Reference Genome Anchoring of High-Density Markers for Association Mapping and Genomic Prediction in European Winter Wheat

Olufunmilayo Ladejobi; Ian J. Mackay; Jesse Poland; Sebastien Praud; Julian M. Hibberd; Alison R. Bentley

doi:10.3389/fpls.2019.01278

Reference Genome Anchoring of High-Density Markers for Association Mapping and Genomic Prediction in European Winter Wheat

Olufunmilayo Ladejobi, Ian J. Mackay, Jesse Poland, Sebastien Praud, Julian M. Hibberd, Alison R. Bentley^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

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Abstract

In this study, we anchored genotyping-by-sequencing data to the International Wheat Genome Sequencing Consortium Reference Sequence v1.0 assembly to generate over 40,000 high quality single nucleotide polymorphism markers on a panel of 376 elite European winter wheat varieties released between 1946 and 2007. We compared association mapping and genomic prediction accuracy for a range of productivity traits with previous results based on lower density dominant DArT markers. The results demonstrate that the availability of RefSeq v1.0 supports higher precision trait mapping and provides the density of markers required to obtain accurate predictions of traits controlled by multiple small effect loci, including grain yield.

Original language	English
Article number	1278
Journal	Frontiers in Plant Science
Volume	10
Early online date	8 Nov 2019
DOIs	https://doi.org/10.3389/fpls.2019.01278
Publication status	First published - 8 Nov 2019
Externally published	Yes

Keywords

genomic selection
mapping
next-generation sequencing
quantitative traits
trait dissection

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10.3389/fpls.2019.01278

fpls-10-01278Final published version, 1.77 MBLicence: CC BY

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title = "Reference Genome Anchoring of High-Density Markers for Association Mapping and Genomic Prediction in European Winter Wheat",

abstract = "In this study, we anchored genotyping-by-sequencing data to the International Wheat Genome Sequencing Consortium Reference Sequence v1.0 assembly to generate over 40,000 high quality single nucleotide polymorphism markers on a panel of 376 elite European winter wheat varieties released between 1946 and 2007. We compared association mapping and genomic prediction accuracy for a range of productivity traits with previous results based on lower density dominant DArT markers. The results demonstrate that the availability of RefSeq v1.0 supports higher precision trait mapping and provides the density of markers required to obtain accurate predictions of traits controlled by multiple small effect loci, including grain yield.",

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AU - Ladejobi, Olufunmilayo

AU - Mackay, Ian J.

AU - Poland, Jesse

AU - Praud, Sebastien

AU - Hibberd, Julian M.

AU - Bentley, Alison R.

PY - 2019/11/8

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N2 - In this study, we anchored genotyping-by-sequencing data to the International Wheat Genome Sequencing Consortium Reference Sequence v1.0 assembly to generate over 40,000 high quality single nucleotide polymorphism markers on a panel of 376 elite European winter wheat varieties released between 1946 and 2007. We compared association mapping and genomic prediction accuracy for a range of productivity traits with previous results based on lower density dominant DArT markers. The results demonstrate that the availability of RefSeq v1.0 supports higher precision trait mapping and provides the density of markers required to obtain accurate predictions of traits controlled by multiple small effect loci, including grain yield.

AB - In this study, we anchored genotyping-by-sequencing data to the International Wheat Genome Sequencing Consortium Reference Sequence v1.0 assembly to generate over 40,000 high quality single nucleotide polymorphism markers on a panel of 376 elite European winter wheat varieties released between 1946 and 2007. We compared association mapping and genomic prediction accuracy for a range of productivity traits with previous results based on lower density dominant DArT markers. The results demonstrate that the availability of RefSeq v1.0 supports higher precision trait mapping and provides the density of markers required to obtain accurate predictions of traits controlled by multiple small effect loci, including grain yield.

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KW - mapping

KW - next-generation sequencing

KW - quantitative traits

KW - trait dissection

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ER -

Reference Genome Anchoring of High-Density Markers for Association Mapping and Genomic Prediction in European Winter Wheat

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Keywords

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