African Cattle Genomics Exchange Fri, 25 May 2018 09:27:47 +0000 en-US hourly 1 Support for Genomics Reference Resource for African Cattle Mon, 22 Aug 2016 13:49:51 +0000 Summary of discussion to-date on the topic: Do you consider building a genomics reference resource for African cattle to be a worthwhile investment – why or why not?


In favour?

The majority of people who commented on this question were in favour of establishing the resource, with some raising pertinent issues related to resource utility and design (see below). These participants were challenged to expand on how they thought the resource would be useful (responses are still coming in)

A minority of people did not feel the resource was a current priority – in relation to AnGR use they felt emphasis would be better placed on establishing basic, functional genetic improvement programs (linked to delivery systems), as well as capacity building on animal breeding / genomics in general.


Key points raised in relation to increasing the utility of the resource or on resource design:

  • Design must lead to exciting and useful results generated from the early investment, to provide incentives for future investments
  • Animals should be strategically sampled e.g. influential sires
  • Link to phenomic characterization of animals will increase the utility of the resource



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Future applications of genomics in African livestock systems Mon, 22 Aug 2016 11:46:02 +0000 What genetic or genomic applications have the most potential to positively impact on the rural poor in Africa – in the near future and longer term?


Main themes discussed on this topic to-date are:

The need for a holistic outlook on improving the performance of African livestock was stressed by many. Points raised here included:  the need for  supportive policy; the need for strong livestock product markets, as well as ability of livestock keepers to access these markers;  intervention package to address the various livestock production constraints (including on feed, health etc.); and means for farmers to access new technologies, such as public-private partnerships, amongst others.  In general, these issues are a subset of those commonly recognized by those working in the African livestock sectors.


Of the potential applications of genomics / genetics in African livestock systems, the only one discussed in any detail was genomic selection.  Here discussion centered around

1)Whether / how African livestock systems could capitalize on the opportunity of genomic selection, given current  system constraints.  Some example comments are:

  • “Genomic tools are not a silver bullet. …(for)  any livestock improvement effort to bear fruit requires that the basics need to be in place i.e. the conventional livestock recording systems which are not existent in most developing countries”
  • “Application of genomic tools is constrained by inefficient breeding programmes and policies in our African countries”
  • “Current genomic tools offer a ray of hope but the basic infrastructure for conventional animal performance recording are still necessary”

2) How reference populations could be created – with the suggestion of using data from government institutions linked to data from (the often few) producers who record. The latter to assist in dealing with issues related to GxE

3) An example was given of a project on Kenyan dairy cattle (mainly cross-bred) where genomic prediction was undertaken (using GBLUP and Bayes C) based on about 1000 animals with phenotypes (milk records) and genotypes, with resultant accuracies of 0.3 to 0.4.


The need for recording schemes – with appropriate incentives for farmer engagement – was also a common theme. The only incentive explicitly discussed, however, was the use of records to help improve farm management decisions (seen as being more immediate than that related to generation of genetically improved animals). There was general agreement that farmers needed capacity building in recording, and that timely feedback (on the records) was important.


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Current use of genomics / genetics in African livestock systems Wed, 17 Aug 2016 14:48:58 +0000 Below is a summary of contributions to date on the topic “What (real) examples of the application of genomic or genetic information to African livestock production systems (regardless of species) do we have to-date, and what was successful or not successful about these, and why”

Updated 22nd August, 2016

Application Country Species / traits Intended use Actual use Contributor
Genetic diversity/population structure Nigeria Goats,

some sheep, chicken,

few cattle

Abdulmojeed Yakubu
Cameroon Cattle To inform breeding and conservation decisions Ngono Ema
Pathogen detection / disease diagnostics Nigeria Swine, cattle, poultry Animal health applications, championed by

National Veterinary Institute

Oladeji Bamidele


Abdulmojeed Yakubu

Breed composition of admixed populations Senegal Cattle Comparison of productivity and household profit for keeping different breed-types – to create an evidence base for a genetic improvement strategy Karen Marshall
Rwanda Cattle  Identification of bull calves as a source of germplasm and breeding lines, in relation to a ‘One Cow per Family’ program Mizeck Chagunda
Kenya Cattle-dairy Feeding into test of genomic prediction ability (see below) Raphael Mrode
Breeding program using genomic predictions Kenya Cattle – dairy Test of genomic prediction ability  (using GBLUP & Bayes C; 1000 genotyped and phenotyped crossbred animals)


Raphael Mrode
Identification of underlying genes / gene-networks Nigeria Cattle (local) – heat tolerance & productivity Genetically improved animals Oladeji Bamidele


See what others have contributed and contribute your insights and suggestions

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Welcome to the Cattle Genomics in Africa web forum Tue, 16 Aug 2016 07:06:14 +0000 Dear colleagues,

Today we are launching our discussion. During the coming two weeks we will focus on:

  • Current and future applications of genomics to cattle in Africa – in particular, which applications are likely to make a difference to poor livestock keepers and animal source food consumers, and what capacities and resources are required to achieve this.
  • The potential to create a genomic reference resource on African cattle – a publically-available set of sequence information on cattle breeds in Africa,  and critically which breeds to prioritize for this.


