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Plant Genetic Diversity

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					Plant Genetic Diversity and Molecular Marker Assisted Breeding

                      A training course


        A project for the Generation Challenge Program




                         Workplan
                       March 11, 2005




                  Marilyn Warburton
            CIMMYT Genetic Resources Program
                mwarburton@cgiar.org
Introduction.

The GCP Training Program (subprogram 5) will offer a series of regional courses
(Africa, Asia and Latin America) focusing on the main subjects of each of the
Subprograms. Subprogram 3, Trait Capture for Crop Improvement, has as the main goal
the increased efficiency of crop breeding, particularly using new tools such as
biotechnology. The uptake of new tools depends on the ability of national partner
scientists to use the new technologies, which may include the need for capacity building
in some cases. Therefore, the training courses offered in the regions for Subprogram 3,
entitled “Plant Genetic Diversity and Molecular Marker Assisted Breeding”, is geared
towards National Program scientists with the desire and possibilities to utilize markers
(via diversity analyses and Marker Assisted Selection) in their breeding programs. The
course proposed here will be offered in conjunction with a National Program in the
region (Latin America) who has a demonstrated track record in both training and
utilization of biotechnology in crop improvement.

The Instituto Nacional de Investigaciones Agropecuaria (INIA) in Chile is the country’s
national program for investigations in agriculture and fisheries, funded by the Ministry of
Agriculture. INIA has been in operation for 40 years and has regional offices in all states
of the country. The main office is in the capital, Santiago, where they have extensive
laboratories in many disciplines, including biotech. INIA’s mission is to “generate,
adapt, and transfer technologies” to the agriculture sector in Chile, which is completely
compatible with what the Generation Challenge Program is working on worldwide.
Located in Santiago, the La Platina Experiment Station is convenient for travel to Chile,
and has good accommodation facilities nearby. Laboratories and classrooms are
available for the workshop. In addition to INIA staff, several nearby universities could
provide resource people for the classes. Resource staff from CIMMYT, CIAT, and CIP
(the Latin American CG centers) will be called upon, as necessary to complement the
resource people from Universities and NARs from Chile and other countries in Latin
America. The identification of resource people has begun already, and should be finished
by July 1, 2005.

Objective.

The objective of this proposed project is to organize a training course in Chile on “Plant
Genetic Diversity and Molecular Marker Assisted Breeding,” The course is tentatively
planned for a 3-week period to be determined in October, 2005.

Resource personnel and coordination.

Dr. Marilyn Warburton will lead the organization of the course, in conjunction with Drs.
Fulton and Chandra, who are organizing similar courses in Africa and Asia, respectively.
It is hoped that all three courses will cover the same topics, and the three coordinators
have worked together to create a list of topics (see below). Dr. Warburton is the head of
the Diversity project in the Applied Biotechnology Center in CIMMYT, Mexico, and has
considerable experience in teaching and workshop organization. She has also been
involved with the GCP since its inception. She will be responsible for the agenda,
scheduling, invitations of participants and resource people, evaluations and report, and
also for the day-to-day leadership of the course on site.

Dr. Patricio Hinrichsen of INIA, La Platina has agreed to assist in coordination,
particularly in identifying an appropriate locale of the course in Chile, accommodations
for participants, and related on-site issues. Scientists from INIA throughout Chile are
being invited to attend as resource people, and specific scientists from Universities in
Chile, with particular strengths in topics that will be presented in the workshop, are also
being identified.

Topics and Participants.

The list of topics to be presented in the workshop are included at the end of the proposal.
Teaching materials are being developed by Drs. Poisson and Thijssen as commissioned
activities in subprogram 5; in addition, considerable training materials have been
developed at CIMMYT for previous classes and workshops on Genetic Diversity,
Genetic Mapping, QTL Mapping, and Marker Assisted Selection. These will be used to
enhance what becomes available from Drs. Poisson and Thijssen.

Participants will be selected from a pre-defined list of national partner institutes whom
are part of the GCP, and as second priority from a list approved by the GCP, subprogram
5 leadership (Table 2). The participants will be selected by a committee set up by the
Subprogram 5 leaders, and Drs. Warburton and Hinrichsen. All final materials used and
powerpoint presentations (with the permission of the presenters), along with a list of
participants names and contact information, will be given to each participant on a CD
upon completion of the course.

