Using genomic information on cattle in Africa

  • Here we are discussing the applications of genomic (or genetic) information on cattle in Africa, both in the near future (next 5 years) and longer term.

    Some potential applications are given below (see also this post on the potential role of genomics for African cattle)

    Genomics_Use2

     

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

    (1)  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

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

    (2) Which genomic or genetic applications have the most potential to positively impact on the rural poor in Africa – in the near future and the longer term.

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

    (3) Is phenomics – the ability to measure livestock performance – a bigger challenge than genomics in African livestock systems and, if so, how can we increase phenomic capabilities

    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.

     

    Genomics_Use1

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121 Comments

 

  1. Chanda Nimbkar August 19, 2016 Reply

    Hi Karen, So far as I know, very little, if anything, is being done to set up reference populations in India. The issue is further complicated because of the existence of many breeds. Some preliminary discussions have been held about reference populations of cows and buffaloes but not in other species. Under the National Dairy Plan, populations of cows and buffaloes with good phenotypic records are being built up. But things are at a preliminary stage.

    This forum is very welcome indeed. One of the problems in India is the scarcity of impact-oriented genomic studies and paucity of information exchange between scientists involved in genomics and breeders and practitioners.

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

      Thanks Chanda. Africa also has the problem of scarcity of impact-oriented genomic studies, and it would be great to see more focus on this.

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

    Hi all - looking forward to more contributions on current genomics / genetics work being performed on livestock systems in Africa, and what you think are the key applications of genomics / genetics that will impact positively on Africa's rural poor. A summary of discussions to date on the first point can be found here.

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    • Profile gravatar of Sahar Ahmed
      Sahar Ahmed August 19, 2016 Reply

      Dear All

      It is important to establish an African genetic consortium for African cattle and other animals. This will help a lot for genetic improvement, especially most the African countries have the same environmental condition (adaptation of animals for environmental stress) , some countries have the same breeds. For animal resistance: in most African countries animals facing the disease (adaptation of animals for environmental stress)

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  3. Charles Kariuki August 17, 2016 Reply

    Dear all,

    In my view I think African livestock producers find themselves in a rather difficult position. First, with the flow of information and germplasm, many producers dream of owning super performing animals with the believe that this will translate to profitability. However, due to the constrained production circumstances they mostly make minimal profits if not losses (see the report from Tegemeo institute for more details). On the other hand, growth in human population is creating more demand for animal products. Therefore, producers find themselves in a situation where there is demand for animal products and don’t know to economically benefit from it. How to make livestock farming economically resilient should be the driver of present and future research in the animal production domain.

    African genotypes have been over time labelled as inferior. This thinking emanates from a narrow perception of production that focuses on the product without considering the resources required and the market forces. Animals within developing world have over years been naturally selected for survival. Present needs require that selection be focused towards production. How increased productivity translates to increased profitability for the farmer is key to sustainable increased productivity.

    It is my personal view that the biggest problem is that farmers in developing world are being forced to progress in genetic terms at a rate they have not been adequately prepared for (in terms of knowledge and production inputs). Besides, the markets are also not prepared for high cost products e.g., despite the changes in inputs costs, prices for milk fluctuate marginally; going up and down. This is likely an indication that consumers are not prepared to pay more.

    Influx of exotic high performance breeds (driven by marketers who don’t give a balanced view to farmers) is not going to solve the farmer’s problems. In my view, slow genetic progress that incorporates the participation of the producers is key to increasing productivity in an economically sustainable way. This calls for the establishment of local breeding programs for developing countries. Such programs can target local germplasm e.g. for goats, chickens and beef cows or can be geared towards adapting the imported genotypes to the production systems in developing countries e.g. for dairy cattle. This is where genomic selection becomes a key pillar. With GS it is possible to actualize a breeding program for a situation where there is minimal recording by producers (a key limitation for genetic improvement in the tropics). Reference populations can be created from government institutions incorporating the few producers who record. Other producers are more likely to join in the future in the breeding efforts when they observe and see the benefits or the privileges. In this way two thngs are achieved: a) we breed animals to suit our needs and b) more importantly demystify genetic improvement of animals among farmers. With more involvement of producers the industry is bound to improve drastically.

