Maize Data Analysis and Management Workshop – Harare 2009 – already held!

23-27 FEBRUARY 2009 – HARARE

Monday 23 February

STATISTICS AND BIOMETRICS FOR MAIZE BREEDERS – PART I – JOSE CROSSA

Written notes on Basic Statistical Methods will be given. The notes will include:

• t-test
• Hypothesis test
  • One tail test
  • Two tail test
• Covariance, correlation, and covariance analyses
• Simple Linear regression
• ANOVA (Analysis of Variance)
• Data transformation

Time Activity

PHENOTYPING

08:00

Basic Quantitative Genetic

• Phenotypic and Genotypic Values
• Average effect of an allele
• Average effect of an allele substitution
• Concepts on GENERAL COMBINING ABILITY and SPECIFIC COMBINING ABILITY
• Heritability
• One Factor Design

10:00 break

10:30

Within Site analyses

• Basic Experimental designs
  • Incomplete block design

12:30 Lunch

13:30

Across Site analyses

• Stability Analyses
  • Regression on the site mean
  • AMMI and SREG
• Selection Indices based on phenotypic data. Multi trait environment
• Practice – Computer SAS programs for various analyses useful for breeders

18:00 End

Tuesday 24 February

STATISTICS AND BIOMETRICS FOR MAIZE BREEDERS – PART II – JOSE CROSSA

Time Activity

GENOTYPING

08:00

Basic on Linear models (fixed, random, and mixed)

• When a factor should be considered fixed and when random?
• What is the main difference between a factor being random or fixed?
• Genotypes – fixed or random? Environments fixed or random?

Marker Assisted Breeding

• Traditional uses of molecular markers in breeding programs, Advantages and limitations
• New development in marker technology — SNPs
• Marker Assisted Recurrent Selection
• Genome wide selection

10:00 break

10:30

Selection Indices using phenotypic and molecular marker data

• Results from Simulation studies for DTMA

12:30 Lunch

13:30

Selection Indices using phenotypic and molecular marker data

• Results from Simulation studies for DTMA

15:00 SAS Program for mixed-model analysis of multi-location trials – Gary Atlin

16:00 Practice

• Computer SAS programs for various analyses useful for breeders

18:00 End

*Examples will use SAS and ASREML

Wednesday 25 February

FIELD VISIT, MECHANISATION AND ELECTRONIC CAPTURE IN THE FIELD

Time  Activity

08:00

Field Visit -Cosmos, Vivek, John MacRobert

• Mechanisation
• FieldLog – Electronic data collection
• Barcoding

11:00 Best practices for mechanization – Cosmos

11:45 Data Management in Maize FieldBook – Hector

12:30 Lunch

DATA MANAGEMENT IN MAIZE FIELD BOOK AND ICIS – PART I – B. VIVEK, JEAN SABADO AND HECTOR SANCHEZ

Time  Activity

13:30

Querying in MaizeFinder

15:00 break

15:30 Pedigree Parsing Using the Parser

16:30 Discussions about FieldBook, FieldLog, and Parser

18:00 end

Thursday 26 February

DATA MANAGEMENT IN MAIZE FIELD BOOK AND ICIS – PART II – B. VIVEK, JEAN SABADO AND HECTOR SANCHEZ

Time Activity

08:00

An Introduction to ICIS

• GMS (Genealogy Manaegement System)
• DMS (Data Management System)

08:45 The ICIS Launcher

09:00 Querying for Pedigrees with GMS SRCH

09:30 Creating a Pedigree List with SetGen Application

10:15 break

10:45 Calculating Coefficient of Parentage using the Browse Application

11:15 Advancing Lines and Generating Crosses with SetGen Application

• Advancing Lines
• Generating Crosses

12:30 lunch

13:30

ICIS Workbook

• Generating a FieldBook, Recording Observation Data
• Loading a study into the DMS
• Retrieving a study

15:30 break

16:00 ICIS underneath Maize FieldBook

• Importing SetGen List
• Making Stocklists (New Pedigrees Being Saved into GMS)
• Exporting to a SetGen List

16:30 Discussions about MaizeFinder and ICIS/IMIS

17:30 Best practices for software use and data backup

18:00 end

Friday 27 February

QTL MAPPING – JIANKANG WANG

Time Activity

08:00 Introduction to QTL mapping

09:00 The inclusive composite interval mapping (ICIM) for additive and epistasis QTL

10:30 break

11:00 QTL mapping applications by ICIM

12:00 The integrated software QTL IciMapping

13:00 Lunch

DISCUSSIONS RESULTING IN A BRIEF DOCUMENTED RECORD OF BEST PRACTICES

Time Activity

14:00 Using pre-harvest yield ratings to reduce harvesting and speed turn-around for Stage 1 testcrosses– Gary

14:30 Molecular breeding schemes: Best-bet MARS and AB-QTL research plan templates– Gary, Sarah, Kassa, Yunbi

15:30 break

16:00 Work flow between breeders/phenotypers, molecular breeders, outside labs, and bioinformatics, their roles and timelines – Sarah, Kassa, Hector, Yunbi, Gary

17:00 Best practices for monitoring breeding progress – Pancho