Expected outcomes.

Key outcomes of this workshop include the training of at least 12 regional Latin
American scientists from six countries in plant genetic diversity assessment and
molecular marker-assisted breeding concepts and techniques. This will not only increase
research capabilities of the scientists involved, but will pave the way for further strong
and extensive collaborations among those scientists, the CGIAR, and INIA, Chile,
including re-training and problem solving in the region and establishment of a regional
network, one of the key goals of the GCP.

All participants and resource persons will fill out an evaluation form at the end of the
course so that both key areas of satisfaction and recommended changes for the future can
be assessed. Participants will also be familiarized with the GCP-sponsored Resource
Center (http://irc.igd.cornell.edu) during the course in case they have questions or
concerns that arise after they return home. This should assist participants in implementing
what they have learned and serve to keep them in touch with the international scientific
community.
Timeplan.

Phase I. Possible sources of participants identified, advertisements sent, applications
gathered, tentative resource persons identified and invited, tentative agenda drafted.
Plants to be used identified and sown as needed.
        Deadline: July 1

Phase II. Participants selected and contacted for confirmation of attendance. Laboratory
and conference space at host institute identified and reserved. Resource persons
confirmed. Laboratory procedures confirmed, supplies ordered as needed.
       Deadline: August 15

Course held (October). Evaluations collected. Report sent to GCP by November 1, 2005.


Table 1: Budget.


Laboratory supplies & equipment                          $19,000
Accommodations & Meals                                   $20,000
   (12 participants, 3 full-time resource persons)
Additional Resource persons                              $4,000
   (4 persons, ave. 4 nights)
Administrative assistance, INIA                          $1,000
Administrative assistance, CIMMYT                        $1,000
Field trip(s)                                            $2,000
Materials (course manual, CDs, etc)                      $500
Communications (mail, phone, fax)                        $500
Travel, Resource persons, international                  $20,000
Travel, Resource persons, regional                       $5,000
Travel, Participants                                     $17,000
Per diems                                                $10,000

Total                                                    $100,000
Course Schedule:

Unit 1: About Genetic Markers
       DNA Basics
       Comparing techniques
              Review: Amplified Fragment Length Polymorphism (AFLP). Sequence-
              tagged site markers, RFLPs, RAPDs/Arbitrary techniques, SNPs,
              Diversity Arrays, Microsatellites
       The Polymerase Chain Reaction
       Procedures / lab demonstrations concentrating on SSRs
       AFLP Data Interpretation and Analysis
       Considerations to choose a technique
              Cost, repeatability, type of variation being revealed, local constraints

Unit 2: Plant Genetic Diversity
        Sampling strategies,
        Basics of population genetics,
        Linkage disequilibrium concept (as it relates to pop. structure and consequences
        for association mapping)
        Measures of genetic distance and genetic diversity,
        Clustering and ordination methods, and
        Use of genetic diversity software.


Unit 3: Linkage Map Building
        Designing a linkage mapping study for marker identification,
        Mendel’s laws,
        Single-locus analysis,
        Two-locus analysis for estimation and detection of linkage,
        Linkage grouping, Locus ordering,
        Marker coverage and map density,
        Use of linkage mapping software.


Unit 4: Phenotyping
        Importance of reliable phenotyping in marker identification,
        Planning a phenotyping study,
         Accuracy and precision, Basics of experimental design,
        Choosing an appropriate experimental design,
        Selection of environments and replications,
        Biometric analysis (including spatial analysis) of phenotyping data,
        Use of software for designing and analyzing phenotyping trials.

Unit 5: Marker Identification through QTL Analysis and Association Mapping.
        The key idea behind identifying trait-linked markers,
        Basics of quantitative genetics in relation to different mapping populations,
       Single-marker analysis,
       Multiple-marker analysis without a linkage map,
       Interval mapping,
       Composite interval mapping,
       Significance thresholds,
       Resampling techniques (cross-validation and bootstrapping),
       Association mapping to identify markers without a linkage map in a breeding
       population and diverse germplasm.




Unit 6: Applications
        Estimation of key MAS parameters
        Practical applications in plant genetic diversity analyses and marker-assisted
        breeding
        Commercial applications of marker-assisted breeding
        Resources for Scientists: Resource Center, Agora, etc.
        Cost/benefit analysis (MAS vs. phenotypic selection, considerations)
Table 2: List of institutions from which participants in the course will be drawn. Second
priority will be given to non-GCP affiliated institutions (shaded in green).

