COCONUT - ONLINE

  

OILPALM-ONLINE 
 
ICA4-2001-10066

( Link2Palm )
 

Construction and exploitation of high density DNA marker and physical maps in the perennial tropical oil crops coconut and oil palm: from biotechnology towards marker-assisted breeding

 

Shared-cost research project: 1.8.2001 - 31.7.2004

Total cost:    Euro                          EC contribution:    Euro

 

PARTICIPANTS:

Prof. Dr. Wolfgang ROHDE (P1 Coordinator) - Max-Planck-Institut fuer Zuechtungsforschung (MPIZ)

Carl-von-Linne-Weg 10, D 50829 Koeln, Germany

TEL:++49221 5062 420, FAX: ++49 221 5062 413, email: rohde@mpiz-koeln.mpg.de, Website: http://www.mpiz-koeln.mpg.de/~rohde/index.html

Subcontractor to P1: Dr. Alois KULLAYA (S2) - Mikocheni Agricultural Research Institute (MARI)

P.O. Box 6226, Dar es Salaam, Tanzania

TEL: ++255 51–700552 or 74606, FAX: ++255 51-75549, email: arim@africaonline.co.tz 

     

Dr. Enrique RITTER (P2) - NEIKER, Centro de Arkaute

Apartado 46, E-01080 Vitoria, Spain

TEL: ++34-945-121313, FAX: ++34-945-281422, email: eritter@neiker.net,Website: http://www.neiker.net

Subcontractor to P2: Dr. Carlos OROPEZA (S1) - Centro de Investigación Científica de Yucatán (CICY)

Km 7.5, Carr. Mérida-Progreso, A.P. 87, Cordemex 97310 Mérida, Yucatán, México

FAX: ++52 - 99 813900, TEL: ++52 - 99 813914, email: cos@cicy.mx 

 

     

Dr. Norbert BILLOTTE (P3) - CIRAD

Avenue Agropolis, 34398 Montpellier Cedex 5, FRANCE

TEL: ++33 04 67 61 71 16, FAX: ++33 04 67 61 71 83, email: norbert.billotte@cirad.fr

Subcontractor to P3: Dr. Jean-Louis KONAN (S3) - CNRA Station Cocotier Marc Delorme

BP13, Abidjan 07, Côte d’Ivoire

 

          

Dr. Maria Judith B. RODRIGUEZ (P4) - Philippine Coconut Authority (PCA)

Albay Research Center (ARC), Banao, Guinobatan 4503, Philippines

TEL: 063-059-4846614, FAX: 063-059-4846615, email: pcaarcvb@globalink.net.ph

 

   

Dr. Dwi ASMONO (P5) - Indonesian Oil Palm Research Institute (IOPRI)

P.O. Box 1103,Medan 20001, INDONESIA

TEL: (0622) 21926, FAX: (0622) 24605, email: dasmono@psiantar.wasantara.net.id

 

    

Dr. Suan-Choo CHEAH (P6) - Malaysia Palm Oil Board (MPOB)

6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang Selangor, MALAYSIA. 

P.O Box 10620, 50720 Kuala Lumpur, MALAYSIA. 

FAX: 603-89259446 email: cheah@mpob.gov.my

      

 

Mr. ASMADY (P7) - SOCFINDO (P.T. SOCFIN INDONESIA) 

Jl. K.L. Yos Sudarso N° 105 MEDAN 20115 P.O. Box 1254 Medan 2001 INDONESIA

FAX: (62) 61 661 43 90, email: socfindo@indosat.net.id

 

 

Commission disclaimer

This web-page does not necessarily reflect the Commission's views and in no way anticipates its future policy in this area. Its content is the sole responsibility of the publishers. The information contained herein, including any expression of opinion and any projection or forecast, has been obtained from or is based upon sources believed by the authors to be reliable but is not guaranteed as to accuracy or completeness. The information is supplied without obligation and on the understanding that any person who acts upon it or otherwise changes his/her position in reliance thereon does so entirely at his/her own risk".

 

Commission acknowledgement

This project is carried out with the financial support from the Commission of the European Communities (project N° ICA4-2000-10010), Directorate General Research - INCO-Dev. It does not necessarily reflect its views and in no way anticipates the Commission’s future policy in this area.

 
Objectives

The general objectives of this project are:

  1. to provide the methodological basis and molecular tools for improving the breeding efficiency in the two perennial tropical oil crops coconut and oil palm.

  2. to develop these DNA marker-based breeding strategies in collaboration with the most important countries in coconut and oil palm production and to directly transfer to developing countries small-scale technological solutions for the genetic improvement of these tropical oil crops.