    Regards,
    Kariuki

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    • Andrew Marete August 18, 2016 Reply

      Hi,
      Thanks for this constructive dialogue, I work on dairy genomics and bioinformatics in particular quantitative trait nucleotides affecting complex dairy traits and gene by gene interactions in the same. I suppose the main challenge in developing countries, as many have pointed out, is not only lack of proper performance recording, but routine uniform recording. This is key in reducing all the noise in the data and potentially increase the accuracy of prediction from analysis of such data. From my previously work at ILRI Nairobi, I recall a platform for dairy recording was in beta phase, am not sure if this platform is still in use. One solution would be to set up a central database where farmers send a FREE short text (from any cell) with performance recording data. This can either be interactive SMS or Structured SMS. In both instances, it involves a series of commands initiated by the farmer entering either his national ID/ farm id, then selects the animal(s) and records the performance and any other metadata deemed necessary. This eliminates data entry errors, and need for major data editing cost. The best traits to consider first would be production traits (moderate to high heritability, easy to record).
      As pertaining to GS, there is need for a customized chip specifically for the Bos Indicus species, the current available SNP bead chips explain less than 45% of the variation of the tropical breeds. This means that even if one does GS, they will only be trying to capture less than 45% of the variation. This is very far from would be ideal since complex traits are influenced by many genes each with a small effect, as such, many genes that are not yet discovered in our populations would, probably, be overlooked. With the data already available in our research stations and partner institutions, and with partnership of SNP bead chip companies, we can easily develop a chip specifically for our breeds (or borrow a leaf from India who have developed a lot in the last decade in this field)
      At the end of the day, we have to come up with solutions that incentivize the farmer to participate in such programs, such incentives could be Cow performance certificates from accredited breeding organizations and loans in form of cows, just to name but a few.

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

        Thanks Andrew. Note that in relation to paper-less data recording, it is possible to use new tools create for mobile devices - such as open data kit - to collect data along the lines you suggested. We have been testing this - along with provision of feedback to farmers based on their data.

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

        A customised SNP-chip is one potential outcome of the genomics reference resource - further discussions on the potential genomics reference resource are taking place under 'discuss building'

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    • Profile gravatar of Kabuni Thomas
      Kabuni Thomas August 18, 2016 Reply

      l agree that we have a potential genetic resources to be exploited from our livestock although we have not effectively exploited enough these potentials for the improvement of livestock productivity and livelihood of the poor rural farmers. The inability of these failures is contributed by a number of factors but the most important ones include; animal factors (herd fertility problems, and inbreeding etc.) and human factors (inefficient breeding programmes and breeding policy). As already discussed previously, it should be careful noted that until when the underlying issues above are well tackled and properly solved is where we can now realise the best outcomes resulted from the application of genomic tools. The better performance produced from dairy cattle is because these animals have less fertility and inbreeding problems as compared to the beef cattle. Again much genomic works/researches/projects have been conducted using dairy cattle compared to beef cattle. Therefore, it is now the right time to intervene in the beef cattle industry which accounts high contribution to the livestock sector and improve the performance of beef cattle owned by majority of our pastoral and agro-pastoral farmers using genomic tools.

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    • biomickwatson August 18, 2016 Reply

      Hi Charles

      I totally agree that we must focus on benefits to the farmers, and as you say, profit is an important driver. I also agree that the aim cannot and should not be to create "high cost products" - as you say the market is not there (and nor should we expect people to pay more). Yet crosses of African breeds with western breeds show large performance increases; if we can only capture and understand the genetic basis for those increases, then we can perhaps influence the local breeds.

      As you rightly point out, there are two approaches - using reference populations in government institutions, or a distributed approach using farmers. The former is more expensive; the latter is harder but engages more people. I think what's clear is we need good livestock recording and good phenotypes

      Cheers
      Mick

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

        .... though at present there are few (if any) government institutions with sufficient animal numbers and recording capabilities to generate the needed data for reference populations

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

      HI - yes I agree that there has been a lot of confusion related to the term superior - many people think of this only in the terms of e.g. milk yield or growth rate, rather than also adaptability to harsh environmental conditions, disease resistance etc. Breeding animals is suit the needs of the production system / environment they are in, is very key.

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

      Yes I agree that increased productivity requires a 'intervention package' approach - jointly addressing genetics, feeding, and health-care amongst others. Also, that farmers need access to markets, a voice in value chain governance etc.

      I would like to hear more from experts in genomic selection on their thoughts in relation to size of reference populations, and level of ongoing phenotypic recording.

