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Moderated conference on Genomics in Food and Agriculture

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Moderated conference on Genomics in Food and Agriculture, hosted by the FAO Biotechnology Forum, March 2013
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All messages from FAO e-conference on genomics now available in a single PDF
End of FAO e-mail conference on genomics
61: Genomics of rhizobacteria
60: Re: Establishing a global genomics/breeding forum?
59: Omics tools versus conventional plant breeding
58: Animal 'omics'
57: Development of mapping populations for crop species
56: Re: Genomics of crop beneficial bacteria
55: Genomics in tropical forestry
54: Re: Establishing a global genomics/breeding forum?
53: Re: Establishing a global genomics/breeding forum?
52: Genomics for livestock in tropical countries
51: Genomics in livestock
50: Re: Establishing a global genomics/breeding forum?
49: Re: Establishing a global genomics/breeding forum?
48: Establishing a global genomics/breeding forum?
47: The status of genomics application in Iraq
46: Property rights
Reminder that are in last days of this FAO e-conference on Genomics
45: Re: Locally important crops
44: Re: Impact of genomics technologies so far
43: Genetic promise
42: Partnerships in genomics
41: Locally important crops
40: Re: Two points about genomics
39: Two points about genomics
38: Impact of genomics technologies so far
37: Access to genomics technology for developing countries
36: Progress on chickpea
Now beginning the last week of the FAO e-mail conference on genomics !
35: Re: Molecular markers, MAS and plant genetic resources
34: Re: Young scientists from developing countries and genomics
33: Past and future impacts of crop genomics in Indonesia
32: Bridging the genomic divide
31: Genomics of tropical fruits
30: Young scientists from developing countries and genomics
29: Re: Genomics of crop beneficial bacteria
28: Challenges and opportunities for genomics-assisted breeding in developing countries
27: Genomics of crop beneficial bacteria
Halfway stage of the FAO e-mail conference on genomics !
26: Re: Genomics for livestock improvement in developing countries
25: Capitalising on the possibilities of genomics
24: Molecular markers, MAS and plant genetic resources
23: Re: Role of genomics in livestock improvement in developing countries
22: Genomics for livestock improvement in developing countries
21: Re: Genome assisted selection in livestock
20: Perspectives on genomics in livestock in developing countries
19: Re: Role of genomics in plant and livestock improvement in developing countries
18: Re: Distinguishing 3 categories of use of genomic technologies
17: Genome assisted selection in livestock
16: Distinguishing 3 categories of use of genomic technologies
15: Genomics to help developing countries?
14: Re: Role of genomics in plant and livestock improvement in developing countries
13: Genomics for livestock improvement in developing countries
12: Omic studies in the least developed countries should have to emphasize on adaptation traits
11: Re: Genomics-based crop improvement
10: Role of genomics in plant and livestock improvement in developing countries
9: Genomics and related omics to aquatic resources - fish resources
8: Future contribution of genomics to indigenous breeds
7: What have been the impacts of genomics so far...
6: Re: Genomics-based crop improvement
Update on the FAO genomics e-conference
5: Fermentation of cysteine
4: Opportunities of genomics for the livestock and plant sector of the "tropics"
3: Re: Genomics-based crop improvement
2: Importance of software for genomics applications
1: Genomics-based crop improvement
Welcome to the FAO e-mail conference on Genomics !
Background document to the FAO e-conference on Genomics

Biotech-Mod3
Tue, 26 Mar 2013 18:01:08 +0100
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Dear Participants,

We have now put all of the messages from this FAO e-mail conference on Genomics in Food and Agriculture into a single PDF and made it available on the web.

The PDF file contains in chronological order:

- the first 2 messages I sent before the conference began (one of which contained the Background Document),
- the 61 messages from participants posted during the 3-week conference
- the final message I posted on 25 March 2013 closing the conference, providing also a brief summary about participation.

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Biotech-Mod3
Mon, 25 Mar 2013 17:54:56 +0100
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Dear Participants,

The last messages (numbers 58 to 61) have now been posted so Conference 19 of the FAO Biotechnology Forum, entitled "Impacts of genomics and other 'omics' for the crop, forestry, livestock, fishery and agro-industry sectors in developing countries", is now officially closed.

The FAO Biotechnology Forum was established in order to provide quality balanced information on agricultural biotechnologies in developing countries and to make a neutral platform available for people to exchange views and experiences on this subject. We hope that you found the conference interesting, constructive and beneficial.

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Biotech-Mod3
Mon, 25 Mar 2013 17:51:57 +0100
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This is Doris Zuñiga, again.

Several researchers in Latin America have demonstrated the importance of the growth promoting plant bacteria among which are the nitrogen-fixing in various crops, the soybean crop is very important in Brasil and Argentina and pastures in Uruguay (Biofertilizantes en Iberoamérica: Una visión técnica, científica y empresarial. 2007. Edited by M.L. Izaguirre-Mayoral, C. Labandera and J. Sanjuan. 98 pages. http://www.biofag.org.ar/actividades/publicaciones/Libro-Biofag2007.pdf [2 MB]).

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Biotech-Mod3
Mon, 25 Mar 2013 17:51:25 +0100
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This is Denis Murphy again.

