Capacity Building Corner
Plant Genetic Diversity Analysis and Marker Assisted Breeding Workshop
Santiago, Chile
3 - 21 October 2005
A training workshop commissioned by the Generation Challenge Program was held in Santiago, Chile to provide both conceptual and hands-on training in the use of plant genetic diversity and molecular marker assisted breeding. Emphasis was placed on practical applied usage and improving the links between plant breeding, germplasm management and utilization, and molecular biology methods, with a particular focus on the use of microsatellite markers. Sessions included DNA-based markers, PCR-based markers, comparing molecular marker techniques, diversity analyses, population genetics, phenotyping and statistical analyses, linkage mapping and QTL discovery & analysis, marker-assisted breeding strategies, and practical applications. Laboratory practicals included DNA extractions, PCR, electrophoresis, and the use of microsatellites. Computer practicals included SSR diversity, mapping and breeding software, and the use of public databases.
In addition, the International Foundation for Science (IFS) and the GCP collaborated to promote and award research grants according to the IFS?s scheme to provide opportunities for young researchers to use molecular genetics methodologies to address important genetic diversity or breeding issues.
Students in the course included 17 women and 8 men from 8 countries (Argentina, Bolivia, Brazil, Chile, Colombia, Cuba, Ecuador, and Peru). Most held permanent positions as young scientists in universities or National Agriculture programs, and a few were finishing up their dissertations. A few worked more with germplasm, while most worked in the lab. The 11 resource people came from 7 different countries to present the theoretical or practical lectures. The course was very well evaluated by students, resource people, and donors, who were very complimentary of the course materials, lectures, and interactions with other participants. Below you will find links to important documents and presentations from the course.
NOTE: Links marked with ** are larger than 1 MB and may take longer to download.
LOGISTICS
Final Workshop Schedule
List of participants
Course Evaluation Form
PRESENTATIONS
Unit 1
Comparing Techniques
Basic Genetic Concepts: A short review
**AFLP Data Interpretation and Analysis. Sequence-tagged site markers, RFLPs, RAPDs/Arbitrary techniques, SNPs, Diversity Arrays, Microsatellites
Polymerase Chain Reaction
Unit 2
Cluster Analysis (finding groups)
**Genetic Diversity Analysis with Molecular Marker Data: Learning Module--Basic Concepts of Population Genetics
**AFLP Data Interpretation and Analysis. Sequence-tagged site markers, RFLPs, RAPDs/Arbitrary techniques, SNPs, Diversity Arrays, Microsatellites
Reducing the Dementionality and Doing Graphics of Multivariate Data
Sampling
**Genetic Diversity Analysis with Molecular Marker Data: Learning Module--Introduction
Unit 3
**Crossing Analysis--Linkage grouping-locus ordering
**Genomic Libraries, Yacs, BACs, PACs. Physical maps, fingerprint, and Sequencing strategies
Positional Cloning: From the genetic map to grabbing the gene
**Plant Comparative Genetics
**Designing a Linkage Mapping Study for Marker Identification
Mechanisms of Mendelian heredity-Cytogenetics
Mendel's Laws
Single-Loci Analysis
Two-Locus Analysis
Unit 4
Design 0
Design 1
Design 2
Incomplete Block Designs
Unit 5
Composite Interval Mapping Resampling Techniques
**Linkage Disequilibrium Concept (as it relates to pop. structure)
Windows QTL Cartographer
**QTL Mapping
Unit 6
Taller: Preparacion de solicitudes de subsidio para proyectos cientificos
The Genetics of Radiocaesium Accumulation by Plants
La IFS, una organizaci?n que apoya el trabajo de cient?ficos j?venes en pa?ses en desarrollo
**Practical Applications in Plant Genetic Diversity Analyses and Marker Assisted Breeding
**Key MAS Parameters
**Resistencia al fr?o en tomate: aspectos fisiol?gicos y agron?micos
Capacity Building and Enabling Delivery
HANDOUTS
Unit 1
**Introduction
**Population Genetics
Appendix 1 to Basic Concepts in Population Genetics
**Introducion to Cuantitive Genetics
**Introducion a la genetica cuantitativa
Unit 5
