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Sent: 10 June 2005 09:06
Subject: 32: DNA genebank
This is Richard Wang, Research Geneticist, USDA-ARS (United States Department of Agriculture - Agricultural Research Service). I work on germplasm improvement of forage crops.
In early 1980's, I suggested that pure DNA samples should be stored in genebanks to preserve genes in anticipation that someday scientists can utilize desirable genes directly from the DNA molecules. This form of germplasm preservation is already a reality in Australia and U.K. I hope it will become a common practice in all genebanks.
USDA-ARS Forage and Range Res Lab
Utah State University
695 N 1100 E
Logan, UT 84322-6300
rrcwang (at) cc.usu.edu
Sent: 10 June 2005 10:23
Subject: 33: Re: Introducing biotechnology in rural areas = sausages to a new born baby
This is Kioumars Ghamkhar from Australia, again. I am sorry I did not properly introduce myself in my first email. I'm a plant molecular biologist and systematist at CLIMA (Centre for Legumes in Mediterranean Agriculture), University of Western Australia: http://www.clima.uwa.edu.au.
Regarding message 29 (June 9) from Roger DJOULDE DARMAN:
I think we have lost the point here. No rural farmer is supposed to use polymerase chain reaction (PCR) or any molecular technique in the lab. This is apparently the molecular diversity scientists' responsibility to undertake these tests and satisfy the farmers to use the outcomes and end products of these screening and/or breeding programs. Farmers in developing countries are and will be more than happy to use the accessions and/or varieties that we suggest if we prove that the suggested accessions are improved ones within a huge, or at least relatively large, collection. They do not really care what methods we have used as long as we provide them with the right thing and do not say "sorry, I was wrong" in a couple of years after their field trials. That is exactly why we need a global effort and coordination to establish a standard dataset and methodology for our molecular research.
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
Sent: 10 June 2005 10:29
Subject: 34: Re: DNA genebank
This is Kioumars Ghamkhar from Australia, again.
Regarding message 32 (June 10) from Richard Wang:
There is already a DNA bank in the United States at the Missouri Botanic Gardens although it is not a "real DNA bank" as we know it but it is one step forward, having the leaves stored in silica gel. The best DNA bank, though, is at Kew Botanic Gardens in the UK as you said, but I am not aware of any well-established DNA bank in Australia.
Although I agree that DNA banks are good sources of conserving genetic resources, I draw your attention to the fact that there are advantages and disadvantages for both DNA banks and seed banks forcing people to prefer seed banks at this stage, particularly in the countries with less funding support for these purposes:
This information is from a talk by A.H.D. (Tony) Brown (CSIRO plant industry, Canberra, Australia) at the Centre for Legumes in Mediterranean Agriculture (CLIMA) last year, comparing these two storage systems, which has been a bit modified by myself:
Disadvantages of DNA banks:
1. Contamination diagnosis is difficult in DNA banks while it is much more obvious in seed banks.
2. Morphological screening is not possible at any stage to double check any wrong going practice in DNA banks.
3. DNA banks need highly skilled technicians for maintenance while seed banks do not really.
Advantages of DNA banks:
1. No quarantine issues for countries such as Australia with strict quarantine rules for seeds and any other parts of plants.
2. Quick availability for research.
3. Almost immortal for storage purposes.
Of course, there are even more advantages and disadvantages, with the latter decreasing over time and in future, but certainly for now we are better off sticking to seed banks.
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
Sent: 10 June 2005 11:10
Subject: 35: Re: Molecular characterisation of animal genetic resources
I am Hans Lenstra, Faculty of Veterinary Medicine, Utrecht University, Netherlands. I am a molecular biologist and have coordinated a large-scale European project on cattle genetic diversity (GenRes CT98-118, 1999-2002) and have participated in a sheep-goat diversity project Econogene (2001-2005, coordinated by Prof. P. Ajmone-Marsan, Piacenza).
Ilse Köhler-Rollefson (Message 31, June 9) is asking the right questions about livestock conservation. Of course there is more in our world than DNA.
