Estimates of genetic parameters and effect of inbreeding on milk yield and composition in South African Jersey cows

The effect of inbreeding on the 305-d yields of milk, fat and protein, and the percentages of fat and protein in the first three lactations was estimated using records on the South African Jersey cows that participated in the National Dairy Animal Improvement Scheme. Inbreeding coefficients were estimated using the entire pedigree records of the Jersey breed and ranged from 0 to 42%. Data were analyzed using a repeatability animal model. The statistical model included the fixed effects of herd-year-season, age of the cow at calving, calving interval, inbreeding as a discrete or continuous variable and random effects of direct additive genetic, permanent environment of the cow and the residual effects. The multitrait derivative-free REML algorithm was used to obtain estimates of the variance components, ratios and empirical best linear unbiased estimates of the effects of inbreeding. Estimates of heritability were 0.26 (±0.009), 0.19 (±0.008), 0.23 (±0.008), 0.39 (±0.009), and 0.53 (±0.009) for milk, fat and protein yields and fat and protein percent, respectively. Corresponding estimates of the ratio of permanent environmental effect of the cow to total phenotypic variance were 0.20 (±0.008), 0.18 (±0.007), 0.21 (±0.007), 0.14 (±0.008) and 0.13 (±0.008). The regression coefficients for yields (kg) of milk, fat and protein were -15.42 (±1.13), -0.64 (±0.05), and -0.59 (±0.04), and 0.0011 (±0.0005) and 0.0003 (±0.0003) for percent (%) of fat and protein for each 1% increase in inbreeding, respectively. These results provide evidence of inbreeding depression for milk yield and composition traits in the South African Jersey population. Keywords: Dairy cattle, inbreeding depression, 305-d yield South African Journal of Animal Science Vol. 38 (2) 2008: pp. 119-12

The effect of herd of origin by year on post-weaning traits of young beef bulls at centralized testing centres in South Africa

The effects of herd of origin by year on the average daily gain (ADG), average daily feed intake (DFI), shoulder height (SDH) and scrotal circumference (SCR) of beef bulls at centralized test centres in South Africa were investigated using data of Bonsmara cattle. Data consisted of post-weaning traits of beef bulls tested between 1990 and 2003, with available weaning weight (WWT) and weaning management group information as well as weaning weights of their contemporaries. A multiple-trait animal model including ADG, DFI, SDH and SCR, together with WWT was used. The model for WWT (adjusted to 205 days of age and age of dam by sex of calf classes) included the fixed effect of management group and random effects of direct additive genetic and dam effects, while the model for post-weaning traits included fixed effects of test group and age of the bull at the end of test (fitted as linear and quadratic regressions) and random effects of direct additive genetic and herd of origin by year (HY) effects. Variance components were estimated using REML procedures. Heritability estimates were 0.27, 0.34, 0.36, 0.51 and 0.46 for WWT, ADG, DFI, SDH and SCR, respectively. The contribution of HY effects to the phenotypic variance of ADG, DFI, SDH and SCR were 9%, 10%, 6% and 5%, respectively. Inclusion of HY effect resulted in the re-ranking of sires, with rank correlations ranging from 0.86 to 0.98 among the top sires, across traits. These results suggest that the HY effect should be included in the model for the national genetic evaluation of post-weaning traits of beef bulls measured at centralized testing centres in South Africa. South African Journal of Animal Science Vol. 36(1) 2006: 33-3

