[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.]

-----Original Message-----
From: Biotech-Mod1
Sent: 21 June 2005 11:52
To: 'biotech-room1@mailserv.fao.org'
Subject: 64: Re: Fish genetic resources - Malaysia

This is from Ron Jones, Canada, again.

Subha Bhassu's comments (message 62 June 20) make some key points when putting our discussion into a fisheries/aquatics context. Most of the molecular/biotech work in fisheries is done on commercial or potentially commercial species, such as Subha's work done on relatedness in tilapia stocks and the giant freshwater prawn. The expense of biotech analyses for developing countries will probably mean that the priorities will focus on those important commercial applications and species (breeding, disease diagnostics, genetics for re-stocking/supplementation. Who actually benefits from this is, of course, another question. Researchers from developed countries, with robust grants, will continue to explore the marvellous historical evolutionary relationships among interesting populations. How can we apply this knowledge to reducing hunger and alleviating poverty through better design (or conservation) of aquatic systems? Where are the salinity/cold tolerant; disease resistant; fast growing; tasty; tilapia stocks?

It will always be important to determine stock origins and levels of inbreeding/introgression in founder stocks for any commercial production of aquaculture species. I think that national/international organizations can play key supportive or facilitative roles in both the governance and capacity building for genetic technologies respectively through creative co-management arrangements. It is my opinion that the conservation of aquatic genetic resources will require simultaneous applications of good in situ natural resource governance AND strategic applications of technology to characterize, protect and intelligently use these genetic resources. There are niche roles to play by each level of government, academia and NGOs, which will require collective creativity and willingness to implement. I think academic researchers will have to venture out of the lab (we can publish your results later) and find some interesting genetic problems on which to apply this technology thereby rekindling scientific explorations in solving key problems related to hunger, poverty and biodiversity.

It was interesting to hear that the 2 (east/west) stocks of giant freshwater prawn were first determined by less charismatic methods of morphology and allozymes. We really do have to take a hard look why we choose a specific technological pathway.

Ron Jones
Consultant,
International Development Research Centre (IDRC)
Ottawa,
Canada
channastri (at) netscape.net

[The reference in the last paragraph is to the results mentioned in Subha's message showing that M. rosenbergii (freshwater prawn) is classified into two form, the western and eastern forms. While that 2004 paper, by de Bruyn et al. in Molecular Phylogenetics and Evolution, is available for subscribers only, a 2003 article in Naga (the WorldFish Center Quarterly) by P.B. Mather and M. de Bruyn, entitled "Genetic diversity in wild stocks of the giant freshwater prawn (Macrobrachium rosenbergii): Implications for aquaculture and conservation" summarises the results, writing "We, therefore, set out to document genetic diversity in wild M. rosenbergii stocks from across the natural range from southern Asia, to SE Asia and into the Asia-Pacific region. Molecular genetic analysis of a 472 base-pair segment of the 16S rRNA mtDNA gene, sampled from individuals representing 18 wild populations of M. rosenbergii, supports previous allozyme and morphological work that has identified two distinct forms of M. rosenbergii (De Man 1879; Johnson 1973; Lindenfelser 1984). The boundary between the two major clades corresponds with Huxley’s extension (Huxley 1868) of Wallace’s Line (Fig. 2), a well-known biogeographical break that runs through Indonesia" (http://www.worldfishcenter.org/naga/naga26-4/pdf/naga-26-4-article1.pdf) ...Moderator].

-----Original Message-----
From: Biotech-Mod1
Sent: 21 June 2005 14:57
To: 'biotech-room1@mailserv.fao.org'
Subject: 65: Re: Molecular characterisation of animal genetic resources

I am M. S. Tantia, Senior Scientist working at National Bureau of Animal Genetic Resources, Karnal, India.

I certainly agree that molecular characterization with microsatellite markers, which are mostly neutral to selection, are excellent tools to study population parameters and identify unique populations/breeds requiring efforts for their improvement and conservation. But in most of the developing countries, like India, due to small size of the animal holding (1 to 3 for large ruminants), no field recording systems exist on the ground. The population sizes at organized herds for certain breeds are also very small. In such a situation, the molecular data can effectively be utilized for diversity studies but, due to lack of pedigree and phenotypic records, how can we use molecular markers (marker assisted selection) for improvement of livestock?

In India, we have some naturally existing breeds/populations which have the extremes of a trait - for example, milk production. You find populations which are milch type producing on average 1500-2000 kg per lactation and, on the other hand, there are draft populations hardly producing 300-500 kg. Can we use some methodology to find quantitative trait loci (QTLs) from molecular markers in the absence of pedigree or phenotype data?

M S Tantia
Senior Scientist,
NBAGR,
Karnal 132 001,
India
mstantia (at) nbagr.ernet.in

[This conference focuses on the use of biotechnologies (including molecular markers) for the characterisation and conservation of genetic resources for food and agriculture. Methods for using markers for QTL detection or for genetic improvement are not a theme for discussion in the conference, so anyone wishing to address M.S. Tantia's questions are requested to contact him directly. Conference 10 of this Forum (entitled "Molecular marker assisted selection as a potential tool for genetic improvement of crops, forest trees, livestock and fish in developing countries", that ran from 17 November to 14 December 2003) has already addressed this area. The Background Document, 85 messages posted and the Summary Document from the conference are all available at http://www.fao.org/biotech/C10doc.htm ...Moderator].