However, there are now several examples of DNA telling us something we did not know before:- about the species origin of domestic cattle, horse, goat, sheep, dog, etc. (Bruford, M.W., D.G. Bradley, G. Luikart, 2003. DNA markers reveal the complexity of livestock domestication. Nat. Rev. Genet. 4: 900-910)
Many papers are focused on a few local breeds with often a modest number of DNA markers. Now we have the large datasets generated by the above-mentioned projects and these contain a wealth of information. With the forthcoming papers of the European Cattle Genetic Diversity Consortium and the Econogene Consortium we hope to prove our point!
About the use of genetic data for conservation: this is quite a thorny subject. My view may appear provocative, but is based on the analysis of datasets of a size that for livestock were not available before. Genetic distances appear not at all to be reliable criteria for the value of a breed, since it tells more about the degree of genetic isolation than about unique properties. A Holstein population derived from one fibroblast would show up as more valuable than an old landrace with a lot of unique alleles! This is now leading (at least for livestock) to criticism of the popular Weitzman approach for estimating conservation priorities. We find that newer methods (marker-estimated kinship analysis, developed by Herwin Eding) make more sense.
However, like it or not, with the current state of art I would not dare to condemn any breed on the basis of DNA markers alone! Indeed, the perceived value of a breed is often linked to regional tradition and this is not in the DNA. On the other hand, DNA data give most relevant data about the history of a breed, e.g. by revealing ancient alleles or by detection of outcrossing, and this may very well contribute to decisions about conservation. Eventually, DNA has the future! Mutations coding for breed-specific phenotypes are being found. A new trend will be the male Y-chromosome, more vulnerable to extinction than autosomal DNA and potentially relevant for masculine traits.
Dr. J.A. Lenstra
Faculty of Veterinary Medicine
3584 CL Utrecht
+31-30-2534992, fax 2518126
at home +31-30-6375622
J.A.Lenstra (at) vet.uu.nl
Sent: 10 June 2005 11:11
Subject: 36: Re: Molecular characterisation of animal genetic resources
This is Olivier Hanotte. I am a molecular geneticist working at the International Livestock Research Institute (ILRI-Nairobi) where I am leading the ILRI project on Animal Genetic resources which has a strong biotechnology component.
I am particularly welcoming Ilse Köhler-Rollefson's comments (Message 31, June 9) and would like to take this opportunity to comment on a couple of issues raised by her message.
I think we can all recognize the importance of characterizing our livestock breeds/species/population to better utilize it for the short and long term benefit of the farmers and for the long term benefit of the global community.
Importantly, we have to understand that the word characterization engulfed a lot of areas, of which biotechnology (molecular characterization) is only one of them.
Rightly we should ask ourselves the question, what has been then the deliverable of molecular characterization.
One area, as pointed out by Ilse Köhler-Rollefson, has been the unraveling of center of domestication and in some case dispersal routes etc. I would like to broaden this and say that molecular characterization has helped us to understand the origin and also the today genetic make-up of our livestock.
Have we learned anything through genetic methods that we did not know before? Broadly speaking, I think it is not the way we should be stating the question. Molecular characterization, archeology, linguistic, indigenous knowledge etc. are providing information which allows us to complete a puzzle about origin and history of agriculture. One kind of evidence pointing in a specific direction is good, several distinct sources of evidence is much better, much more convincing and exchanges of information between these fields can only better guide future research, initiative etc.
This understanding of the genetic make-up is also opening new doors for conservation and utilisation. One of which is to provide putative criteria for priority decision for conservation, these could be genetic uniqueness, level of diversity etc. Should the molecular criteria be the main criteria? If we think about ex-situ conservation, I think it should be a very important criteria (selection of animals representative of the diversity of the breeds conserved etc.).
But if we think about in situ conservation at the farmer community level we should be extremely careful here and realize that in-situ conservation and genetic improvement/utilization (through which we will have an impact at the farmers level and therefore on poverty) are not the same thing.
Undoubtedly, we should be targeting poverty alleviation and improvement of indigenous breeds is one possible avenue. Such an approach will result only on a subset of the indigenous livestock diversity conserved but in a likely sustainable way. A subset, but an important subset for the future
Biotechnology tools and information can help breeding improvement (pedigree reconstruction, marker-assisted selection etc.). Let's not forget that the raw genetic material for selection and therefore genetic improvement is diversity.