Analysis of stayability in South African Angus cattle using a threshold model

The objectives of the study were to estimate genetic parameters for stayability in the South African Angus cattle and to compare the sire and animal threshold models. Data and pedigree information were obtained from the Integrated Registration and Genetic Information System of South Africa. Stayability was defined as a probability that a cow remained in the herd until four (STAY4), five (STAY5), six (STAY6), seven (STAY7) and eight years of age (STAY8), given that she was a dam. Cows that were in the herd by a specific age were assigned a “1” or a “0”, otherwise. The proportions of successful stayability were 0.63, 0.57, 0.49, 0.42, and 0.37 for STAY4, STAY5, STAY6, STAY7 and STAY8, respectively. Estimates of genetic parameters were obtained from sire and animal threshold models using AIREML algorithm. The model included the fixed effect of contemporary group and random effects of sire or animal genetic effect and the residual. Heritability estimates from the sire model were 0.26 ± 0.08, 0.26 ± 0.09, 0.30 ± 0.09, 0.24 ± 0.10 and 0.27 ± 0.11 for STAY4, STAY5, STAY6, STAY7 and STAY8, respectively. Corresponding estimates from the animal model were 0.20 ± 0.11, 0.20 ± 0.11, 0.20 ± 0.12, 0.18 ± 0.13 and 0.20 ± 0.14. Estimates from the sire and animal models were consistent. Results from the current study indicate that direct selection for stayability could be effective. However, the long generation interval required to obtain accurate estimates of genetic merit may slow genetic progress for stayability at older ages

Alternative models for genetic evaluation of feed intake by Afrikaner cattle

The objectives of this study were to evaluate statistical models of potential utility for genetic evaluation of feed intake and to estimate the (co)variance components and genetic parameters that would be necessary for their use in a national cattle evaluation scheme. Data were from Afrikaner bulls that were tested between 1974 and 2016 in Phases C (n = 1 250) and D (n = 11 083) of the National Beef Recording and Improvement Scheme. Statistical analyses in which the number of traits varied and contemporary group effects were considered either random or fixed were conducted using multiple-trait derivative-free restricted maximum likelihood. Contemporary group effects were important. When they were considered random, the estimated phenotypic variance of feed intake increased and its heritability reduced from approximately 0.43 ± 0.09 to approximately 0.30 ± 0.06. Use of average daily gain, recorded either concurrently with the feed intake measure (ADGC) or from related bulls reared on-farm (ADGD), had relatively little effect on estimated heritability of feed intake. Thus, considering contemporary group effects random consistently increased the accuracy of the estimated breeding values. Relatively small genetic correlations between ADGC and ADGD complicated the ultimate application of data recorded in Phase C and the use of data recorded in Phase D in decoupling the phenotypes for feed intake and growth in an evaluation of feed efficiency. Some modification of testing procedures may be necessary to facilitate this application of the results.Keywords: accuracy, contemporary group, genetic parameters, performance testin

Genome-wide identification of breed-informative single-nucleotide polymorphisms in three South African indigenous cattle breeds

Access to genotyping assays enables the identification of informative markers that discriminate between cattle breeds. Identification of these markers can assist in breed assignment, improvement and conservation. The objective of this study was to identify breed informative markers to discriminate between three South African indigenous cattle breeds. Data from BovineSNP50 and GeneSeek Genomic Profiler (GGP-80K) assays were generated for Afrikaner, Drakensberger and Nguni, and were analysed for their genetic differentiation. Hereford and Angus were included as outgroups. Breeds were differentiated using principal component analysis (PCA). Single-nucleotide polymorphisms (SNPs) within the breeds were determined when minor allele frequency (MAF) was ≥ 0.05. Breed-specific SNPs were identified using Reynolds Fst and extended Lewontin and Krakauer's (FLK) statistics. These SNPs were validated using three African breeds, namely N’Dama, Kuri and Zebu from Madagascar. PCA discriminated among the breeds. A larger number of polymorphic SNPs was detected in Drakensberger (73%) than in Afrikaner (56%) and Nguni (65%). No substantial numbers of informative SNPs (Fst ≥ 0.6) were identified among indigenous breeds. Eleven SNPs were validated as discriminating the indigenous breeds from other African breeds. This is because the SNPs on BovineSNP50 and GGP-80K assays were ascertained as being common in European taurine breeds. Lower MAF and SNP informativeness observed in this study limits the application of these assays in breed assignment, and could have other implications for genome-wide studies in South African indigenous breeds. Sequencing should therefore be considered to discover new SNPs that are common among indigenous South African breeds and also SNPs that discriminate among these indigenous breeds

Rate of inbreeding and effective population size in four major South African dairy cattle breeds