I think this has been a very useful discussion in bringing out some important genomics related issues from the wider community.

One point that I raised earlier (Message 25) was about more regional collaboration, especially in developing countries, and the establishment of larger and better resourced regional centres for genomics and related disciplines. This echoes some of the sentiments of a previous e-mail conference entitled "Learning from the past: Successes and failures with agricultural biotechnologies in developing countries over the last 20 years" which was held by the FAO Biotechnology Forum in 2009 (http://www.fao.org/biotech/biotech-forum/conference-16/en/). To

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Biotech-Mod3
Mon, 25 Mar 2013 17:50:58 +0100
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I am Sathish Kumar Ponniah, plant molecular breeder working as extension specialist at the University of Arkansas at Pine Bluff, United States. I thank the moderator for the useful discussion.
 
I have been following the discussion for the past few weeks. I would like to thank the discussions by Beatrix Tappeser (Message 24) and Wayne Parrott (Message 35) for highlighting 'omics' tools that are used as plant breeding techniques in the current scenario. As we are progressing to improve plant breeding techniques, 'omics' tools form a very good addition to the conventional techniques. In the next-generation sequencing era, markers

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Biotech-Mod3
Mon, 25 Mar 2013 17:50:28 +0100
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This is Acacia Alcivar-Warren from Environmental Genomics Inc, a small consulting firm in Massachusetts, USA, and an unpaid part-time volunteer at the UNA SALUD/ONE HEALTH Genomics & Epigenetics Program of the Fundación para la Conservación de la Biodiversidad Acuática y Terrestre (FUCOBI) of Ecuador.

I agree with Dr. Dubock (Message 54) that the conference is lacking on "animal 'omics'" information. On March 14, 2013, I sent a message to the AnGenMap Discussion Mailing List (http://www.animalgenome.org/community/discuss) distributed to 2365 members, some of whom are members of the National Animal Genome Research Program (NRSP-8, funded by the United States Department of Agriculture [USDA]) that include cattle,

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Biotech-Mod3
Sun, 24 Mar 2013 07:47:48 +0100
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This is Harjit Singh Rekhi, Professor of Crop Genetics and Breeding, University of West Indies, Trinidad and Tobago (on sabbatical leave from a Canadian Federal Agency).

I support the establishment of Global Genomics/Breeding Forum (Messages 48 - 50, 53).

To make such initiatives useful to the developing countries, in addition to other things, there would be need to provide support for development of mapping populations for the crops important to developing countries. Earlier, in Message 60 of Conference 16 of the FAO Biotechnology Forum on "Learning from the past: Successes and failures with agricultural biotechnologies in developing countries over the

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Biotech-Mod3
Sun, 24 Mar 2013 07:37:08 +0100
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This is Doris Zuñiga of the Universidad Nacional Agraria La Molina, Peru.

I am very grateful for all the contributions of scientists about the impact of genomics. I work with plant growth promoting rhizobacteria and it is significant to have the identification using the total or
partial genomic of these bacteria so that they can be applied to the field for crop improvement. Yet in a few places in our country is being implemented in a limited way these bacteria as inoculants in replacement of chemical fertilizers and also for the control of phytopathogenic with good results.

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Biotech-Mod3
Sun, 24 Mar 2013 07:36:59 +0100
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This is from Milton Kanashiro, Empresa Brasileira de Pesquisa Agropecuária (Embrapa), Brazil.

I am really sorry I could not enter into the Conference earlier. Working with tropical forests, focusing more on natural forest management, I do think genomics is very important tools when the level of domestication and selection is already highly developed. At this moment, molecular genetics is very important to access population diversity and the main priority is the basic and tedious job of correct species identification. In the Amazon forest, there are several commercial timber species with a very complex taxonomy puzzle to solve, which I take

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Biotech-Mod3
Sun, 24 Mar 2013 07:27:46 +0100
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Hello, Adrian Dubock again.

Good to hear from Dr Rajeev Varshney (Message 53) about ICRISAT’s plans, which seem to go some way towards what participants in this conference are asking for. One aspect which seems to be missing is “animal ‘omics”.

Another point: In my experience, competition keeps institutions on their toes, with benefits for speed and focus of progress. For benefit to humanity ‘cooperative-competition’ is to be encouraged too. So Professor Denis Murphy’s idea should also be promoted.

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Biotech-Mod3
Sat, 23 Mar 2013 06:39:02 +0100
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This is Rajeev Varshney again.

I am quite excited to see the ongoing discussions by Denis Murphy (Message 48), Adrian Dubock (Message 49) and David Steane (Message 50) on establishing a global genomics/breeding forum. In fact as a part of CGIAR Generation Challenge Pragramme (GCP), GCP established the Integrated Breeding Platform (IBP) for facilitating crop breeding using advanced tools (https://www.integratedbreeding.net/). And very recently, we have established the Agricultural Genomics Network (AGN) as a part of GCP/IBP (https://www.integratedbreeding.net/agricultural-genomics). Though this portal is still under development, with an objective of making genetic research and breeding applications cost-effective by enhancing adoption of modern

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Biotech-Mod3
Fri, 22 Mar 2013 15:57:06 +0100
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Let me introduce myself: my name is Michel Naves, from the french Institut National de la Recherche Agronomique (INRA) and I work in animal breeding and genetics of local animal breeds in French West Indies. I am really greatly interested by this conference as I am involved in a research program on the improvement and management of the local tropical breeds, mainly on Creole cattle. Other colleagues in my team work on small ruminants and pigs. In our work, we tackle the use of genomic tools (and other -omics), for i) the identification and quantification of variability within/between breeds, ii) 

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Biotech-Mod3
Fri, 22 Mar 2013 15:41:42 +0100
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I am Dr. A. Sudhakar, Ph.D in Animal Genetics and Breeding and presently working with the National Dairy Development Board, India.

