Development of the beef genomic pipeline for BREEDPLAN single step evaluation

Connors, Natalie; Cook, Jim; Girard, Christian; Tier, Bruce; Gore, Klint; Johnston, David; Ferdosi, Mohammad

Author(s)

Connors, Natalie

Cook, Jim

Girard, Christian

Tier, Bruce

Gore, Klint

Johnston, David

Ferdosi, Mohammad

Publication Date

2017

Abstract

Single step genomic BLUP (SS-GBLUP) for BREEDPLAN beef cattle evaluations is currently being tested for implementation across a number of breeds. A genomic data pipeline has been developed to enable efficient analysis of the industry-recorded SNP genotypes for incorporation in SS-GBLUP analyses. Complex data collection, along with format and/or naming convention inconsistencies challenges efficient data processing. This pipeline includes quality control of variable formatted data, and imputation of genotypes, for building the genomic relationship matrix required for implementation into single step evaluation.

Citation

Proceedings of the Association for the Advancement of Animal Breeding and Genetics, v.22, p. 317-320

ISSN

1328-3227

Link

https://hdl.handle.net/1959.11/23151

Language

Publisher

Association for the Advancement of Animal Breeding and Genetics (AAABG)

Title

Development of the beef genomic pipeline for BREEDPLAN single step evaluation

Type of document

Conference Publication

Entity Type

Publication

Author(s)	Connors, Natalie Cook, Jim Girard, Christian Tier, Bruce Gore, Klint Johnston, David Ferdosi, Mohammad
Publication Date	2017
Abstract	Single step genomic BLUP (SS-GBLUP) for BREEDPLAN beef cattle evaluations is currently being tested for implementation across a number of breeds. A genomic data pipeline has been developed to enable efficient analysis of the industry-recorded SNP genotypes for incorporation in SS-GBLUP analyses. Complex data collection, along with format and/or naming convention inconsistencies challenges efficient data processing. This pipeline includes quality control of variable formatted data, and imputation of genotypes, for building the genomic relationship matrix required for implementation into single step evaluation.
Citation	Proceedings of the Association for the Advancement of Animal Breeding and Genetics, v.22, p. 317-320
ISSN	1328-3227
Link	https://hdl.handle.net/1959.11/23151
Language	en
Publisher	Association for the Advancement of Animal Breeding and Genetics (AAABG)
Title	Development of the beef genomic pipeline for BREEDPLAN single step evaluation
Type of document	Conference Publication
Entity Type	Publication

Development of the beef genomic pipeline for BREEDPLAN single step evaluation

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