Efficient designs for fine-mapping of quantitative trait loci using linkage disequilibrium and linkage

S H Lee; Julius Herman Van Der Werf

Efficient designs for fine-mapping of quantitative trait loci using linkage disequilibrium and linkage

S H Lee
, Julius Herman Van Der Werf

School of Environmental & Rural Science

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

Abstract

This study showed that common half sib designs can obtain sufficient linkage disequilibrium (LD) information for fine-mapping of quantitative trait loci (QTL). A design of two large half sib families was applied to a hypothetical population with an effective size (Ne) of 1000 simulated for 6000 generations. 70 ~ 75% of replicates could position QTL within 0.75 cM when mutation age was more than 200 generations in mapping using multi-allelic markers. When Ne was linearly decreasing (1000 to 100) in the last 50 generations, the accuracy of QTL mapping was decreased to only 50 to 70% of replicates that could position QTL within 0.75 cM. Provided that QTL allele segregates in the dam population, it is advantageous to use the same half sib design in linkage mapping and fine-mapping making gene mapping cost effective in livestock populations.

Original language	English
Title of host publication	Proceedings of the Association for the Advancement of Animal Breeding and Genetics
Editors	Abigail Henderson
Place of Publication	Armidale, Australia
Publisher	Association for the Advancement of Animal Breeding and Genetics (AAABG)
Pages	9-13
Volume	15
ISBN (Print)	0958629927
Publication status	Published - 2003
Event	AAABG 2003: 15th Conference of the Association for the Advancement of Animal Breeding and Genetics - Melbourne, Australia Duration: 7 Jul 2003 → 11 Jul 2003

Conference

Conference	AAABG 2003: 15th Conference of the Association for the Advancement of Animal Breeding and Genetics
City	Melbourne, Australia
Period	7/07/03 → 11/07/03

Keywords

Quantitative Genetics (incl Disease and Trait Mapping Genetics)

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https://hdl.handle.net/1959.11/4517

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Lee, S. H., & Van Der Werf, J. H. (2003). Efficient designs for fine-mapping of quantitative trait loci using linkage disequilibrium and linkage. In A. Henderson (Ed.), Proceedings of the Association for the Advancement of Animal Breeding and Genetics (Vol. 15, pp. 9-13). Association for the Advancement of Animal Breeding and Genetics (AAABG). https://hdl.handle.net/1959.11/4517

Lee, S H ; Van Der Werf, Julius Herman. / Efficient designs for fine-mapping of quantitative trait loci using linkage disequilibrium and linkage. Proceedings of the Association for the Advancement of Animal Breeding and Genetics. editor / Abigail Henderson. Vol. 15 Armidale, Australia : Association for the Advancement of Animal Breeding and Genetics (AAABG), 2003. pp. 9-13

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title = "Efficient designs for fine-mapping of quantitative trait loci using linkage disequilibrium and linkage",

abstract = "This study showed that common half sib designs can obtain sufficient linkage disequilibrium (LD) information for fine-mapping of quantitative trait loci (QTL). A design of two large half sib families was applied to a hypothetical population with an effective size (Ne) of 1000 simulated for 6000 generations. 70 \textasciitilde{} 75\% of replicates could position QTL within 0.75 cM when mutation age was more than 200 generations in mapping using multi-allelic markers. When Ne was linearly decreasing (1000 to 100) in the last 50 generations, the accuracy of QTL mapping was decreased to only 50 to 70\% of replicates that could position QTL within 0.75 cM. Provided that QTL allele segregates in the dam population, it is advantageous to use the same half sib design in linkage mapping and fine-mapping making gene mapping cost effective in livestock populations.",

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

author = "Lee, \{S H\} and \{Van Der Werf\}, \{Julius Herman\}",

year = "2003",

language = "English",

isbn = "0958629927",

volume = "15",

pages = "9--13",

editor = "Abigail Henderson",

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 2003: 15th Conference of the Association for the Advancement of Animal Breeding and Genetics ; Conference date: 07-07-2003 Through 11-07-2003",

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Lee, SH & Van Der Werf, JH 2003, Efficient designs for fine-mapping of quantitative trait loci using linkage disequilibrium and linkage. in A Henderson (ed.), Proceedings of the Association for the Advancement of Animal Breeding and Genetics. vol. 15, Association for the Advancement of Animal Breeding and Genetics (AAABG), Armidale, Australia, pp. 9-13, AAABG 2003: 15th Conference of the Association for the Advancement of Animal Breeding and Genetics, Melbourne, Australia, 7/07/03. <https://hdl.handle.net/1959.11/4517>

Efficient designs for fine-mapping of quantitative trait loci using linkage disequilibrium and linkage. / Lee, S H; Van Der Werf, Julius Herman.
Proceedings of the Association for the Advancement of Animal Breeding and Genetics. ed. / Abigail Henderson. Vol. 15 Armidale, Australia: Association for the Advancement of Animal Breeding and Genetics (AAABG), 2003. p. 9-13.

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

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AU - Lee, S H

AU - Van Der Werf, Julius Herman

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N2 - This study showed that common half sib designs can obtain sufficient linkage disequilibrium (LD) information for fine-mapping of quantitative trait loci (QTL). A design of two large half sib families was applied to a hypothetical population with an effective size (Ne) of 1000 simulated for 6000 generations. 70 ~ 75% of replicates could position QTL within 0.75 cM when mutation age was more than 200 generations in mapping using multi-allelic markers. When Ne was linearly decreasing (1000 to 100) in the last 50 generations, the accuracy of QTL mapping was decreased to only 50 to 70% of replicates that could position QTL within 0.75 cM. Provided that QTL allele segregates in the dam population, it is advantageous to use the same half sib design in linkage mapping and fine-mapping making gene mapping cost effective in livestock populations.

AB - This study showed that common half sib designs can obtain sufficient linkage disequilibrium (LD) information for fine-mapping of quantitative trait loci (QTL). A design of two large half sib families was applied to a hypothetical population with an effective size (Ne) of 1000 simulated for 6000 generations. 70 ~ 75% of replicates could position QTL within 0.75 cM when mutation age was more than 200 generations in mapping using multi-allelic markers. When Ne was linearly decreasing (1000 to 100) in the last 50 generations, the accuracy of QTL mapping was decreased to only 50 to 70% of replicates that could position QTL within 0.75 cM. Provided that QTL allele segregates in the dam population, it is advantageous to use the same half sib design in linkage mapping and fine-mapping making gene mapping cost effective in livestock populations.

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

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M3 - Conference contribution

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

A2 - Henderson, Abigail

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

CY - Armidale, Australia

T2 - AAABG 2003: 15th Conference of the Association for the Advancement of Animal Breeding and Genetics

Y2 - 7 July 2003 through 11 July 2003

ER -

Efficient designs for fine-mapping of quantitative trait loci using linkage disequilibrium and linkage

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