Conservation status and historical relatedness of South African communal indigenous goat populations using a genome-wide single-nucleotide polymorphism marker.

Indigenous goats form the majority of populations in smallholder, low input, low output production systems and are considered an important genetic resource due to their adaptability to different production environments and support of communal farming. Effective population size (N e ), inbreeding levels, and the runs of homozygosity (ROHs) are effective tools for exploring the genetic diversity and understanding the demographic history in efforts to support breeding strategies to use and conserve genetic resources. Across populations, the current N e of Gauteng was the lowest at 371 animals, while the historical N e across populations suggests that the ancestor N e has decreased by 53.86%, 44.58%, 42.16%, and 41.16% in Free State (FS), North West (NW), Limpopo (LP), and Gauteng (GP), respectively, over the last 971 generations. Genomic inbreeding levels related to ancient kinship (F ROH > 5 Mb) were highest in FS (0.08 ± 0.09) and lowest in the Eastern Cape (EC) (0.02 ± 0.02). A total of 871 ROH island regions which include important environmental adaptation and hermo-tolerance genes such as IL10RB, IL23A, FGF9, IGF1, EGR1, MTOR, and MAPK3 were identified (occurring in over 20% of the samples) in FS (n = 37), GP (n = 42), and NW (n = 2) populations only. The mean length of ROH across populations was 7.76 Mb and ranged from 1.61 Mb in KwaZulu-Natal (KZN) to 98.05 Mb (GP and NW). The distribution of ROH according to their size showed that the majority (n = 1949) of the detected ROH were > 5 Mb in length compared to the other categories. Assuming two hypothetical ancestral populations, the populations from KZN and LP are revealed, supporting PC 1. The genomes of KZN and LP share a common origin but have substantial admixture from the EC and NW populations. The findings revealed that the occurrence of high N e and autozygosity varied largely across breeds in communal indigenous goat populations at recent and ancient events when a genome-wide single-nucleotide polymorphism (SNP) marker was used. The use of Illumina goat SNP50K BeadChip shows that there was a migration route of communal indigenous goat populations from the northern part (LP) of South Africa to the eastern areas of the KZN that confirmed their historical relatedness and coincides with the migration periods of the Bantu nation.

Genetic relationship between weaning weight and milk yield in Nguni cattle.

A study was conducted to estimate the genetic relationship between weaning weight and milk yield in Nguni cattle. Milk yield data (n=125) were collected from 116 Nguni cows from Mara Research Station located in Limpopo Province and Loskop South Farm located in Mpumalanga Province using the weigh-suckle-weigh technique. Weaning weight data (n=19 065) were obtained from stud Nguni cattle from 146 herds distributed throughout South Africa. Estimates of (co)variance components for milk yield and weaning weight were calculated using PEST and VCE softwares. The average weaning weight, age of the calf at weaning and 24-h milk yield was 158.94 kg, 210 days and 5.25 kg/day, respectively. Heritability estimates for milk yield, direct and maternal weaning weight were 0.22±0.238, 0.47±0.039 and 0.25±0.029, respectively. Estimates of genetic correlations for milk yield and maternal weaning weight, milk yield and direct weaning weight, direct and maternal weaning weight were 0.97±0.063, -0.71±0.416 and -0.56±0.247, respectively. The results indicate that maternal weaning weight is genetically highly predictive of milk yield in Nguni cattle. Maternal breeding values for weaning weight could therefore be used as a selection criterion to improve milk yield in Nguni cattle.

Effect of agro-ecological zone, season of birth and sex on pre-weaning performance of Nguni calves in Limpopo Province, South Africa.