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    • Profile gravatar of Raphael Mrode
      Raphael Mrode August 19, 2016 Reply

      I just want to comment on the point made by Charles in terms of basing GS on data from government Institutions and few producers initially. Actually this is a very good approach and one may regard reference population from government institutions and few producers as a nucleus herd of some sort where more detailed phenotyping could be implemented as well. However, if these reference population animals are managed differently from the small holder systems, then we may have an issue of GxE to address. Therefore it will be necessary a deliberate attempt be made to include records from the small holder system. Actually we are developing a proposal for goat improvement based on this concept in some Africa countries. If you are interested in being a part, let me know

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      • Profile gravatar of Abdulmojeed Yakubu
        Abdulmojeed Yakubu August 20, 2016

        Hello Raph! Please I am highly interested in your proposed goat project. Please do not forget to include Nigeria.

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      • Aliyu umar August 20, 2016

        I joined the appeal to include Nigeria

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  4. Profile gravatar of Baitsi Podisi
    Baitsi Podisi August 17, 2016 Reply

    My comments are based on my past experience as a researcher in Botswana and my involvement in management of farm animal genetic resources at national and international levels.

    My take is that genomic tools are not a silver bullet. Therefore 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. Record keeping is quiet a challenge for most farmers. Tracking the mating is also a headache especially in communal grazing systems where bulls of different breeds can mate with cows with no control. The dairy sub-sector has a higher chance of making progress because of the ease of implementing recording and of managing breeding through A.I.

    Otherwise within herd selection programmes in Government Research stations have limited chance of success due to no strategies of involving the communities to sustain the genetic progress e.g. in open nucleus set-up.

    While A.I. is generally performs well in most settings for dairy & beef systems, MOET results remain very poor. Improving capacity for MOET is necessary for breed multiplication.

    Given the high costs of past molecular characterization studies related to breed diversity in some developing countries. Such resources would have been better spent on phenotypic characterization to support development of breed standards and designing of breed selection programmes which are absent in most developing countries.More over because often such studies were undertaken with very limited number of markers due to budget constraints.
    Current genomic tools offer a ray of hope but the basic infrastructure for conventional animal performance recording are still necessary.

    Baitsi

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

      Yes excellent points.

      I completely agree that well-designed, robust and sustainable breed improvement programs are absolute requirements (without that, genomic selection cannot add value), and that many issues need to be addressed to achieve this - institutional arrangements, farmer incentives, delivery systems etc.etc.

      Given your experience, what are your thoughts on how we can encourage donors and stakeholders to invest in phenomic characterisation?

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    • Profile gravatar of Kabuni Thomas
      Kabuni Thomas August 17, 2016 Reply

      Thanks Baitsi you have said it well, however to my opinion ineffective application of genomic tools is constrained by inefficient breeding programmes and policies in our African countries and that is why it is difficult for the implementers to disseminate genomic technologies to our farmers, because farmers have not been hold accountably and been bound by these programmes and policies. Therefore, in situation like this serious reformation has to be undertaken for the transformation of our African Livestock Production Systems.

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    • biomickwatson August 18, 2016 Reply

      Thanks Baitsi. You mention that "record keeping is quite a challenge for most farmers". What can we do to make it less challenging?

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      • Baitsi Podisi August 18, 2016

        It depends on what type of data needs to be collected. For growth traits (live weights, birth, weaning, yearling etc) which involve animal handling requires equipment (weigh scales), infrastructure (crushes) and concerted human effort especially with beef animals which tend to become restless when handled. The cattle owners need to see the value of such tedious work which calls for farmer education and supporting legal framework for them to reap the benefits of producing performance tested animals. With credible bodies to accredit the quality of identified elite animals justifies the investment by farmers.

        About 10yrs back we operated a pilot beef cattle performance recording and evaluation scheme in Botswana. We used mobile scales drawn behind a 4x4 van in sometimes sandy terrain and a requirement for a farmer to have a crush to participate in the scheme. Ultimately farmers were encouraged to buy their own scales or bear the inconvenience of sharing a mobile scale.

        Cheaper tools such as weigh bands and the use of ICT tools to collect and send data offers a convenient option which is not readily harnessed due to low literacy among farm workers who are left to tend the animals in remote locations with low mobile phone network penetration. A proliferation of phone Apps offers a good opportunity to facilitate data collection. Provision of farmer training and timely feedback to farmers is paramount to get buy-in.

