Animal Breeding Genomic Selection for Improved Animal health: A review of challenges and opportunities in Zimbabwe (original) (raw)
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Frontiers in Genetics
The African livestock sector plays a key role in improving the livelihoods of people through the supply of food, improved nutrition and consequently health. However, its impact on the economy of the people and contribution to national GDP is highly variable and generally below its potential. This study was conducted to assess the current state of livestock phenomics and genetic evaluation methods being used across the continent, the main challenges, and to demonstrate the effects of various genetic models on the accuracy and rate of genetic gain that could be achieved. An online survey of livestock experts, academics, scientists, national focal points for animal genetic resources, policymakers, extension agents and animal breeding industry was conducted in 38 African countries. The results revealed 1) limited national livestock identification and data recording systems, 2) limited data on livestock production and health traits and genomic information, 3) mass selection was the commo...
A review of genomic selection - Implications for the South African beef and dairy cattle industries
South African Journal of Animal Science, 2013
The major advancements in molecular technology over the past decades led to the discovery of DNAmarkers, sequencing and genome mapping of farm animal species. New avenues were created for identifying major genes, genetic defects, quantitative trait loci (QTL) and ultimately applying genomic selection (GS) in livestock. The identification of specific regions of interest that affect quantitative traits aimed to incorporate markers linked to QTL into breeding programs by using marker assisted selection (MAS). Most QTL explained only a small proportion of the genetic variation for a trait with limited impact on genetic improvement. Single nucleotide polymorphism (SNP) markers created the possibility to genotype cattle in a single assay with hundreds of thousands of SNPs, providing sufficient genomic information to incorporate into breeding value estimation. Genomic selection is based on the principle of associating many genetic markers with phenotypic performance. A large database of genotyped animals with relevant phenotypes pertinent to a production system is therefore required. South Africa has a long history of animal recording for dairy and beef cattle. The challenge for implementation of GS would be the establishment of breed-specific training populations. Training populations should be genotyped using a high density SNP panel, and the most appropriate genomic prediction algorithm determined. The suitability of commercially available genotyping platforms to South African populations should be established. The aim of this review is to provide an overview of the developments that occurred over the past two decades to lay the foundation for genomic selection with special reference to application in the South African beef and dairy cattle industry.
Livestock Genomics for Developing Countries – African Examples in Practice
Frontiers in Genetics
African livestock breeds are numerous and diverse, and typically well adapted to the harsh environment conditions under which they perform. They have been used over centuries to provide livelihoods as well as food and nutritional security. However, African livestock systems are dynamic, with many small-and medium-scale systems transforming, to varying degrees, to become more profitable. In these systems the women and men livestock keepers are often seeking new livestock breeds or genotypes-typically those that increase household income through having enhanced productivity in comparison to traditional breeds while maintaining adaptedness. In recent years genomic approaches have started to be utilized in the identification and development of such breeds, and in this article we describe a number of examples to this end from sub-Saharan Africa. These comprise case studies on: (a) dairy cattle in Kenya and Senegal, as well as sheep in Ethiopia, where genomic approaches aided the identification of the most appropriate breed-type for the local productions systems; (b) a cross-breeding program for dairy cattle in East Africa incorporating genomic selection as well as other applications of genomics; (c) ongoing work toward creating a new cattle breed for East Africa that is both productive and resistant to trypanosomiasis; and (d) the use of African cattle as resource populations to identify genomic variants of economic or ecological significance, including a specific case where the discovery data was from a community based breeding program for small ruminants in Ethiopia. Lessons learnt from the various case studies are highlighted, and the concluding section of the paper gives recommendations for African livestock systems to increasingly capitalize on genomic technologies.
Genomics to benefit livestock production: improving animal health
Revista Brasileira de Zootecnia, 2016
The primary principle underlying the application of genomics is that it has the most value for difficult and expensive to measure traits. These traits will differ between species and probably also between markets. Maintenance of health will be one of the biggest challenges for efficient livestock production in the next few decades. This challenge will only increase in the face of demand for animal protein, resistance to existing drugs, and the pressure to reduce the use of antibiotics in agriculture. There is probably genetic variation in susceptibility for all diseases but little has been done to make use of this variation to date. In part this is because it is very difficult as well as expensive to measure this variation. This suggests that genomics should provide one of the ways of tackling the challenge of improving animal health. This paper will discuss the concepts of resistance, variation in susceptibility, and resilience; provide examples and present some recent results in cattle and pigs; and briefly discuss the application of gene editing in relation to disease resistance.
