Slides for short course on 'omics assisted breeding methods.
Dates and Location Monday, November 12 to Thursday, November 15
Lecturers
- Malachy Campbell (MC)
- Hiroyoshi Iwata (HI)
- Diego Jarquin (DJ)
- Gota Morota (GM)
- Emi Tanaka (ET)
- Jessica Tressou (JT)
What do workshop participants expect?
What workshop participants need
- Their own laptop
- R v3.5 and RStudio XX installed
- Special packages need in the WS (BGLR, MTM, rrBLUP)
- For the R-Inla introduction: INLA, sp, fields, geoR, viridisLite + tidyverse
Participants Approximately 90 participants (50 - 70)
Day 1
- 9:00-10:10: Basic statistical computing in R (MC) - R Markdown
- 10:10-10:20: Break
- 10:20-12:00: Data visualization in R (ET) - ggplot2 + desplot
- 12:00-13:00: Lunch
- 13:00-14:00 Introduction to Quantitative Genetics (GM)
- 14:00-14:10: Break
- 14:10-15:40: Least squares and Linear mixed model (MC, JT)
- Lab slides [PDF Slides][.Rmd]
- Exercises [HTML][.Rmd]
- Data [.csv]
- 15:40-15:50: Break
- 15:50-16:50 Bayesian methods (JT)
- 17:30-19:30 Social mixer
Day 2
- 9:00-9:30 Genomic heritability (MC, GM) [PDF Slides][.Rmd]
- 9:30-9:40 Break
- 9:40-12:00 GWAS (HI)
- 12:00-13:00 Lunch
- 13:00-14:00 GBLUP and RR-BLUP (MC, GM)
- Lab slides [PDF Slides][.Rmd][Data]
- 14:00-15:00 Bayesian alphabet (DJ)
- 15:00-15:10 Break
- 15:10-16:10 Classical GxE including FW, AMMI, and biplot (HI, DJ)
- 16:10-17:10 GxE covariates (HI, DJ)
Day 3
- 9:00-11:00 Introduction to ASReml-R (ET)
- 11:00-11:10 Break
- 11:10-12:00 Theoretical part of factor analytic model (ET)
- 12:00-13:00 Lunch
- 13:00-14:00 Application of factor analytic model to GxE analysis with ASReml (ET)
- 14:00-14:10 Break
- 14:10-15:10: Bayesian factor analytic model (DJ, GM)
- 15:10-15:20: Break
- 15:20-16:20 Spatial analysis (ET) Gilmour et al. (1997)
- 16:20-17:00 Introduction to R-INLA (JT)
Day 4
- 9:00-12:00 Multi-trait methods for GWAS and GP (HI, DJ, GM)
- 12:00-13:00 Lunch
- 13:00-15:00 Bayesian network (MC, GM) [PDF Slides][.Rmd]
- 15:00-15:10 Break
- 15:10-17:00 Experimental design + Optimal designs (ET)