        Baitsi

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  5. Profile gravatar of Kabuni Thomas
    Kabuni Thomas August 17, 2016 Reply

    Among Animals' Assisted Reproductive Technologies (AART) (eg. AI, MOET, Semen sexing, Gene cloning, etc.), AI stand to be the best way of applying genetic information due to its potentiality and positive impact to the poor rural African farmers. The uniqueness/specialities of AI as compared to other AART is that: The uptake of AI to farmers is simple and easy to practice, it is not very expensive, and easy availability and accessibility of AI technicians. However, for better performance AI programmes should include oestrus synchronisation protocols because of fertility problems (poor ovulation and irregular oestrus) in our herds which then will tend to maximize the reproductive performances of our cattle. To make the AI programme simple and more effective , FTAI (Fixed Time Artificial Insemination) can be used as a substitute of normal AI (Artificial Insemination) simply because in FTAI there is no need of detecting oestrus prior to insemination instead insemination is done based on fixed time. Under this regime farmers can be sure of increasing their productivity (i.e. increased pregnancy and conception rates, calving rates, increased weaning rates, and reducing calving intervals etc.) within their herds. Hence the livelihood of the farmers will be improved as well in general.

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

      Thanks. We have a project here (ILRI) looking at scaling of fixed-time AI. Also, we are testing a recording and feedback tool for AI service providers that is mobile-phone based (and aimed at increasing AI success rate, as well as improving service provision)

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  6. Mizeck Chagunda August 17, 2016 Reply

    Dear Karen and All. Firt thanks for this initiative and for moderating the discussion. Just like your example of the work you carried out in Senegal, we (Univeristy of Rwanda and SRUC of Scotland), are currently doing some work in Rwanda with smallholder dairy farmers through a PEARL project funded by BMGF. Due to lack of pedigree information in most cases, wewill use genomic approaches to assign breed-types to individuals. I strongly agree that we need to keep recording the phenotypes. I think that one thing we need to seriously think about on the continent is the aspect of stoping to consider individual projects as stand-alone activities. We need to start thinking of communities of projects and everything we collect some data or consider traits to measure, we should think of how the individual project data sets can contribute to the community without compomising the ability to address the individual projects' specific objectives.

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

      Excellent points, and great that genomic information will be used for breed composition also in Rwanda dairy

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

      What is the underlying objective of the project - is it a breed comparison?

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      • Mizeck Chagunda August 17, 2016

        The underlying objective is not breed comparison per say. Its just part of it. We are working with farmers that received cows through the One Cow per Family Programme (Girinka). As you might be aware, in such programmes the focus is on passing on the first heifer to another farmer. One of our questions is, can we start identifying the bull calves as a source of germplasm and breeding lines? Given the different breeds and their crosses that are used and sparse pedigree data, genomic approaches will help us in this process. I hope this explains it in a nutshell.

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

    And please don't forget to participate in the survey - use the 'take survey' button on the top bar

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  8. karenmarshallilri August 17, 2016 Reply

    Hi All. Thanks for the discussion to date on topic 1 - current applications of genetics or genomics to African livestock systems. We have collected a few examples of these, but please keep contributing. I will summaries all examples at the of the forum.

    I would also like to add a new discussion topic - 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?

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  9. Profile gravatar of Kabuni Thomas
    Kabuni Thomas August 16, 2016 Reply

    In most cases farmers fail to restore the fitness of animals lost during inbreeding as a result of this, it affect animals' ability to survive, reproduce, and contribute progeny to the next generation. The impact of fitness on profitability of livestock/cattle production enterprise is observed in the sense that, a unit increase in genetic gain obtained in number of calves weaned influences profit to a great extent than increases or similar magnitude in growth traits. This is manifested mostly in extensive tropical production systems where calving rates are very low. Therefore, immediate and rapid improvement of low heritable fitness traits is advocated because it has been observed to be feasible by exploiting heterosis through crossbreeding.

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  10. Profile gravatar of Kabuni Thomas
    Kabuni Thomas August 16, 2016 Reply

    Kasonta J.S. and Nitter, G. 1990. Efficiency of nucleus breeding schemes in dual-purpose cattle of Tanzania. Animal Production. 50(2):245-251.

    Katyega P.M.J. 1987. Mpwapwa cattle of Tanzania. FAO/UNEP Animal Genetic Resources Information Bulletin. 6:23-26.