Frontiers in Genetics
South Africa (SA) holds a unique position on the African continent with a rich diversity in terms of available livestock resources, vegetation, climatic regions and cultures. The livestock sector has been characterized by a dual system of a highly developed commercial sector using modern technology vs. a developing sector including emerging and smallholder farmers. Emerging farmers typically aim to join the commercial sector, but lag behind with regard to the use of modern genetic technologies, while smallholder farmers use traditional practices aimed at subsistence. Several factors influence potential application of genomics by the livestock industries, which include available research funding, socioeconomic constraints and extension services. State funded Beef and Dairy genomic programs have been established with the aim of building reference populations for genomic selection with most of the potential beneficiaries in the well-developed commercial sector. The structure of the beef, dairy and small stock industries is fragmented and the outcomes of selection strategies are not perceived as an advantage by the processing industry or the consumer. The indigenous and local composites represent approximately 40% of the total beef and sheep populations and present valuable genetic resources. Genomic research has mostly provided insight on genetic biodiversity of these resources, with limited attention to novel phenotypes associated with adaptation or disease tolerance. Genetic improvement of livestock through genomic technology needs to address the role of adapted breeds in challenging environments, increasing reproductive and growth efficiency. National animal recording schemes contributed significantly to progress in the developed sector with regard to genetic evaluations and estimated breeding values (EBV) as a selection tool over the past three decades. The challenge remains on moving the focus to novel traits for increasing efficiency and addressing welfare and environmental issues. Genetic research programs are required that will be directed to bridge the gap between the elite breeders and the developing livestock sector. The aim of this review was to provide a perspective on the dichotomy in the South African livestock sector arguing that a realistic approach to the use of genomics in beef, dairy and small stock is required to ensure sustainable long term genetic progress.
Unintended consequences of selection for increased production on the health and welfare of livestock
Archives Animal Breeding
Modern farming technologies, including quantitative selection and breeding methods in farm animal species, resulted in increased production and efficiency. Selection for increased output in both intensive and extensive production systems has trade-offs and negative outcomes, often more pronounced in intensive systems. Animal welfare and health are often adversely affected and this influences sustainable production. The relative importance of animal welfare differs among developed and developing countries due to the level of economic development, food security and education, as well as religious and cultural practices which presents challenges for sound scientific research. Due to breeding goals in the past set on growth performance, traits such as fertility, welfare and health have been neglected. Fertility is the single most important trait in all livestock species. Reduced fertility and lameness, claw health and mastitis results in unnecessary culling and reduced longevity. Selection pressure for growth accompanied with inbreeding has resulted in a number of genetic defects in beef, sheep and pigs. This review demonstrated the importance of inclusion of animal welfare concepts into breeding objectives and selection strategies. Accurate phenotyping of welfare traits is a limiting factor in the implementation of mitigating strategies, which include diagnostic testing, control of inbreeding and genomic selection.
Genomic selection - Revolutionary breeding practice in Domestic animals
Veterinary World, 2012
With more and more Single Nucleotide Polymorphisms (SNPs) being identified throughout the genome, some of those SNPs will be found to be located within candidate genes, allowing the researchers to use the candidate gene approach on a genomewide scale. SNPs have some drawbacks but when compared to other markers they are more efficient and SNP consortium is growing to meet the requirements of genome-wide scans. Genomic selection should be able to at least double the rate of genetic gain in the dairy industry but the incorporation of genomic information into the breeding programs must be carefully considered. One needs to have around 2000 genotypes means a large reference population (population with both phenotype and genotype recorded) to achieve meaningful increases in accuracy. The available information, selection objectives, production circumstances and benefit/cost analysis must be evaluated in order to decide whether or not the population is suitable for GS implementation, and which would be the most convenient way, if any, for its implementation. Animal breeders will need to lead the way on the integration of genomic and phenotypic data into a new era of genome-enabled animal improvement and management.
