Genome wide association studies in dairy cattle using high density SNP scans

H W Raadsma; M S Khatkar; G Moser; M Hobbs; Ronald Crump; J A L Cavanagh; Bruce Tier

Genome wide association studies in dairy cattle using high density SNP scans

H W Raadsma, M S Khatkar, G Moser, M Hobbs, Ronald Crump, J A L Cavanagh, Bruce Tier

Animal Genetics and Breeding Unit

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

Abstract

Use of high density Single Nucleotide Polymorphic (SNP) marker information allows for prediction of genetic merit via genome wide selection and for localization of markers in gene regions of biological interest through Genome Wide Association Studies (GWAS). We report on a replicated GWAS in dairy cattle using 1,945 progeny tested bulls genotyped with three high density SNP panels representing 63,678 informative SNP. Single SNP genotypes were analysed against deregressed EBV for protein percent and fat percent using a mixed linear model accounting for SNP and animal polygenic effects. The 127,356 analyses (63,678 informative SNP by two traits) across the two data sets identified 143 and 87 significant (P<0.05, corrected for False Discovery Rate) associations for protein % in data set 1 and 2 respectively, whilst for fat % 102 and 61 significant associations were identified in the two data sets respectively. Outputs from selected SNP analyses are discussed for significance and pleiotropic effects and compared against integrated QTL meta-assembly from public domain studies.

Original language	English
Title of host publication	Proceedings of the Association for the Advancement of Animal Breeding and Genetics
Editors	Alex Safari, Bill Pattie, Barrie Restall
Place of Publication	Armidale, Australia
Publisher	Association for the Advancement of Animal Breeding and Genetics (AAABG)
Pages	151-154
Volume	18
ISBN (Print)	9780646521039
Publication status	Published - 2009
Event	AAABG 2009: 18th Conference of the Association for the Advancement of Animal Breeding and Genetics - Barossa Valley, Australia Duration: 27 Sept 2009 → 2 Oct 2009

Conference

Conference	AAABG 2009: 18th Conference of the Association for the Advancement of Animal Breeding and Genetics
City	Barossa Valley, Australia
Period	27/09/09 → 2/10/09

Keywords

Animal Breeding
Genomics

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Raadsma, H. W., Khatkar, M. S., Moser, G., Hobbs, M., Crump, R., Cavanagh, J. A. L., & Tier, B. (2009). Genome wide association studies in dairy cattle using high density SNP scans. In A. Safari, B. Pattie, & B. Restall (Eds.), Proceedings of the Association for the Advancement of Animal Breeding and Genetics (Vol. 18, pp. 151-154). Association for the Advancement of Animal Breeding and Genetics (AAABG). https://hdl.handle.net/1959.11/5240

Raadsma, H W ; Khatkar, M S ; Moser, G et al. / Genome wide association studies in dairy cattle using high density SNP scans. Proceedings of the Association for the Advancement of Animal Breeding and Genetics. editor / Alex Safari ; Bill Pattie ; Barrie Restall. Vol. 18 Armidale, Australia : Association for the Advancement of Animal Breeding and Genetics (AAABG), 2009. pp. 151-154

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title = "Genome wide association studies in dairy cattle using high density SNP scans",

abstract = "Use of high density Single Nucleotide Polymorphic (SNP) marker information allows for prediction of genetic merit via genome wide selection and for localization of markers in gene regions of biological interest through Genome Wide Association Studies (GWAS). We report on a replicated GWAS in dairy cattle using 1,945 progeny tested bulls genotyped with three high density SNP panels representing 63,678 informative SNP. Single SNP genotypes were analysed against deregressed EBV for protein percent and fat percent using a mixed linear model accounting for SNP and animal polygenic effects. The 127,356 analyses (63,678 informative SNP by two traits) across the two data sets identified 143 and 87 significant (P<0.05, corrected for False Discovery Rate) associations for protein \% in data set 1 and 2 respectively, whilst for fat \% 102 and 61 significant associations were identified in the two data sets respectively. Outputs from selected SNP analyses are discussed for significance and pleiotropic effects and compared against integrated QTL meta-assembly from public domain studies.",

keywords = "Animal Breeding, Genomics",

author = "Raadsma, \{H W\} and Khatkar, \{M S\} and G Moser and M Hobbs and Ronald Crump and Cavanagh, \{J A L\} and Bruce Tier",

year = "2009",

language = "English",

isbn = "9780646521039",

volume = "18",

pages = "151--154",

editor = "Alex Safari and Bill Pattie and Barrie Restall",

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

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

note = "AAABG 2009: 18th Conference of the Association for the Advancement of Animal Breeding and Genetics ; Conference date: 27-09-2009 Through 02-10-2009",

