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 Inidces 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
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