Frontiers in Genetics
Genomic selection (GS) has resulted in rapid rates of genetic gains especially in dairy cattle in developed countries resulting in a higher proportion of genomically proven young bulls being used in breeding. This success has been undergirded by well-established conventional genetic evaluation systems. Here, the status of GS in terms of the structure of the reference and validation populations, response variables, genomic prediction models, validation methods, and imputation efficiency in breeding programs of developing countries, where smallholder systems predominate and the basic components for conventional breeding are mostly lacking is examined. Also, the application of genomic tools and identification of genome-wide signatures of selection is reviewed. The studies on genomic prediction in developing countries are mostly in dairy and beef cattle usually with small reference populations (500-3,000 animals) and are mostly cows. The input variables tended to be pre-corrected phenotypic records and the small reference populations has made implementation of various Bayesian methods feasible in addition to GBLUP. Multi-trait single-step has been used to incorporate genomic information from foreign bulls, thus GS in developing countries would benefit from collaborations with developed countries, as many dairy sires used are from developed countries where they may have been genotyped and phenotyped. Cross validation approaches have been implemented in most studies resulting in accuracies of 0.20-0.60. Genotyping animals with a mixture of HD and LD chips, followed by imputation to the HD have been implemented with imputation accuracies of 0.74-0.99 reported. This increases the prospects of reducing genotyping costs and hence the cost-effectiveness of GS. Next-generation sequencing and associated technologies have allowed the determination of breed composition, parent verification, genome diversity, and genome-wide selection sweeps. This information can be incorporated into breeding programs aiming to utilize GS. Cost-effective GS in beef cattle in developing countries Mrode et al. Genomic Selection for Cattle in Developing Countries may involve usage of reproductive technologies (AI and in-vitro fertilization) to efficiently propagate superior genetics from the genomics pipeline. For dairy cattle, sexed semen of genomically proven young bulls could substantially improve profitability thus increase prospects of small holder farmers buying-in into genomic breeding programs.
Impact of genomics on animal agriculture and opportunities for animal health
Trends in Biotechnology, 2008
Livestock production is an important source of animal protein worldwide. In the developed world meat consumption will remain steady but demand is forecast to grow enormously in developing countries. The use of genomics will speed genetic improvement and increase levels of production quickly in the developed world but might face problems in the developing world, including scientific, economic and political challenges. Considerable increases in public and private research funding will be required to develop and utilize novel tools and collections of detailed trait information on appropriate animals. The development of policies protecting the environment and managing all genetic resources will also be needed. Advances in livestock genomics have major implications for increasing food output as well as improving human health.
Genomics Research: Livestock Production
Encyclopedia of Biotechnology in Agriculture and Food, 2010
The major emphasis of animal genomic research has been to increase the productivity and disease resistance ability of economically important farm animal breeds to meet the ever increasing demands of animal products. Traditionally, the approach of livestock improvement was based on the classical breeding where in the parents of the next generation were selected based on their phenotype without knowing the genetic variation underlying the traits of interest. To this end, genomic tools have helped to move away from this "Black box" approach and understand the complex genetic components of phenotypic variation. Through structural and comparative genomics it had become possible to identify the genomic regions/quantitative trait loci (QTL) harboring the performance altering genes. However, the QTL search followed by fine mapping could prove useful to a limited extent as detection of casual mutations underlying QTL's was time consuming and cost extensive. These limitations restricted the extensive implementation of marker assisted selection technology in the commercial breeds. Recent advances in genomic research including whole genome sequencing, expression array, and highly multiplexed and high throughput single nucleotide polymorphism (SNP) genotyping platforms have a large impact on the ability for genome mining and pinpoint genes that influence biological and economically important traits. In future, selection decision based on the genomic breeding values complemented with other quantitative genetic evaluation approaches can very well lead to improve genetic gain in livestock species. In this chapter, an effort has been made to describe the issues, scope and needs those confront the animal genomics community in today's industry driven era.