Oyanedel Lecture Outline
Marker Identification through QTL Analysis and Association Mapping Outline for part 1
ADDITIONAL READINGS
Unit 1
**Laurent Excoffier, et al. -- Analysis of Molecular Variance Inferred from Metric Distances Among DNA Haplotypes: Application to Human Mitochondrial DNA Restriction Data
Unit 2
Jorge Franco, et al. -- A Sampling Strategy for Conserving Genetic Diversity when Forming Core Subsets
Lucia Gutierrez, et al. -- Comparing a Preliminary Racial Classification with a Numerical Classification of the Maize Landraces of Uruguay
JC Reif, et al. -- Genetical and Mathematical Properties of Similarity and Dissimilarity Coefficients Applied in Plant Breeding and Seed Bank Management
J. Franco, et al. -- A method for combining molecular markers and phenotypic attributes for classifying plant genotypes
Unit 3
**Walter R. Fehr -- Artificial Hybridization and Self-Pollination
**Merideth W. Bonierbale, et al. -- RFLP Maps Based on a Common Set of Clones Reveal Modes of Chromosomal Evolution in Potato and Tomato
Maria-Theresa Cervera, et al. -- Dense Genetic Linkage Maps of Three Populus Species (Populus deltoides, P. nigra and P. trichocarpa) Based on AFLP and Microsatellite Markers
Steven D. Tanksley, et al. -- Chromosome landing: A paradigm for map-based gene cloning in plants with large genomes
MD Gale -- Plant Comparative Genetics after 10 Years
Catherine Feuillet -- High gene density is conserved at syntenic loci of small and large grass genomes
M. Claverie, et al. -- High-resolution mapping and chromosome landing at the root-knot nematode resistance locus Ma from Myrobalan plum using a large-insert BAC DNA library
**GA Churchill, et al. -- Empirical Threshold Values for Quantitative Trait Mapping
Monica Morales, et al. -- A physical map covering the nsv locus that confers resistance to Melon necrotic spot virus in melon (Cucumis melo L.)
MJ Kearsey -- The Principles of QTL Analysis (a minimal mathematics approach)
Unit 5
Alpert and Tanksley -- High-resolution mapping and isolation of a yeast artificial chromosome contig containing fw2.2: A major fruit weight quantitative trait locus in tomato
Roderick D. Ball -- Bayesian Methods for Quantitative Trait Loci Mapping Based on Model Selection: Approximate Analysis Using the Bayesian Information Criterion
Barton and Keightley -- Understanding Quantitative Genetic Variation
**de Vicente and Tanskley -- QTL Analysis of Transgressive Segregation in an Interspecific Tomato Cross
**John Doebley -- The Genetics Of Maize Evoluation
Rebecca W. Doerge -- Mapping and Analysis of Quantitative Trait Loci in Experimental Populations
Anne Frary et al. -- Quantitative Trait Locus Key to the Evolution of Tomato Fruit Size
M. Frisch et al. -- Duplicate marker loci can result in incorrect locus orders on linkage maps
**I. Hoeschele et al. -- Advances in Statistical Methods to Map Quantitative Trait Loci in Outbred Populations
Ritsert C. Jansen -- Interval Mapping of Multiple Quantitative Trait Loci
Chen-Hung Kao et al. -- Multiple Interval Mapping for Quantitative Trait Loci
Kearsey and Farquhar -- QTL Analysis in Plants: Where are we now?
M.J. Kearsey -- The Principles of QTL Analysis (a mathematical approach)
Maarten Koornneef et al. -- Naturally Occurring Genetic Variation in Arabidopsis Thaliana
Christoph Lange and John C. Whittaker -- Mapping Quantitative Trait Loci Using Generalized Estimating Equations
**Rodney Mauricio -- Mapping Quantitative Trait Loci in Plants: Uses and Caveats for Evolutionary Biology
Manfred Mayer -- A simulation study on the accuracy of position and effect estimates of linked QTL and their asymptotic standard deviations using multiple interval mapping in an F2 scheme
Albrecht E. Melchinger et al. -- Quantitative Trait Locus (QTL) Mapping Using Different Testers and Independent Population Samples in Maize Reveals Low Power of QTL Detection and Large Bias in Estimates of QTL Effects
Renata Mihaljevic et al. -- Congruency of Quantitative Trait Loci Detected for Agronomic Traits in Testcrosses of Five Populations of European Maize
Ilan Paran et al. -- Quantitative traits in plants: beyond the QTL
Andrew H. Paterson -- What has QTL mapping taught us about plant domestication?