At first I would like to thank the enablers of the e-Conference (John Ruane and the FAO team) and contributors by sharing their experiences.

I would like to highlight a few areas where knowledge of genomics is used currently:

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Biotech-Mod3
Fri, 22 Mar 2013 15:17:35 +0100
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This is David Steane again.

I particularly like the comments of Adrian Dubock (Message 43) and the contributions of Denis Murphy. As an animal breeder, I consider our efforts are rather more complicated than those of plant breeders. While I believe that we need much more information about the environments in which certain genotypes are normally expected to perform before we can best use the techniques, this does not mean opposition to 'omics - simply caution that we do not get things wrong - especially as it is the farmers who suffer such mistakes. I do, however, believe that there is need for more

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Biotech-Mod3
Fri, 22 Mar 2013 15:11:46 +0100
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This is Adrian Dubock again.

I am sure I will not be the only one to support the development of the concept proposed by Denis Murphy (Message 48).

It seems that this opportunity for information sharing and creation of critical mass of capability would go some way to addressing the clearly expressed frustration of many conference participants from developing countries.

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Biotech-Mod3
Fri, 22 Mar 2013 06:07:51 +0100
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This is Denis Murphy again, from the University of Glamorgan, UK.

I greatly appreciate all the comments from colleagues throughout the world and applaud the opportunity provided by John Ruane and the team at FAO for us to communicate together in this way.

I especially welcome the comments of Adrian Dubock (Message 43) as somebody who has worked with a major biotech company (Syngenta) and currently works on the at-times controversial golden rice project. It is now 14 years since I heard Ingo Potrykus announce the successful production of golden rice at a conference in London and the variety has

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Biotech-Mod3
Fri, 22 Mar 2013 05:57:33 +0100
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I am Sahar Al-bayatti, a livestock geneticist working for the Ministry of Agriculture in Iraq, the national coordinator (NC) for animal genetic resources (AnGR) and a member of the biosafety committee working on GMO legislation for the Ministry of Environment.

First, I would like to thank the organizers of this important e-conference. I have been following the very useful discussions. It is clear from ongoing discussions that genomics has an important role in agriculture and agro-industry sectors. But this as Rajeev Varshney said (Message 28) is happening in either developed countries or in private sectors. I think it is early

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Biotech-Mod3
Thu, 21 Mar 2013 13:22:17 +0100
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This is Darmono Taniwiryono, a senior research scientist at the Indonesian Biotechnology Research Institute for Estate Crops (IBRIEC) in Bogor, Indonesia. Estate Crops cover oil palm, Hevea rubber, cacao, coffee, tea, and sugarcane. I had been the head of that institute for quite sometime, ended just recently this year. Now I become part of the Center for Agricultural Policy Studies (CAPS), based in Jakarta, Indonesia, as an Institutional Development Officer of Biotechnology Program. 

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Biotech-Mod3
Thu, 21 Mar 2013 11:06:12 +0100
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Dear Participants,

This is just to remind you all that we are in the very last days of this FAO e-mail conference on "Impacts of genomics and other 'omics' for the crop, forestry, livestock, fishery and agro-industry sectors in developing countries".

The last day for receiving messages is Sunday 24 March 2013. The final messages will be posted on Monday 25 March and the conference is then closed.

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Biotech-Mod3
Thu, 21 Mar 2013 11:04:46 +0100
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This is Rajeev Varshney (again), working for two CGIAR organizations, namely the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT, www.icrisat.org) and the Generation Challenge Programme (www.generationcp.org) and I sent Message 28. 

I agree with Raul Castillo (Message 41) and support genomics research and genomics-assisted breeding for less-studied (many times called 'orphan crops') but locally important crops. But the good news is that the power of genomics technologies and collaboration can transform any so-called 'orphan crop' to 'genomics resources rich crop'. ICRISAT and its partner institute have demonstrated this in several cases. For instance, pigeonpea (Nature Biotechnology 
30, 83-89; http://www.nature.com/nbt/journal/v30/n1/full/nbt.2022.html)

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Biotech-Mod3
Thu, 21 Mar 2013 11:04:30 +0100
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This is Shashi Bhushan Tripathi from The Energy and Resources Institute (TERI), New Delhi, India.

