Fine mapping QTL with haplotypes determined from dense single nucleotide polymorphic markers

Yuandan Zhang; Bruce Tier; Rachel Hawken

Fine mapping QTL with haplotypes determined from dense single nucleotide polymorphic markers

Yuandan Zhang, Bruce Tier, Rachel Hawken

Animal Genetics and Breeding Unit

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

Abstract

We use publicly available methods to impute missing genotypes, infer haplotypes and partition haplotypes into blocks for large numbers of single nucleotide polymorphic data on two sections of chromosomes. Haplotype trend regression was used to associate these haplotype blocks with a continuously distributed trait. A number of significant regions of chromosomes, that were not found when tested with single-marker tests, were identified. This study demonstrated a feasible framework to fine-mapping QTL using haplotypes of SNP markers.

Original language	English
Title of host publication	Proceedings of the Association for the Advancement of Animal Breeding and Genetics
Editors	AAABG: Association for the Advancement of Animal Breeding, Genetics
Place of Publication	Armidale, Australia
Publisher	Association for the Advancement of Animal Breeding and Genetics (AAABG)
Pages	119-122
Volume	17
ISBN (Print)	1921208139
Publication status	Published - 2007
Event	AAABG 2007: 17th Conference of the Association for the Advancement of Animal Breeding and Genetics - University of New England, Armidale, Australia Duration: 23 Sept 2007 → 26 Sept 2007

Conference

Conference	AAABG 2007: 17th Conference of the Association for the Advancement of Animal Breeding and Genetics
City	Armidale, Australia
Period	23/09/07 → 26/09/07

Keywords

Quantitative Genetics (incl Disease and Trait Mapping Genetics)

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https://hdl.handle.net/1959.11/4128

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Zhang, Y., Tier, B., & Hawken, R. (2007). Fine mapping QTL with haplotypes determined from dense single nucleotide polymorphic markers. In AAABG. Association for the Advancement of Animal Breeding, & Genetics (Eds.), Proceedings of the Association for the Advancement of Animal Breeding and Genetics (Vol. 17, pp. 119-122). Association for the Advancement of Animal Breeding and Genetics (AAABG). https://hdl.handle.net/1959.11/4128

Zhang, Yuandan ; Tier, Bruce ; Hawken, Rachel. / Fine mapping QTL with haplotypes determined from dense single nucleotide polymorphic markers. Proceedings of the Association for the Advancement of Animal Breeding and Genetics. editor / AAABG: Association for the Advancement of Animal Breeding ; Genetics. Vol. 17 Armidale, Australia : Association for the Advancement of Animal Breeding and Genetics (AAABG), 2007. pp. 119-122

@inproceedings{8d24cf1ae89949bfb267a9e765355a85,

title = "Fine mapping QTL with haplotypes determined from dense single nucleotide polymorphic markers",

abstract = "We use publicly available methods to impute missing genotypes, infer haplotypes and partition haplotypes into blocks for large numbers of single nucleotide polymorphic data on two sections of chromosomes. Haplotype trend regression was used to associate these haplotype blocks with a continuously distributed trait. A number of significant regions of chromosomes, that were not found when tested with single-marker tests, were identified. This study demonstrated a feasible framework to fine-mapping QTL using haplotypes of SNP markers.",

keywords = "Quantitative Genetics (incl Disease and Trait Mapping Genetics)",

author = "Yuandan Zhang and Bruce Tier and Rachel Hawken",

year = "2007",

language = "English",

isbn = "1921208139",

volume = "17",

pages = "119--122",

editor = "\{Association for the Advancement of Animal Breeding\}, AAABG: and Genetics",

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 2007: 17th Conference of the Association for the Advancement of Animal Breeding and Genetics ; Conference date: 23-09-2007 Through 26-09-2007",

}

Zhang, Y, Tier, B & Hawken, R 2007, Fine mapping QTL with haplotypes determined from dense single nucleotide polymorphic markers. in AAABG Association for the Advancement of Animal Breeding & Genetics (eds), Proceedings of the Association for the Advancement of Animal Breeding and Genetics. vol. 17, Association for the Advancement of Animal Breeding and Genetics (AAABG), Armidale, Australia, pp. 119-122, AAABG 2007: 17th Conference of the Association for the Advancement of Animal Breeding and Genetics, Armidale, Australia, 23/09/07. <https://hdl.handle.net/1959.11/4128>

Fine mapping QTL with haplotypes determined from dense single nucleotide polymorphic markers. / Zhang, Yuandan; Tier, Bruce; Hawken, Rachel.
Proceedings of the Association for the Advancement of Animal Breeding and Genetics. ed. / AAABG: Association for the Advancement of Animal Breeding; Genetics. Vol. 17 Armidale, Australia: Association for the Advancement of Animal Breeding and Genetics (AAABG), 2007. p. 119-122.

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

TY - GEN

T1 - Fine mapping QTL with haplotypes determined from dense single nucleotide polymorphic markers

AU - Zhang, Yuandan

AU - Tier, Bruce

AU - Hawken, Rachel

PY - 2007

Y1 - 2007

N2 - We use publicly available methods to impute missing genotypes, infer haplotypes and partition haplotypes into blocks for large numbers of single nucleotide polymorphic data on two sections of chromosomes. Haplotype trend regression was used to associate these haplotype blocks with a continuously distributed trait. A number of significant regions of chromosomes, that were not found when tested with single-marker tests, were identified. This study demonstrated a feasible framework to fine-mapping QTL using haplotypes of SNP markers.

AB - We use publicly available methods to impute missing genotypes, infer haplotypes and partition haplotypes into blocks for large numbers of single nucleotide polymorphic data on two sections of chromosomes. Haplotype trend regression was used to associate these haplotype blocks with a continuously distributed trait. A number of significant regions of chromosomes, that were not found when tested with single-marker tests, were identified. This study demonstrated a feasible framework to fine-mapping QTL using haplotypes of SNP markers.

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

UR - http://trove.nla.gov.au/work/35062558?selectedversion=NBD42373479

M3 - Conference contribution

SN - 1921208139

VL - 17

SP - 119

EP - 122

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

A2 - Association for the Advancement of Animal Breeding, AAABG:

A2 - Genetics, null

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

CY - Armidale, Australia

T2 - AAABG 2007: 17th Conference of the Association for the Advancement of Animal Breeding and Genetics

Y2 - 23 September 2007 through 26 September 2007

ER -

Zhang Y, Tier B, Hawken R. Fine mapping QTL with haplotypes determined from dense single nucleotide polymorphic markers. In Association for the Advancement of Animal Breeding AAABG, Genetics, editors, Proceedings of the Association for the Advancement of Animal Breeding and Genetics. Vol. 17. Armidale, Australia: Association for the Advancement of Animal Breeding and Genetics (AAABG). 2007. p. 119-122

Fine mapping QTL with haplotypes determined from dense single nucleotide polymorphic markers

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