Genome Structure in Australian Holstein Friesian Cattle Revealed by Combined Analysis of Three High Density SNP Panels

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

Genome Structure in Australian Holstein Friesian Cattle Revealed by Combined Analysis of Three High Density SNP Panels

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

Animal Genetics and Breeding Unit

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

Abstract

We genotyped overlapping samples of Australian dairy bulls using three different SNP chips (15k, 25k and 54k). These chips have different but complementary coverage hence increasing the number of animals and the density and coverage of SNPs to 74k in a combined dataset. A combined analysis of the data from these three SNP chips showed a four fold increase in the coverage of the genome by haplotype blocks over bovine hapmap reported previously (Khatkar et al. 2007). An analysis of contiguous runs of homozygosity revealed long stretches (up to 49.39 Mb) of homozygosity on chromosome 1 in many bulls. Distribution of these segments of homozygosity in a sample of bulls is presented. The results for one chromosome are described in detail.

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	247-250
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

Genome Structure and Regulation
Animal Breeding

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https://hdl.handle.net/1959.11/5272

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Khatkar, M. S., Tier, B., Hobbs, M., Khatkar, D., Cavanagh, J. A. L., Crump, R., Moser, G., & Raadsma, H. W. (2009). Genome Structure in Australian Holstein Friesian Cattle Revealed by Combined Analysis of Three High Density SNP Panels. In A. Safari, B. Pattie, & B. Restall (Eds.), Proceedings of the Association for the Advancement of Animal Breeding and Genetics (Vol. 18, pp. 247-250). Association for the Advancement of Animal Breeding and Genetics (AAABG). https://hdl.handle.net/1959.11/5272

Khatkar, M S ; Tier, Bruce ; Hobbs, M et al. / Genome Structure in Australian Holstein Friesian Cattle Revealed by Combined Analysis of Three High Density SNP Panels. 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. 247-250

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title = "Genome Structure in Australian Holstein Friesian Cattle Revealed by Combined Analysis of Three High Density SNP Panels",

abstract = "We genotyped overlapping samples of Australian dairy bulls using three different SNP chips (15k, 25k and 54k). These chips have different but complementary coverage hence increasing the number of animals and the density and coverage of SNPs to 74k in a combined dataset. A combined analysis of the data from these three SNP chips showed a four fold increase in the coverage of the genome by haplotype blocks over bovine hapmap reported previously (Khatkar et al. 2007). An analysis of contiguous runs of homozygosity revealed long stretches (up to 49.39 Mb) of homozygosity on chromosome 1 in many bulls. Distribution of these segments of homozygosity in a sample of bulls is presented. The results for one chromosome are described in detail.",

keywords = "Genome Structure and Regulation, Animal Breeding",

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year = "2009",

language = "English",

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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",

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Khatkar, MS, Tier, B, Hobbs, M, Khatkar, D, Cavanagh, JAL, Crump, R, Moser, G & Raadsma, HW 2009, Genome Structure in Australian Holstein Friesian Cattle Revealed by Combined Analysis of Three High Density SNP Panels. 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. 247-250, 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/1959.11/5272>

Genome Structure in Australian Holstein Friesian Cattle Revealed by Combined Analysis of Three High Density SNP Panels. / Khatkar, M S; Tier, Bruce; Hobbs, M 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. 247-250.

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

TY - GEN

T1 - Genome Structure in Australian Holstein Friesian Cattle Revealed by Combined Analysis of Three High Density SNP Panels

AU - Khatkar, M S

AU - Tier, Bruce

AU - Hobbs, M

AU - Khatkar, D

AU - Cavanagh, J A L

AU - Crump, Ronald

AU - Moser, G

AU - Raadsma, H W

PY - 2009

Y1 - 2009

N2 - We genotyped overlapping samples of Australian dairy bulls using three different SNP chips (15k, 25k and 54k). These chips have different but complementary coverage hence increasing the number of animals and the density and coverage of SNPs to 74k in a combined dataset. A combined analysis of the data from these three SNP chips showed a four fold increase in the coverage of the genome by haplotype blocks over bovine hapmap reported previously (Khatkar et al. 2007). An analysis of contiguous runs of homozygosity revealed long stretches (up to 49.39 Mb) of homozygosity on chromosome 1 in many bulls. Distribution of these segments of homozygosity in a sample of bulls is presented. The results for one chromosome are described in detail.

AB - We genotyped overlapping samples of Australian dairy bulls using three different SNP chips (15k, 25k and 54k). These chips have different but complementary coverage hence increasing the number of animals and the density and coverage of SNPs to 74k in a combined dataset. A combined analysis of the data from these three SNP chips showed a four fold increase in the coverage of the genome by haplotype blocks over bovine hapmap reported previously (Khatkar et al. 2007). An analysis of contiguous runs of homozygosity revealed long stretches (up to 49.39 Mb) of homozygosity on chromosome 1 in many bulls. Distribution of these segments of homozygosity in a sample of bulls is presented. The results for one chromosome are described in detail.

KW - Genome Structure and Regulation

KW - Animal Breeding

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

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

UR - http://www.aaabg.org/proceedings18/files/khatkar247.pdf

M3 - Conference contribution

SN - 9780646521039

VL - 18

SP - 247

EP - 250

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 -

Khatkar MS, Tier B, Hobbs M, Khatkar D, Cavanagh JAL, Crump R et al. Genome Structure in Australian Holstein Friesian Cattle Revealed by Combined Analysis of Three High Density SNP Panels. 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. 247-250

Genome Structure in Australian Holstein Friesian Cattle Revealed by Combined Analysis of Three High Density SNP Panels

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Keywords

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