I am writing in response to the point made by Dr Rai (Message 38) regarding the impact of marker-assisted selection (MAS) in plant breeding so far and my comments are from the Indian perspective only. We are working on marker-assisted breeding in several crops such as Indian mustard, Jatropha and Chilies for the past 10 years. I would like to state that the potential of MAS has not yet been realized to any level which could be considered significant. I would like to list some

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Biotech-Mod3
Thu, 21 Mar 2013 11:04:17 +0100
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This is from Adrian Dubock, Golden Rice Project Manager, and Executive Secretary to the Golden Rice Humanitarian Board.

It is good to see the excitement that the realization of genetics for improving food security generates. It is also good to see that the excitement is tempered with realistic prudence concerning where in the expected long time line to precise genetic management for useful phenotypes we are. As a  case in point, I was involved with the announcement of the determination of the genome of rice by Syngenta (for whom I then worked) in about 2001 - more than a decade ago. It hasn't

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Biotech-Mod3
Thu, 21 Mar 2013 11:04:00 +0100
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This is Sanjeev Raikar from SGS India Pvt Ltd, Hyderabad, Head Biotech Operations.

After going through a few of the messages which have mostly stressed on how and when genomics would be efficiently put to use in breeding activities especially if we were to improve the wide variety of crops mostly in our tropical developing countries.... Many views have been expressed such as lack of thorough understanding of genomics as a tool by breeding scientists in developing countries, the constant upgradation of equipments, changing methodology or protocols, the millions of dollars involved in upgradation of equipments, and above all the

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Biotech-Mod3
Wed, 20 Mar 2013 17:54:08 +0100
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This is Raul O. Castillo, Director, Sugarcane Research Center of Ecuador.

I've been following the interesting conference on genomics and I am impressed with so many people presenting their practical views and also the number of scientists working in this issue who have gone further with gene sequencing and gene identification for several crop plants and some animal species. However, most of the research is done for the economically important crops of worldwide consumption. Minor crops of local consumption are hardly studied or included in such projects. Albeit, these crops feed millions of people living in the less developed world

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Biotech-Mod3
Wed, 20 Mar 2013 16:45:44 +0100
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This is from Sinclair Mantell, Nakhlatec International Development Advisors, Sweden.

Denis Murphy (Message 39) should be congratulated by members of the forum for presenting very effectively the perspective and reality of the practical field-level impact of -omics in the domains of tropical livestock and crop production in low to middle income countries (notice the emphasis on production as against breeding!).

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Biotech-Mod3
Wed, 20 Mar 2013 06:24:44 +0100
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This is Denis Murphy again, from the University of Glamorgan, UK.

Two main points I’d like to raise:

1. About genomics in general. Together with our international colleagues, we are working on several projects aimed at the annotation of whole genome sequences in a variety of plant species from the model Arabidopsis to large commercial crops such as oil palm. We are also trying to analyze the genomes of crop pathogens, such as the fungal Ganoderma spp that infect oil palm crops.

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Biotech-Mod3
Tue, 19 Mar 2013 11:52:32 +0100
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This is KN Rai again from ICRISAT, India.

Most of the discussions on the subject has gone on challenges and opportunities, and these are truly interesting. But the response/inputs to the first main conference question (i.e. what have been impact of genomics technologies so far) remains unaddressed and still not forthcoming, and this is vital for the breeders to appreciate the application power of these technologies and their cost effectiveness. There is no doubt in anybody's mind that these are the technologies which will be routinely applied effectively in the future, but how far away is this future (a few

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Biotech-Mod3
Tue, 19 Mar 2013 09:48:48 +0100
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This is from Prof. Sudarsono of IPB, Bogor, Indonesia again.

I would like to add some opinions on the importance of training and more data access about the genomic sequences. I would agree with Rajeev Varshney's statement (Message 28) that we, in the developing countries may not be able to keep up with the changing technology and the cost of the genome sequencing even if it is continually going down. [Rajeev wrote ".. several colleagues in developing countries still feel that they should be able to undertake genomics-assisted breeding only if they are involved in generation of genotyping data. As

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Biotech-Mod3
Tue, 19 Mar 2013 09:15:06 +0100
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This is Dele Raheem. I am a Food Scientist currently at the Arctic Centre (a multi-disciplinary centre) and part of the University of Lapland, Finland, as a visiting researcher.
 
It is a great opportunity to read various contributions on how these "omics" can make positive impacts in developing countries as exemplified by Message 35 by Wayne Parrott and Message 33 by Sudarsono. As more opportunity to carry out research develops in this area there are bound to be new opportunities. Research in developing countries is often hampered by challenges including funding to get access to the right equipment which retards

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Biotech-Mod3
Mon, 18 Mar 2013 14:47:31 +0100
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Dear Participants,

This is just to remind you all that we are now entering the third and final week of this FAO e-mail conference on "Impacts of genomics and other 'omics' for the crop, forestry, livestock, fishery and agro-industry sectors in developing countries" which runs from 4 to 24 March.

As described in the conference Background Document, the first sequenced genomes of domesticated animals and plants were released about 10 years ago and an ever increasing number of important species have been sequenced each year since then; the genomes of several thousand micro-organisms have now been sequenced; and the knowledge

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Biotech-Mod3
Mon, 18 Mar 2013 14:45:56 +0100
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My name is Wayne Parrott, and I run a soybean genetics program at the University of Georgia, United States. To begin with, I want to thank the organizers of the conference.

