Building a genomic reference resource on African cattle

  • Here we will discuss the need and potential for a Genomics Reference Resource for African Cattle – which is a collated and publicly accessible set of sequence information on African cattle breeds. The sequence information would be contributed by African countries and potentially other partners to the initiative, with the intent that such information will help facilitate the application of genomics to benefit the African cattle sectors.

    For more on this potential initiative, please see this post on a ‘Genomics reference resource for Africa

    Genomics_Building1

    We are currently discussing two topics in relation to this (and more topics will follow as the forum progresses):

    (1)  Do you consider building a genomics reference resource for African cattle to be a worthwhile investment – why or why not?

    Click here for a summary of contributions on this topic to-date

    (2) What are the strategic research questions we can answer, or applications we can facilitate, with such a resource

    Please submit your contributions on these by posting below. Use the comment box (scroll down) to add a new comment, or reply to existing comments using the reply button.

     

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59 Comments

 

  1. Profile gravatar of Djemali M'Naouer
    Djemali M'Naouer August 23, 2016 Reply

    It seems that my photo disappeared just after I posted it. Only my name remained which is essential.
    Using phenomics and genomics can mislead some of us. Genomics is ok to me, but what's phenomics? What is behind phenomics?
    Anyway, back to the subject and I will stick to what I think phenomics is or are! I read through the word phenomics, any science or technique linked to phenotypes of the animals including their performances. This is a big gap in Africa (at least the majority of African countries). There is an absence of complete and coherent animal breeding strategies similar to what we find in developed countries. I do not consider university or research institutions flocks or herds as representatives of what it should be done in our countries involving farmers with a majority of small farmers under low input systems. The challenge is here. The priority of national and international efforts, in my opinion should be at this level. Genomics should be a complementary component and not the alternative for Africa. This is why building capacities through training is essential, bringing farmers together to promote their native breeds is also a promising pathway for the future of Animal Genetic Resources in Africa.

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  2. monia August 23, 2016 Reply

    Information generated by farm animals in Africa can help farmers better manage theirs animals and make better selection decisions if these infoemation are well processed. Africa Animal Genetic Ressources information can lead to a continent data bank useful to farmers and researchers. Empowering Africa Farmers toform breed Associations can be the first step to this goal

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  3. Profile gravatar of Ben Abdallah
    Ben Abdallah August 23, 2016 Reply

    Establishing Animal genetic resources programs including identification, recording and genetic evaluation and dissemination of adapted genes is an important step for Africa. This is the plus of phenomics.

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  4. Profile gravatar of Sabrine
    Sabrine August 23, 2016 Reply

    Phenomics and genomics should go together in Africa to achieve comfortable levels in animal genetic resources management and conservation

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  5. monia August 23, 2016 Reply

    For African Cattle reference in genomics,inventories should be done in all African countries to identify cattle breeds and populations

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  6. Profile gravatar of Karen Marshall - forum organiser
    Karen Marshall - forum organiser August 23, 2016 Reply

    In relation to our current discussion topic (applications of a reference resource) I would like to add a starting suggestion.

    The use of genomic information to determine breed composition of admixed animals is being increasingly used (there were several examples of this in mentioned in this forum - most commonly in relation to performance comparison of different breeds / genotypes). However this requires the availability of reference information (genomic information on the underlying breeds present in the admixed animals) . If we had this reference information available and linked to a 'smart tool' to determine breed composition, researchers would no longer need to obtain the reference information on a project by project basis. Do others see utility in this?

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  7. Asma August 22, 2016 Reply

    In establishing cattle reference using genomics, universities in Africa can play a key role if they are organized in a Network toward this objective

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    • Profile gravatar of Karen Marshall - forum organiser
      Karen Marshall - forum organiser August 23, 2016 Reply

      Yes - and National Agricultural Research Institutes should also be involved

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  8. Baitsi Podisi August 22, 2016 Reply

    The issue of an African genebank is already in the cards under the AU-IBAR animal genetics project. The planned genebank will be hosted the African Union Panafrican Veterinary Vaccine Centre (AU- PANVAC)

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    • karenmarshallilri August 23, 2016 Reply

      Thanks Baitsi - Great to hear of an African genbank. Which country is the AU-PANVAC in, and when is the genebank expected to be operational?