Olivier Hanotte, PhD
Animal Genetic Resources
International Livestock Research Institute (ILRI)
P.O. Box 30709
PLEASE NOTE NEW PHONE NUMBERS
Tel + 254 20 4223466 (office) + 254 20 4223140 (home)
Fax +254 20 4223001
Mobile + 254 (0)734 333071
E-mail o.hanotte (at) cgiar.org
ILRI via USA-Direct Tel + 1 650 8336660, Fax 1 650 833 6661
Sent: 10 June 2005 14:06
Subject: 37: Characterization of fish biodiversity
My name is Kazhila Croffat Chinsembu from the University of Namibia in Windhoek, again.
This time I am onto the subject of ecology and evolution of cichlid fishes of Southern Africa. So far, the only fisheries contribution has been from Ron Jones (Messages 14 and 15, June 7).
Let me draw your attention to the recent work by Joyce et al. reported in Nature volume 435 of 2005. It has revealed that the situation is different in Southern African rivers. Haplochromine cichlids in five Southern African rivers (Upper Congo, middle/upper Zambezi, Okavango, Cunene and Limpompo) show species richness and ecomorphological diversity similar to that in Lake Victoria and Lake Malawi. They found numerous sympatric haplochromines different in shape and size. Within this Southern African radiation, mitochondrial (mt) DNA haplotypes comprised six clades within which a large number of closely related haplotypes have arisen from a small number of more divergent haplotypes. On the other hand, several morphologically different and geographically distant species have very similar haplotypes. These phylogenetic relationships suggest a species flock that emerged rapidly and simultaneously in many geographically distant rivers, in which very similar haplotypes are found several thousand kilometers apart, yet for which strongly differentiated haplotypes are found within single populations. [African cichlids are extremely species-rich, making up an estimated 5% of all vertebrate species, and are much studied for evolutionary reasons. Haplochromine refers to one of the major lineages of African cichlids. Sympatric species are those which occupy the same area at the same time. A clade is a group of species with a common evolutionary ancestry. The paper referred to is Joyce, D.A. et al., 2005. "An extant cichlid fish radiation emerged in an extinct Pleistocene lake", Nature, 435, 90-94 - address for correspondence regarding the paper is ole.seehausen (at) aqua.unibe.ch ...Moderator].
Through the use of geological evidence, Joyce et al contend that the high diversity among Southern African river cichlids arose from palaeolake Makgadikgadi, a lake that disappeared about 2000 years Before Present. The centre of this extinct lake is now a saltpan north of the Kalahari Desert. They showed that the lake paleo-Makgadikgadi hosted a rapidly evolving cichlid species radiation (comparable in morphological diversity to that in the extant African Great lakes) that later seeded all major river systems of Southern Africa with ecologically diverse cichlids.
Now as a follow up to the above study, we propose to conduct the following research here in Namibia. Here is a short description of the proposed research:
Despite the huge biodiversity of cichlids in Southern African rivers, few known species have been documented in northern Namibian rivers (11 Serranochromine species were found in the Okavango river; 7 Serranochromine and 2 Thoracochromis species were found in the Cunene river - Joyce et al). Targeted biogeographical, ecological and phylogenetical studies to map out the species richness, ecomorphological diversity and phylogenetical relationships of known cichlids in Namibian rivers have not yet been conducted. Although the paleolake Makgadikgadi hypothesis is plausible (Joyce et al 2005), data to demonstrate the dispersal of species from a single centre of diversification and the subsequent coexistence of multiple species are not yet available.
While unidentified species are being discovered (2 Sargochromis species were discovered at the Kalembeza/Zambezi junction - Joyce et al), the scope to discover new species of cichlids still remains unfulfilled and selection pressures that lead to adaptive evolution and explosive speciation are not yet fully understood. Forces that limit coexistence such as ecological competition versus mating competition and introgression in cichlid fishes of Namibia have also not been elucidated.
Further, important genes and genetic variations responsible for phenotypic differences among cichlid species in rivers of northern Namibia are still to be identified.
Given that cichlids are commercially important food fishes in northern Namibia, inadequate information about their biodiversity and underlying mechanisms hampers correct decision-making in fisheries management, conservation, utilization, breeding and aquaculture.