Beatrix Tappeser (Message 24) gave a really great overview of the current state of genomic applications to breeding. Yet, although the use of marker assisted selection (MAS) is routine and widespread in a few crops, such as maize and soybean, the bottom line is that the technology is still in its infancy. I want to share my experience in soybean, and as well as where I see this technology

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Biotech-Mod3
Sat, 16 Mar 2013 06:32:19 +0100
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This is Gabriel Ataguba, from the Department of Fisheries & Aquaculture, University of Agriculture, Makurdi, Nigeria.

I quite agree with Dr Danlami Moses Ogah (Message 30). Training and equipment are the necessary tools we as young scientists in developing countries in Sub-Saharan Africa need to enable us to grasp this technology. I do research in fish breeding and genetics and I have tried to get laboratories to help me carry out basic DNA work (PCR - RAPD, AFLP) but I could not get any to get it done. We as young scientists in developing countries urgently need the support of

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Biotech-Mod3
Sat, 16 Mar 2013 06:31:43 +0100
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This is Sudarsono, from the Department of Agronomy and Horticulture, Faculty of Agriculture, Bogor Agricultural University (IPB), Bogor, Indonesia. I am a university lecturer who runs a plant molecular biology lab (PMB Lab) where a number of PhD and MSc students are conducting their thesis and dissertation researches.

Regarding the topic of discussion "what have been the impacts (positive and/or negative) so far of genomics and the other 'omics' for the crop, forestry, livestock, fishery and agro-industry sectors in developing countries?":

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Biotech-Mod3
Sat, 16 Mar 2013 06:02:05 +0100
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This is Tarek Yehia Soliman Kapiel, I am currently working as Assistant Professor of Plant Biotechnology, Al Baha University, Kingdom of Saudi Arabia.

I am following the important topics of the conference and the thought-provoking discussions from the 1st e-mail, and I would like to share some notes and recommendations regarding the current situation of the genomic research in developing countries.

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Biotech-Mod3
Fri, 15 Mar 2013 16:33:50 +0100
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This is Martin Tiznado, from the Centro de Investigación en Alimentación y Desarrollo (CIAD), Hermosillo, Mexico.

Regarding "What are the impacts (positive and/or negative) of genomics and other 'omics' likely to be in the near future (e.g. the next five years) for the crop, forestry, livestock, fishery and agro-industry sectors in developing countries?":

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Biotech-Mod3
Fri, 15 Mar 2013 11:19:49 +0100
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My name is Dr. Danlami Moses Ogah. I am a lecturer in the Department of Animal Science, Nasarawa State University, Keffi, Shabu, Lafia Nigeria. My specialty is in animal breeding and genetics.
 
Thanks for the opportunity for me to make my input. Actually some of us young scientists from developing countries are excited in hearing and reading about application of genomics to improve production. But the majority of us have no idea about genomics, no laboratory for us to carry out researches, no funding and facilities. I solicit FAO to develop programmes that will assist scientists from Africa to

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Biotech-Mod3
Fri, 15 Mar 2013 11:01:56 +0100
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This is Uche Godfrey Okeke again.

I strongly agree with Humberto Peralta's opinion (Message 27) on viewing agriculture as a complex system. Microbes, especially fungi and bacteria, are having profound interactions with especially the plant roots for different purposes including nutrient exchange, nutrient recycling and transfer, reduction of elements into that which can be utilized by plants, warding off pathogenic organisms, forming complex matrices for structural adaptation, aiding in plant signal transduction for adaptation in their environment and so much more.

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Biotech-Mod3
Thu, 14 Mar 2013 22:07:05 +0100
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This is Rajeev Varshney, working for two Consultative Group on International Agricultural Research (CGIAR) organizations, namely the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT, www.icrisat.org) and the Generation Challenge Programme (www.generationcp.org).

I have been following very useful discussions and submissions from a large number of colleagues. I am very excited to see contributions from both young as well as senior colleagues. It is clear from ongoing discussions that genomics has an important role in crop, forestry, livestock, fishery and agro-industry sectors. While we have success stories not only in crops, but in other sectors as well, we all

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Biotech-Mod3
Thu, 14 Mar 2013 21:51:51 +0100
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This is from Humberto Peralta, researcher at the Center for Genomic Sciences, National University of Mexico in Cuernavaca (Mexico).

Genomics can also be used to enhance yield of crops by studying the whole array of genes from beneficial microorganisms, but also by modifying specific genetic targets on them. Currently, there is a huge amount of sequenced bateria (3841 to date, http://www.genomesonline.org). There is genome information available for nitrogen fixing bacteria such as Rhizobium (bean, pea, vetch symbiont), Sinorhizobium (alfalfa symbiont), Bradyrhizobium japonicum (soy symbiont) etc. and also other plant-growth promoting rhizobacteria (PGPR) such as Herbaspirillum, Azospirillum, Azotobacter, and Frankia. Microorganisms

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Biotech-Mod3
Thu, 14 Mar 2013 09:12:25 +0100
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Dear Participants,

We are now at the halfway stage of this FAO e-mail conference on "Impacts of genomics and other 'omics' for the crop, forestry, livestock, fishery and agro-industry sectors in developing countries" which runs from 4 to 24 March.