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      • Baitsi Podisi August 23, 2016

        The African Union Panafrican Veterinary Vaccine Centre (AU-PANVAC), provides vaccine quality control for African vaccine producing laboratories to meet international standards. The Centre promotes standardization and quality control of biological products and provides training and support services for vaccine production laboratories. It is based in Debre Zeit, Ethiopia.

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  9. Profile gravatar of Karen Marshall - forum organiser
    Karen Marshall - forum organiser August 22, 2016 Reply

    Welcome to week two of this forum!

    This week I wanted to concentrate on the design of the potential Genomics Reference Resource for African Cattle, but to do so we need to be more specific on the current discussion topic "What are the strategic research questions we can answer, or applications we can facilitate, with such a resource", as this knowledge will inform the design. Please do contribute your thoughts on this apparently challenging question.

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    • Djemali August 22, 2016 Reply

      Africa needs to establish its Continental Animal Gene Bank. This will help Africa to have its own cattle genomics reference. Is it a dream? Let's make it happen.

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    • Profile gravatar of Sabrine
      noomane August 22, 2016 Reply

      Creation of an African Platform in molecular genetics is a major step toward African cattle reference in Genomics .

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  10. Profile gravatar of Asma
    Asma August 19, 2016 Reply

    Funding Animal Genomics in Africa will not serve Africa in the first place. It will help more parties that sell equipments and lab needs. Africa needs first to build ilt capacities in training and education in animal breeding and genomics.

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    • Profile gravatar of Karen Marshall - forum organiser
      Karen Marshall - forum organiser August 19, 2016 Reply

      Thanks for raising the excellent point on capacity. I will raise capacity building needs as a specific point in the forum next week.

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    • Profile gravatar of Dr.  V. E. Olori
      Dr. V. E. Olori August 20, 2016 Reply

      I think these things are going on in the background gradually. For example I came aross a new company started recently; www.africanbio.com; which can become a key player both in terms of training and service provision. It is African. I beleive funding if properly channeled can speed up capacity building and development of key infrastructure locally.

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  11. Profile gravatar of Djemali M'Naouer
    Djemali M'Naouer August 18, 2016 Reply

    Investment in building a genomics reference for African cattle and African Animal Genetic Resources in general is worthwhile. But what is new in that. The CBD signed since 1992 identified the importance of animal genetic resources management and conservation and stressed the need to help countries in need (technical and funds) to do so.
    My concern is should Animal Genomics be the priority for African countries? The answer is NO. Africa Animal Genomics should be The World priority of course (Go back to CBD paragraphs).Animal Genetic Resources priority No1 in Africa should be going back to the basics (Farmers Breed Associations formation, suitable chain production establishments with small farmers playing key roles, suitable breeding strategies with their complete ingredients: identification, recording, evaluation , dissemination of adapted productive animals, and sustainable breeding and crossbreeding programs).

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  12. Baitsi Podisi August 18, 2016 Reply

    With respect to Yakubu's comment on the need for financial and political commitment, all is not gloom and doom as African Leaders have done a positive thing in adopting the Livestock Development Strategy for Africa (LiDeSA) (http://www.au-ibar.org/strategy-documents) which is new advocacy tool to mobilise support and investment in livestock in Africa. What remains is for the technocrats and other stakeholders at country levels to domesticate the strategy within their respective countries.

    Baitsi

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    • Profile gravatar of Karen Marshall - forum organiser
      Karen Marshall - forum organiser August 18, 2016 Reply

      Thanks for sharing the link to this cornerstone document. Advocacy on investment in African Livestock is indeed critical.

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  13. Profile gravatar of Karen Marshall - forum organiser
    Karen Marshall - forum organiser August 18, 2016 Reply

    Many people have said this resource will be useful, but there has been limited discussion on how it will be used, who will benefit from its use etc.

    It would be great to build on the perceptive comment of John Gibson –essentially that the resource design must lead to exciting and useful results generated from the early investment, to provide incentives for future investments.