    Mchau K.W. 1988. Production characteristics of Mpwapwa cattle. 1. Lactation yield and length. World Animal Review 65:11-17.

    Das S.M., Mgheni M., Msechu J.K.K. and Mpiri D.B. 1989. Association between milk production and reproductive efficiency traits in Mpwapwa cattle and their crosses. TSAP Conference Series (Tanzania). Tanzania Society of Animal Production, Morogoro. 13:167-182.

    http://agtr.ilri.cgiar.org/index.php?option=com_content&view=article&id=116&Itemid=132

    Karen these are some of the published papers and link where you can get the information of Mpwapwa breed cattle, however, expect to receive some more recent woks done on mpwapwa breed cattle, although more papers and project information found in Tanzania Society of Animal Production (TSAP) have not been published online.

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  11. Profile gravatar of Kabuni Thomas
    Kabuni Thomas August 16, 2016 Reply

    Sure Karen l will let you have the link whereby you can read works and projects which have been done on Mpwapwa breed. Preferably as soon after this.

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  12. Profile gravatar of Kabuni Thomas
    Kabuni Thomas August 16, 2016 Reply

    The success of developing tools for record keeping and feedback to farmers will rely on how famers are aware of the importance of record keeping in the breeding programme to be established in the sense that what are the breeding goals?, breeding objectives?, breeding criteria?, breeding strategy?, and reproduction method?. More importantly, record keeping scheme should have a monitoring scheme mainly to trace genetic progress/gain of the programme and check if the targets have been realised/met.

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

      Thanks Kabuni. How do we engage with the farmers and get them on board? How do we convince them that the effort is worth it?

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      • kabuni thomas August 17, 2016

        Best farmers have to be selected and get involved in any breeding programme to represent the rest of the farmers, also these projects have to located on-farm where farmers feel a sense of belonging/ownership and will effectively participate and cooperate to implement the objectives of the programme. Therefore, once the programme is successful it will be easier for the other farmers to adopt the it.

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    • Karen Marshall – forum organiser August 17, 2016 Reply

      Also, importantly, how farmers can improve their management practice based on record keeping. This, I feel, is likely to be a key incentive as it is immediate

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

      Yes and the record keeping could also inform farm management decisions - which I think is a more immediate incentive than monitoring genetic progress.

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  13. Profile gravatar of Kabuni Thomas
    Kabuni Thomas August 16, 2016 Reply

    As a researcher working with Tanzania Livestock Research Institute (TALIRI), we managed to create a dual purpose breed of cattle (for both meat and milk production) which is a synthetic/composite breed mainly composed of five different eco-types/lines namely; TSZ, Boran, Ayrshire, Sahiwal, and Red Sindhi. This breed was named Mpwapwa breed a name of a place where it was created. The benefits of this breed is that, it has the ability to withstand harsh tropical climatic conditions, resistant to diseases and has higher milk and meat production potentials compared to other indigenous cattle breeds. At the moment strategies are underway for the multiplication and distribution of Mpwapwa breed cattle to the farmers in order to improve their herd and livelihoods. However, the other cattle breeds in the country needs to be upgraded as well based on the interaction of their genetic composition and the environment.

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

      Thanks Kabuni. Is there a reference where I can read more on the Mpwapwa breed?

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  14. Kehinde Soetan August 16, 2016 Reply

    I think its time to have a database on genetic characterization of indigenous African cattle breeds. This could help in bringing out their good traits like disease resistance, good milk yield and other undiscovered/untapped resources. This will be a step further in selection of required traits and improving protein intake of African countries and also reducing poverty.

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

      Thanks, and also see the 'discuss building' page, where this is more discussion on this topic

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

      I am interested in your opinion about how best to make this type of data available and usable to African scientists

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

      Hi - Thanks for your comment. Please expand on what you would like debated - as this is a great forum for that.

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  15. 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 - 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.

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

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  16. Profile gravatar of Kabuni Thomas
    Kabuni Thomas August 16, 2016 Reply

    In most of our African farmers, the issue of getting quality bulls or quality semen to be used during the breeding season is another factor limiting the success of applying genomic or genetic information to our livestock production systems. As we all know that before implementing any breeding programme it is advised to have quality bulls or semen simply because heterosis/genetic gain can not over-come low quality genetic inputs. Therefore,that is why the quality of progeny will always depend on the quality of parents.