GENERATION CHALLENGE PROGRAMME
LIST OF AMERICAN NARS - CONTACT
INFORMATION

                                                             POSITION (if
     INSTITUTION              CONTACT           REGION                      COUNTRY
                                                               known)

AMERICA


Banco de Germoplasma       Ing Atilio David   Central       Department
                                                                            Honduras
CURLA                      Lobo Erazo         America       Coordinator


                                                            Director of
                                              Central       Genetic
CATIE                      Andreas Ebert                                    Costa Rica
                                              America       Resources
                                                            Division
Center for Nuclear         Ms. Silvana
                                              South
Energy in Agriculture      Creste Dias                                       Brazil
                                              America
(CENA)                     Souza
Center for Technological
                           Ms. Alba de las
Applications and Nuclear                      Caribbean                     Cuba
                           Mercedes Álvarez
Development (CEADEN)

Centro De Investigacion    Andrew C. James    Central       Investigator
                                                                            Mexico
Cientifica De Yucatan      Kay                America       Level A

                                                            Investigadora
Centro de
                                                            principal del
Investigaciones en         Ana Mercedez       Central
                                                            proyecto        Costa Rica
Biologia Celular y         Espinoza           America
                                                            biotecnología
Molecular
                                                            de arroz
Corporacion Colombiana
de Inverstigacion                             South
                           Lilian Duplat                                     Colombia
Agropecuaria                                  America
(CORPOICA)
Corporacion Colombiana
de Inverstigacion
Agropecuaria               Ms. Luisa          South
                                                            Researcher       Colombia
(CORPOICA) - Genetic       Fernanda Páez      America
Resources and Vegetal
Biotechnology Program
Centro Nacional de
Investigaciones
                                              South
Agropecuarias (INIA-       Ms. Marta Osorio                 Researcher      Venezuela
                                              America
CENIAP) - Biotechnology
Unit
Fundacion Simon I.
Patiño, Centro de
                                               South
Investigaciones             Ms. Teresa Avila                              Bolivia
                                               America
Fitoecogenéticas de
Pairumani (CIFP)


Centro Nacional de
                            Dr. José Eduardo   Central                    El
Tecnología Agropecuaria
                            Vides              America                    Salvador
y Forestal (CENTA)


                                                         National
Centro Regional de
                                                         Coordinator of
Investigación Carillanca,   Ivette Seguel                                 Chile
                                                         Genetic
INIA
                                                         Resources
CORPOICA - Programa
                                               South
Nacional Recursos           Mario Lobo                                    Colombia
                                               America
Genéticos Vegetales
Instituto de
Investigaciones
                            Ms. Mónica         South     Research
Agropecuarias INIA-                                                       Chile
                            Mathias            America   Assistant
Remehué - Department
of Vegetal Production
Corporacion Colombiana
                                                         Director Of
de Inverstigacion                              South
                            Tito Efrain Diaz             Research &       Colombia
Agropecuaria                                   America
                                                         Innovation
(CORPOICA)

                                               South
DENAREF/INIAP               Cesar Tapia                                   Ecuador
                                               America

Dirección de Parques
                                                         Dirección de
Nacionales y Vida
                            Victor Santander             Investigación    Paraguay
Silvestre, Ministerio de
                                                         Agrícola
Agricultura
Federacion Nacional de
                            Miguel Diago       South
Arroceros de Colombia                                                     Colombia
                            Ramirez            America
(FEDEARROZ)
                                               South
Fundación PROINPA           Ximena Cadima                                 Bolivia
                                               America
Fundacion Simon I.
Patiño, Centro de
                            Ms. Andrea         South
Investigaciones                                                           Bolivia
                            Davila             America
Fitoecogenéticas de
Pairumani (CIFP)
Promocion en
Investigacion de            Ms. Yola Sánchez   South
                                                         Researcher       Bolivia
Productoa Andinos           Canedo             America
(PROINPA)
                             Juan Fernando
Honduran Foundation for                          Central
                             Aguilar Moran,                                  Honduras
Agricultural Research                            America
                             PhD

                             PhD. . Silvana      Central
ICTA                                                                         Guatemala
                             Maselli             America


