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Agriculture see Forum website.
Note, participants are assumed to be speaking on their own behalf, unless they state otherwise.]
Sent: 28 June 2005 10:40
Subject: 88: Using different molecular marker systems
This is Ted Kisha in Pullman, United States, again.
First, I would like to thank everyone not only for the discussion of a universal molecular marker database, but on the subject of molecular markers for the estimation of genetic diversity in general. These two topics, of course, are inseparable.
I would like to say that ANY molecular marker data is useful, and no marker type should be discounted. It's true that random amplified polymorphic DNA (RAPD) markers have some problems with reproducibility. Any molecular marker system that is a multi-order chemical reaction is going to be subject to competition among annealing sites for primers. Problems can result from symplasty, repetitive DNA, or differences in the reaction conditions. This is a problem with AFLP (amplified fragment length polymorphism) also. It's not as noticeable using AFLP, because ignoring non-reproduceable, quantitative markers still leaves many more very strong, scoreable markers. I would ask anyone who has used AFLP to review their work. They will see that there is variance from gel to gel for every run. It is just so much easier to ignore this variability when there are so many more "good" markers to choose from. This problem is exacerbated when researchers use software to score gels, instead of an eyeball and some common sense. [The symplast is the continuum of cytoplasm within a plant tissue connected by plasmodesmata (fine protoplasmic threads that connect adjacent plant cells). Repetitive DNA is DNA sequences that are present in a genome in many copies...Moderator].
It is true that microsatellite data is more reproducible, and usually has a higher information content per locus, but the number of loci analyzed is limited by time and money.
Any marker system can also be subject to other problems like clustering about the centromere or telomere, or being in tight groups within heterochromatin. That's why the database should be curated, and a select "core" of markers, even within a select core of primer sets (AFLP), should be adopted for universal comparison. [The centromere or telomere are specific regions of the chromosome. Heterochromatin are regions of the chromosomal material that are stained intensely by certain dyes...Moderator].
I would also agree that it would be useful to compare at least two different marker systems for agreement in the resulting relationships.
I am going to pursue the establishment of a database locally, with hopes that it might someday be adopted on a larger scale. I would encourage anyone interested to keep in touch following this conference.
Thank you everyone,
Theodore J. Kisha
Washington State University
Pullman, WA 99164-6402
e-mail: kisha (at) mail.wsu.edu
Sent: 28 June 2005 10:46
Subject: 89: Biotechnology in animal genetic resources research - Philippines
I am Dr. Sonwright B. Maddul, professor at the Benguet State University in La Trinidad, Benguet, Philippines.
I fully agree with my compatriot, Emma Sales (Message 84, June 27), that much innovation is desired in less developed and developing countries when it comes to biotechnology, considering the huge investment that it requires. This is especially true in livestock research and development (R&D). While there are people trained in biotechnology, inadequacy of equipment in laboratories or the lack of it, has stiffled the progress in this field. Our University, being government-owned, does not even have a biotech lab for livestock. But this has not dampened our interest nor our spirit to do simple R&D on livestock. Since 2003, we have started The Animal Genetic Resources (TANGERE) Conservation Program which established the Highland Pig Farm and Native Chicken Farm. Our research included physical characterization of the native pigs and chickens found in the highlands of northern Luzon, and monitoring their productive and reproductive performance ex-situ. We have not yet done the molecular characterization due to absence of a lab. In fact, we are waiting for collaborators.
Dr. Sonwright B. Maddul,
Department of Animal Science,
Benguet State University
La Trinidad, Benguet,
smaddul (at) yahoo.com
Sent: 28 June 2005 10:55
Subject: 90: Re: Capacity building // Decentralised banks
This is Dr. Seetharam Annadana, India, replying to Kioumars Ghamkhar (Message 85, June 27):
Capacity building is a two way process between developed and developing countries. Developed countries have an arrogance that they know all, and their way is the way to do it. However, such attitudes have failed in really developing nations as a lot of socio-economic considerations have to be taken into consideration for any developmental activity. Developing countries are also complex. Sometimes they grumble saying the fund is not enough so why put an effort, otherwise they make unnecessary delays in moving files and getting approvals making the donor feel the recipient is not interested.
