Genomic Relationships and GBLUP

Plant Breeding and Genomics June 12, 2014|Print

Author:

Fikret Isik, North Carolina State University

This tutorial describes calculations of realized genomic relationships from DNA markers and the application of GBLUP for genomic estimated breeding values in animal and plant breeding. Two demos are provided using R and ASReml software. The tutorial was recorded as a live webinar on August 1, 2013.

Learning Objectives

  • Estimate realized genomic relationships (G matrix) using SNP markers with different methods
  • Compare realized genomic relationships with pedigree based genetic relationships (A matrix)
  • Calculate genomic estimated breeding values using the inverse of the G matrix 

Software Links 

R Statistical Software (Open Source)
Bioconductor: GeneticsPed Package (Open Source)
ASReml

Supplemental Files (attached below)

R Scripts
     Calculate genomic relationships: Gmatrix_webinar.R
     Calculate inverse of G Matrix: Ginverse_Webinar.R
Data Files Used in Demostrations
     ped.ped
     C165pedmatrix.csv
     data.csv
     Genotype_c.csv
     Marker.txt

Part 1 Introduction and Marker Matrices

Part 2 Calculating Genomic Relationships (G matrix): R Demonstration 

Part 3 Genetic evaluation with ABLUP and GBLUP: ASReml Demonstration

Full Recording

About the Presenter

Fikret T. Isik

Fikret Isik is Associate Professor and Associate Director of North Carolina State University Cooperative Tree Improvement Program. Dr. Isik has been awarded with USDA Secretary’s Honor Award, NATO post-doctoral fellowships, and the Turkish Higher Education Council honorary Associate Professor of genetics. He is currently involved in the following areas of research: 1) genomic prediction methods in forest tree breeding and development of tree breeding strategies for genomic era; 2) development of a quantitative model of the pathways and regulation of lignin biosynthesis in poplar and 3) pathogen by pine genotype interactions in the fusiform rust - Pinus taeda pathosystem.

Related Publication

Zapata-Valenzuela, J., Whetten, R. W., Neale, D. B., McKeand, S. E., & Isik, F. (2013). Genomic Estimated Breeding Values Using Genomic Relationship Matrices in a Cloned Population of Loblolly Pine. G3: Genes| Genomes| Genetics.

Recommended Reading

Forni, S., Aguilar, I., & Misztal, I. (2011). Different genomic relationship matrices for single-step analysis using phenotypic, pedigree and genomic information. Genetics Selection Evolution, 43(1).

Henderson, C. R. (1984). Linear models in animal breeding.

Lynch, M., & Walsh, B. (1998). Genetics and analysis of quantitative traits.

Mrode, R. A., & Thompson, R. (2005). Linear models for the prediction of animal breeding values. Cabi, UK.

VanRaden, P. M. (2008). Efficient methods to compute genomic predictions. Journal of Dairy Science, 91(11), 4414-4423.

Funding Statement

Development of this resource was supported in part by the National Institute of Food and Agriculture (NIFA) Solanaceae Coordinated Agricultural Project, Dry Bean Root Health East Africa, National Institute of Food and Agriculture (NIFA) Coordinated Agricultural Project Conifer Translational Genomics Network and NC State University Cooperative Tree Improvement Program. Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the view of the United States Department of Agriculture.

 

Attachments:

GBLUP_Webinar_Slides.pdf (2.18 MB)

Supplementary Files.zip (872.53 KB)

PBGworks 1614