    Thus I propose the next discussion topic as “What are the strategic research questions we can answer, or applications we can facilitate, with such a resource” (the definitions of which will feed into later discussions on resource design)

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  14. Profile gravatar of Karen Marshall - forum organiser
    Karen Marshall - forum organiser August 17, 2016 Reply

    And please don't forget to take the survey - the 'take survey' button is on the top bar

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  15. Profile gravatar of Raphael Mrode
    Raphael Mrode August 17, 2016 Reply

    In developed countries, individual countries have realized that they could not build adequate genomic reference resources on their due cost and the number of animals required. Consequently we have blocks of countries such as the North American Consortium consisting of USA, Canada, Italy and UK and the Euro-genetic consisting of France, Germany, Finland etc, exchanging genomic information. In small breeds such as the Brown Swiss, several countries pool their genomic information together to reduce cost and to achieve adequate numbers for meaningful genomic analysis. Therefore the building of an Africa genomic reference resource must cut across country bounders and strategic. Just as John Gibson remarked, we must move beyond mere characterization to actual implementation procedures that will have impart on productivity. Thus sampling of animals should be strategic; influential sires could be sampled so that we collect data from their daughters leading to genomic analysis that has practical application.

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    • Profile gravatar of Oladeji Bamidele
      Oladeji Bamidele August 17, 2016 Reply

      since it is termed 'African' then it should be at least representative of all the breeds with proven impact on the locals; interms of the performance & productivity. There are practically no substantial up-to-date records for these animals which means there may be a considerably reliance on the knowledge of the farmers to identify the influential sires and also track the progenies. The Establishment of a farmer research network may be helpful both for these strategic sampling as well as subsequent dissemination of the results for practical application and impact

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      • Profile gravatar of Karen Marshall - forum organiser
        Karen Marshall - forum organiser August 17, 2016

        Thanks - we will come back to the issue or breed prioritization later in the survey, as we will have to make some initial choices as the resource builds up

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    • Profile gravatar of Karen Marshall - forum organiser
      Karen Marshall - forum organiser August 17, 2016 Reply

      Yes I agree on strategic selection of animals - we can priorities influential animals when we have that information, but unfortunately their are few cases of this. It would be great if others could comment on breeding / recording programs on African cattle of which they are aware

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    • Profile gravatar of Abdulmojeed Yakubu
      Abdulmojeed Yakubu August 18, 2016 Reply

      I quite agree with the submission of Raph. One of the long-range objectives of the cattle Genome Program is to identify all coding sequences, genes and other functional elements in genomic DNA. Given that physical maps are being rapidly assembled and that the rate of accumulation of large-scale sequence data is increasing, there is a critical need for robust, high-throughput, and cost-effective methods and strategies to identify and map functional elements in the genome. An Indiana local dairy farmer claimed that DNA marker-technology has helped him boost production to 40 litres of milk per cow, per day, Although the 50K test continues to be used for high-end breeding stock and screening young artificial insemination (AI) sire entries, a simpler, cheaper test called the 3K test, which identifies about 3,000 carefully chosen SNPs, has been developed to allow herd owners to make use of genomic testing on a wider basis. Provided that at least one parent has been tested with the 50K test, the more economical 3K test can be used with only a small loss in accuracy due to the use of a method called imputation, which uses knowledge of the parental genome in the calculations. Recently, more SNPs and improved accuracy have been added to the 3K test, now called the 6K test. Due to the cost implication, I will recommend the use of 6K genomic application. The smallholder dairy farmers may be organized into a formidable group in such a way that they can pool resources together in order to be able to pay for the genomic services inform of public-private partnership. Such genomic services should be highly subsidized by the government in power so that the farmers will be able to afford them.

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  16. John Gibson August 17, 2016 Reply

    It has proven challenging to attract significant funding to understand and harness the genetic of Africa's livestock genetic resources. A contributing factor in this has been the lack of compelling evidence-based arguments for how R&D that explores genetic diversity can generate information that translates to practical outcomes. Having high quality information on the diversity of African cattle breeds is an essential starting point for the efficient and effective design of research for development that can harness this genetic diversity. Efficient/effective design is critical because if funding agencies see exciting and useful results generated by early investments the incentives for future investments will be high; but if early investments yield little of any value, prospects for larger and longer-term investments will be poor. I strongly support the creation of an initial genomics reference resource that includes a targeted generation of sequence/genotype information for an initial set of breeds that represent the wide diversity of African cattle. I urge that the design of this initial genomics reference resource (which breeds?; how many animals; what genomic/genetic information?) be driven by the need to generate information that will allow the design future investments that have the highest probability of generating results of high scientific quality and practical relevance (and hence will maximise the probability of longer-term investment in this space).

