OPTIBOV: Genetic Characterization of Cattle Populations for Optimal Performance in Africa Eco Systems

A large variety of local indigenous and commercial cattle breeds has been produced as a result of domestication and selection. This variety ensures the capability and adaptability of livestock to fulfil its role in food production under different circumstances, now and in the future. Local breeds exhibit unique adaptive features to harsh environments, which can be useful for adjusting mainstream breeds to climate change. Simply transferring high producing commercial animals to the African continent, will not be the solution due to low performance and even low survival under these harsh environments (ecosystems). The aim of the OPTIBOV project is to improve production and survival of traditional/indigenous breeds adapted to the local environments in Africa. This will secure the future of these well adapted traditional/indigenous local breeds. With combined effort from partners across the globe, the OPTIBOV project will help maintain traditional cattle breeds, capture adaptation, use known variations in production, train, educate & involve stakeholders to perform optimal breeding.

The project is coordinated in The Netherlands (Wageningen University and Research Centre). Participating institutions include; Makerere University, Uganda; Natural Resources Institute Finland; Agricultural Research Council Pretoria, South-Africa; University of Porto, Portugal; Cairo University, Egypt; and Taurus Foundation Netherlands.

Project members include; Dr Richard Crooijmans, Wageningen University, The Netherlands; Dr Donald Kugonza, Department of Agricultural Production, Makerere University; Prof Juha Kantanen, Natural Resources Institute Finland; Dr Nasser Ghanem, University of Cairo, Egypt; Dr Linky Makgahlela, Pretoria, South Africa; and Dr Catarina Ginja from Portugal.

The project is supported by LEAP-Agri, a joint Europe Africa Research and Innovation (R&I) initiative related to Food and Nutrition Security and Sustainable Agriculture (FNSSA).

An important deliverable of the project is a new genotyping assay specific for African cattle breeds which will include markers associated with specific traits.

 Expected outcomes and impact:                         

1. A uniform bovine phenotype scoring list for adaptation traits.
2. Genome-wide information of the traditional breeds. Giving knowledge on the amount of diversity but also on the amount of inbreeding, detection of potential genetic defects and selective sweeps related to adaptation to a specific environment.

• The obtained information can be used to improve traits by selection of animals within or over breeds such as longevity, production and resistance to diseases. This will increase production, longevity and reduces cost for medical treatments which will result in breed performance in the next generations.

1. Training of young researchers will be conducted to use the latest technology and techniques and how to implement the findings in breeding.
2. Involvement of all stakeholders up to farmers by creating an APP, database and website to submit data and actively participate within the research.

Hybrid seminar

On 25^th April 2022, the project team met at the College of Agricultural and Environmental Sciences (CAES), Makerere University to share updates on activities in the respective countries. The hybrid seminar was hosted by Dr Donald Kugonza and Dr Morris Agaba.

Seminar presentations/issues being researched

1. Traditional cattle genomics: search for adaptive markers – Dr Richard crooijmans, Wageningen University in The Netherlands;
2. Developments in SNP genotyping and next generation sequencing in South African indigenous cattle – Dr AA Zwane, a Researcher in Animal Breeding and Genetics, Agricultural Research Council-Animal Production (ARC-AP), Irene, Pretoria, South Africa;
3. Molecular responses of heat stress during early embryonic development and alleviation strategies – Dr Nasser Ghanem from the Department of Animal Production, Faculty of Agriculture, Cairo University, Egypt;
4. Application of genomics for livestock genetic improvement – Dr Linky Makgahlela, ARC-Animal Production, South Africa;
5. Genomic characterization of northern native cattle breeds – Prof. Juha Kantanen, Natural Resources Institute Finland;
6. Phenotypic and Genotypic Characterisation of Ankole, Ntuku and Nganda cattle of Uganda – Dr. Behabura Generous Betunga, an MSc. Animal Science student in the Department of Agricultural Production, CAES;
7. Investigating the production and adaptive traits of indigenous cattle to eastern Uganda ecosystems – Waibi Sarah, an MSc. Livestock Development student at the College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University;
8. The use of Genomic Tools to Improve Cattle, an Archaeogenomics Perspective – Dr Catarina Ginja

Issues arising from the research

1. Developments in SNP genotyping and next generation sequencing in South African indigenous cattle – Dr AA Zwane

• There is notable difference in using single nucleotide polymorphism (SNP) data and whole genome sequence (WGS) data in characterizing SA indigenous cattle breeds
• WGS data holds the potential for the improvement of indigenous livestock breeds due to the in-depth analysis genome-wide
• Genetic diversity studies give the understanding of population structure, demographic history, introgression and heterozygosity levels in South Africa indigenous cattle
• Identification of selective signatures provides insight into selection events that have shaped the genomes of indigenous cattle breeds, and allows the identification of important genes
• This will allow genomic selection, sooner, in the indigenous breeds, and more studies are needed for other indigenous livestock species

