[For further information on the Electronic Forum on Biotechnology in Food and
Agriculture see Forum website.
Note, participants are assumed to be speaking on their own behalf, unless they state otherwise.]
Sent: 24 June 2005 13:22
Subject: 79: Re: Simpler techniques for molecular characterization of forest trees
This is D. Vijay again
This is in reply to Alice Muchugi's message (message 77, June 23). I agree that random amplified polymorphic DNA (RAPD) is comparable with the other techniques but its important drawback is the absence of reproducibility, as the technique itself implies it is a random technique and its sensitivity to chemicals and conditions is also another factor. In general, the decamer primers used in RAPD have a lower annealing temperature thus in such low stringent conditions the reproducibility is doubtful. With the advancement of technology, new techniques which are more robust, reliable and reproducible have been developed and we have to adopt them. Even the articles which Alice Muchugi mentioned have references for the non reproducibility of RAPD markers (e.g. Neale and Harry, 1994; Demeke et al., 1997; Karp et al., 1997) and the excerpt from Garcia et al, 2004, Genetics and Molecular Biology, 27, 579-588 “Our results indicate that, apart from the RAPD markers, the other DNA marker systems provided consistent information for diversity studies on tropical maize populations and produced genetic distance estimates which were in good agreement.” Thus, this is the main reason why the leading journals are not accepting the RAPD data. [In RAPD analysis, DNA primers of an arbitrary 10 base pair sequence (decamer) are generated and the polymerase chain reaction (PCR) is used to amplify DNA segments in the genome that are flanked by sequences which anneal (pair with) to the primers...Moderator].
I agree that funding is the main problem for scientists in the developing world but use of outdated technology because of its low cost is not the answer. Here, we should take the help rendered by several international organisations to the developing world. Another important aspect is the concentration of resources rather than their excessive distribution - like use of common laboratories/facilities rather than individual laboratories, so that we can really work out something productive.
Coming to the conservation of forest genetic resources, as E.M. Muralidharan said earlier in his message (message 67, June 21) the usage of DNA banks could be helpful along with other methods of conservation like seed banks, gene sanctuaries, circa-situ and ex situ conservation (Alice Muchugi, message 68, June 21).
Vijay D., PhD
International Plant Genetic Resources Institute
IPGRI Office for South Asia
NASC complex, Pusa Campus
New Delhi - 110 012,
E-mail: vijaydunna (at) gmail.com
References used in text:
- Neale DB and Harry DE (1994) Genetic mapping in forest trees: RFLPs, RAPDs and beyond. Ag Biotech News Inf 6:107N-113N.
- Demeke T, Sasikumar B, Hucl P and Chibbar RN (1997) Random Amplified Polymorphic DNA (RAPD) in cereal improvement. Maydica 42:133-142.
- Karp A, Edwards K, Bruford M, Vosman B, Morgante M, Seberg O, Kremer A, Boursot P, Arctander P, Tautz D and Hewitt G (1997) Newer molecular technologies for biodiversity evaluation: Opportunities and challenges. Nature Biotechnol 15:625-628.
- Antonio A.F. Garcia, Luciana L. Benchimo, Antônia M.M. Barbosa, Isaias O. Geraldi, Cláudio L.Souza Jr. and Anete P. de Souza. 2004. Comparison of RAPD, RFLP, AFLP and SSR markers for diversity studies in tropical maize inbred lines. Genetics and Molecular Biology, 27, 4, 579-588 http://www.scielo.br/pdf/gmb/v27n4/22428.pdf
Sent: 24 June 2005 13:27
Subject: 80: Re: Simpler techniques for molecular characterization of forest trees
Just answering Alice Muchugi's concern (message 77, June 23):
I suggest inter-simple sequence repeat (ISSR) techniques, as I did in my previous messages. It is more efficient, still cheap and it is not based on random selection of primers.
Dr Kioumars Ghamkhar
Centre for Legumes in Mediterranean Agriculture (CLIMA)
University of Western Australia
35 Stirling Highway
Crawley WA 6009
Voice: 61 8 6488 7120
Fax: 61 8 6488 1140
E-mail: kioumars (at) cyllene.uwa.edu.au
[For more information on ISSR markers, see Kioumars' message 28, June 9...Moderator]
Sent: 24 June 2005 13:31
Subject: 81: Re: Molecular markers - Populations the same? - Inbreeding
This is S.G. Tan, geneticist, Dept of Biology, Faculty of Science, Univ. Putra Malaysia.
With reference to message 71 (June 22) from Miguel Toro, I totally agree with him that inbreeding depression is a well known phenomenon. However, unfortunately many of our aquaculturalists seem to be unaware of it or choose to ignore it. They usually also do not keep breeding records. Thus, it is often a surprise to them when molecular typing results show that their problem stocks are inbred. After being shown the molecular typing results, then only will they follow the suggestion that they do outcrossing to improve their stocks. Such is often the reality on the ground level in developing countries.
