Genomics for the advancement of livestock production: A South African perspective

Most of the growth of human populations worldwide will be in developing countries, including South Africa. Natural resources are under immense pressure and animal scientists are faced with the challenges for increased efficiency and long-term sustainability of livestock production. Since the completion of the Human Genome Project, animal genomes have been mapped with genomics, enabling new opportunities for application in farm animal species. The use of microsatellite markers has made significant contributions to the insight in genetic characterisation of indigenous and local developed breeds in most farm species in South Africa and Africa. The single nucleotide polymorphic (SNP) marker discovery and development of commercial SNP arrays made genomic selection possible and genomic enhanced breeding values (GEBVs) are used widely in the First World. In South Africa, genomic programmes for beef and dairy cattle were established in 2015 and 2016, with the focus on building training populations for genomic selection. The SA Bonsmara breed was the first to receive GEBV. The availability of hard-to-measure phenotypes is limited, and these are the traits that hold the most potential for genomic selection and answering to the challenges of methane (CH4) emissions and higher efficiency. Genome editing, which involves zinc-finger nucleases (ZFNs), transcription-activators such as endonucleases (TALEN) and RNA-programmable genome editor (CRISPR/CAS9), includes the most recent technology for application in precision genetics. Welfare and ethical concerns will be an important consideration in the acceptability of genome editing to consumers. Applications that benefit the animals are more acceptable to the public. The use of genome editing to produce polled cattle is one of the first applications with a direct welfare impact as it nullifies the need for painful dehorning. In this paper, genomic technology is reviewed with the focus on the most recent research trends and commercial application of genomics towards the genetic improvement of livestock with specific reference to South Africa.Keywords: Genetic diversity, genomic selection, gene editing, microsatellite markers, SN

Test-day models for South African dairy cattle for participation in international evaluations

Variance components and breeding values of production traits and somatic cell score of South African Guernsey, Ayrshire, Holstein and Jersey breeds have been estimated using a multi-lactation repeatability test-day model, including tests of the first three lactations as repeated measures and fitting the permanent environmental effect across lactations. Multitrait evaluations were done for the production traits (milk, butterfat and protein) and single trait evaluations for somatic cell score. Heritability estimates were comparable with yield and somatic cell score estimates obtained by test-day models from other countries (17-24% for milk yield; 10-13% for butterfat yield; 14-19% for protein yield and 6-8% for somatic cell score). Proofs of qualifying sires were sent to the International Bull Evaluation Service (INTERBULL) for participation in the March 2005 test runs. Genetic correlations between South Africa and other participating countries, estimated by INTERBULL, compared well with those amongst the other participating countries. Trend validation tests were successful using this methodology for all traits and breeds except for somatic cell score of the Guernsey breed, due to insufficient data for this trait. South Africa can now participate in routine INTERBULL evaluations to obtain Multiple Across Country Evaluation (MACE) breeding values, using this methodology. South African Journal of Animal Science Vol. 36(1) 2006: 58-7

Genetic diversity and population structure of locally adapted South African chicken lines: Implications for conservation

In this study microsatellite markers were applied to investigate the genetic diversity and population structure of the six local chicken lines kept in the “Fowls for Africa” program, for better clarification of parameters for breed differentiation and genetic conservation of this valuable resource. The lines included the Black Australorp, Potchefstroom Koekoek, New Hampshire, Ovambo, Lebova- Venda and a Naked Neck line. Unbiased estimates for heterozygosity ranged from 50% in the Potchefstroom Koekoek to as high as 65% in the Naked Neck chickens. FIS values varied from as low as 0.16 for the Black Australorp line to as high as 0.35 for the Ovambo chickens. The FST values indicated moderate to high genetic differentiation between the Naked Neck and New Hampshire (0.11); Ovambo and Naked Neck lines (0.12), and Naked Neck and Lebowa- Venda (0.14). A total of 13% of the total genetic variation observed was between the chicken lines and 87% within the lines, supporting moderate genetic differentiation. Population structure was assessed using STRUCTURE where the Black Australorp was genetically best defined. Although six clusters for the different populations could be distinguished, the other lines were not as clearly defined, with individual birds tending to share more than one cluster. Results support a broad classification of these lines and further investigation of unique alleles is recommended for conservation of the lines within the program. Keywords: Native chicken, microsatellite markers, genetic variation, population structure, South Africa South African Journal of Animal Science Vol. 38 (4) 2008: pp. 271-28

Comparison of breeding values and genetic trends for production traits estimated by a Lactation Model and a Fixed Regression Test-day Model

A comparison of breeding values and genetic trends of production traits from two models is made. One set of breeding values and trends was estimated by the September/October 2003 South African National Genetic Evaluation, using a Lactation Model (LM). The other set was obtained in the 2004 South African National Genetic Evaluation, using a Fixed Regression Test-day Model (TDM). This comparison is made for Ayrshire, Guernsey, Holstein and Jersey cows participating in the South African Dairy Animal Improvement Scheme. Specific differences between the two models were documented, with differences in statistical methodology and inclusion of test-day records of the first three parities in the TDM vs. only first lactation 305-day yields in the LM, as the main differences. Significant reranking of especially cows and unproven sires occurred between the models. Genetic trends of the TDM were not as steep as those from the LM, as the trait that was selected was first lactation yield, while the TDM trends reflect genetic progress over the first three parities. South African Journal of Animal Science Vol. 36(2) 2006: 71-7