2. Application of genomics for livestock genetic improvement – Linky Makgahlela, ARC-Animal Production, South Africa
3. Genomics drives biological efficiency of production, boosts livestock contribution for sustainable protein source
4. Genomics promises cutting-edge solutions: Nutritional needs of all human beings, while safeguarding natural resources, and preventing environmental degradation

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  Genomics enables farmers to increase efficiency, decrease production costs & prophylactics and limits expenditure of resources

1. Research (and capacity development) ongoing for better understanding of breeds and to put science to practice

3. Genomic characterization of northern native cattle breeds – Prof. Juha Kantanen, Natural Resources Institute Finland

The gene expression analysis of the northern Eurasian breeds revealed;

1. Several differentially expressed genes (DEG) that were associated with the eicosanoid metabolic process (ALOX15, ALOX5 and HPGD) in northern Finncattle and with immunity (CCL4, CCL5 CX3CR1, CXCR6 and PRF1) and the regulation of lipid transport (ABCA1, ABCG1, IRS2 and THBS1) in Yakutian cattle.
2. The genes involved in the immune system are also associated with environmental adaptation.

• The eicosanoid metabolic process was previously found to be involved in the hibernation of brown bears (Ursus arctos) and indigenous peoples associated with seasonal changes. These findings indicate a convergent evolution that may have occurred in different mammalian species living in northern and sub‐arctic environments.

4. Phenotypic and Genotypic Characterisation of Ankole, Ntuku and Nganda cattle of Uganda – Behabura Generous Betunga, Makerere University

The Ugandan cattle herd is comprised of 93.3 percent of indigenous breeds and their crossbreeds which are mainly; Long-horned cattle of Uganda(Sanga) (Bos taurus indicus); Zenga breeds (Sanga and Zebu crosses); East African short-horn Zebu (Bos indicus). The OPTIBOV breeds of interest in Uganda are; Long horned Ankole cattle (South-Western Uganda); Nganda cattle (Central-Uganda) and Ntuku cattle (Mid-Western Uganda). The study aims to carry out phenotypic characterization for performance traits and draw a genomic growth curve for Ankole, Ntuku and Nganda cattle under different management systems for a period of 0 to 18 months in Uganda. It also aims to carry out genetic characterization and measure the genetic relationship between the Ankole, Ntuku and Nganda cattle in Uganda; and to assess selection techniques (natural and human mediated) of Ankole, Ntuku and Nganda cattle of Uganda. Meetings have been held with farmers and animals selected for sampling and samples collected for analysis

Issues arising include;

1. The Indigenous cattle breeds are at the threat of genetic erosion. There is need for Phenotypic & genotypic Characterization for the performance traits of the Ankole, Ntuku & Nganda cattle breeds
2. The Ankole, Ntuku & Nganda cattle breeds in Uganda are adoptable under agro-climatic conditions. Conditions are much better in central Uganda given the feeding traits of Nganda cattle

• OPTIBOV project cattle species of interest in Uganda include: Long horned Ankole Cattle in South Western Uganda, Nganda cattle in Central & Ntuku cattle in Mid-Western Uganda

5. Investigating the production and adaptive traits of indigenous cattle to eastern Uganda ecosystems

Cattle is a valuable source of income, employment & a major source of nutrition to people in the East especially Karamoja & Bukedi in Tororo. Angoria Ting & Cheptoyoi are the indigenous cattle breeds in Karamoja: Karamajong women prefer rearing goats to cows. The study aims to;

1. To phenotypically characterize the performance and adaptive traits of the Nkedi and Karimajong cattle
2. To develop indices for assessing the productivity of the Nkedi and Karimajong cattle

• To assess status and risk of erosion of the two indigenous cattle genetic resources

 Meeting with Makerere University Vice Chancellor

In the course of the seminar, the OPTIBOV project team paid a courtesy call on Makerere University Vice Chancellor, Prof. Barnabas Nawangwe who congratulated them upon winning the research grant. “As we celebrate 100 years of teaching, research and innovation, such projects are vital in pushing forward our agenda of transforming Makerere into a research-led University,” he noted, pledging to accord the researchers all the support they need to achieve the project objectives.

 The project leader at Makerere University, Dr Donald Kugonza expressed gratitude to the Vice Chancellor for the support he accorded the team in their bid for the project.

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