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    • Profile gravatar of Peter Freeman
      Peter Freeman August 17, 2016 Reply

      Might be good to take a post-funding look at existing evidence-based arguments, such as they are, and take it from there. At CTLGH we're keen to tap into past and present PROJECTS and their knowledge artefacts, which tend to disappear from view once funding is secured and spent, The compelling arguments are locked up in (often eloquent) project proposals and reports that are tossed aside once they do their job of winning funding, and the focus turns to "research impact" of academic publications rather than real world impact outlined in the project proposals. We need to join up projects to show their collective impact, and knowledge gaps, and then point these out to investors.

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      • Profile gravatar of Karen Marshall - forum organiser
        Karen Marshall - forum organiser August 19, 2016

        Yes, and those of us involved in Research for Development projects, are being increasingly asked to provide evidence on project outcomes (or, as you put it, real world impact)

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    • Profile gravatar of Mick Watson
      Mick Watson August 17, 2016 Reply

      John, very interested in your comments on this! How do we maximise the translation of genomics into results that change lives?

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    • Profile gravatar of Karen Marshall - forum organiser
      Karen Marshall - forum organiser August 17, 2016 Reply

      Thanks for your insightful comment. Yes I agree that we need early results / applications to stimulate future investments. Could you give some examples of what you have in mind.

      I will come back to the issue of which breeds, how many animals, what information etc. a bit later in the forum

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  17. Profile gravatar of Abdulmojeed Yakubu
    Abdulmojeed Yakubu August 16, 2016 Reply

    I agree with earlier contributors that building a genomics reference resource for African cattle is a necessity. If we take a cursory look at the existing GenBanks and databases, one will discover that there is little information on African cattle. Having a reliable database will facilitate research work on genomics selection. Today genomic breeding values (GEBV) are routinely used for making selection decisions, which has resulted in reducing the generation interval and increasing genetic gain compared to classical progeny testing systems in dairy cattle. populations

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    • Profile gravatar of Peter Freeman
      Peter Freeman August 17, 2016 Reply

      Can we move from taking cursory looks to actually mapping (or making lists of) the existing Genbanks and databases? Who would be well placed to do that? Do they know about us and could we get them interested?

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      • Profile gravatar of Mick Watson
        Mick Watson August 17, 2016

        We have started a bit of this, we'll be able to do more once recruitment has finished!

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      • Profile gravatar of Abdulmojeed Yakubu
        Abdulmojeed Yakubu August 18, 2016

        I think we can leverage on the initiatives of AU-IBAR and exploit the potential of ILRI-BecA to work out modalities for GenBanks and databases for African Livestock species. Through the strong financial backing and political will of African Nations and the support of international funding bodies, we may be able to make a headway.

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  18. Profile gravatar of Oladeji Bamidele
    Oladeji Bamidele August 16, 2016 Reply

    A genetic reference resource for African Cattle is very necessary. I think it is long overdue considering the rich genetic resource of Cattle for improving livelihoods. It will help to better understand and exploit the genetic variation between/within the cattle sub-species of African descent. Although the sequenced genome of the Hereford cow is largely representative of both sub-species, however, there are increasing indications that there are sub-species differences in the bovine genomic architecture and having a reference resource particularly suited for these tropically adapted breeds will help their targeted genetic improvement.

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    • Profile gravatar of Mick Watson
      Mick Watson August 17, 2016 Reply

      I suspect "the devil is in the detail" - the current Hereford assembly has errors in it, and also there will be quite a lot of structural variation between cattle breeds in Africa and the Hereford reference. We are also working on difficult-to-assemble regions such as MHC

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  19. Profile gravatar of Karen Marshall - forum organiser
    Karen Marshall - forum organiser August 16, 2016 Reply

    Great that this discussion is continuing after a technical hitch on comment submission.

    The current discussion topic is - Do you consider building a genomics reference resource for African cattle to be a worthwhile investment – why or why not?

    It would be great to hear from more African countries on this!