-----Original Message-----
From: Biotech-Mod1
Sent: 21 June 2005 14:58
To: 'biotech-room1@mailserv.fao.org'
Subject: 66: Re: Molecular characterisation of animal genetic resources

This is Salah Galal, again. In response to Miguel A. Toro (Message 63, June 20):

You picked the wrong example - Holstein. I am talking about breeds or populations where hardly no intentional breeding programs took place and they share similar, if not the same, origins and geographical zones. These are what are sometimes called 'landraces'. Of course molecular techniques can establish with a certain degree of probability if these populations are/are not the "same".

Salah Galal, Ph.D.
Professor, Animal Production Department
Faculty of Agriculture
Ain Shams University
Hadaeq Shubra 11241
Cairo,
Egypt
sgalal (at) tedata.net.eg
Tel: +202 444 1711
Fax: +202 444 4460

[Miguel Toro (Message 63) had written
"1) Establishing that two breeds are genetically similar does not guarantee that the genetic improvement program of one of them can be applied to the other, because this depends on the existence or not of genotype x environment interaction. For example, the Holstein is a universal breed but probably a different genetic improvement program should be implemented in a tropical or in a temperate climate.
2) I cannot see ‘exactly’ how molecular markers could be used to decide if two breeds are or are not the same. First: a) molecular markers refer to neutral or non-coding genetic variation; b) it is well known that genetic distances are not very useful in this context because they ignore within breed variation. An inbred line (just because a handful of animals became isolated in a small area during a few generations) would be classified as a very different breed despite not having interest at all"...Moderator].

-----Original Message-----
From: Biotech-Mod1
Sent: 21 June 2005 15:00
To: 'biotech-room1@mailserv.fao.org'
Subject: 67: DNA banks - forest genetic resources

This is E.M. Muralidharan from India again.

I had in an earlier message (Message 22, June 6) asked about the relevance of DNA banks. My interest was in the context of conservation of forest genetic resources and, more specifically, tropical forest genetic resources (much of it in developing nations) that are in danger of mass erosion due to degradation of the habitat. The situation is perhaps quite different from that of the agricultural or domesticated animal genetic resources that are being discussed more often in this conference. These areas manage to attract attention and funds for obvious reasons. On the other hand, forest genetic resources, especially that of the wild species, fail to get priority. Other than through national parks or sanctuaries, I don't see how the multitude of species (including unidentified species with unknown economic prospects for the future) can ever be preserved without incurring a huge expenditure. It thus appears that a great extent of such resources are destined to be lost for ever in the coming years. And it appears that scientists alone cannot change the scenario.

If simple, rapid and cost-effective DNA extraction and storage procedures applicable to several taxa are developed, will DNA banks be the sensible way to keep something for posterity? The primary advantage that I see here is the possibility of rapid collection, inventorizing and long-term storage of genetic material with minimal space requirements. For the same reason, I don't find the storage of leaves, eggs or other tissue parts under silica gel, cryoproservation etc. as ideal. Wherever feasible, the more conventional conservation methods would of course be used. DNA banks would also mean that the disadvantages of storing DNA (Messages 34 (June 10, Kioumars Ghamkhar) and 47 (June 13, D. Vijay)) are overcome and we presume that having DNA is better than species going extinct - leaving nothing at all. How much of a priority should this activity be given?

Dr. E.M. Muralidharan
Scientist, Biotechnology
Kerala Forest Research Institute
Peechi, Thrissur, Kerala State
680653,
India
Email: emmurali (at) kfri.org

-----Original Message-----
From: Biotech-Mod1
Sent: 21 June 2005 15:07
To: 'biotech-room1@mailserv.fao.org'
Subject: 68: Application of biotechnology in forest genetic resources conservation

I am Alice Muchugi, a lecturer in the Department of Biochemistry and Biotechnology of Kenyatta University, Kenya, with special interest in conservation of indigenous forest tree genetic resources. I am currently a PhD research fellow at the World Agroforestry Centre (ICRAF).

I agree with the Moderator's concern that little mention has been made about forestry despite the global concern on reduced forest cover and forest genetic erosion especially in developing countries. However, the debate on biotechnology application in forestry follows the same trend of crop plants. Forest resources are threatened by the increased population as more land is taken up for settlement and farming. The problem is compounded where there is commercial exploitation of indigenous species. Again, when new forests have to be established in most of these developing countries the focus is on exotics. There is therefore a great need to think seriously about the indigenous forest genetic conservation which also happens to be a rich biodiversity habitat (for flora and fauna). There are two areas where biotechnology is being employed in conservation of the forest tree genetics.