Both donors and recipients, I think, must work under some international framework and, if necessary, make use of a body for monitoring.
Dr. Seetharam Annadana
CTO: ASR BIOTEC and ASR HERBALS
Director Technical: AgriGrowMore (M) Sdn. Bhd.
71/2, 21st A Main, Marenahalli, JP Nagar,
seetharam (at) hotmail.com
Wageningen University: http://www.wageningen-ur.nl
Contract Research: http://www.plant.wageningen-ur.nl
Molecular Markers: http://www.keygene-genetics.com
Biologistics International: http://www.biologistics.us
ASR HERBALS: http://www.asrherbals.com
Sent: 28 June 2005 13:22
Subject: 91: Re: Biotechnology and genetic resources in war-hit countries
This is Edo Lin, independent consultant.
Janaki Krishna (Message 86, June 27) brings up the issue of the management of genetic resources in war and conflict. Although strictly speaking outside the scope of this conference, I would like to contribute to this topic as, in several parts of Africa and elsewhere, war and low intensity conflicts tend to become endemic and threaten not only genetic resource conservation but directly affect the livelihoods of millions of people.
In many developing countries, genetic resources conservation takes place in-situ by small scale farmers and is supported by seed exchange between individuals and communities (the informal seed sector). This system of conservation and exchange is based on trust and loyalty which is threatened when, through conflict, trust is destroyed, people and communities are,displaced, seed stores in villages are looted and crops in the field are destroyed. In addition conflicts may destroy (and have done so in several countries) institutional genebanks.
Participants interested in this issue and also the problem of genetic resource rehabilitation post conflict can find a free report at the IPGRI website: http://www.ipgri.cgiar.org/publications/pdf/245.pdf (660 KB). The 1997 report, by Paul Richards and Guido Ruivenkamp, entitled "Seeds and survival: Crop genetic resources in war and reconstruction in Africa", gives three detailed case studies concerning rice genetic resources during conflicts in Sierra Leone, Guinea Bissau and Liberia and proposes a reorientation of the rehabilitation efforts post conflict.
Ceres Consulting International
309, rue de Bombon
tel and fax: +33 164387844
e-mail: ceres.consult (at) free.fr
Sent: 28 June 2005 15:36
Subject: 92: Capacity and economic issues - Madagascar
This is from Xavier Rakotonjanahary, plant breeder at FOFIFA, a national research institute, Madagascar.
I followed with interest the debate on the role of biotechnology on characterization/conservation of crop, forest animal and fishery genetic resources in developing countries. I would like to contribute on capacity and economic issues.
Many people in their messages have emphasized the weak capacity of using biotechnology in characterization/conservation, in developing countries. It is understandable that, in general, national policy is poverty alleviation, food self sufficiency and increased agricultural productivity and that research activities are not a priority. However, characterization and conservation activities which are the basis for any breeding progam are included in the national research sector. It will take time for the developing countries to reach a level where biotechnology could be used as an efficient tool for this purpose. International organizations, like FAO, the World Bank and the international centers should have an efficient way to promote and support the application of biotechnology in characterization/conservation in developing countries. This could be done by organizing at the regional level some group trainings, workshops or seminars,...and by funding some projects. They also could play a role in disseminating information, give recommendations on how a molecular technique is suitable, simpler and low cost.
Public private partnerships in developing countries could play an important role, but only on the condition that characterization and conservation has an evident economic impact, which is not the case for the moment. In most cases, the private sector is more interested in genetic material from outside, which has proven better performance in the country of origin.
About weighting genetic differences with respect to non-genetic differences, the former should be ranked at a lower level because socio-economic traits such as culture, market value, degree of endangerment are more related to humankind, which is to be considered the top priority.
From my personal view, genetic differences for traits which have been under selection are also more important than genetic diversity at neutral loci, even for characterization and conservation purposes. The best combination is that there is linkage between adaptative trait or trait of economic importance and a molecular marker.
Before I end my contribution, I would like to address my appreciation to the moderator of the conference for providing an updated and insightful background and to all participants for sharing their experience or giving recommendation and useful comments.