What do I seek? I seek the collaboration and help of any organisation that may help us to conduct the field work as well as laboratory experiments. Information about sources of financial support is also welcome.
Kazhila Croffat Chinsembu, MSc
Lecturer, University of Namibia
Private bag 13301
Tel: 264-61-206 3426
Fax: 264-61-206 3791
Email: kchinsembu (at) unam.na
[People interested in collaboration should contact Kazhila directly...Moderator].
Sent: 10 June 2005 14:24
Subject: 38: Re: Core collection // Markers and morphology // Tissue culture
This is from Dr. Zosimo Huaman, PROBIOANDES, Lima, Peru. I was the curator of large potato and sweetpotato collections conserved at the International Potato Center. We selected core collection for those crops. At present I am a consultant on Biodiversity issues to promote public awareness in Peru to conserve in situ the diversity of 182 crop species domesticated by our ancestors and several thousands of other plant species with known uses.
On the issue of core collections, molecular markers are the most valuable source to get data on genetic diversity of a given crop or plant species. However, at the time of selecting a core collection, one has to take into account other characters such as ecogeographical data, disease and pest reaction, morphological diversity, etc. One has also to make sure to include rare alleles.
From a cluster of accessions with similar genetic constitution, it would be better to select an accession representing the group that has some desirable character such as disease or pest resistance, higher nutritive value, etc. Therefore, the collection should be evaluated for some of the most important biotic or abiotic factors that limit productivity of that crop.
Researchers in developing countries many times do not have the equipment nor the supplies needed to get molecular data. Therefore, the recipes that we get from researchers from industrialized countries are many times difficult to implement. However, the selection of core collections are extremely important to make sure that at least the most genetically diverse accessions in the collection are maintained. This is a better choice instead of losing accessions in the collections at random due to natural or man made causes.
Dr. Zosimo Huaman
Calle El Herraje # 120
Urb. Rinconada Baja, La Molina
email: z.huaman (at) probioandes.com
Sent: 10 June 2005 14:45
Subject: 39: Re: DNA genebank
This is Glaucia S.C. Buso, from Embrapa Genetic Resources and Biotechnology, Brazil.
Responding to Kioumars Ghamkhar (Message 34, June 10):
Is there any well-established DNA bank in any country? What should be the criteria to keep DNA samples for long time conservation? Is there any publication that establishes these criteria or requirements?
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
[Responding also to Message 34, Rajeev Varshney from IPK-Gatersleben, Germany, rajeev (at) ipk-gatersleben.de, writes to say that he thinks that Robert Henry from Southern Cross University has also established a DNA Bank in Australia (http://www.scu.edu.au/research/cpcg/sxn3/staff.php?id=1) ...Moderator].
Sent: 10 June 2005 16:20
Subject: 40: Re: DNA genebank
This is Elizabeth A. Widjaja from Botany Division, Research Centre for Biology, Indonesian Institute of Sciences, Bogor, Indonesia.
I am not a geneticist, but only a plant taxonomist. I would like to join in this e-conference to know what people talk in biotech e-conference to give me an idea because I am just a new person in the Subsidiary Body on Scientific, Technical and Technological Advice (SBSTTA) Focal Point from the developing countries so I need to learn everything regarding to the Convention on Biological Diversity (CBD).
Responding to Glaucia S.C. Buso (Message 39, June 10): In our research centre we have a collection of DNA bank although it is not a real one, because we keep the leaves and stored in silica gel or as dried extracts. Most of our DNA plant collection is kept in silica gel and comes from the threatened species. On the other hand, we also have DNA fauna collection such as bird, mammals and others - mostly kept as blood, hairs and extract collection.
