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

When

May 16 - June 3, Athens, GA
From 9:00am to 5:00pm

Course Venue

Department of Animal and Dairy Science
425 River Road, Athens GA 30602
Classroom #114
Google street view

General info ... the big day is coming!

1) The course check-in will be at 8:50am Monday May 16 (classroom #114)
2) We have 25 desktops available for the lab session, but due to the high number of participants, we encourage you to bring your personal laptop
3) Once you are at UGA, you should be able to connect to the welcome_to_UGA network as a guest (pwd will be provided)
4) Course participants will have access to a linux server, so no previous preparation is needed


Week 1.

Introduction to programming in Fortran 95/2003


PDF Computational techniques in animal breeding

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


PDF Introduction to renumf90
PDF Parallelization

Week 3. (Monday free - Memorial Day)

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


PDF Genomic matrices in preGSf90

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


PDF Quality control of genomic data

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


PDF GWAS in ssGBLUP

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


PDF Genomic analyses with emphasis on single-step
PDF Efficient inversion of genomic relationship matrix
PDF ssGBLUP in practice
PDF Assignments

Instructors:

Ignacy Misztal (UGA), Shogo Tsuruta (UGA), Daniela Lourenco (UGA), Yutaka Masuda (UGA), and Ignacio Aguilar (INIA, Uruguay)

Attendance:

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 only by those interested in application programs and genomic applications.

Prerequisites:

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.

Fees:

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 - no fees
  • Prospective graduate students please contact Daniela Lourenco (danilino@uga.edu)

Forms of Payment:

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

Deadline Application:

April 6
Download the Registration Form

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

Logistics:

The closest airport to Athens is in Atlanta. A local hotel provides accommodation at < $250/week. Detailed information will be available later at http://nce.ads.uga.edu/~ignacy/course.html

Athens information

Pictures

Sandy Creek Park

Picnic in Summer Course at UGA’s Animal Breeding and Genetics is a chance to relax in beautiful nature Georgia. On May 25th, casual outdoor evening was a great opportunity to gather with new friends. Attendees shared and enjoyed a fun and memorable experience at Sandy Creek Park.

Study Hard, Play Hard!

Animal Breeding and Genetics Team had 51 attendees from all over the world to join UGA Edgar L. Rhodes Center for Animal and Dairy Science for a 3-weeks summer course. Many attendees said the team’s lectures and assignments have helped to understand about the newest methods of animal breeding and genetics. During the summer course, participants, who embrace same passion for animal genetics and breeding in different species and countries, exchanged opinions and listened to each other through social activities such as Picnic in Sandy Creek Park, Gala Dinner at Terrace Room in State Botanical garden of Georgia, and Beer brewery tour for Terrapin.

“I was happy to have been able to create a bond with many scientists in my filed,” said one of the participants. “I learned the most advanced system for animal breeding with their computer programs.”

course_information_-_uga_2016.txt · Last modified: 2016/07/15 22:06 by dani
 
Recent changes RSS feed Donate Powered by PHP Valid XHTML 1.0 Valid CSS Driven by DokuWiki