ESALQ - USP, Brazil

05 - 09 August 2019

Five-day course in genomic analyses with emphasis on single-step GBLUP

Taught by Daniela Lourenco and Andre Garcia (University of Georgia, USA)

BLUPF90 programs BLUPF90 Download

QMSim genomic data simulator QMSim Download

Xming Xming X Window System Server - for Windows

XQuatz X Quartz - for Mac

Putty 64-bit: putty.exe (the SSH and Telnet client itself)

WinSCP WinSCP File Transfer

Editor Notepad++ Notepad++ 64-bit Installer

Course Outline

BLUPF90 Manual

Introduction to BLUPF90 suite programs

Day 1

• Introduction to blupf90 family

• Lab1

• Files for Lab1

• Script for lab1

Day 2

• Genomic data

• Introduction to QMSim - simulating datasets

• Introduction to Linux commands - data manipulation

• Lab2

• Files for Lab2

Day 3

• The promise of genomics for breeding and genetics

• Quality control of genomic data in preGSf90

• Constructing genomic relationship matrix (G) in preGSf90

• Lab3

• Files for Lab3

• Script for lab3

Day 4

• Introduction to single-step GBLUP

• Lab4

• Files for Lab4

• Script for lab4

Day 5

• SNP effects and GWAS with ssGBLUP

• Lab5

• Files for Lab5

• Script for lab5

• Assignments - All labs

• Lourenco et al., 2019a

• Lourenco et al., 2019b

• Legarra et al., 2018

• Misztal et al., 2017