First, a very big thank you to each of the 21 people who have already posted a message to the conference.

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Biotech-Mod3
Wed, 13 Mar 2013 13:44:47 +0100
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This is Okoro, Victor Mela Ph.D, animal breeder and geneticist, Federal University of Technology, Owerri, Nigeria.
 
I agree with Abdulmojeed Yakubu (Message 13) where he posited that a lot has not been exploited in animal genomics in Africa, citing Dr. I.G. Imumorin in his lecture “Potential exists for application of biotechnology to livestock improvement in the areas of disease resistance, nutrition and reproduction”. Since most of our indigenous breeds are characteristically of low output and in most cases disease resistant, there is need to use genomic technologies in the improvement of these breeds in a mutual way that will

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Biotech-Mod3
Wed, 13 Mar 2013 10:12:51 +0100
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This is Professor Denis J Murphy, University of Glamorgan, United Kingdom. I previously worked with FAO on the ABDC-10 biotechnology meeting in Mexico in 2010 and in framing the crop sector background document which covered several aspects of crop genomics. More recently, I have been working on crop genomics at several levels from the use of bioinformatics to analyse next generation genome sequencing data to more applied uses of molecular marker development in crops such as oil palm. 

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Biotech-Mod3
Wed, 13 Mar 2013 10:11:22 +0100
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My name is Beatrix Tappeser from the German Federal Agency for Nature Conservation. I am a biologist and the head of the division GMO regulation and biosafety at the Agency.

We were interested in the use of plant genetic resources together with marker assisted breeding (instead or in addition to GMO development) and commissioned a project to researchers of the University of Kassel, Germany (Sarah Brumlop MA, Prof. Maria Finckh) to explore the potentials of marker assisted selection (MAS) in supporting agricultural biodiversity.

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Biotech-Mod3
Tue, 12 Mar 2013 16:23:54 +0100
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This is Gilbert Msuta, a Livestock Research Scientist at the National Livestock Research Institute in Tanzania. I am a recent graduate of Msc. Animal Science from Melbourne University, Australia, where I wrote my thesis on the Application of Bioinformatics tools to identify key candidate genes regulating residual feed intake (RFI) and other traits in dairy cattle. 

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Biotech-Mod3
Tue, 12 Mar 2013 14:31:27 +0100
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My name is Richard Osei-Amponsah, Lecturer of Animal Breeding and Genetics at the University of Ghana in Legon, Ghana.

I thank the organisers of this e-mail conference for the opportunity to discuss an important issue that has an impact on our efforts to attain food security.

I agree with other contributors on the potential benefits of genomics in plants and animal breeding. If a technology exists that can help us increase food production, reduce diseases and ensure that we get the best of investments from agriculture then it makes sense to utilise that technology.

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Biotech-Mod3
Tue, 12 Mar 2013 09:52:05 +0100
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From David Steane again (Message 8).

I, too, agree with John Gibson's assessment of the situation. That is precisely why I am suggesting that the importance of genomics in the context of real contributions to sustainable agriculture depends on obtaining more comprehensive data than that used in the simplistic, naive schemes being used at the present time. The information on environmental conditions is crucial to any understanding of the genetic performance - sequencing offers an opportunity to find such links.

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Biotech-Mod3
Tue, 12 Mar 2013 09:51:47 +0100
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This is from Mark Boggess, National Program Leader - Food Animal Production 101, Animal Production and Protection, in the United States Department of Agriculture Agricultural Research Service (USDA-ARS).

I would like to support the arguments made by Uche Godfrey Okeke and John Gibson with an additional perspective or two.
 
I agree that the remarkable progression of genomic theory and application is potentially providing extraordinary opportunity for small-holders and livestock industry programs in developing countries, especially when combined with next generation sequencing. I am confident that properly administered and developed there will be extraordinary progress in areas of critical need relating

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Biotech-Mod3
Mon, 11 Mar 2013 13:56:39 +0100
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This is Uche Godfrey Okeke, again. Greetings again to everyone and special thanks to everyone contributing in these discussions.

I am very pleased with the statement from John Gibson (Message 17) stating: " genetic improvement is too often based on wishful thinking rather than critical assessment of farmer livelihoods, needs and demands......research geneticists have a poor track record in both developed and developing world of producing products that farmers actually want".

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Biotech-Mod3
Mon, 11 Mar 2013 12:46:45 +0100
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This is from David Jordan, Sorghum Breeder, Queensland Alliance for Agriculture and Food innovation at the University of Queensland, Brisbane, Australia.

I think John Gibson (Message 16) makes some excellent points which are equally relevant to plant breeding. In order for application of genomic selection methods to generate good returns there is a requirement for a large suite of supporting skills and infrastructure (high level of conventional plant breeding capacity, DNA extraction, data management systems, seed and DNA inventory and tracking systems, statistics, rapid generation turn around, perhaps double haploid systems etc). In many cases, these are hard or impossible

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Biotech-Mod3
Mon, 11 Mar 2013 09:35:33 +0100
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This is from John Gibson, again.

