Development of the beef genomic pipeline for BREEDPLAN single step evaluation

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

Development of the beef genomic pipeline for BREEDPLAN single step evaluation

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

Animal Genetics and Breeding Unit

Research output: Contribution to journal › Conference article › peer-review

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.

Original language	English
Pages (from-to)	317-320
Journal	Proceedings of the Association for the Advancement of Animal Breeding and Genetics
Volume	22
Publication status	Published - 31 Dec 2017
Event	AAABG 2017: 22nd Conference of the Association for the Advancement of Animal Breeding and Genetics - Townsville, Australia Duration: 2 Jul 2017 → 5 Jul 2017

Keywords

Animal Breeding

Access to Document

Handle.net

Persistent link

Cite this

@article{e80c3bc1e8b942b68c575aaaa031376b,

title = "Development of the beef genomic pipeline for BREEDPLAN single step evaluation",

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.",

keywords = "Animal Breeding",

author = "Natalie Connors and Jim Cook and Christian Girard and Bruce Tier and Klint Gore and David Johnston and Mohammad Ferdosi",

year = "2017",

month = dec,

day = "31",

language = "English",

volume = "22",

pages = "317--320",

journal = "Proceedings of the Association for the Advancement of Animal Breeding and Genetics",

issn = "1328-3227",

publisher = "Association for the Advancement of Animal Breeding and Genetics (AAABG)",

note = "AAABG 2017: 22nd Conference of the Association for the Advancement of Animal Breeding and Genetics ; Conference date: 02-07-2017 Through 05-07-2017",

}

TY - JOUR

T1 - Development of the beef genomic pipeline for BREEDPLAN single step evaluation

AU - Connors, Natalie

AU - Cook, Jim

AU - Girard, Christian

AU - Tier, Bruce

AU - Gore, Klint

AU - Johnston, David

AU - Ferdosi, Mohammad

PY - 2017/12/31

Y1 - 2017/12/31

N2 - 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.

AB - 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.

KW - Animal Breeding

UR - http://www.aaabg.org/aaabghome/

M3 - Conference article

SN - 1328-3227

VL - 22

SP - 317

EP - 320

JO - Proceedings of the Association for the Advancement of Animal Breeding and Genetics

JF - Proceedings of the Association for the Advancement of Animal Breeding and Genetics

T2 - AAABG 2017: 22nd Conference of the Association for the Advancement of Animal Breeding and Genetics

Y2 - 2 July 2017 through 5 July 2017

ER -

Development of the beef genomic pipeline for BREEDPLAN single step evaluation

Abstract

Keywords

Access to Document

Handle.net

Fingerprint

Cite this