Quantitative Genomics and Modern Breeding: from theory to practice (using BLUPF90 programs)

When
August 26 - 30

Location
Florence, Italy
Plesso C9 - Aule Agraria - Università di Firenze See on Google Maps

Instructors
Dr. Daniela Lourenco – University of Georgia, USA
Dr. Christian Maltecca – North Carolina State University, USA
Dr. Francesco Tiezzi – University of Florence, ITA

Course Description
This course offers a focused exploration of quantitative genetics and genomics, providing theoretical understanding and practical applications. Participants will gain comprehensive insights into key genetic principles applied to breeding, covering the fundamental aspects of estimation, selection, and prediction processes crucial for advancing modern breeding practices.

Intended audience
Advanced graduate students, postdocs, faculty, and professionals interested in breeding programs and using genomic information to predict genetic merit.

Course Schedule
Check the full schedule here

Day 1

• Mixed models related to breeding and genetics
• Introduction to BLUPF90 programs for the analyses of Mixed Models
• Estimation of breeding values and VCE: blupf90+
• Estimation of breeding values and VCE - Bayesian: gibbsf90+

Day 2

• Genetic resemblance, diversity, and covariance
• Introduction to genomic data
• Theory of GBLUP and ssGBLUP
• Creation of genomic relationship matrices and quality control in preGSf90
• Using blupf90+ and gibbsf90+ for GBLUP and ssGBLUP

Day 3

• Multi Environmental and Multivariate Models
• Genotype by Environment and longitudinal models
• Multivariate, random regression, and reaction norm models using blupf90+ and gibbsf90+

Day 4

• Methods for GWAS: linear, nonlinear, and ML models
• SNP effects and GWAS from GBLUP-based models
• Multi-Omics and functional Annotation

Day 5

• Beyond genomics, predicting phenotypes

Registration Cost
Before May 1st, 2024: 650 euros
Before July 1st, 2024: 750 euros
Starting July 1st, 2024, 850 euros

The registration cost includes access to the course, coffee breaks, lunch, and a social dinner.

Registration link
Register here

Local organizing committee
Dr. Francesco Tiezzi – University of Florence, ITA
Prof. Riccardo Bozzi – University of Florence, ITA

BLUPF90 programs BLUPF90 Download

Download BLUPF90 programs before August 19 and make sure they are working. Choose the proper OS according to your laptop.

It allows one to run Unix commands from a PC:

MobaXterm Enhanced terminal for Windows with X11 server, tabbed SSH client, network tools, and more.

Editor Notepad++ Notepad++ 64-bit Installer

It allows one to use Linux graphical applications remotely:

Xming Xming X Window System Server - for Windows

XQuatz X Quartz - for Mac

Install R according to the OS you use: R

1) The preferred OS for the course is Linux. If you want to use Windows, please download MobaXterm so that you can use some Linux bash commands inside Windows.

2) If you have problems executing the BLUPF90 binaries in Windows, it may be related to the lack of OpenMP libraries (“The program can't start because libiomp5md.dll is missing from your computer…”). Click here to solve this issue.

3) If you have problems executing the BLUPF90 binaries in Linux or MacOS, change the permission for the file using the following command

chmod a+x <filename>

or

chmod 777 <filename>

4) In some laptops, it is necessary to use the following command before the BLUPF90 program name

./ <filename>

5) If you try to run any program and get a message about segmentation fault, this is because the program tried to access an inappropriate memory area or accessed it abnormally.

When the program fails (crashes) without any messages, most likely, a segmentation fault has occurred.

There are possible reasons for this error.

• Missing configuration in your computing environment
• Running out of free memory
• A bug in the program

Please type the following command before running the BLUPF90 programs.

ulimit -s unlimited

BLUPF90 Manual

Bases for Genomic Prediction

Step-by-step on how to run ssGBLUP

Day 1

• Linear mixed models - a short review
• Linear mixed models - examples
• Introduction to the BLUPF90 Software Suite
• Lab1
• Data for Lab1
• Solutions for Lab1

Day 2

• Resemblance
• Theory of GBLUP and single-step GBLUP
• Validating Genomic Predictions
• Lab2
• Data for Lab2
• Solutions for Lab2

Day 3

• Multi-trait, GxE
• Multivariate, RRM, and RNM using BLUPF90
• Shaeffer's notes on RRM
• Linux bash scripting
• Lab3
• Data for Lab3
• Solutions for Lab3

Day 4

• SNP effects, IP, and GWAS in ssGBLUP
• Functional Annotation
• Lab4
• Data for Lab4

Day 5

• Multi-omics
• Multi-omics - examples