You are already a member of the community. To join the discussion please log in at

We look forward to your participation.

Karen Marshall

The International Livestock Research Institute & the Centre for Tropical Livestock Genetics and Health.


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Genomic reference resource Mon, 25 Jul 2016 16:25:24 +0000 Genomic Reference Resource for African Cattle

A collated set of sequence and genotype information on cattle breeds in Africa is currently not available.  Such a resource is important at is can underpin the design of genomic tools for different applications.

The Dairy Genomics Program of the Centre for Tropical Livestock Genetics and Health (  proposes to help generate this important resource by collating data already available in public database and (where access is granted) with private research groups, and through the generation of new data obtained in collaboration with African and potentially other partners.

The initial target for the resource is 25  African cattle breeds with sequence information on at-least 10 individuals per breed, by the of end-2017.  The expectation that the number of breeds, and individuals per breed, will increase over time, as the initiative gains momentum and additional resources become available.

The genomic reference resource will be a database – accessible to all stakeholders and which is well documented– of genomic information on African cattle breeds, linked to meta-data, such as GPS location of where the animals were sampled, a, amongst other.

                              Benefit sharing on AnGR use: All data newly generated under this initiative will be generated in collaboration with partners who wish to participate, utilising appropriate access and benefit sharing agreements.  The expectation is that all data will be made publicly available.


Potential role of genomics Mon, 25 Jul 2016 16:23:40 +0000 Potential role of genomics for genetic improvement strategies for cattle in Africa

African cattle 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 and food and nutritional security to their keepers.  However a number of African cattle production systems are changing, including via intensification where livestock keepers are able to provide a higher levels of inputs (for example, in relation to animal feed and health-care).  These livestock keepers are thus seeking cattle breeds that are both adapted to the local environmental conditions and productive.  Such livestock can be made available through appropriate genetic improvement strategies.

The most appropriate genetic improvement strategy for any developing country livestock system will vary depending on the specific context, with options including breed-substitution, cross-breeding, within-breed improvement, or a combination of these. Supporting such strategies at national or regional levels is a major undertaking, requiring amongst others appropriate policy, institutional arrangements, underlying data collection, analysis and feedback platforms, attention to incentives for livestock keeper engagement, and involvement of a range of partners including the national research system and private sector.  Attention to these is critical for the genetic improvement strategy to be sustainable and provide impact at scale.

Genomic approaches can assist in the development and / or implementation of genetic improvement strategies.  For example genomic information can be used to:

  • assign breed composition to animals of otherwise unknown breed or cross-breed type – for use in studies comparing the performance of, or household income from keeping, different breeds or cross-breeds, and thus identification of the most appropriate breed-type
  • help in the identification of genes / gene-networks underpinning important livestock adaptation or production traits – leading to the creation of new or improved breed-types
  • enable livestock breeding programs –through provision of information on breed composition or the relatedness of animals in situations where pedigree has not been recorded


Further strategic thinking on which specific applications of genomics, to the varied cattle systems in Africa, are most likely to lead to positive impact – on the livelihoods of the rural poor, food and nutritional security, or environmental sustainability – is required.  This will require significant stakeholder input to find the intersection between what is technically feasible and what is relevant, and a priority, to the low-input cattle systems in Africa.

This will be a key focus area of the Dairy Genomics Programme of the Centre for Tropical Livestock Genetics and Health  in its initial years  (click here for more on the Dairy Genomics Program and here for more on CTLGH)


First stakeholder engagement Mon, 25 Jul 2016 16:22:52 +0000 This is the first stakeholder engagement of the Dairy Genomics Program of the Centre for Tropical Livestock Genetics and Health  – on Cattle Genomics in Africa

The Dairy Genomics Program of the newly established Centre for Tropical Livestock Genetics and Health (CTLGH) aims to facilitate the application of genomics to cattle in the Tropics, and particularly Africa. This will be achieved through:

  • a stakeholder engagement process to identify key applications that will lead to improving the livelihoods of the rural poor in Africa, and advocacy on these;
  • supporting the developing of tools and methodological approaches;
  • capacity building;
  • and partnering in research and resource mobilisaion.

For more on the Dairy Genomics Program of CTLGH see website and the ILRI project profile.

We welcome your input into this process through this forum – which will focus on:

  • current and future applications of genomics to cattle in Africa: Potential role of genomics
  • which breeds to prioritise for inclusion in a Genomics Information Resource for African cattle (a publically available set of sequence information on cattle breeds in Africa): Genomics reference resource



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