Implementation of single-step genomic BREEDPLAN evaluations in Australian beef cattle

David Johnston; Mohammad Ferdosi; Natalie Connors; Vinzent Boerner; Jim Cook; Christian Girard; Andrew Swan; Bruce Tier

Implementation of single-step genomic BREEDPLAN evaluations in Australian beef cattle

David Johnston, Mohammad Ferdosi, Natalie Connors, Vinzent Boerner, Jim Cook, Christian Girard, Andrew Swan, Bruce Tier

Animal Genetics and Breeding Unit

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

Abstract

Single-step GBLUP (ssGBLUP) procedures have now been implemented into Australia's BREEDPLAN genetic evaluation system for beef cattle. This major remodelling required the development of many new features and modifications to existing procedures. The first requirement was the construction of a flexible but robust set of procedures for handling and processing of raw SNP genotypes to enable the construction of suitable genomic relationship matrices. The analytical processes were modified to replace with and for the explicit fitting of genetic groups. A new accuracy algorithm was developed and the solver was revised. Examples from Australian Angus and Brahman breeds comparing current BLUP evaluation with ssGBLUP are presented to show the resultant changes and effects of implementing the new genomic evaluations.

Original language	English
Pages (from-to)	269-277
Journal	Proceedings of the World Congress on Genetics Applied to Livestock Production
Volume	Theory to Application 1
Publication status	Published - 2018
Event	WCGALP 2018: 11th World Congress on Genetics Applied to Livestock Production - Aotea Convention Centre, Auckland, New Zealand Duration: 7 Feb 2018 → 16 Feb 2018

Keywords

Agriculture, Land and Farm Management
Quantitative Genetics (incl. Disease and Trait Mapping Genetics)

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Johnston, D., Ferdosi, M., Connors, N., Boerner, V., Cook, J., Girard, C., Swan, A., & Tier, B. (2018). Implementation of single-step genomic BREEDPLAN evaluations in Australian beef cattle. Proceedings of the World Congress on Genetics Applied to Livestock Production, Theory to Application 1, 269-277. http://www.wcgalp.org/proceedings/2018/implementation-single-step-genomic-breedplan-evaluations-australian-beef-cattle

@article{15c25309e4e742098aaf1135af060dac,

title = "Implementation of single-step genomic BREEDPLAN evaluations in Australian beef cattle",

abstract = "Single-step GBLUP (ssGBLUP) procedures have now been implemented into Australia's BREEDPLAN genetic evaluation system for beef cattle. This major remodelling required the development of many new features and modifications to existing procedures. The first requirement was the construction of a flexible but robust set of procedures for handling and processing of raw SNP genotypes to enable the construction of suitable genomic relationship matrices. The analytical processes were modified to replace with and for the explicit fitting of genetic groups. A new accuracy algorithm was developed and the solver was revised. Examples from Australian Angus and Brahman breeds comparing current BLUP evaluation with ssGBLUP are presented to show the resultant changes and effects of implementing the new genomic evaluations.",

keywords = "Agriculture, Land and Farm Management, Quantitative Genetics (incl. Disease and Trait Mapping Genetics)",

author = "David Johnston and Mohammad Ferdosi and Natalie Connors and Vinzent Boerner and Jim Cook and Christian Girard and Andrew Swan and Bruce Tier",

year = "2018",

language = "English",

volume = "Theory to Application 1",

pages = "269--277",

journal = "Proceedings of the World Congress on Genetics Applied to Livestock Production",

publisher = "Massey University",

note = "WCGALP 2018: 11th World Congress on Genetics Applied to Livestock Production ; Conference date: 07-02-2018 Through 16-02-2018",

}

Johnston, D, Ferdosi, M , Connors, N, Boerner, V, Cook, J, Girard, C, Swan, A & Tier, B 2018, 'Implementation of single-step genomic BREEDPLAN evaluations in Australian beef cattle', Proceedings of the World Congress on Genetics Applied to Livestock Production, vol. Theory to Application 1, pp. 269-277. <http://www.wcgalp.org/proceedings/2018/implementation-single-step-genomic-breedplan-evaluations-australian-beef-cattle>

TY - JOUR

T1 - Implementation of single-step genomic BREEDPLAN evaluations in Australian beef cattle

AU - Johnston, David

AU - Ferdosi, Mohammad

AU - Connors, Natalie

AU - Boerner, Vinzent

AU - Cook, Jim

AU - Girard, Christian

AU - Swan, Andrew

AU - Tier, Bruce

PY - 2018

Y1 - 2018

N2 - Single-step GBLUP (ssGBLUP) procedures have now been implemented into Australia's BREEDPLAN genetic evaluation system for beef cattle. This major remodelling required the development of many new features and modifications to existing procedures. The first requirement was the construction of a flexible but robust set of procedures for handling and processing of raw SNP genotypes to enable the construction of suitable genomic relationship matrices. The analytical processes were modified to replace with and for the explicit fitting of genetic groups. A new accuracy algorithm was developed and the solver was revised. Examples from Australian Angus and Brahman breeds comparing current BLUP evaluation with ssGBLUP are presented to show the resultant changes and effects of implementing the new genomic evaluations.

AB - Single-step GBLUP (ssGBLUP) procedures have now been implemented into Australia's BREEDPLAN genetic evaluation system for beef cattle. This major remodelling required the development of many new features and modifications to existing procedures. The first requirement was the construction of a flexible but robust set of procedures for handling and processing of raw SNP genotypes to enable the construction of suitable genomic relationship matrices. The analytical processes were modified to replace with and for the explicit fitting of genetic groups. A new accuracy algorithm was developed and the solver was revised. Examples from Australian Angus and Brahman breeds comparing current BLUP evaluation with ssGBLUP are presented to show the resultant changes and effects of implementing the new genomic evaluations.

KW - Agriculture, Land and Farm Management

KW - Quantitative Genetics (incl. Disease and Trait Mapping Genetics)

M3 - Conference article

VL - Theory to Application 1

SP - 269

EP - 277

JO - Proceedings of the World Congress on Genetics Applied to Livestock Production

JF - Proceedings of the World Congress on Genetics Applied to Livestock Production

T2 - WCGALP 2018: 11th World Congress on Genetics Applied to Livestock Production

Y2 - 7 February 2018 through 16 February 2018

ER -

Implementation of single-step genomic BREEDPLAN evaluations in Australian beef cattle

Abstract

Keywords

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