Prof. Dr. S.G. Tan BSc.(Hons. Malaya), PhD. (Hawaii),J.S.M. (Malaysia).
Professor of Genetics.
Dept. of Biology,Faculty of Science,
Universiti Putra Malaysia,
43400 UPM Serdang,
email:sgtan (at) fsas.upm.edu.my
Sent: 24 June 2005 17:22
Subject: 82: Animal genetic resources - Documentation, evaluation, conservation and utilization
I am Mahmoud Abdel Aziz, Professor of animal breeding and genetics, Alexandria University, Egypt. This is my second contribution to the conference.
Work needed for the future:
The complete study of animal genetic resources involves documentation, evaluation, conservation and utilization. In developing countries, I assume there is no systematic efforts that have been made so far to ensure collection and conservation of animal genetic resources. I also assume that most research work has been conducted on experimental herds of research centers and universities. Experimental data are completely different from field data. Although the former should be more accurate and organized, they are small in number. Therefore, the results and recommendations obtained from experimental herds cannot be applied and generalized on field data. In my opinion, comprehensive breeding plans should be developed. These plans should broadly fall under the following functions: 1. Identification and classification of native breeds based on ecological, genetic and economic criteria. 2. Preservation and conservation 3. Utilization.
1. Documentation: There may be a great deal of information on the distribution, population number and production performance of the various types of livestock. However, much of this information is not readily available to research workers because it is unpublished or published in local documents, reports and journals that have a very restricted and limited distribution. It is imperative that this information be collected and collated in a readily available form to identify gaps of knowledge, and areas where research efforts should be maximized, to fully document productivity of local strains and to assess their adaptation to specific climate-management-production systems to ensure that such strains are not displaced by so-called improved breeds (exotic breeds and crosses) before their present or potential value is known, to allow research workers to know the extent of information in their area of interest, and hence, to minimize the chance of repetition and to allow planners and administrators to make rationale decisions with regard to national development programs to maximize rates of improvement. There is no room for complacency, and the need for action is urgent.
2. Evaluation: While documentation will provide basic information on the indigenous types of livestock, there is a vital need for comparative evaluation studies. The conditions under which such evaluation is made must be the normal environment. Further evaluation should be performed in a potential environment. Such conditions might be available on experimental stations or larger commercial enterprises. It should be noted that large enterprises are basically established on importing exotic breeds, with no attention given to native livestock. The evaluation experiments must be carried out to a properly designed and prepared plan. Evaluation must be made on total performance, including not only productivity measures but also reproductive rate, mortality and disease resistance. Overall economic merit should also be considered. Studies on biochemical genetic polymorphisms are one of the ways to study the population in order to express their genetic differences and/or similarities by detection of alleles that are genetically conserved during the evolution process. Based on the expected results, native animals can be judged, evaluated and then, morphological, conformation and production standards ought to be established for each.
3. Conservation: The task of conservation of livestock is very complex problem. In any developing country, I assume that 90% of the animals are owned by small farmers. In addition, socio-cultural conditions make the problem more complicated. Under these circumstances, it is necessary to identify individuals, families and groups of specific genetic importance. Individuals that show promise for selecting breeding should be conserved by appropriate means. They must be maintained in an adequate number in well managed units. Distinctiveness is a difficult quality to define. A breed can be defined as a population which conforms to stipulated standards, which breed true for type, and which is distinct from other breeds. There are no recognized measures of distinctiveness. There are two questions that need answers. Are local breeds worth conserving ? Are local breeds in certain region similar? Small farmers or farmers of limited resources are abundant in any developing country. They are easily visible. They are located in remote areas lacking the necessary infrastructure, and hence, the exposure to modern technology. There should be some consideration to the small farmers who keep the majority of livestock resources.
4. Utilization: In developing countries, there is not any breeding program operating nationwide for improving productivity of any livestock species. It is necessary to design breeding programs for that purpose. These programs require the rapid assembly and evaluation of large amount of information. Its full development depends on the evaluation of data processing machinery and analytical methods. However, the environment may adversely affect the design aspects in two aspects: a) There may be severe limitations to animal productivity by a combination of climate, nutrition, health, and management practices. b) The infrastructure which supports such programs is entirely lacking. Difficulties of cost, literacy, communication may greatly inhibit the consistent operation of these programs. Both aspects must be taken into consideration in designing the program. Improved local populations must be initiated from within. This naturally requires a domestic selection program. Any crossbreeding strategy may be required at some point in the program, but it must not replace it. The genetic model underlying the selection program requires a knowledge of heritabilities, genetics and phenotypic correlations, phenotypic variances and appropriate economic weights. A key element in the implementation of any selection scheme is the new breeding and reproduction technologies including, of course, artificial insemination.
Mahmoud Abdel Aziz
Department of Animal Production
Faculty of Agriculture
University of Alexandria
fassad9 (at) yahoo.com
[Further messages on this subject should focus more on the potential role that biotechnology can play for the characterisation/conservation of the animal genetic resources...Moderator].