A One-week Course on Genetic Analysis and Plant Breeding

Organized by the Genetic Resources Program, CIMMYT

Funded by the Generation Challenge Program

21 - 25 January 2013, CIMMYT, Mexico

Objectives of the course

Through lectures, practices and discussions, you will learn:

l  Plant breeding methodology

l  Applied population and quantitative genetics

l  Estimation of recombination between two linked loci

l  Construction of genetic linkage maps

l  Principles of QTL mapping and statistical comparison of different mapping methods

l  Identification of quantitative trait genes with additive (and dominance) effects

l  Identification of quantitative trait genes with epistasis effects

l  QTL by environment analysis

l  Modeling of plant breeding

l  Comparison and optimization of plant breeding strategies

l  Integration of known gene information into conventional plant breeding

Who should attend?

CIMMYT staff and visitors in CIMMYT headquarter, and CIMMYT’s partners across Mexico who are interested in applied quantitative genetics, linkage analysis, linkage map construction, QTL mapping, simulation and optimization of breeding strategies will benefit from this course. Participants should be familiar with basic methods in plant genetics, plant breeding and statistics. You are welcome to bring your genetic data to this course.

Costs: There will not be any charge for this course and lunches will be provided by CIMMYT. Each participant will have to cover his/her own travelling and accommodation expenses, if any.

Computers: Each participant must bring a laptop computer that can run Microsoft Windows applications. A USB memory stick will be distributed to all participants at the beginning of the course. This contains the lecture presentations, the QTL IciMapping integrated software V3.3, QU-GENE simulation tools, exercises and answers, etc.

Location: Sasakawa Conference Room in the Main Building, CIMMYT (International Maize and Wheat Improvement Center), Km. 45, Carretera México-Veracruz, El Batán, Texcoco CP 56130, Edo. de México MEXICO

Accommodations: On your own.

Contact details: Please address any enquires and the registration to Daniela Flores Castillo, CIMMYT Training Office, Tel: +52 (55) 5804 2004 ext 2025, Fax: +52 (55) 5804 7558/59, Email: cimmyt-to@cgiar.org or d.f.castillo@cgiar.org. For any technical issues, please contact Dr. Jiankang Wang, E-mail: jkwang@cgiar.org.

Detailed Program

Day 1 (Monday, Jan. 21): Introduction of Population and Quantitative Genetics

Maize and wheat breeding methodology and achievements at CIMMYT; Genetic population and population structure; mating systems; Hardy-Weinberg Equilibrium; Linkage disequilibrium; Additive and dominance genetic model; Genetic analysis in biparental populations; Genetic analysis in random mating populations; Mating designs and estimation of genetic variance and heritability; Prediction of genetic gain; and correlated selection etc.

9:00 – 12:30

Opening Lecture: Maize and Wheat Breeding at CIMMYT: Methodology, Achievement and Perspective (Dr. Marianne Banziger, DDG of CIMMYT, m.banziger@cgiar.org)

Group photo in front of the Main Building

Lecture 1.1: History and Contents of Quantitative Genetics

Lecture 1.2: Introduction of Population Genetics

Practical 1.1: Find the structure of genetic populations

Practical 1.2: Find the number of effective factors under multi-factor hypothesis  

12:30 – 13:30 Working lunch break

13:30 – 17:00

Lecture 1.3: Classical Quantitative Genetics I

Lecture 1.4: Classical Quantitative Genetics II

Practical 1.3: ANOVA and estimation of heritability

Practical 1.4: Genetic mating designs, estimation of genetic variances and genetic gain

Day 2 (Tuesday, Jan. 22): Genetic Linkage Analysis

Generation transmission matrix; Expected frequencies of genotypes at two loci; Estimation of recombination frequency between two loci in biparental genetic populations; Genetic interference and mapping function; Linkage map construction; Handling redundant markers; and Integration of multiple linkage maps to generate a consensus map etc.