The study was conducted to determine the effect of agro-ecological zone, season of birth and sex on Nguni calves' pre-weaning performance. Production indices such as birth weight (BW), weaning weight (WW), pre-weaning average daily gain (P-ADG) and pre-weaning gain (P-WG) were assessed in the different agro-ecological zones. Herd records on performance of 826 Nguni calves' from nine Nguni herds representing different agro-ecological zones: arid zone (n = 217); semi-arid zone (n = 296); dry sub-humid zone (n = 118) and humid zone (n = 195) were used for the analysis of pre-weaning calf performance. General linear model (GLM) procedure of SAS (2013) was used to analyse data, whereas mean separation was conducted using Tukey's HSD test. Agro-ecological zone had a great influence (P < 0.01) on performance levels arising from pasture conditions which were dependent on rain, temperature, topography and soil type. Fluctuations in WW, P-ADG and P-WG performance across agro-ecological zones depicted the sensitivity of Nguni calves' to postnatal stress. Calves' in humid zone had higher performance with 121.21 kg for WW, 96.83 kg for P-WG and 0.477 kg/day for P-ADG. The lowest WW (114.51 kg), P-WG (89.98 kg) and P-ADG (0.438 kg/day) were observed in arid zone. Male calves were heavier at weaning (128.18 kg), P-ADG (0.503 kg/day) and total gain (103.03 kg); however, similar BW of 25 kg was observed for both male and female calves. Season had a significant (P < 0.05) effect on BW, P-ADG and P-WG. The P-ADG was 0.461 kg/day for calves born in summer and 0.449 kg/day for calves born in winter season. Calves born in summer gained 94.69 kg and calves born in winter gained 92.10 kg. Summer calves gained 2.59 kg more than winter calves. Summer heifer calves performed poorly whilst summer male calves outperformed heifer calves in terms of WW, P-WG and P-ADG. Pre-weaned calves in humid zone outperformed all calves in other agro-ecological zones. It was concluded that acceptable levels of growth are achievable from Nguni cattle under the different agro-ecological zones of Limpopo province, South Africa.

Relationship between linear type and fertility traits in Nguni cows.

The objective of the study was to assess the dimensionality of seven linear traits (body condition score, body stature, body length, heart girth, navel height, body depth and flank circumference) in Nguni cows using factor analysis and indicate the relationship between the extracted latent variables and calving interval (CI) and age at first calving (AFC). The traits were measured between December 2012 and November 2013 on 1559 Nguni cows kept under thornveld, succulent karoo, grassland and bushveld vegetation types. Low partial correlations (-0.04 to 0.51), high Kaiser statistic for measure of sampling adequacy scores and significance of the Bartlett sphericity test (P1. Factor 1 included body condition score, body depth, flank circumference and heart girth and represented body capacity of cows. Factor 2 included body length, body stature and navel height and represented frame size of cows. CI and AFC decreased linearly with increase of factor 1. There was a quadratic increase in AFC as factor 2 increased (P<0.05). It was concluded that the linear type traits under study can be grouped into two distinct factors, one linked to body capacity and the other to the frame size of the cows. Small-framed cows with large body capacities have shorter CI and AFC.

Genetic analysis of body weights of individually fed beef bulls in South Africa using random regression models.

The aim of this study was to estimate genetic parameters for body weights of individually fed beef bulls measured at centralized testing stations in South Africa using random regression models. Weekly body weights of Bonsmara bulls (N = 2919) tested between 1999 and 2003 were available for the analyses. The model included a fixed regression of the body weights on fourth-order orthogonal Legendre polynomials of the actual days on test (7, 14, 21, 28, 35, 42, 49, 56, 63, 70, 77, and 84) for starting age and contemporary group effects. Random regressions on fourth-order orthogonal Legendre polynomials of the actual days on test were included for additive genetic effects and additional uncorrelated random effects of the weaning-herd-year and the permanent environment of the animal. Residual effects were assumed to be independently distributed with heterogeneous variance for each test day. Variance ratios for additive genetic, permanent environment and weaning-herd-year for weekly body weights at different test days ranged from 0.26 to 0.29, 0.37 to 0.44 and 0.26 to 0.34, respectively. The weaning-herd-year was found to have a significant effect on the variation of body weights of bulls despite a 28-day adjustment period. Genetic correlations amongst body weights at different test days were high, ranging from 0.89 to 1.00. Heritability estimates were comparable to literature using multivariate models. Therefore, random regression model could be applied in the genetic evaluation of body weight of individually fed beef bulls in South Africa.

Effect of pre-weaning selection on estimates of genetic parameters and breeding values for post-weaning growth rate of beef bulls on test.

