genetic correlations for calving interval (CI), calving date (CD), calving date with a penalty score (CDP) and age at first calving (AFC) were estimated as traits of the dam. The estimated heritabilities for CI, CD, CDP and AFC obtained in this study were 0.01, 0.04, 0.06 and 0.40 respectively with a repeatability of 0.07, 0.12 and 0.13 for CI, CD and CDP. Genetic correlations between traits varied from low to moderate, except for high correlations between CD and CDP (0.98), CI and CD (0.75) and between CI and CDP (0.79). Heritabilities, genetic correlations and repeatabilities of CD and CDP obtained in this study suggest that CD and CDP are the same traits and that selection for CDP rather then for CD does not have any additional advantages. Due to the additional advantages of CD over CI and the fact that CD is a less biased measurement of the female reproductive complex, CD and AFC (because of its high heritability) may be considered as selection criteria for improvement of reproduction in beef cattle herds. (South African Journal of Animal Science, 2001, 31(1): 41-48)

The object of this study was to estimate heritabilities and sire breeding values for stayability and reproductive traits in a composite multibreed beef cattle herd using a threshold model. A GFCAT set of programmes was used to analyse reproductive data. Heritabilities and product-moment correlations between predicted breeding values for stayability at 36, 48, 60, 72 and 84 months of age, calving success and longevity were estimated. The estimated heritabilities on the underlying scale for these traits were 0.06, 0.10, 0.06, 0.03, 0.11, 0.03 and 0.08 respectively. Product-moment correlations between breeding values for stayability traits were low. The highest correlation of 0.22 was obtained between the ages of 36 and 48 months. Heritability estimates and correlations between traits appear to be of such a low magnitude that selection for these characteristics would result in limited genetic improvement, and also indicate that sires had little influence on the stayability, longevity or calving success of their daughters. (South African Journal of Animal Science, 2001, 31(1): 25-32)

(South African J of Animal Science, 2000, 30, Supplement 1: 102-104)