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Related Experiment Video

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Infinium Assay for Large-scale SNP Genotyping Applications
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Single-Step Genomic Evaluations from Theory to Practice: Using SNP Chips and Sequence Data in BLUPF90.

Daniela Lourenco1, Andres Legarra2, Shogo Tsuruta1

  • 1Department of Animal and Dairy Science, University of Georgia, Athens, GA 30602, USA.

Genes
|July 18, 2020
PubMed
Summary

Single-step genomic evaluation integrates all available animal data for breeding. This method, single-step genomic best linear unbiased prediction (ssGBLUP), efficiently combines genotypes, phenotypes, and pedigree information.

Keywords:
genome-wide associationgenomic predictiongenomic selectionsingle-step genomic BLUP

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Area of Science:

  • Animal Breeding and Genetics
  • Genomics
  • Quantitative Genetics

Background:

  • Single-step genomic evaluation is a standard in livestock breeding, integrating diverse data types seamlessly.
  • It combines pedigree, phenotype, and genotype information without complex post-analysis processing.
  • Incorporating data from both genotyped and non-genotyped animals is straightforward.

Purpose of the Study:

  • To review the theoretical developments and practical implementation of single-step genomic best linear unbiased prediction (ssGBLUP).
  • To highlight the flexibility and global adoption of ssGBLUP within the BLUPF90 software suite.
  • To demonstrate ssGBLUP applications using SNP data, from regular chips to sequence data.

Main Methods:

  • Focuses on single-step genomic best linear unbiased prediction (ssGBLUP), a method using SNP data to construct the genomic relationship matrix.
  • Discusses the implementation of ssGBLUP in the BLUPF90 software suite since 2009.
  • Explores theoretical advancements and numerical examples for ssGBLUP.

Main Results:

  • ssGBLUP has been successfully implemented and refined in the BLUPF90 software suite.
  • The method is flexible for various models, traits, phenotypes, and numbers of genotyped animals.
  • ssGBLUP is utilized globally for livestock genomic evaluations.

Conclusions:

  • Single-step genomic evaluation, particularly ssGBLUP, is a robust and widely adopted methodology in livestock breeding.
  • The BLUPF90 implementation of ssGBLUP offers flexibility and efficiency for integrating genomic data.
  • Continued advancements support the use of ssGBLUP with diverse genomic data, including sequence data.