National Center for Applied Research for Rural Development (FOFIFA)
BP 1690, Antananarivo, 101
E-mail: r.xavier (at) simicro.mg
Tel office 261 20 22 238 35
Mobile 261 33 12 060 08
Sent: 28 June 2005 16:18
Subject: 93: Re: Using different molecular marker systems
This is Glaucia S. Cortopassi Buso, from Brazil, again.
I agree with all of the observations of Ted Kisha (Message 88, June 28). Sometimes we don't have much time to choose or apply the best marker. In our lab, in some cases, we have to analyse the diversity of plants which were never studied before as fast as we can, because the site where these species are will be flooded. The faster marker is still random amplified polymorphic DNA (RAPD) and we think that if we take some precautions to choose the robust and reproducible bands (doing repetitions) and to perform an accurate data analysis (applying bootstrapping to check the confidence of marker number, etc) we have trustful results.
I agree that amplified fragment length polymorphism (AFLP) have the same problems as RAPD and it is more expensive and difficult to implement.
In addition to the case of flooding, we have many species for which simple sequence repeats (SSRs) have not been developed, and not enough funds for research, therefore we have used RAPD as a marker and the analysis frequently corroborates the morphological one, giving more confidence in our results.
I also agree with Alice Muchugi (Message 77, June 23) that renowned journals are refusing to publish studies with RAPDs and this may be harmful for the research with species that are not in the focus of developed countries where the best marker systems are developed and applied.
Glaucia Salles Cortopassi Buso, Ph.D.
Laboratorio de Genetica
Embrapa - Recursos Geneticos e Biotecnologia
Parque Estacao Biologica 70770-900
Caixa Postal 02372
Brasilia - DF
fone: 61- 448-4647
buso (at) cenargen.embrapa.br
Sent: 28 June 2005 16:29
Subject: 94: Use what the countries have to make decisions on conservation
This Alice Muchugi from Kenya, again.
If we address the application of biotechnology (especially of molecular marker technology) in developing countries, D. Vijay (Message 79, June 24) will agree with me that it is not possible in the near future to say that we will be at a par with the developed countries. His options of pulling resources together, as well as using laboratories of international organizations are okay (and I also suggested it previously). As Ted Kisha (Message 88, June 28) comments, every marker system has its disadvantages. My question is; With the unavailability of the two above solutions, and considering the threat to biodiversity, would it not be advisable to use what the countries have to make decisions on conservation? This can be combined with morphological traits as suggested by PK Gupta (Message 87, June 27).
We are lucky that, in Kenya, we have several international organizations with very good laboratories and our national research institutes have a few advanced equipments too. These have made a great contribution to the application of biotechnology in various fields of medicine and agriculture locally. However, I do know the problems being experienced by colleagues in other African countries as we interact while visiting these laboratories.
Finally, on pooling of resources, as several participants are suggesting: A good example is the Biosciences East and Central Africa (BECA; www.biosciencesafrica.org) facilities located in the International Livestock Research Institute (ILRI). I do hope that developing countries in other regions will, in future, have such a facility to help in the advancement of biotechnology.
PhD Research Fellow
Genetic Resource Unit,
World Agroforestry Centre (ICRAF)
PO Box 30677-00100
tel: +254-20-7224000 Ext 4273
email: a.muchugi (at) cgiar.org
Sent: 28 June 2005 17:46
Subject: 95: Characterization of genetic resources using molecular markers
This is from Hubert Dulieu, Professor Emeritus of Plant Genetics, University of Burgundy, Dijon, France. I have done developmental genetics studies on somatic mutations in plants (in vivo and in vitro) since the 1960's and molecular/population genetics since 1989.