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    • Profile gravatar of Raphael Mrode
      Raphael Mrode August 17, 2016 Reply

      Thanks Kabuni for the comments. Usually the provision of semen from bulls of high genetic merit to farmers is better managed by AI companies. We lack this infrastructure in most Africa countries. Currently, there is a project in Tanzania and Ethiopia exploring the possibility of establishing a public-private efficient AI service to farmers. This could provide a framework for other countries

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

    In Cameroon, I worked on four indigenous cattle (Arab Shuwa, Ngaoundere Gudali, Namchi and White Fulani) to assess their genetic diversity using microsatellites.That study demonstrates that the genetic diversity of Cameroonian indigenous cattle seems to have been affected by gene flow between breeds. Therefore,adopting effective breeding management practices will facilitate the conservation of those breeds and preserve their special characteristics. I want to emphasize on Ngaoundere Gudali because of its exceptional potentialities for milk and meat productions.Unfortunately, without a good policy from decision makers on AnGR in Cameroon, the problem will be difficult to overcome.

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

      Thanks! Do you know what the milk potential of the Ngaoundere Gudali is?

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

      How do we influence the policy makers?

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  18. Profile gravatar of Kabuni Thomas
    Kabuni Thomas August 16, 2016 Reply

    Although there seem to be much work being done on the phenotypic characterisation of our livestock, nevertheless we have achieved low genetic gain or progress and this is because we have done very little work on the genotypic characterisation which could actually assist us in correctly identifying the genetic potential of our animals and making right decisions in our established breeding programmes by correctly selecting and matching the genotype of cows and sires for genetic improvement and better performance of our animals.

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

      Yes by using genomic information in breeding program (in lieu of pedigree, for genomic breeding values) we have an opportunity to overcome some of the past constraints - however continued phenotypic collection will be critical as part of that, as without these records the use of the genomic information is limited.

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

      Indeed - it's very clear we need strong genotypic data alongside well defined phenotypic data from the same animals.

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    • Profile gravatar of Adamu Isa Mani
      Adamu Isa Mani August 17, 2016 Reply

      Genomic selection will be difficult to implement in African continent because of the high cost of sequencing in addition to poor record keeping attitude of farmers. Worst still, where researches are conducted at stations by institutions, farmers are not usually involved, and this, makes it hard for the farmers to adopt whatever comes from the research stations. If farmers can be persuaded to keep records as well as involving them and their goals in researches conducted at stations, we may achieve something in that direction.

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      • Charles Kariuki August 17, 2016

        Adamu, genotyping is much cheaper compared to progeny testing in dairy cattle!

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

        Yes in developed country dairy systems the use of genomic selection has reduced the cost of progeny testing. But do we have this evidence for African systems that are not analogous? I think more cost:benefit modelling studies would be useful to this end - particularly on the issue of what scale of operation is required.

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  19. Profile gravatar of Roy Kimotho
    Roy Kimotho August 16, 2016 Reply

    I think we should have a genetic database of all African domestic animal, that would help scientists to have a molecular tool to target animal diseases and the emerging and re-emerging animal diseases. At the moment such information is not widely available to all scientists and also such information is on a limited number of farm animals.

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

      I agree and I would be interested in your opinion on how best we could make such data available and usable by the African scientific community

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  20. kabuni thomas August 16, 2016 Reply

    Formation of breed (sire-dam) complementarity, creation of synthetic/composite breeds, and exploitation of heterosis are examples of some of the direct application of genomic or genetic information achieved mainly through crossbreeding and selection as genetic improvement techniques (breeding strategies) to African livestock production systems. However, these benefits of genomic or genetic information have not been successfully exploited by our farmers due to fact that most farmers lack precise knowledge of breeding, cultural and social-economical barriers as well as the level of development and infrastructure which have impaired the introduced breeding programmes in order to harness the genetic potential of our indigenous livestock/cattle. Instead on the other hand it is clearly observed that most farmers have no defined breeding programmes and as a result of this, they have practiced inbreeding for quite a long time to an extent of deteriorating heterosis and fitness in their herds. Record keeping and pasture availability also seem to be a problem to most farmers to achieve successful breeding programmes. Therefore, the existing identified constrains above should be marked as areas for intervention for successful application of genetic information to our African livestock production systems.

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

      Yes, the constraints you raised on livestock productivity in general, and animal breeding in particular, are key and all need addressing. We are working for tools on record-keeping and feedback to farmers using devices such as mobile-phones, which look promising

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      • Gilbert August 17, 2016

        indeed Karen, unless farmers see the value of what they are recording for, their involvement in record keeping might be compromised. The technology ought to help these farmers see an immidiate value for their records.

