• Event
  • Scientific training

Bioinformatics for Breeding

The increasing number of genomic tools and resources which facilitate large-scale analysis of genotypes and traits are leading to novel, quicker approaches to breeding.

Start date:

21 February 2017

End date:

24 February 2017

Time:

08h30 - 17h00

Venue:

Earlham Institute

Registration deadline:

08 January 2017

Cost:

£300

About the event.

What is the workshop about?

The increasing number of genomic tools and resources which facilitate large-scale analysis of genotypes and traits are leading to novel, quicker approaches to breeding. This course will introduce participants to the sequencing-based methods and bioinformatics tools available to apply genomic approaches to breeding.

The practical course will feature a collection of methods and bioinformatics tools fundamental for modern breeding, especially for crops. Next generation sequencing (NGS) has made large collections of open-source diversity genomic data possible, such as SNPs, that can be used as molecular markers for breeding. Combined with phenotypes, genome-wide association studies provide breeders with an understanding of the molecular basis of complex traits.

What will it cover?

  • SNP calling/discovery and SNPs effects and context
  • NGS techniques for genotyping
  • Genetic markers, linkage analysis, and genetic maps
  • High-throughput phenotyping and image analysis
  • Association mapping (GWAS)
  • Genome-wide predictions, modelling and simulations
  • Genomic selection

Target Audience

The course is aimed at researchers or pre-breeders working in plant (or animal) improvement and interested in applying NGS approaches in the early future, as well as to plant bioinformaticians with basic knowledge about crop breeding.

Pre requisties

Some experience in bioinformatics would be an advantage but not mandatory, some knowledge of R/Rstudio and Linux & Command-line will be needed - basic training will provided at the beginning of the course.

Programme.

Day 1 - 21 February 2017

Time

Topic

10:00 - 12:00

'Learn Linux from scratch' This is an optional course available to all delegates attending the Bioinformatics for Breeders workshop.

12:00 - 13:00

Lunch and registration

13:00 - 13:15

Welcome and introduction

13:15 - 14:00

Introduction to working remotely in a HPC cluster

14:00 - 14:45

Introduction to R/RStudio

14:45 - 15:15

Coffee break

15:15 - 16:00

Lecture: Cristobal Uauy (JIC): “Understanding diversity to drive crop improvement”

16:00 - 17:00

Hands-on - FASTQ to BAM: How to align reads and references

17:00 - 19:30

Pizza & Beer

Day 2 - 22 February 2017

Time

Topic

09:00 - 09:30

Morning coffee

09:30 - 10:15

Lecture: Ji Zhiu (EI): “High-throughput phenotyping”

10:15 - 11:30

Hands-on SNP calling

11:30 - 12:00

Coffee break

12:00 - 13:15

Hands-on SNP discovery

13:15 - 14:15

Lunch

14:15 - 15:30

Hands-on SNP effects and genomic context

15:30 - 16:00

Coffee break

16:00 - 17:00

Practical lecture: Wiktor Jurkowski (EI): “Phenotyping data standards and platforms”

17:00 - 17:30

Q&A and wrap up

Day 3 - 23 February 2017

Time

Topic

09:00 - 09:30

Morning coffee

09:30 - 10:15

Lecture: Alison Bentley (NIAB): Crop breeding in the NGS age

10:15 - 11:30

Hands on genetic markers, recombination and LD

11:30 - 12:00

Coffee break

12:00 - 13:15

Hands-on Linkage analysis & Genetic maps

13:15 - 14:15

Lunch

14:15 - 15:30

Hands-on association mapping (GWAS)

15:30 - 16:00

Coffee break

16:00 - 17:00

A quick look to Genomic predictions, models and for crop breeding

17:00 - 17:30

Q&A - wrap up

Day 4 - 24 February 2017

Time

Topic

09:00 - 09:30

Morning coffee

09:30 - 10:45

Hands-on Genomic selection

10:45 - 11:15

Coffee break

11:15 - 12:30

Hands-on Genomic selection - cont.

12:30 - 13:15

Q&A - Feedback and wrap up

13:15 - 14:15

Lunch