Short course UGA 2018 - Programming and computer algorithms in animal breeding with focus on single-step GBLUP and reality of genomic selection

EDIT on March 16th

:!: All new applications will be put on a waiting list.


May 7 - 25, Athens, GA
From 9:00am to 5:00pm

Course Venue

Department of Animal and Dairy Science
425 River Road, Athens GA 30602

Week 1.

Introduction to programming in Fortran 95/2003

Week 2.

Monday - Wednesday:

  1. Advanced programming in Fortran 95/2003
  2. Computer algorithms useful in animal breeding

Thursday - Friday:

  1. Introduction to BLUPF90 family programs
  2. Associated programs: renumf90, inbupg,…
  3. Modeling:
    1. Basic models: single-trait, multiple trait, maternal,…
    2. Advanced models: random-regression, competition, threshold, censored,…
  4. Variance components estimation

Week 3. (Preliminary)

Monday - Tuesday. Basics of Single step

  1. Why single step
    1. Issues with pseudo-observations and indices with PA
    2. Double counting
    3. Pre-selection
  2. Derivation of H and H-1
  3. What G
    1. Derivation from SNP BLUP
    2. Blending
    3. Effect of number of SNP
    4. Properties with different gene frequencies
    5. Other types of G
  4. G and Imputation

Wednesday. Single-step continued

  1. Quality control for G
    1. Calling rate
    2. Parental exclusions
    3. Distributions of diagonals of G
    4. Differences between matched G and A22
    5. Heritability of gene content
    6. Elimination of sex and “0” chromosomes
    7. Eigenvalues/eigenvectors – population stratification
  2. G and A22
    1. Properties of A22 as a function of base year
    2. A22 and incomplete pedigree recording
    3. Matching G to A22
    4. Adjusting A22 to G: metafounders or data cutting
    5. Correlations between G and A22 elements
      1. Genomic and pedigree inbreeding
      2. Runs of homozygosity
    6. Crossbreeding and G

Thursday. Meaning of GEBV, validation and GEBV/SNP conversions

  1. Decomposition of GEBV into PA, DGV, CD, PC and PI
    1. Weights, species and status of animals
  2. Validation techniques for genomics
    1. R2 for dairy bulls
    2. Predictability for animals with records
    3. Cross-validation when few genotyped animals with records (e.g., mortality or disease resistance)
    4. Selection bias for in realized accuracies
  3. Procedures for approximating accuracies with genomic information
  4. Conversion of DGV to SNP effects
    1. Indirect prediction
    2. GWAS
      1. Calculation of SNP weights
      2. LD blocks or SNP regions
      3. Options in postGSf90

Friday. Single-step without limits and practical issues

  1. Computations with very large number of genotypes
    1. Structure of genotyped animals
    2. Unsymmetric equations and SNP methods
    3. APY algorithm for G-1 with millions of genotypes
    4. Computing with new sparse matrix YAMS
    5. YAMS and APY – no limits?
    6. APY and sequence data
    7. APY or indirect prediction?
  2. Select practical issues
    1. UPG in dairy/sheep and external subpopulations
  3. Single-step in commercial applications
  4. Research in animal breeding at UGA and related places
    1. Reality of practical breeding
    2. Heat stress
    3. Realistic competition model
    4. Selection as optimization – nothing is free


Ignacy Misztal, Shogo Tsuruta, Daniela Lourenco, and Yutaka Masuda (UGA)
Andres Legarra and Zulma Vitezica (France)
Ignacio Aguilar (Uruguay)


The course can be attended in full or partially. The attendance in Weeks 1-2 is limited to 25 and in Week 3 is limited to 35. Those attending for 2-3 weeks will have priority.
Those familiar with basics of Fortran 95 can skip Week 1. Those familiar with the BLUPF90 software can skip Week 2.
Thursday-Friday of Week 2 and Week 3 will involve very limited programming and can thus be attended by those interested in application programs and genomic applications.


Participants are expected to be familiar with mixed model equations and quantitative genetics.
Familiarity with Linux / Unix environments a plus.
Knowledge of programming in any programming language a strong plus.


The fees will be the same regardless of the number of weeks attended

  • Industry - $1200
  • Academic - $700
  • Graduate student - $500
  • Graduate students from USA who are part of AG*IDEA institution - might be able to waive the registration fee
  • Prospective graduate students please contact Daniela Lourenco (

Forms of Payment:

Cash, checks (US) or wire transfers (instructions)
We are unable to accept credit card or PayPal payments

Deadline Application:

April 6
As of March 16th, all new applications will be put on a waiting list
Download the Registration Form

To speed up the process, email your registration form to Susan Bradley

Please mail the registration form and check (made payable to University of Georgia) to:
Susan Bradley
University of Georgia Animal and Dairy Science
425 River Road
Athens, GA 30602 USA


The closest airport to Athens is in Atlanta. For transportation to and from the Atlanta airport, see:


Housing at the university dorms will be available. The registration will be open in April:
On-campus hotel (Georgia Center) is also an option:
An extended stay hotel provides accommodation at ~ $250/week (DO NOT book before reading reviews):
Other housing options can be booked through regular booking websites and Airbnb.

Athens information:

course_information_-_uga_2018.txt · Last modified: 2018/03/17 00:33 by dani
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