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

      I agree with this, so how do we do this? How do we engage with farmers and convince them of the need to engage with our efforts?

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

        To this end, I would like to see a study on farmer incentives for engaging in recording schemes - we are working on the assumption that feedback to farmers (based on information they have submitted) that assists them in management decisions (health-care, feeding, breeding etc.) will provide this incentive, but that is yet to be well tested

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  21. Oladeji Bamidele August 16, 2016 Reply

    The most significant application of genomics in livestock production systems (swine, cattle, poultry) in NG has been in disease diagnosis and characterization of animal disease pathogens e.g ASF, CBPP, Tryps etc. The National Veterinary Institute in NG has been championing this with huge success in improving livestock health. In recent times there has been some genetic & genomics studies conducted on heat tolerance & Productivity (i.e. growth, development) using the local cattle breeds although these are yet to translate to actual impact. The genetic improvements in cattle has been largely limited to the private dairy farms (Shonga, WAMCO etc). Those farms have successfully bred Holstein*White Fulani (Bunaji) and Jesse*White Fulani for milk production. I know the National Veterinary Institute initiated a breeding programme years ago to develop an adaptive but highly productive dairy breed using the Holstein as a base for the Whitefulani/N'Dama. This was a laudable project but it wasn't successful and as at 2004, only one cross bred was available and the records gone. The West African Milk Company (WAMCO) an affiliate of FrieslandCampina recently launched a project aimed at developing the smallholder dairy production system in NG. Part of their objectives is to improve the local dairy breeds/develop a 'better' breed. For such projects, having a genomic reference resource for African cattle breeds will guide their choice & application of genomics.
    I think the limitations to the successful utilization of genomics to improving livestock and in particular cattle may not be unrelated to the inadequacies in both human (skill/capacity) and financial resources as well as the political will to sustain such initiatives.

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      Karen Marshall - forum organiser August 16, 2016 Reply

      Thanks Oladeji, and I fully agree that a supportive political environment (amongst other factors) is key to sustaining breeding initiatives, whether they are utilising a genomic approach or not.

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      Mick Watson August 17, 2016 Reply

      With the characterisation of pathogens you mention, did this lead to anything useful e.g. better vaccines or better intervention strategies? How do we improve our ability to tackle disease?

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

        Yes, this has improved the vaccine production with actual impact as most of the vaccines being used for poultry & cattle are produced locally. A recommended minimum standards for bio security especially for diseases like ASF, AI has also being adopted.

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    • Aliyu umar August 17, 2016 Reply

      NAPRI/ ABU is having a programme for local farmers to improve milk production through crossing fresian to Bunaji or white fulani since late 1960s and the success is much to explain their quite a lot of publications in line with that. NAPRI has Beef research programme, dairy research programme and Animal reproduction and artificial insemination programme working together to desiminate technologies and breeding bulls for farmers in Nigera. Beef research programme has out station in Talata mafara at Zamfara state mainly for research using Sokoto gudali breed and it was reported to be the breed of choice for beef ( Madziga et al. , 2014 , shehu et al ., 2014 etc. ). Like wise white fulani was evaluated to be a dual purpose breed for milk and meat production. The dairy stock of NAPRI composed of Friesian-Bunaji and they are giving an excellent result ( 20L/ day).

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        Karen Marshall - forum organiser August 19, 2016

        Great to hear of these activities are the link or genetic improvement to dissemination programs.

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

    I am an example of use of use of genomic information in relation to a project on dairy cattle in Senegal. We wanted to compare the productivity and household profit of keeping different breeds and cross-breeds of dairy cattle, and had monitored more than 3000 animals over a 2 year period to this end. However we were unable to assign a breed-type to individual animals due to lack of pedigree recording, so instead used a genomic approach to do this (based on 50k SNP-chip information). This worked well. and results (see https://cgspace.cgiar.org/handle/10568/72865 for a result summary) will be shared back with decision makers on AnGR use in Senegal, for evidence-based decision making.

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  23. Profile gravatar of Raphael Mrode
    Raphael Mrode August 16, 2016 Reply

    It might be useful to kick this topic by briefly looking at the application of genetic information to African livestock production systems initially and gradually move on to application of genomic information. In this respect, I am aware that there has been a lot of cross breeding in several livestock species in Africa or may be some community breeding programs. Can people share some of such experiences in terms of success or otherwise?