Many messages concern the first topic of the conference: Characterization of genetic resources. This is an important point where DNA technology must be used. One of the problems is the repeatability among different labs. We agree with the observations that some markers (microsatellites, sequence tagged sites (STS), inter-simple sequence repeat (ISSR))) are more faithful than others (amplified fragment length polymorphism (AFLP) and random amplified polymorphic DNA (RAPD)). Unfortunately, microsatellites and STS, which are sequence-based markers, require more preliminary research: cloning, screening, sequencing and, finally, genetic mapping. Remember that fingerprinting kits are produced for human DNA that are used universally. Some biotech companies should be encouraged to produce kits for the most important species used in the world. Nevertheless, AFLPs are highly informative and can now be performed without radioactive elements for many actual applications of fingerprinting cultivars, varieties and species.
I would like to point out a property of hypervariable markers which does not seem to have been discussed by our colleagues (probably except P.K. Gupta, Message 44, June 13): Many molecular markers reveal intraspecific/populational polymorphism which is not highly correlated with performances nor with phenotypic characters. Indeed, the level of polymorphism in panmictic (random mating) populations revealed by microsatellites is so high (number of alleles per locus can reach 40 or more) that it leads to overestimations 1) of genetic distances and 2) of the part of polymorphism of interest for the breeders, i.e. concerning the regulatory/structural genes responsible for the realization of the characters/phenotypes. Molecular characterization of genetic resources used for breeding should be more pertinent if sequences from functional genes could be used, many of which are not identified at the DNA level today. Remember, however, that increasing databanks of expressed sequences exist, as well as complete genes from which primers can be chosen freely and applied to related species. Remember also that genetic distances can be calculated from phenotypic characters if the observer is attentive and able to correctly code the alternative forms of each character - I doubt that such distances should be less efficient than molecular distances for preparing the use of germplasm to be bred.
Emeritus Professor of Plant genetics,
University of Burgundy,
(personal address: 6, rue des roses, 21 110 France
tel : 0032 380 37 82 88).
hdulieu (at) u-bourgogne.fr
Sent: 28 June 2005 18:06
Subject: 96: Germplasm conservation and conservation of endangered species
This is from Hubert Dulieu, France, again.
Concerning the second topic of this conference i.e. conservation of genetic resources, it is necessary to distinguish between a) germplasm conservation and b) conservation of endangered species, which refers to population genetics.a) Germplasm conservation:
My opinion tends to remain simple and realistic: if a germplasm (associated or not with molecular data) cannot be maintained alive and reproduced normally in culture or at least in collections, its probability to be lost in a next future remains high (many species disappear as well as ancient cultivars), in spite of sophisticated processes used (in vitro culture, DNA banks, cryopreservation). Simply because the probability of technical problems, catastrophes, etc. is of the same order of magnitude as losses due to human destruction by abandonment or to environmental changes. Concerning DNA banks, I should prefer phage genomic libraries, relatively easy to prepare and to preserve, from which every gene can be isolated in the future. However, I am tempted to think that using more technology to try correcting counter-effects of misuses of technology (mainly the destruction of traditional agricultural systems), resembles the eternal promethean dream of humans, unable to resolve the crucial dilemma of pursuing the logics of the intensive production of consumer goods at the expense of the environment. This remark is not contradictory to the development of scientific projects for identifying characters (physiological, ecological, molecular) of resources species and varieties whose culture and use must be maintained and/or radiated in all the favourable countries possible.b) Conservation of endangered species:
Population analyses with highly informative neutral markers (namely microsatellites) should be recommended for endangered wild species (animals, fish, forest trees, etc.). Such studies should allow us to evaluate the genetic polymorphism which is necessary to maintain, in order to suppress or delay the risks of extinction. There are typical examples where bottlenecks have been detected by molecular markers, leading to decisions favouring protection. These very important applications of molecular biotechnology to population genetics and management are true for all countries. One single example: forest trees of indigenous species in Europe were subjected both to phenotypic counter-selection during their multi-secular history and efforts are presently encouraged to regenerate populations naturally. It must be demonstrated that such populations have maintained their genetic basis sufficiently large, both to maintain diversity and to apply directed phenotypic selection (two apparently antagonistic goals, except for forest geneticists). This must be done by molecular analyses of populations.
Emeritus Professor of Plant genetics,
University of Burgundy,
(personal address: 6, rue des roses, 21 110 France
tel : 0032 380 37 82 88).
hdulieu (at) u-bourgogne.fr