Data on South African Angus cattle consisting of 45 259 records on weaning weight (WWT), 4 360 records on average daily gain from on-farm test (ADG-D) and 1 118 from centralized test (ADG-C) were analyzed to evaluate the effect of pre-weaning selection on estimates of genetic parameters and subsequent estimated breeding values (EBV) for post-weaning average daily gain. (Co)variance components and genetic parameters for weaning weight (WWT), ADG-C and ADG-D were estimated by REML procedures fitting three different animal models. Model 1 was a univariate model of WWT, ADG-C or ADG-D and did not account for the effect of pre-weaning selection on post-weaning ADG. Model 2 was a two-trait model of WWT and either ADG-C or ADG-D. Model 3 was a multi-trait animal model including WWT, ADG-C and ADG-D. Estimates of heritability for ADG-C were 0.39 +/- 0.080, 0.42 +/- 0.060 and 0.44 +/- 0.010 from Model 1, 2 and 3 respectively. Corresponding estimates for ADG-D were 0.18 +/- 0.020, 0.19 +/- 0.020 and 0.21 +/- 0.020 respectively. Rank correlations based on EBVs for ADG-C for all bulls were 0.92, 0.83 and 0.94 for Model 1 vs. Model 2, Model 1 vs. Model 3, and Model 2 vs. Model 3, respectively and they indicated a possible re-ranking of bulls when including or excluding a correlated pre-weaning trait. Rank correlations for ADG-D also followed a similar trend. Inclusion of pre-weaning information in genetic analysis for post-weaning average daily gain is necessary to account for selection at weaning.

The influence of stocking density on body weight, egg weight, and feed intake of adult broiler breeder hens.

The influence of stocking density on BW, egg weight (EW), and feed intake (FI) in Ross broiler breeder hens (n = 120) was investigated during the late medium egg production period (from 50 to 54 wk of age). Birds were randomly allocated to 6 pens in densities of 15, 20, and 25 birds/pen, giving rise to a floor space allowance of 5, 6.67, and 8.33 birds/m(2), respectively. Each density was replicated twice, and the order among the 6 pens was chosen at random. Data were analyzed using the repeated measures techniques of the Statistical Analysis System, considering the covariance structure of the observed data. There was a significant effect attributable to stocking density, time (in days), and their interaction for BW, EW, and FI. Birds in density of 6.67 per m(2) were lighter but had heavier eggs than birds in density of 5 per m(2); however, birds in density of 8.33 per m(2) had similar BW and EW with birds in the other 2 groups. The mean FI were statistically different among the 3 groups, with a reduction in FI as density increases. Total egg production within the 3 density groups and average egg production per bird were also analyzed using categorical data techniques. The results indicated that stocking density influenced egg production, with birds at higher density producing fewer eggs per bird. Although generous floor space allowances were allocated per bird in this experiment, stocking density influenced the performance of broiler breeder hens.

Genetic relationships between sex-specific traits in beef cattle: mature weight, weight adjusted for body condition score, height and body condition score of cows, and carcass traits of their steer relatives.

Data from the first four cycles of the Germplasm Evaluation Program at the U.S. Meat Animal Research Center (USMARC) were used to investigate genetic relationships between mature weight (MW, n = 37,710), mature weight adjusted for body condition score (AMW, n = 37,676), mature height (HT, n = 37,123), and BCS (n = 37,676) from 4- to 8-yr old cows (n = 1,800) and carcass traits (n = 4,027) measured on their crossbred paternal half-sib steers. Covariance components among traits were estimated using REML. Carcass traits were adjusted for age at slaughter. Estimates of heritability for hot carcass weight (HCWT); percentage of retail product; percentage of fat; percentage of bone; longissimus muscle area; fat thickness adjusted visually; estimated kidney, pelvic, and heart fat percentage; marbling score; Warner-Bratzler shear force; and taste panel tenderness measured on steers were moderate to high (0.26 to 0.65), suggesting that selection for carcass and meat traits could be effective. Estimates of heritability for taste panel flavor and taste panel juiciness were low and negligible (0.05 and 0.01, respectively). Estimates of heritability from cow data over all ages and seasons were high for MW, AMW, and HT (0.52, 0.57, 0.71; respectively) and relatively low for BCS (0.16). Pairwise analyses for each female mature trait with each carcass trait were done with bivariate animal models. Estimates of genetic correlations between cow mature size and carcass composition or meat quality traits, with the exception of HCWT, were relatively low. Selection for cow mature size (weight and/or height) could be effective and would not be expected to result in much, if any, correlated changes in carcass and meat composition traits. However, genetic correlations of cow traits, with the possible exception of BCS, with HCWT may be too large to ignore. Selection for steers with greater HCWT would lead to larger cows.