}

Raadsma, HW, Khatkar, MS, Moser, G, Hobbs, M, Crump, R, Cavanagh, JAL & Tier, B 2009, Genome wide association studies in dairy cattle using high density SNP scans. in A Safari, B Pattie & B Restall (eds), Proceedings of the Association for the Advancement of Animal Breeding and Genetics. vol. 18, Association for the Advancement of Animal Breeding and Genetics (AAABG), Armidale, Australia, pp. 151-154, AAABG 2009: 18th Conference of the Association for the Advancement of Animal Breeding and Genetics, Barossa Valley, Australia, 27/09/09. <https://hdl.handle.net/1959.11/5240>

Genome wide association studies in dairy cattle using high density SNP scans. / Raadsma, H W; Khatkar, M S; Moser, G et al.
Proceedings of the Association for the Advancement of Animal Breeding and Genetics. ed. / Alex Safari; Bill Pattie; Barrie Restall. Vol. 18 Armidale, Australia: Association for the Advancement of Animal Breeding and Genetics (AAABG), 2009. p. 151-154.

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

TY - GEN

T1 - Genome wide association studies in dairy cattle using high density SNP scans

AU - Raadsma, H W

AU - Khatkar, M S

AU - Moser, G

AU - Hobbs, M

AU - Crump, Ronald

AU - Cavanagh, J A L

AU - Tier, Bruce

PY - 2009

Y1 - 2009

N2 - Use of high density Single Nucleotide Polymorphic (SNP) marker information allows for prediction of genetic merit via genome wide selection and for localization of markers in gene regions of biological interest through Genome Wide Association Studies (GWAS). We report on a replicated GWAS in dairy cattle using 1,945 progeny tested bulls genotyped with three high density SNP panels representing 63,678 informative SNP. Single SNP genotypes were analysed against deregressed EBV for protein percent and fat percent using a mixed linear model accounting for SNP and animal polygenic effects. The 127,356 analyses (63,678 informative SNP by two traits) across the two data sets identified 143 and 87 significant (P<0.05, corrected for False Discovery Rate) associations for protein % in data set 1 and 2 respectively, whilst for fat % 102 and 61 significant associations were identified in the two data sets respectively. Outputs from selected SNP analyses are discussed for significance and pleiotropic effects and compared against integrated QTL meta-assembly from public domain studies.

AB - Use of high density Single Nucleotide Polymorphic (SNP) marker information allows for prediction of genetic merit via genome wide selection and for localization of markers in gene regions of biological interest through Genome Wide Association Studies (GWAS). We report on a replicated GWAS in dairy cattle using 1,945 progeny tested bulls genotyped with three high density SNP panels representing 63,678 informative SNP. Single SNP genotypes were analysed against deregressed EBV for protein percent and fat percent using a mixed linear model accounting for SNP and animal polygenic effects. The 127,356 analyses (63,678 informative SNP by two traits) across the two data sets identified 143 and 87 significant (P<0.05, corrected for False Discovery Rate) associations for protein % in data set 1 and 2 respectively, whilst for fat % 102 and 61 significant associations were identified in the two data sets respectively. Outputs from selected SNP analyses are discussed for significance and pleiotropic effects and compared against integrated QTL meta-assembly from public domain studies.

KW - Animal Breeding

KW - Genomics

UR - http://trove.nla.gov.au/work/36420775

UR - http://aaabg.org/aaabg18/

UR - http://www.aaabg.org/proceedings18/files/raadsma151.pdf

M3 - Conference contribution

SN - 9780646521039

VL - 18

SP - 151

EP - 154

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

A2 - Safari, Alex

A2 - Pattie, Bill

A2 - Restall, Barrie

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

CY - Armidale, Australia

T2 - AAABG 2009: 18th Conference of the Association for the Advancement of Animal Breeding and Genetics

Y2 - 27 September 2009 through 2 October 2009

ER -

Raadsma HW, Khatkar MS, Moser G, Hobbs M, Crump R, Cavanagh JAL et al. Genome wide association studies in dairy cattle using high density SNP scans. In Safari A, Pattie B, Restall B, editors, Proceedings of the Association for the Advancement of Animal Breeding and Genetics. Vol. 18. Armidale, Australia: Association for the Advancement of Animal Breeding and Genetics (AAABG). 2009. p. 151-154

Genome wide association studies in dairy cattle using high density SNP scans

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Keywords

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