Pedigree information on the registered South African Ayrshire (n = 47 116), Guernsey (n = 18 766), Holstein (n = 892 458) and Jersey (n = 314 403) breeds was analyzed to determine the rate of inbreeding and effective population sizes for the period 1960 to 2003. Inbreeding coefficients were calculated using the Animal Breeder's Tool Kit. The mean inbreeding coefficients for 2003 were 2.02%, 2.04%, 2.30%, and 3.05% for the Ayrshire, Guernsey, Holstein and Jersey, respectively. The corresponding rates of inbreeding per year were 0.05%, 0.05%, 0.06%, and 0.07% indicating that inbreeding is accumulating at a slightly higher rate in Jersey compared to the other three breeds. However, the rates of inbreeding in the current study are still considerably lower than the acceptable rate of less than 0.5% per year. Estimates of effective population sizes were 148, 165, 137, and 108 for the Ayrshire, Guernsey, Holstein and Jersey, respectively. Results indicate that the impact of inbreeding on genetic variability is still minimal. However, the impact of inbreeding on phenotypic performance on traits of economic importance was not investigated in the current study and should therefore receive future consideration. South African Journal of Animal Science Vol. 36(1) 2006: 50-5

Evaluation of the BovineSNP50 genotyping array in four South African cattle populations

The BovineSNP50 genotyping array is a product with a wide range of applications in cattle such as genome-wide association studies, identification of copy number variation and investigation of genetic relationships among cattle breeds. It also holds potential for genomic selection, especially for traits that are expensive and difficult to measure. The successfulness of this chip for any of these applications depends on the degree of polymorphisms in the cattle breeds. The SNP50 array has not been validated in any South African cattle population and this could lead to overestimating the number of polymorphic SNPs available for application in it. This study is a first attempt to evaluate the Bovine64SNP50 genotyping array in the South African cattle population. Ninety six bovine samples, consisting of 45 Holstein, 29 Nguni, 12 Angus and 10 Nguni x Angus crossbred animals, were genotyped with the BovineSNP50 infinium assay. The results of this study demonstrated that 40 555 SNPs were polymorphic (MAF >0.05) in these breeds and indicate potential for application in South African cattle populations. Genomic information generated from the BovineSNP50 can now be applied in genetic prediction, genetic characterization and genome-wide association studies.The authors would like to thank the ARC-Biotechnology Platform for making their laboratory resources available for genotyping samples. Financial support from the ARC is greatly appreciated. Provision of semen on Holstein bulls by Taurus Co-operative is also acknowledged.http://www.sasas.co.za/am201

Genetic diversity in South African Nguni cattle ecotypes based on microsatellite markers

The Nguni cattle breed is a landrace breed adapted to different ecological regions of South Africa. A number of ecotypes are recognised based on phenotype within the breed, but it is not known if they are genetically distinct. In this study, molecular characterisation was performed on Makhathini (MAK), Pedi (PED), Shangaan (SHA) and Venda (VEN) Nguni cattle ecotypes. Two Nguni cattle populations, not kept as separate ecotypes, from the University of Fort Hare (UFH) and Agricultural Research Council Loskop South farm (LOS) were also included. Genotypic data was generated for 189 unrelated Nguni cattle selected based on pedigree records using 22 microsatellite markers. The expected heterozygosity values varied from 69 % (UFH) to 72 % (PED) with a mean number of alleles ranging from 6.0 to 6.9. The F ST estimate demonstrated that 4.8 % of the total genetic variation was due to the genetic differentiation between the populations and 92.2 % accounted for differences within the populations. The genetic distances and structure analysis revealed the closest relationship between MAK, PEDI and SHA ecotypes, followed by SHA and VEN. The UFH population clustered with the MAK ecotype, indicating that they are more genetically similar, while the LOS cattle grouped as a distinct cluster. Results suggest that the genetic differentiation between the PED and SHA ecotypes is low and can be regarded as one ecotype based on limited genetic differences. The results of this study can be applied as a point of reference for further genetic studies towards conservation of Nguni cattle ecotypes.Limpopo Department of Agriculture and Agricultural Research Council - Animal Production Institute (ARC-API).http://link.springer.com/journal/112502017-02-20hb201