First, molecular markers can be used to identify areas of focus in conservation of genetic diversity for specific species. Deductions on gene flow will also guide in ex-situ establishment of species in conserving diversity. Secondly, where circa-situ and ex-situ conservation have to be practiced, planting material of good genetic base is a problem for most of these indigenous species. Some have recalcitrant seeds or very little is available. Here, tissue culture techniques can play a major role in multiplication of available propagules. Suspension cultures and cryopreservation may be another aspect that can be approached in conservation (though Message 22 (June 8, E.M. Muralidharan) discourages this) as well as the DNA bank in form of plant material. [With circa situ conservation, germplasm is collected from a site and conserved in sites nearby. Geneflow is therefore a possibility between the sites, unlike ex situ conservation, where germplasm is collected from a site and conserved in a completely different site...Moderator].

Compared to temperate species, there is very [little?...Moderator] work that has been carried out on tropical tree species, where most of these developing countries fall. As already highlighted, the major limitation in its biotechnology application is in both physical and human resources. Since the floral distribution cuts across political boundaries, molecular characterization is best approached from ecological/geographical perspective. This, therefore, calls for greater collaboration among scientists within the regions in exchange of plant materials and knowledge gathered. Maybe a tropical tree biotechnology forum, if formed, can help in networking. This will finally reduce the technology cost for individual countries. I also feel that due to the pressure on loss of forest biodiversity, cheaper applications such as the RAPD markers (which are being discontinued in well developed laboratories) can still be employed in the preliminary studies to form a basis of conservation strategies. The collaboration of the Consultative Group on International Agricultural Research (CGIAR) centers and the national agricultural research systems (NARs) has also helped to improve on the capacity building problems for developing countries (I have had my MSc and PhD training under this) and should therefore be greatly fostered.

Alice Muchugi
PhD Research Fellow
Genetic Resource Unit,
World Agroforestry Centre (ICRAF)
PO Box 30677-00100
Nairobi, Kenya
tel: +254-20-7224000 Ext 4273
fax: +254-20-7224001
email: a.muchugi (at) cgiar.org
http://www.worldagroforestrycentre.org

-----Original Message-----
From: Biotech-Mod1
Sent: 21 June 2005 15:08
To: 'biotech-room1@mailserv.fao.org'
Subject: 69: Economic value of genetic diversity measure in aquaculture

This is S.G. Tan, again, a geneticist from the Dept of Biology, Fac. Science, University Putra Malaysia.

In Malaysia, it has been found through the use of molecular genetic markers (be they protein level ones like allozymes, whenever possible or DNA markers like microsatellites, when the need arises) that the level of genetic variation is low in many cultured stocks of prawns and seabass. This has resulted in low fertility levels and abnormalities being found in them. Such information has vast economic implications because if the situation is not remedied through the introduction of more genetic variation, the cultured stocks will continue to deteriorate with time and the aquaculture industry will suffer economically. Hence, in developing countries, it does make sense to invest in genetic marker studies of economically important species even though we do not have the luxury of studying the non economic species as well at this stage of our development.

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,
Malaysia.
email: sgtan (at) fsas.upm.edu.my
Fax: 603-86567454/89432508

-----Original Message-----
From: Biotech-Mod1
Sent: 21 June 2005 17:38
To: 'biotech-room1@mailserv.fao.org'
Subject: 70: Molecular markers - genetic distances - livestock

Again from Hans Lenstra from Utrecht, Netherlands.

I would like to respond to the discussion of Salah Galal and Miguel Toro [Messages 60 and 66...Moderator] on the basis of observation on datasets of cattle, sheep and goat (European Union (EU) Resgen project (CT98-118) and EU Econogene project).

Miguel Toro is right that a large genetic distance often mainly reflects genetic isolation - examples are Danish red cattle, a subpopulation of Betizu cattle, Mallorquina cattle, fighting cattle. However, the large genetic distance of Italian Chianina cattle from other breeds seems to reflect an ancient history. Despite its reputation, Holstein populations are quite heterozygous and genetic distances to other breeds are not at all extremely long. Genetic isolation is not at all restricted to highly selected breeds and is also common for island breeds (e.g., Greek Skopelos sheep) or may be caused in the wild by habitat fragmentation.

On the other hand, short genetic distances may very well confirm that populations are closely related, if not identical, like German Brown Bavaria and German Brown Wuertemberg, or the Swiss Evolene and Eringer.

For the non-selected cattle breeds, a zebu component may create a large genetic distance, but as pointed out by Salah Galal, breeding is not strict and there may be considerable overlap between breeds.

In general, in all three species we see a clear difference between phenotypic distinctness and molecular diversity. North-Western European breeds are clearly distinct with long genetic distances. However, allele richness as a measure for molecular diversity is clearly higher in South-Eastern Europe and still higher in Asia, where uniqueness of breeds is less conspicuous (but certainly valuable, like local adaptation and disease resistance). So phenotypic distinctness and molecular diversity may both be valid reasons for conservation, but are often negatively correlated.

Dr. J.A. Lenstra
Faculty of Veterinary Medicine
Yalelaan 8
3584 CL Utrecht
Netherlands
+31-30-2534992, fax 2518126
at home +31-30-6375622
J.A.Lenstra (at) vet.uu.nl