                             MSc. Salvador       Central
IICA                                                                         Belize
                             Monge               America



                             PhD. Francisco      Central
IICA                                                                         Costa Rica
                             Encizo              America


                                                           Gerente de la
                             Ana Lorena          Central   Unidad de
INBio                                                                        Costa Rica
                             Guevara             America   Bioprospección
                                                           INBio
INIFAP, Programa de          Mario Aguilar San   Central
                                                                             Mexico
Recursos Geneticos           Miguel              America

Instituto de Botánica del                        South
                             Guillermo Seijo                                 Argentina
Nordeste (IBONE)                                 America
Instituto de Investigación   Ing. Priscila                 Chair of the
                                                 Central
Agropecuaria de Panamá       Alvarado de                   Management        Panamá
                                                 America
(IDIAP)                      Gonzalez                      Committee
                                                           Regional
Instituto de
                             Julio Cesar         South     Director For
Investigaciones                                                              Chile
                             Kalazich            America   Chile’s Region
Agropecuarias (INIA)
                                                           10

Instituto de                 Dr. Juan Manuel
                                                 Central
Investigaciones              Hernández                                       Mexico
                                                 America
Forestales (INIFAP)          Casillas

Instituto Nacional
                                                           Director de
Autonomo de                  Julio César         South
                                                           Investigaciones   Ecuador
Investigaciones              Delgado Arce        America
                                                           del INIAP
Agropecuarias, Iniap

Instituto Nacional de
Investigación                                    South
                             Sergio Ceretta                                  Uruguay
Agropecuaria (INIA),                             America
Uruguay
Instituto Nacional de
                                                 South
Investigación y Extensión    Ms. Emma Rivas                                  Peru
                                                 America
Agraria (INIA)
Instituto Nacional de
                                                             Responsible of
Tecnología Agropecuaria
                            Dr. Sergio           South       the Plant
(INTA) - Estación                                                             Argentina
                            Feingold             America     Biotechnology
Experimental
                                                             Laboratory
Agropecuaria Balcarce
Instituto Nicaraguense de
                            Ing. José Manuel     Central
Tecnología Agropecuaria                                                       Nicaragua
                            Bravo Baez           America
(INTA)

Instituto Nicaragüense de
                            Mr. Rodolfo          Central
Tecnologia Agropecuaria                                                       Nicaragua
                            Valdivia             America
(INTA)

Latin American Center for
                                                 Central     Associate
Competitiviness and         Lawrence P. Pratt                                 Costa Rica
                                                 America     Director
Sustainable Development
Ministerio de Agricultura   Ing. Nevio Bonilla   Central
                                                                              Costa Rica
y Ganadería (MAG-INTA)      Morales              America
                            Orville Agard                    Agricultural
Ministry Of Agriculture                          Caribbean                    Barbados
                            Wickham                          Officer
National Department of
Plan Genetic Resources
                            Ms. Gabriela         South
and Biotechnology, Santa                                     Technician       Ecuador
                            Piedra               America
Catalina Experimental
Station (INIAP)
Programa Nacional de
Recursos Genéticos y                             South
                            Santiago Pastor                                   Perú
Biotecnología                                    America
(PRONIRGEB)/INIA
Promocion e                                                  Coordinator of
Investigacion de            Antonio              South       the Genetic
                                                                              Bolivia
Productos Andinos           Gandarillas          America     Resources
(PROINPA)                                                    Area
Unidad de Recursos
Genéticos E.E. Alberto
                            Ana Berreta                                       Uruguay
Boerger "La Estanzuela",
Banco Base de INIA
                                                             Director Fungi
                                                 South       and Plant
Universidad de Antioquia    Lucia Atehortúa                                   Colombia
                                                 America     Biotechnology
                                                             Laboratory

                                                 South
Universidad del Tolima      Andres Gutierrez                                  Colombia
                                                 America

Universidad Nacional
Agraria La Molina           Ms. Eliana           South       Research
                                                                              Peru
(UNALM) - Instituto de      Yglesias             America     Assistant
Biotecnologia
                                                  Masters in
                                                  Natural
                                                  Resources
                          Ms. Berardo
Universidad Nacional de                 South     Coordinator -
                          Escalante                                Peru
Cajamarca                               America   Responsible of
                          Zumaeta
                                                  the Plant
                                                  Biotechnology
                                                  Laboratory