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  20. Baitsi Podisi August 16, 2016 Reply

    I think reference resource is necessary and will be useful to guide future efforts. Some cattle diversity studies were undertaken by ILRI in the past but were hampered by limited understanding by some stakeholders who failed to submit samples for the initiative. This will create a basis to guide any future interventions as a lot remains unknown on African cattle. The use of the current tools will hep to validate past work which was patchy and lacked power to guide informed decision making on the various breeds and ecotypes. Baitsi

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    • Profile gravatar of Mick Watson
      Mick Watson August 17, 2016 Reply

      Do we know why some stakeholders failed to engage?

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      • Profile gravatar of Oladeji Bamidele
        Oladeji Bamidele August 17, 2016

        I think for this to be successful it has to be partly driven by the farmers/stakeholders themselves as they are the final users of the innovation. The hurdle will be to have a design that easily incorporate the smallholder farmers whose lives we want to improve via genomics tools & application. The benefits needs to be well articulated beyond the science of it.

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  21. Hagos Abraham August 16, 2016 Reply

    No doubt it is quite important. The data will serve as a cornerstone for further research activities concerning genetic diversity, improvement and utility of local cattle breeds in Africa.

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  22. Profile gravatar of Leroy Gregoire
    Leroy Gregoire August 16, 2016 Reply

    It will be of course useful, but the interest of such resources will be mostly conditioned to the provision of phenotypic characterization of individuals sampled (description of the animals, their performance, and their production environment), which remains largely unknown for most of those populations.

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    • Profile gravatar of Karen Marshall - forum organiser
      Karen Marshall - forum organiser August 16, 2016 Reply

      Yes - of genotypes and phenotypes, the latter is the harder and more expensive to get, but of critical importance. It has been difficult to inspire donors to support phenotypic characterization studies, and more advocacy on this issue is definitely needed (and welcomed)

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      • Profile gravatar of Peter Freeman
        Peter Freeman August 17, 2016

        Couldn't agree more. Of course 'advocacy' shouldn't be left to chance - we have to make a business case for WHY donors should get on board. Maybe think of them as 'investors' in tropical livelihoods

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    • Profile gravatar of Karen Marshall - forum organiser
      Karen Marshall - forum organiser August 16, 2016 Reply

      From a practical viewpoint, we can priorities genotyping animals that have additional phenotypic information (for example from an on-going project) where such an option exists. Unfortunately this is not likely to cover many breeds / populations.

      If anyone is aware of ongoing phenotypic data collection activities, please let us know

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    • Profile gravatar of Mick Watson
      Mick Watson August 17, 2016 Reply

      I completely agree with this and many of us are working to ensure that phenotypic data are collected in standard ways that allows and enables downstream analysis

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  23. Profile gravatar of NGONO EMA
    NGONO EMA August 16, 2016 Reply

    Absolutely yes.Such a reference source will help us to move faster in research.If the data collection are done in a good and standard way , instead of first going to the field to collect them, researchers will refer to the genomics reference resource.The challenge is then to have data from different sources and then make them usable for anyone. Such an initiative has been taken in Cameroon in the Universityof Dschang where a Gene Bank for all Central Africa has to be set up.

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    • Profile gravatar of Karen Marshall - forum organiser
      Karen Marshall - forum organiser August 16, 2016 Reply

      Thanks - is the Gene Bank for Central Africa functional or still being established?

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    • Profile gravatar of Mick Watson
      Mick Watson August 17, 2016 Reply

      Genome reference sequences are of huge value to researchers. It would be good to know what challenges exist, if any, in terms of making genome sequence data usable for scientists in Africa.

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  24. Profile gravatar of Peter Freeman
    Peter Freeman August 16, 2016 Reply

    Yes. Absolutely essential to have access to reference resources. Challenge is to harvest, curate, and present data and knowledge from multiple project sources and make them available in useable form for those that need them. This stakeholder engagement is crucial in defining "what knowledge?" , "who needs it?" and "in what form?"

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  25. Profile gravatar of Karen Marshall - forum organiser
    Karen Marshall - forum organiser August 15, 2016 Reply

    Welcome to this discussion on the proposed genomics reference resource for African cattle

    A small team of us will facilitate the discussion by proposing discussion topics and summarizing responses.

    The first discussion topic is given below – please use a new thread for each new point being raised under this discussion topic, and reply within a thread when commenting on a previous post.

    Discussion topic 1: Do you consider building a genomics reference resource for African cattle to be a worthwhile investment – why or why not?

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