QTL Mapping and Breeding Simulation Three Day Course (11th)

Title                           QTL Mapping and Breeding Simulation Three Day Course

 Presenters:            Dr. Jiankang Wang, CIMMYT China and Chinese Academy of Agricultural Sciences

Dr. Rudi Appels, Centre for Comparative Genomics, Murdoch University

When:         Wednesday 6^th – Friday 8^th February 2013

Times:                8.30am until 5.00pm for each day

Where:               Crawley Campus, The University of Western Australia (UWA)

Contact:             Frances Gartrell (admin-icpber@uwa.edu.au)

                     Phone:        (08) 6488 1428          

Supported by:   ICPBER (UWA) and Murdoch University

Who should attend?

Graduate students, geneticists and breeders in Australia who are interested in applied genomics, applied quantitative genetics, linkage analysis, linkage map construction, QTL mapping, simulation and optimization of breeding strategies will benefit from this workshop. Participants should be familiar with basic methods in genetics, breeding and statistics.

Overview

One of the major impacts of the high throughput DNA sequencing capabilities becoming available at a relatively low cost is that identification of single nucleotide polymorphisms (SNPs) can now be identified in very high numbers.  These SNPs provide sequence-based markers for integration into molecular genetic maps and as genomes are sequenced these molecular markers serve to anchor the genome sequences to genetic maps. The ICIM software is new generation mapping software that can handle the range of challenges associated with having thousands of molecular markers instead of hundreds.  The association of markers in a high density marker map with phenotypes assessed in the mapping population is carried out in ICIM using the latest statistical approaches in QTL analysis and visualization of outputs.  The ICIM software also has the facility for integrating different molecular marker maps based on the presence of shared markers.

Learning Objectives

Through lectures, practices and discussions, you will learn:

l  Plant genetics, genomics and breeding methodology

l  Applied 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

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

Registration details

The registration fee for this 3 Day course is $330 AUD or $50 for PhD students or $110 CSIRO / University Staff.  Registration includes a complete set of electronic course notes and morning and afternoon tea for three days.

Numbers are limited and places will be offered on a first-in-first-served basis. Please indicate you would like to attend as soon as possible by direct email to

Frances Gartrell: admin-icpber@uwa.edu.au.

You will receive a registration form by email which you must complete and return as soon as possible, together with payment by either cheque or money order (details on the form). Your place will be confirmed on receipt of the registration form and payment. Please ensure to include your profession to enable lecturers to demonstrate and customise elements towards your subject of interest or research.

Venue

The workshop will be run by the International Centre for Plant Breeding Education and Research (ICPBER) and held the UWA Crawley campus, The University of Western Australia on the Wednesday 6^th February until 8^th February 2013 .

A campus map can be accessed at http://www.uwa.edu.au/campus-map.

PLEASE NOTE:      

Each participant will have to cover his/her own travelling and accommodation expenses.

Free parking will be available at UWA in student / Yellow bays due to Summer Study Break.

Computers: PLEASE NOTE:

Personal Computer usage, software and computers

All course instruction will be on UWA computers with approved software licences. Additionally, instructions will be available on how to download software to individual PC’s, but individual PC’s may not be used during the course time to avoid down-time from individual user laptop issues.

Location: The University of Western Australia , Stirling Highway, Crawley WA 6009, Perth, Australia

Program

Day 1 (Wednesday, Feb. 6)

Introduction of plant genetics, genomics and breeding, quantitative genetics and its application in plant breeding, genetic linkage analysis, and linkage map construction etc.

9:00 – 12:30

Lecture 1.1: Genomics and its applications in plant breeding (Rudi Appels)

Lecture 1.2: Quantitative genetics and its applications in plant breeding (Jiankang Wang)

Group photo and coffee break

Practical 1.1: Find the structure of genetic populations; Find the number of effective factors under multi-factor hypothesis; ANOVA and estimation of heritability (Jiankang Wang)

Practical 1.2: Install the QTL IciMapping software, and Get familiar with the QTL IciMapping software (Parwinder Kaur and Rudi Appels)

12:30 – 13:30 Working lunch break

13:30 – 17:00

Lecture 1.3: Linkage Analysis and Map Construction I (Jiankang Wang)

Lecture 1.4: Linkage Analysis and Map Construction II (Jiankang Wang)

Coffee break

Practical 1.3: Handling the redundancy of markers (Tool BIN in QTL IciMapping) (Parwinder Kaur and Rudi Appels)

Practical 1.4: Linkage map construction (MAP functionality in QTL IciMapping) (Parwinder Kaur and Rudi Appels)

Day 2 (Thursday, Feb. 7)

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 2.1: Single Marker Analysis and the Conventional Interval Mapping (Jiankang Wang)

Lecture 2.2: Inclusive Composite Interval Mapping (ICIM) of additive (dominance) QTL (Jiankang Wang)

Coffee break

Practical 2.1: Construction of the consensus map (CMP functionality in QTL IciMapping) (Parwinder Kaur and Rudi Appels)

Practical 2.2: Use of Single Marker Analysis and Interval Mapping to identify QTL (BIP functionality in QTL IciMapping) (Parwinder Kaur and Rudi Appels)

12:30 – 13:30 Working lunch break

13:30 – 17:00

Lecture 2.3: Inclusive Composite Interval Mapping (ICIM) of epistasis QTL (Jiankang Wang)

Lecture 2.4: LOD Threshold and QTL Detection Power Simulation (Jiankang Wang)

Coffee break

Practical 3.3: Use of Inclusive Composite Interval Mapping to identify QTL (BIP functionality in QTL IciMapping) (Parwinder Kaur and Rudi Appels)

Practical 3.4: Compassion of mapping methods by simulation (BIP functionality in QTL IciMapping) (BIP simulation functionality in QTL IciMapping) (Parwinder Kaur, Rudi Appels and Jiankang Wang)

Day 3 (Friday, Feb. 8)

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

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 3.1: QTL by Environment Interaction, QTL Mapping with Chromosome Segment Substitution (CSS) Lines, and other methods (Jiankang Wang)

Lecture 3.2: Frequently Asked Questions and Answers in QTL Mapping (Jiankang Wang)

Coffee break

Practical 3.1: Identification of QTL by environmental interactions (MET functionality in QTL IciMapping) (Parwinder Kaur and Rudi Appels)

Practical 3.2: QTL mapping with chromosome segment substitution (CSS) lines (CSL functionality in QTL IciMapping) (Parwinder Kaur and Rudi Appels)

12:30 – 13:30 Working lunch break

13:30 – 17:00

Lecture 3.3: Principle of Modeling and Breeding Simulation (Jiankang Wang)

Lecture 3.4: Applications of Breeding Simulation in Plant Breeding (Jiankang Wang)

Coffee break

Practical 3.3: Define a genetic model for the QU-GENE engine (Jiankang Wang)

Practical 3.4: Define a breeding strategy for the simulation tool QuLine and Run a QU-GENE simulation experiment (Jiankang Wang)

17:00 – 17:15

Closing of The QTL Mapping and Breeding Simulation Course