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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