In the livestock world, geneticists understandably hold out hope for the application of genome assisted selection tools in developing world systems. The argument is that in most cases there is no existing genetic improvement program and genomic tools provide an alternative to the establishment of on-going recording and genetic evaluation programs. But genomic selection faces many of the same hurdles that have prevented effective genetic improvement using existing technologies. A few of these include:

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Biotech-Mod3
Mon, 11 Mar 2013 09:30:50 +0100
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This is from Professor John Gibson, Director of The Centre for Genetic Analysis and Applications, Armidale, Australia.

The discussion so far has covered multiple types of use of genomic technologies. I suggest that for both plants and animals it useful to distinguish three broad categories of use:

1) Use to gain information (research) that assists in the subsequent development process (e.g. characterising plant gene bank accessions or livestock breeds; assessing endemic pathogen diversity).

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Biotech-Mod3
Mon, 11 Mar 2013 05:56:27 +0100
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This is from Dr. Paulo Ramos, Environmental analyst from Brazil. I have been working with Agroecology and biodiversity conservation. I am now representing the Brazilian Agroecology Social Organizations as a member of the National Technical Commission for Biosafety (CTNBio).

I would like to thank everybody for sharing experiences here in this e-mail conference.

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Biotech-Mod3
Sun, 10 Mar 2013 07:33:36 +0100
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I am Pushpendra Gupta again (I sent message 1). I like this message 10 by Uche Godfrey Okeke, and would like to submit as follows:

(1) I am also disappointed with the number of messages received (hardly 2 messages per day); what is the reason for this? I believe that not many people have read enough and therefore know enough about the role of genomic selection in crop improvement and never tried to practise it in developing countries including India, not because they don't approve of it, but because they cannot appreciate the technology yet (although the technology still suffers

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Biotech-Mod3
Sun, 10 Mar 2013 07:32:38 +0100
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I am Abdulmojeed Yakubu, a senior lecturer in Animal Breeding and Genetics, Department of Animal Science, Faculty of Agriculture, Nasarawa State University, Keffi, Shabu-Lafia Campus, Lafia, Nigeria.

In Nigeria, while data exist on the application of genomics to improve crop production, little can be said of livestock improvement via biotechnology. In a recent lecture by Dr. I.G. Imumorin of the Department of Animal Science, Cornell University, Ithaca, ''potential exists for application of biotechnology to livestock improvement in the areas of disease resistance, nutrition and reproduction''. In fact, the technology of genomic selection where we select superior animals based on total

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Biotech-Mod3
Sun, 10 Mar 2013 07:32:19 +0100
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I am Takele Taye Desta, a PhD student (Genetics) in The University of Nottingham, United Kingdom.

The majorities of a sort of omics works conducted so far in developing countries are related to genomics and in most instances these have been concentrated on genetic diversity studies. In fact dealing with genetic diversity and population structure is the entry point to work on omic disciplines. However, even these types of basic genomic works are by and large far from complete compared to the high level of genetic diversity existing in the least developed nations.

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Biotech-Mod3
Sat, 9 Mar 2013 19:28:26 +0100
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This is from Dr Chandra Sekhar Mukhopadhyay, Guru Angad Dev Veterinary and Animal Sciences University (GADVASU), India.

In reply to Dr. Drew L. Kershen (Message 6):

The replies are really impressive and hold promise. From my early inititaion in this field, I found that the molecular level solutions have always replaced the predecessor. (perhaps this is the essence of science). Now it is the time of molecular breeding with genomic selection. Can we expect that this will help the developing countries, at least to some extent. If yes, how to solve the problem of recording the proteome, at practical level,

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Biotech-Mod3
Sat, 9 Mar 2013 19:14:33 +0100
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My name is Uche Godfrey Okeke. I have a masters in Bioinformatics and Systems biology and a bachelors in Animal breeding and Genetics. I am currently a Bio-informatician at the DNA Sequencing and Genomics Lab, Institute of Biotech, University of Helsinki, Finland.

I must confess that I am a bit disappointed with the number of people contributing to this topic on the role of genomics in plant and livestock improvement in developing countries especially now that there is a wave of projects focusing on the application of genomic selection in many species of plants and animals across the developed world.

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Biotech-Mod3
Fri, 8 Mar 2013 16:30:18 +0100
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This is from Petros Chigwechokha, Kagoshima University, Japan.

Impacts of genomics are rather difficult to clearly isolate when it comes to aquatic resources. Genomics and its application to aquatic resources, particularly fish, still lags behind compared to other organisms. As rightly indicated in the conference background document, genomic work, most importantly, genome mapping, has been done in zebrafish (Danio rerio), medaka (Oryzias latipes) mostly because these have been widely used as model organisms for more insights into the functions of various genes that are important to human health (e.g. neuraminidase and transferase genes). Such studies have received a lot of attention by their link with human

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Biotech-Mod3
Fri, 8 Mar 2013 10:19:05 +0100
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A message from David Steane - retired and based in Thailand. Before retirement, I lead an FAO project on 'Conservation and Use of Animal Genetic Resources in Asia' after 4-5 years in Rome HQ. Prior to that, I was Head of Animal Breeding and Genetics for the Meat & Livestock Commission in Britain for over 20 years. At present, I am a Board Director of Rare Breeds International and Honorary Adviser on Genetics and Biodiversity to the Department of Livestock Development, Thailand. 