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

    Domestication followed by breed formation and selection schemes has allowed the formation of very diverse livestock breeds adapted to a wide variety of environments and with special characteristics. Although most of the indigenous African cattle breeds have been identified, the majority of African cattle populations remain largely uncharacterized. Nigeria, for instance, is endowed with many cattle breeds having taurine and indicine blood. Among the most popular indigenous breeds of cattle are Bunaji, Sokoto Gudali, Rahaji, Kuri, N’Dama and Muturu. While considerable efforts have been made to characterize them phenotypically, little attempts have been made in the application of genomic techniques. Genomic application especially in the area of genetic diversity/population structure and pathogen detection seems to have better attention in goats (see the work of Okpeku et al., 2011; Sanni et al., 2013; Adefenwa et al., 2013; Yakubu et al., 2013, 2014, 2016; Yakubu, 2015; Ojo et al., 2015; Ajibike et al., 2016; Udeh, 2016; Awojobi et al., 2016) compared to sheep (Agaviezor et al., 2012a and b; 2011Ajayi et al., 2014) and chicken (Adebambo et al., 2010; Adeleke et al., 2011; Olowofeso et al., 2016). Few studies have also been carried out on cattle in the area of molecular genetics (diversity, structure and pathogen detection) and were skewed to particular persons and institutions (see published work of Takeet et al., 2013; 2016a,b and c) and PhD thesis of Mukasa (2014). Most of the genetic characterizations of cattle are in their infancy, and there appears to be no published work on the use of genomics for livestock breed composition, gene discovery, traceability and in breeding programs in Nigeria.

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    • karenmarshallilri August 16, 2016 Reply

      Thanks for starting this discussion, and your detailed overview of the use of genomics on livestock in Nigeria!

      Do you know if the work done on diversity / population structure, or pathogen detection, translated to impact on the ground (e.g. improved cattle productivity)

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      • Profile gravatar of Abdulmojeed Yakubu
        Abdulmojeed Yakubu August 16, 2016

        Thanks Karen. Most of the genetic characterization studies done in Nigeria have been station based and not community based as eearlier indicated. They are products of the research activities of some academics who are desirous of impacting on the farmers, but lack the financial backing to do so. The only major breakthrough is in the area of crossbreeding using artificial insemination where the National Animal Production Reseach Institute (NAPRI), Shika-Zaria, Nigeria has been able to come out with animals with improved productivity. The institute to the best of my knowledge is the apple eye of the Nigerian Government towards improved cow milk production especially at the rural level. This plan s still at the policy and not implementation stage.

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      Mick Watson August 17, 2016 Reply

      Hello! I think this is the kind of project and the kind of idea that all researchers interested in farm animal genomics would be interested in. There are two key questions: (i) what barriers exist to the genomic characterisation of Nigerian cattle and (ii) how do we translate the results into real impact for people?

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        Abdulmojeed Yakubu August 18, 2016

        Thank you Mick. Funding is the greatest obstacle. Lack of basic molecular equipment and facilities for cutting-edge researches is another while there is dearth of experts in the field of genetics and genomics. Also, inconsistency in livestock policies by successive governments have made some good projects to collapse midway. Good research products can only get to the farmers successfully if there is a well coordinated public-private partnership. However, at a small scale, research institutions through extension services could make research findings available to the farmers.

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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 applications of genomics to cattle in Africa.

    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: 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.

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    • Chanda Nimbkar August 18, 2016 Reply

      The performance recording (prolificacy, weights, measurements and milk yield) we (Nimbkar Agricultural Research Institute) have done of Osmanabadi goats (total around 1000 does in six villages in different regions of Maharashtra State over six years) under a project of the Indian Council of Agricultural Research has shown us that usable genetic diversity/superiority is out there and the problem is to detect it reasonably accurately in the absence of records/pedigrees. It would be immensely useful if genomics could provide markers for such detection so that analysis of a DNA sample could indicate the genetic superiority of an animal for the trait of interest. The subset of animals whose DNA samples are to be collected, can be decided based on anecdotal evidence or for example, milk records collected at a competition.

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

        Great to hear about experiences from India!

        Yes what you propose would be immensely beneficial. Can you say more on what India is doing towards building the required reference populations (with both genotyped and phenotyped animals) needed for this?

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