Hans-Peter Piepho -- A Quick Method for Computing Approximate Thresholds for Quantitative Trait Loci Detection
Hans-Peter Piepho et al. -- Marker Pair Selection for Mapping Quantitative Trait Loci
ND Young -- QTL Mapping and Quantitative Disease Resistance in Plants
George Seaton et al. -- QTL Express: Mapping Quantitative Trait Loci in Sample and Complex Pedigrees
H. Friedrich Utz et al. -- Bias and Sampling Error of the Estimated Proportion of Genotypic Variance Explained by Quantitative Trait Loci Determined From Experimental Data in Maize Using Cross Validation and Validation With Independent Samples
MI Vales et al. -- Effect of population size on the estimation of QTL: a test using resistance to barley stripe rust
Peter M. Visscher et al. -- Confidence Intervals in QTL Mapping by Bootstrapping
Joel Ira Weller et al. -- An analytical formula to estimate confidence interval of QTL location with a saturated genetic map as a function of experimental design
Xijiang Yu, et al. -- Theoretical and Empirical Power of Regression and Maximum-Likelihood Methods to Map Quantitative Trait Loci in General Pedigrees
**Zhao-Bang Zeng -- Theoretical basis for separation of multiple linked gene effects in mapping quantitative trait loci
**Zhao-Bang Zeng -- Precision Mapping of Quantitative Trait Loci
Zhao-Bang Zeng et al. -- Estimating the genetic architecture of quantitative traits
Zhao-Bang Zeng et al. -- Modeling Quantitative Trait Loci and Interpretation of Models
Unit 6
CA Urrea et al. -- F1 Hybridization Based on Genetic Distance Using DNA Molecular Data in Tropical and Subtropical Maize Germplasm
Kate Dreher et al. -- Money matters (I): costs of field and laboratory procedures associated with conventional and marker-assisted maize breeding at CIMMYT
Michael Morris et al. -- Money matters (II): costs of maize inbred line conversion schemes at CIMMYT using conventional and marker-assisted selection
FAO -- Electronic Forum on Biotechnology in Food and Agriculture
**Jack CM Dekkers et al. -- The Use of Molecular Genetics in the Improvement of Agricultural Populations
**Russell Lande et al. -- Efficiency of Marker-Assisted Selection in the Improvement of Quantitative Traits
Steven J. Knapp -- Marker-Assisted Selection as a Strategy for Increasing the Probability of Selecting Superior Genotypes
MANUALS
CIMMYT Lab Manual
Fingerprint Instructions
JoinMap 3.0
**QTX Manual
SSR Isolation Campinas
PROTOCOLOS BIOTEC
A simple and efficient method for DNA extraction from grapevine cultivars, Vitis species and Ampelopsis
Electroforesis en gel de poliacrilamida de productos de PCR (RAPD, ISSR, SSR, AFLP)
Extracci?n de ADN- protocolo b?sico
An?lisis de ADN mediante AFLP
Extracci?n DNA
Microsat?lites-protocolo para PCR
PROGRAMS
**Cost Analysis
SAS-Programs
clus_jm.sas
CRD_jm.sas
dist_jm.sas
eje_little.sas
mds_jm.sas
pca_jm.sas
selvar_jm.sas
Software
Arelequin (Zip file)
PRACTICAL DATA SETS
Demo Data
test.jmd (zip file)
DEMO.MAP
demo_bc1_f2.pwd
demoBC1.loc
DEMOCP1.LOC
DEMOCP2.LOC
demoDH2.loc
demoDH.loc
demoF2.loc
demoRIx.loc
JM20DEMO.LOC
JM20DEMO.MAP
sampleF2a.raw
sampleF2b.raw
sampleRIself.raw
test.jmp
Exercises
cmd
OWBcross
OWBmap
OWBmap_inp_In.mcd
OWBmap_inp_In-at (Quick Time Movie)
OWBmap_inp_In-I.qrt
OWBmap_inp_In-I-EQTL
qtlcart.sr
suminfo-t1
Practical Exam
cmd
OROredcross.inp
OROredmap.inp
OROredmap_inp_In.mcd
OROredmap_out_In.mcd
OROredmap_out_In-I.qrt
OROredmap_out_In-O.qrt
OROredmap_out_In-O-O.qrt
suminfo-t1
PHOTOS
Photo 1, Photo 2, Photo 3, Photo 4, Photo 5, Photo 6, Photo 7, Photo 8, Photo 9, Photo 10, Photo 11, Photo 12, Photo 13, Photo 14, Photo 15, Photo 16, Photo 17, Photo 18, Photo 19, Photo 20, Photo 21, Photo 22, Photo 23, Photo 24, Photo 25, Photo 26, Photo 27, Photo 28, Photo 29, Photo 30, Photo 31, Photo 32, Photo 33, Photo 34, Photo 35, Photo 36, Photo 37, Photo 38, Photo 39, Photo 40, Photo 41, Photo 42, Photo 43, Photo 44, Photo 45, Photo 46, Photo 47, Photo 48, Photo 49, Photo 50, Photo 51, Photo 52, Photo 53, Photo 54, Photo 55, Photo 56, Photo 57, Photo 58, Photo 59