Specific scientific and technological objectives are summarised as follows:

  1. Development of molecular resources and construction of high density (HD) reference molecular linkage maps for coconut and oil palm.
    2.
    1. Massive development of microsatellite markers (SSRs) for each species.
    2. Generation of cosmid libraries and development of single nucleotide polymorphism markers (SNPs) for coconut and oil palm.
    3. Construction of HD reference linkage maps for coconut and oil palm based on AFLP, SSR and SNP markers.
    4. Construction of physical maps of coconut and oil palm using individual as well as multidimensionl pools of cosmid clones.
  2. Exploitation of coconut and oil palm reference maps, including alignment of existing coconut maps and establishment of an oil palm consensus map.
    3.
  3. Analysis and comparison of quantitative trait loci (QTLs) in different coconut and oil palm genetic backgrounds.
  4. Comparative genome and QTL analysis in coconut and oil palm.
  5. Establishment of field trial systems to implement marker-assisted breeding strategies in coconut and oil palm .
  6. Dissemination of results and expertise in bioinformatics and biotechnology by international workshops and laboratory courses and via the internet.

 
Description of the work

The research work will be carried out jointly by seven partners (P1-P7) and three subcontractors (S1 to P2; S2 to P1; S3 to P3).

  • The main goal is the construction of a high density map in a reference population of Cocos nucifera for East African Tall (EAT) and in Elaeis guineensis based on an existing 2 x 2 complete factorial genetic design involving dura and tenera parents which will allow to establish a multi-parent reference linkage map. The maps will be based on 1200 to 2250 DNA markers each.

  • In addition to AFLP markers, landmark SSRs and SNPs (published or to be developed) will be integrated into the maps.

  • to exploit these HD maps for molecular breeding and in order to make the information available to the scientific community, to other institutions and companies of the coconut and oil palm sector, a number of actions and research tasks will be performed:

  • The coconut and oil palm HD maps, the parental AFLP profiles, primer combinations and other useful information will be placed on the Internet.

  • The partners will align the HD map in coconut with four existing maps based on common SSR, SNP and co-migrating AFLP markers in order to perform comparative genome analyses.

  • A common subset of primer combinations derived from AFLP, SSR and SNP markers with good genome coverage will be selected, which can be applied to other coconut and oil palm progenies and other users in future applications.

  • These individual populations and the HD maps will be used to perform QTL analysis on a variety of characters of economic interest. They include growth characteristics, flowering, yield, oil content and quality, wax composition and possibly resistance to biotic and abiotic stress. Since several identical characters are evaluated in different genetic backgrounds, it will be possible to compare QTL locations in several genetic backgrounds.

  • The alignment of individual coconut maps with the HD map will provide additional "indirect markers" for corresponding homologous regions in the different genomes. QTLs identified on individual maps can be analysed for example much more precisely based on the information of many additional markers on the HD map.

  • Synteny studies will be performed between oil palm and coconut with respect to polymorphisms, comparative genome structure and QTL analyses for common traits.

  • COS libraries will be constructed for the EAT and LM2T parents of the two reference populations. COS clones for mapped AFLP fragments will be identified using excluding, multidimensional COS pools for both coconut and oil palm. Secondly, randomly picked COS clones will be partially sequenced and mapped by SNP.

  • Field trial systems for future analyses will be set up in coconut and oil palm. In coconut they will consist of 600 genotypes involving 11 parents (fullsib families). In oil palm three types of trials will be planted at two locations consisting of 5000 genotypes and involving at least 20 parents (fullsib families)

  • Dissemination of results and expertise will be followed within the project by training of DC personnel by partners P1 to P3 and through publications.

 

  • More importantly, the project will pursue this issue of dissemination and training "in the region for the region" by a combined workshop / laboratory course in ASIA and locally organised by partner P4 in collaboration with P1. Secondly, the internet will be used as an efficient and readily accessible source of information by constructing the websites coconut-online.org and oilpalm-online.org.

 
Milestones and expected results

  • Obtainment of initial Highdensity (HD) linkage reference maps in coconut and oil palm based on AFLP markers

  • Development of coconut and oil palm SSR primers
  • Results of intra-species polymorphisms and cross-taxa transferability of SSR primers
  • Development of SNP primers for candidate genes in coconut and oil palm

  • Integration of SSR and SNP markers in the HD maps

  • Alignment of HD map with individual coconut maps (AFLP, SSR, SNP locations) and comparative genome analysis. Obtainment of an Integrated Coconut Reference Map.
  • Map alignments and Multi-parent consensus oil palm maps based on SSR markers.

  • Definition of the optimal Molecular Marker Sets (MMS) in both specis

  • Establishment of COS libraries in both species.
  • Physical mapping in both species using pools of COS clones with AFLP analysis or primers developed for individual COS clones.

  • Integration of COS clones in the HD maps.

  • Detection of QTLs for different characters in different populations in both species and comparative QTL analysis

  • Syntheny studies between oil palm and coconut

  • Marker-assisted breeding plan in oil palm and coconut

  • Establishment of Field Trial Systems in coconut and oil palm
  • Realisation of an International workshop /laboratory course at the end of the project