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Sent: 29 June 2005 09:21
Subject: 97: Conservation requires a long term commitment/p>
I am Made Sri Prana, senior researcher, R&D Centre for Biotechnology, Indonesian Institute of Sciences.
Being trained in conservation and utilization of plant genetic resources, I fully agree with the importance of genetic resources conservation of whatever organism it is (plant, animals, microbes) and appreciated the effort of my colleague Sonwright Maddul of the Philippines (message 89, June 28). However, I should say that even just for maintenance of the collection already requires sufficient amount of budget which is not always available in institutions of a developing country. Therefore, it is not uncommon to notice that the whole collection may gradually disappear due to lack of financial support or loss of interest from the boss.
I tend to believe that conservation requires a long term commitment (policy, human resource, funding etc) and certainly it should not be based on personal interest (except in an extreme case). Besides, experience tells us that conservation is best linked with a programme on utilization of the resources conserved. Otherwise, sooner or later, they will disappear simply because it is felt as a mere burden.
Yes, I agree that the key word is "collaborator" or collaboration. Please promote your programme and germplasms collection to the world who knows that at one time somebody from somewhere would be interested to collaborate with you. Let's cross our fingers.
Made S. Prana
PROSEA Network Office,
Research Centre for Biotechnology,
Indonesian Institute of Sciences (LIPI),
pran (at) proseanet.org
Sent: 29 June 2005 10:44
Subject: 98: Re: Characterization of genetic resources using molecular markers
This is Ted Kisha in Pullman, Washington, United States, again.
Hubert Dulieu (Message 95, June 28) brings up an important characteristic of molecular markers to which I had previously alluded (Message 88, June 28), and which has been the subject of considerable research (see K. Weising et al., 2005, DNA Fingerprinting in Plants: Principles, Methods, and Applications, CRC Press). They may reside in neutral, unexpressed regions of the genome, and even be clustered in these regions. I would like to emphasize again the need for a curated set of "core" markers (for each different marker technology) that uniformly and randomly sample the genome, especially in regions of euchromatin where the functional differences of diversity reside. More microsatellite primers are being developed using expressed sequence tags (ESTs) where these become available in GenBank. AFLP markers can be generated using PstI, which preferentially creates markers in unmethylated DNA. Markers should be mapped where possible to ensure uniform distribution.
I agree that measurement of functional diversity is the ultimate goal, but strict adherence to this goal where it may lead to extra expense or delay in germplasm characterization may be unnecessary. Since much of the genetic diversity is a result of adaptation within isolated environments, especially in wild, ancestral germplasm, there could very well be a high correlation between clusters identified by random molecular markers and unique functional characteristics. I believe that an inexpensive, high throughput technology should be the first and most serious consideration. Information from many loci, I believe, is preferential to highly diverse information from only a few loci.
Theodore J. Kisha
Washington State University
Pullman, WA 99164-6402
e-mail: kisha (at) mail.wsu.edu
[To give more details on points made in paragraph 1: Following the classic biology textbook of John W. Kimball, within a cell, the nucleus contains the chromosomes. Each chromosome consists of a single molecule of DNA complexed with an equal mass of proteins. Collectively, the DNA of the nucleus with its associated proteins is called chromatin. The density of the chromatin (that is, how tightly it is packed) varies throughout the nucleus. The dense regions are called heterochromatin (referred to in Message 88, June 28) while the less dense regions are called euchromatin. Heterochromatin is found in parts of the chromosome where there are few or no genes, such as centromeres and telomeres; is densely-packed and is greatly enriched with transposons and other "junk" DNA. Those genes present in heterochromatin are generally inactive; that is, not transcribed. Euchromatin is found in parts of the chromosome that contain many genes and the genes are active (http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/N/Nucleus.html). DNA methylation, where methyl groups (-CH3) are added to DNA, can directly or indirectly silence gene expression. AFLP markers are DNA markers generated by the amplification using the polymerase chain reaction (PCR) of fragments of DNA, cut using restriction enzymes (such as PstI). GenBank was discussed in Message 6...Moderator].
Sent: 29 June 2005 14:26
Subject: 99: Genetic diversity studies: Too much emphasis on markers
This is Miguel Toro, again.
Going back to the question of whether molecular markers can provide an 'objective' method to establishing the 'similarity' between breeds and an objective way of claiming that two breeds are or are not different (raised in several messages - numbers 63, 65, 66, 70, 75, 82, 89, 95, 96 etc.), I would like to point out the following:
If I understand correctly Hans Lenstra's message (nr. 70, June 21), genetic distance based on molecular markers are only partially informative because:
a) they do not take into account within-breed variability;
b) they can reflect or not phenotypic distances;
c) they can reflect or not ancient history.
Therefore it seems that at least three pieces of information are needed: phenotypes, markers and history (and common sense probably). However, I think that there has been too much emphasis on markers, probably because this information is much more easy to obtain. There are hundreds of papers on genetic distances but very few on phenotypic distances (could someone quote some paper on that?).
Miguel Angel Toro Ibanez
Departamento de Mejora Genetica Animal
Instituto Nacional de Investigacion y Tecnologia Agraria y Agroalimentaria (INIA)
Carretera La Coruna km. 7 28040 Madrid
Telf: 34 913476807
Fax: 34 913572293
e-mail: toro (at) inia.es
[To respond to Miguel's question, in Stephen Hall's recent book, "Livestock biodiversity: genetic resources for the farming of the future", he refers to a study where phenotypic information (morphology) was used to create phylogenetic trees. The study (Crepaldi, P. et al, 2001. Diversity in five goat populations of the Lombardy Alps: comparison of estimates obtained from morphometric traits and molecular markers. Journal of Animal Breeding and Genetics, 118, 173-180) considered phenotypic variability (estimated on the basis of six somatic measurements on 60-140 adult goats per Italian breed) whereas genetic variation was measured on the basis of 201 AFLP loci. Results showed that morphometric and molecular marker data produced unrelated distance values and different topology of UPGMA (Unweighted Pair Group Method with Arithmetic Mean) clusters...Moderator].