Adjustment of heterogenous variances and a calving year effect in test-day models for national genetic evaluation of dairy cattle in South Africa

South Africa implemented test-day models for genetic evaluations of production traits, using a Fixed Regression Test-Day Model (FRTDM), which assumes equal variances of the response variable at different days in milk, the explanatory variable. Data at the beginning and at the end of lactation period, have higher variances than tests in the middle of the lactation. Furthermore, first lactations have lower mean and variances compared to second and third lactations. This is a deviation from the basic assumptions required for the application of repeatability models. A modification was therefore implemented to reduce the effect of deviating from this assumption. Test-day milk, butterfat and protein yield records of Jersey cows, participating in the South African Milk Recording Scheme, were therefore pre-adjusted such that the variances are on the same scale. Variance components estimated using the adjusted records were higher than using unadjusted records. Convergence of breeding value estimation is reached significantly faster when using adjusted data (± 4000 iterations) compared to unadjusted records (± 15 000 iterations). Although cow and bull rankings were not influenced much, significant changes in breeding values for individual animals and genetic trends of especially young animals, were found. South African Journal of Animal Science Vol. 36(3) 2006: 165-17

Genetic polymorphism of CSN1S2 in South African dairy goat populations

Alpha-s2 casein has a significant influence on protein content in goat milk, and the technological properties important for cheese processing. Specific alleles (A, B, C, E and F) of the alpha (α)s2-casein gene (CSN1S2) result in higher protein, casein and fat content, and improved coagulation properties, which are useful for improved cheese making. The aim of this study was to investigate the polymorphism and genetic variation of CSN1S2 in South African dairy goats, using DNA sequencing technology. Sixty dairy goats (20 Saanes, 20 British Alpine, and 20 Toggenburg) and 20 meat-type goats were sequenced with four primers to distinguish among the seven known alleles for αs2-casein. A total of four alleles (A, B, C and F) for CSN1S2 were observed among the dairy- and meat-type populations with ten genotypes across the populations. The A allele and the AA genotype were the most frequent across the populations, with the favourable AC genotype being the most frequent (0.300) in the Saanen population. Two unique genotypes were detected in the Toggenburg (BB and BF) and one in the meat-type goats (CF). The results indicate moderate genetic variation for αs2-casein in the South African goat populations (42.3–63.6%). Low positive FST values suggest limited inbreeding. This study confirmed the presence of favourable alleles in the South African goat populations, indicating room for genetic improvement using directional selection for favourable genotypes.Keywords: alpha-s2-casein, genetic variation, goat milk, protein content, Saane

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

Genetic analysis of pre-weaning survival and inbreeding in the Boxer dog breed of South Africa

Abstract Members of the Federation of Boxer Clubs in Southern Africa (FBCSA) have participated in official recording for many years. The aim of the study was to estimate genetic parameters and trends for preweaning survival and to assess inbreeding in the South African Boxer, based on performance and pedigree data. Fitness records were included from 2138 litters recorded between 1988 and 2012 and pedigree information of 32 029 Boxer dogs recorded from 1950 to 2012. The average litter size was 6.14 ± 2.43. More male puppies were born per litter (3.23 ± 1.79) than female puppies (2.91 ± 1.72), with an increase in the proportion of males in larger litter sizes. Heritability values of 0.23 ± 0.08 and 0.25 ± 0.08 were estimated for litter size (LS) and number of puppies alive at two weeks after birth (NA), respectively. Litters larger than five tended to have more puppies born dead or with low survivability. Number of puppies born dead or that died within two weeks after birth increased from 0.43/litter at first parity to 0.82/litter at fifth parity, with a substantial increase of 2.25/litter with low survivability at seventh parity. Average inbreeding levels of the Boxer breed were above 10%, with an inbreeding rate of 0.14%/year since 1982. These results indicate that FBCSA should focus on lowering the levels of inbreeding by avoiding mating closely related animals. The complete recording of fitness traits is encouraged for effective genetic management of the breed

Supplement 1) Peer-reviewed paper

Abstract The FAO publication, Livestock's Long Shadow, indicated that livestock is responsible for 18% of the world's greenhouse gas production thereby creating the perception that livestock is a major cause of global warming. Methane (CH 4 ) makes up 16% of total world gas emissions and is the second most important greenhouse gas (GHG) after carbon dioxide (CO 2 ). Ruminants are important to mankind since most of the world's vegetation biomass is rich in fibre and only ruminants can convert this vegetation into high quality protein sources for human consumption. In spite of this important role of livestock, it is singled out as producing large quantities of GHG that contribute to climate change, since enteric fermentation is responsible for 28% of global CH 4 emissions. However, the net effect from livestock is only a 4.5% contribution to GHG. The livestock industry should be aware of the effect of livestock on climate change and therefore it is important that mechanisms are put in place to mitigate this effect. The improvement of production efficiency through increased production per constant unit, crossbreeding and genetic improvement may be a cost effective and permanent way of reducing the carbon footprint of beef cattle. _______________________________________________________________________________