9:00 – 12:30

Lecture 2.1: Linkage Analysis and Map Construction I

Lecture 2.2: Linkage Analysis and Map Construction II

Practical 2.1: Install the QTL IciMapping software, and Get familiar with the QTL IciMapping software

Practical 2.2: Handling the redundancy of markers (Tool BIN in QTL IciMapping)

Practical 2.3: Linkage map construction (MAP functionality in QTL IciMapping)

12:30 – 13:30 Working lunch break

13:30 – 17:00

Lecture 2.3: Quantitative Genetics and Plant Breeding

Lecture 2.4: Missing Heritability in Human GWAS (Genome-wide Association Study)

Practical 2.4: Estimation of recombination frequency estimation between two loci (Tool 2pointREC in QTL IciMapping)

Practical 2.5: Construction of consensus maps (CMP functionality in QTL IciMapping)

Day 3 (Wednesday, Jan. 23): Mapping Additive (and Dominance) QTL

Quantitative traits and QTL mapping;Principle of QTL mapping; Single Marker Analysis; conventional Interval Mapping; Inclusive Composite Interval Mapping (ICIM) of additive QTLs; ICIM of epistatic QTLs; Choice of LOD threshold to reduce false positives; and Comparison of QTL mapping methods by simulation etc.

9:00 – 12:30

Lecture 3.1: Single Marker Analysis and the Conventional Interval Mapping

Lecture 3.2: Inclusive Composite Interval Mapping (ICIM) of additive (dominance) QTL

Practical 3.1: Use of Single Marker Analysis to identified QTL (BIP functionality in QTL IciMapping)

Practical 3.2: Use of Interval Mapping to identified QTL (BIP functionality in QTL IciMapping)

12:30 – 13:30 Working lunch break

13:30 – 17:00

Lecture 3.3: Inclusive Composite Interval Mapping (ICIM) of epistasis QTL

Lecture 3.4: LOD Threshold and QTL Detection Power Simulation

Practical 3.3: Use of Inclusive Composite Interval Mapping to identified QTL (BIP functionality in QTL IciMapping)

Practical 3.4: Use of Inclusive Composite Interval Mapping to identify epistatic QTL (BIP simulation functionality in QTL IciMapping)

Day 4 (Thursday, Jan. 24): Mapping Epistatic QTL and Segregation Distortion Loci (SDL)

QTL by environmental interactions; QTL mapping with chromosome segment substitution (CSS) lines; Selective genotyping; Bulk Segregant Analysis; Brief introduction of association mapping; QTL mapping in nested association mapping (NAM) populations; and Frequently asked questions in QTL mapping studies

9:00 – 12:30

Lecture 4.1: QTL by Environment Interaction

Lecture 4.2: QTL Mapping with Chromosome Segment Substitution (CSS) Lines and Segregation Distortion Loci Mapping

Practical 4.1: Compassion of mapping methods by simulation (BIP functionality in QTL IciMapping)

Practical 4.2: Identification of QTL by environmental interactions (MET functionality in QTL IciMapping)

Practical 4.3: QTL mapping with chromosome segment substitution (CSS) lines (CSL functionality in QTL IciMapping)

12:30 – 13:30 Working lunch break

13:30 – 17:00

Lecture 4.3: Joint ICIM with the Nested Association Mapping (NAM) Design

Lecture 4.4: Frequently Asked Questions and Answers in QTL Mapping

Practical 4.4: Identification of segregation distortion loci (SDL functionality in QTL IciMapping)

Practical 4.5: QTL mapping in NAM populations (NAM functionality in QTL IciMapping)

Practical 4.6: Use of your own genetic populations in QTL IciMapping

Day 5 (Friday, Jan. 25): Modeling and Simulation of Plant Breeding Programs

Principles of breeding simulation; Modelling of breeding programs; Defining genetic models in QU-GENE; Defining breeding methods in QuLine; Comparing breeding methods through simulation; Some strategic and tactical applications by simulation; and Use of know genes to design the plant breeding

9:00 – 12:30

Lecture 5.1: Principle of Modeling and Breeding Simulation

Lecture 5.2: Strategic Applications of Breeding Simulation

Practical 5.1: Define a genetic model for the QU-GENE engine

12:30 – 13:30 Working lunch break

13:30 – 17:00

Lecture 5.3: Tactical Applications of Breeding Simulation: Use of Known Gene Information in Plant Breeding

Lecture 5.4: Design the Plant Breeding Program

Practical 5.2: Define a breeding strategy for the simulation tool QuLine

Practical 5.3: Run a QU-GENE simulation experiment

17:00 – 17:15

Closing of the One-week Course on Genetic Analysis and Plant Breeding