Dr. Elizabeth Anita Widjaya
Research Center for Biology - Botany Division
Indonesia Institute of Science
c/o the Herbarium Bogoriense, botany Division
Jalan Ir. H. Juanda 22 - P.O. Box 110
+62 251 322 035
Fax: +62 251 325 854; 251 336 538
ewidjaja (at) indo.net.id
Sent: 10 June 2005 17:12
Subject: 41: Developing a core collection - Importance of choice of marker
I am Marie Noelle Ndjiondjop working as a rice molecular geneticist at WARDA - The Africa Rice Center (Cotonou, Benin). In African rice ecosystem, two cultivated rice are found: O. sativa L and O. glaberrima Steud. The objectives of our work is: To exploit the genetic diversity hidden in the rice germplasm found in diverse Africa ecosystems; to identify alleles that control the traits of interest; To identify superior alleles for breeding purposes; To identify and map genes/QTLs associated to traits such as drought, disease and pest and increase the stress adaptiveness of Asian rice with high yield potential; To apply target marker to select gene of interest at the early stage of plant growth in particular when the phenotyping becomes difficult and then enhance efficiency of breeding programs.
I would like to contribute to this important forum discussion by pointing out the importance of the choice of informative molecular marker to develop a core collection.
We have used molecular markers to assess the genetic diversity present in a collection of Oryza glaberrima accessions representative of the cultivated forms. Former studies using isozymes and RFLP markers had generally revealed little allelic diversity among Oryza glaberrima lines (Second 1982; Ishii et al. 1993), while a higher level of variability was revealed in other species of the genus Oryza, particularly Oryza sativa. Second (1982) postulated that lack of diversity of Oryza glaberrima is due to a bottleneck effect during the domestication process. Meanwhile, though less diverse than its Asian counterpart, Oryza glaberrima displays a large range of variation for many morphological and agronomic traits important for breeders (WARDA 1993; Jones et al. 1997).
Recent studies using repetitive sequences derived-molecular markers like minisatellites or retrotransposon probes have detected DNA polymorphism among a few Oryza glaberrima accessions (Dallas 1988; Fukuchi et al. 1993). The polymorphism detected among these varieties of Oryza glaberrima, later confirmed in the diversity analysis of the collection of 200 accessions, reinforces the usefulness of microsatellites in assessing the variability present in the African rice (Semon et al. 2005), while the utilization of marker systems such as isozymes or RFLP had generally failed in the past because of lack of polymorphism. This informative molecular marker will now be used to develop the core collection of O. glaberrima accessions store in our genebank.
Marie Noelle Ndjiondjop
WARDA The Africa Rice Center
m.ndjiondjop (at) cgiar.org
Sent: 10 June 2005 17:31
Subject: 42: Re: Establishing a universal molecular marker data base
My name is Marilyn Warburton, and I work in the Genetic Resources Program of the International Maize and Wheat Improvement Center (CIMMYT). I work on the molecular characterization of maize and wheat using molecular markers.
Currently, we use SSR markers to study diversity, and we have had considerable experience working in conjunction with partner laboratories in other countries. In conjunction with the Asian Maize Biotechnology Network (AMBIONET), we did many studies on the feasibility of combining molecular marker studies in maize from different laboratories. Some relevant results have been published in George et al., 2004 (Molecular characterization of Asian maize inbred lines by multiple laboratories. Theor. Appl. Genet. (109:80-91). The main conclusion of these studies was that if different laboratories use the exact same protocols and platforms for genotyping, with multiple internal controls (same genotypes run in all labs), SOME of the markers (perhaps up to half) can be compared between laboratories. If any of the techniques vary between labs, the number of comparable markers goes down, although using a technique such as the allele kits referred to by Carmen de Vicente in Message 26 (June 9) does help somewhat. However, if different laboratories use different techniques, which is always the case in non-cooperating laboratories, the possibility of combining data sets afterwards is virtually non-existent. We have concluded, both in AMBIONET and the Generation Challenge Program, where large scale genotyping projects are coordinated between several labs, that each lab should run a subset of the markers on all genotypes for the project, rather than each lab running a subset of the genotypes with all the markers. Any other way cannot guarantee no introduction of bias into the study.
We have tried other marker types in the past (AFLP, RFLP, arbitrarily primed markers) and the repeatability between labs goes down for all but RFLPs, but these are simply too much work! We hope to try SNPs in the near future, where repeatability should be much higher.
Molecular Geneticist, Genetic Resources Program
Apdo Postal 6-641
06600 Mexico, D.F.,
Tel.:(52)555-804-2004 ext. 1381
m.warburton (at) cgiar.org