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Fri, 8 Mar 2013 10:03:19 +0100
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This is from Kedar N. Rai, again.

We need to address more main question 1 (i.e. "What have been the impacts (positive and/or negative) so far of genomics and the other 'omics' for the crop, forestry, livestock, fishery and agro-industry sectors in developing countries?"). And just a few selective examples may not be so convincing. I am aware of some success stories of marker-assisted selection (MAS), but the question that those successes could have also been achieved by conventional breeding at much lower cost has not been answered (of course, the conventional approach would have taken a bit longer). Further,

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Biotech-Mod3
Fri, 8 Mar 2013 09:50:15 +0100
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This is from Drew L. Kershen, University of Oklahoma, United States.

In answer to the query in Message 3 by Dr. Rai, requesting examples (a list) of the efficiency of genomics and other biotech tools, I respond with several. Although not a scientist, I work on legal issues related to modern breeding techniques. Due to that work, I have learned some examples or citations as follows.

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Biotech-Mod3
Thu, 7 Mar 2013 13:09:02 +0100
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Dear Participants,

This is just a quick update on the conference so far.

About 500 people have subscribed, coming from a least 50 different countries.

As described in the conference Background Document, the first sequenced genomes of domesticated animals and plants were released about 10 years ago and an ever increasing number of important species have been sequenced each year since then; the genomes of several thousand micro-organisms have now been sequenced; and the knowledge generated from genomics can be applied in several different ways. With this as a background, people are asked to address two main questions in this

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Biotech-Mod3
Wed, 6 Mar 2013 17:29:46 +0100
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This is Jim Currie, MD of Currie Marketing. I have been involved in sales and marketing of food ingredients for 30 years although I did get a BSc Chemistry many years ago !

One of my pet projects is the production of l-cystine and L cysteine by fermentation. There is a good size market for cysteine for flavour production and as a bread additive. Most of the world supply is extracted from chicken and duck feathers and in the past from human hair. All are sources of keratin. The production of fermentation cysteine requires pure strains of bacteria and good operating

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Biotech-Mod3
Wed, 6 Mar 2013 11:47:11 +0100
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This is Olivier Hanotte. I am a livestock geneticist working at the University of Nottingham (UK) for the last 4 years before that I was working for the International Livestock Research Institute (ILRI), a Consultative Group on International Agricultural Research (CGIAR) institute.

In my opinion, the opportunities of genomics for the livestock and plant sector of the "tropics" is more on the new perspectives it is offering rather than new solutions to old problems. Animals and plants breeders know what they are doing. They have done it very well for centuries and will do as well for the coming generations.

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Biotech-Mod3
Wed, 6 Mar 2013 09:08:49 +0100
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I am Kedar N. Rai, working as a pearl millet breeder (using conventional breeding approaches and achieving great successes) at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India. But I do try to read and follow the discussions on application aspects of genomics, and it is with this intent that I joined this e-conference. 

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Biotech-Mod3
Tue, 5 Mar 2013 16:25:26 +0100
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I am Vadivel Arunachalam, Principal Scientist and Head Horticulture section and I work at the Indian Council of Agricultural Research (ICAR) at Goa centre. I worked on computational genomics and mining of genome sequences, expressed sequence tag (EST) libraries for new molecular markers (SSR, SNP, priming sites of RAPD/iSCAR). I authored a book on genomics of cultivated palms published by Elsevier. The book is a review of genomics research on palms (the plants belong to Arecaceae family). We also developed on molecular markers associated with resistance to root (wilt) disease, eriophyid mite pest in coconut. Root (wilt) is a serious disease in coconut palms of 

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Biotech-Mod3
Mon, 4 Mar 2013 16:14:58 +0100
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[Thanks to Professor PK Gupta from India for sending in the first message of this FAO e-mail conference on the "Impacts of genomics and other 'omics' for the crop, forestry, livestock, fishery and agro-industry sectors in developing countries". All messages will be numbered chronologically. If during the conference you notice that you are missing any messages, just contact me at [log in to unmask] ...Moderator]. 

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Biotech-Mod3
Fri, 1 Mar 2013 13:57:25 +0100
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Dear Colleagues,

Welcome to this FAO e-mail conference on "Impacts of genomics and other 'omics' for the crop, forestry, livestock, fishery and agro-industry sectors in developing countries" !! Thank you for joining.

You can send messages now (send them to [log in to unmask]). Messages will be posted from Monday 4 March onwards while the last day for receiving messages will be Sunday 24 March 2013.

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Biotech-Mod3
Thu, 28 Feb 2013 15:37:56 +0100
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Dear Colleagues,

Thank you for subscribing to this FAO e-mail conference on "Impacts of genomics and other 'omics' for the crop, forestry, livestock, fishery and agro-industry sectors in developing countries" which begins in a few days time.

I am now sending you the Background Document to the conference.

It aims to provide information that you, as participants, will find useful for the e-mail conference. The first Section of this 10-page document provides some general background to the subject. Section 2 of the document provides an overview of the current status regarding genomics in food and agriculture. Section 3 briefly discusses

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