Using variable importance measures to identify a small set of SNPs to predict heading date in perennial ryegrass

Abstract Prior knowledge on heading date enables the selection of parents of synthetic cultivars that are well matched with respect to time of heading, which is essential to ensure plants put together will cross pollinate. Heading date of individual plants can be determined via direct phenotyping, w...

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Autores principales:	Stephen L. Byrne, Patrick Conaghan, Susanne Barth, Sai Krishna Arojju, Michael Casler, Thibauld Michel, Janaki Velmurugan, Dan Milbourne
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/f10d2c0d5f0a41799d4096bc29d285d7
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spelling	oai:doaj.org-article:f10d2c0d5f0a41799d4096bc29d285d72021-12-02T15:05:45ZUsing variable importance measures to identify a small set of SNPs to predict heading date in perennial ryegrass10.1038/s41598-017-03232-82045-2322https://doaj.org/article/f10d2c0d5f0a41799d4096bc29d285d72017-06-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-03232-8https://doaj.org/toc/2045-2322Abstract Prior knowledge on heading date enables the selection of parents of synthetic cultivars that are well matched with respect to time of heading, which is essential to ensure plants put together will cross pollinate. Heading date of individual plants can be determined via direct phenotyping, which has a time and labour cost. It can also be inferred from family means, although the spread in days to heading within families demands roguing in first generation synthetics. Another option is to predict heading date from molecular markers. In this study we used a large training population consisting of individual plants to develop equations to predict heading date from marker genotypes. Using permutation-based variable selection measures we reduced the marker set from 217,563 to 50 without impacting the predictive ability. Opportunities exist to develop a cheap assay to sequence a small number of regions in linkage disequilibrium with heading date QTL in thousands of samples. Simultaneous use of these markers in non-linkage based marker-assisted selection approaches, such as paternity testing, should enhance the utility of such an approach.Stephen L. ByrnePatrick ConaghanSusanne BarthSai Krishna ArojjuMichael CaslerThibauld MichelJanaki VelmuruganDan MilbourneNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-10 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Stephen L. Byrne Patrick Conaghan Susanne Barth Sai Krishna Arojju Michael Casler Thibauld Michel Janaki Velmurugan Dan Milbourne Using variable importance measures to identify a small set of SNPs to predict heading date in perennial ryegrass
description	Abstract Prior knowledge on heading date enables the selection of parents of synthetic cultivars that are well matched with respect to time of heading, which is essential to ensure plants put together will cross pollinate. Heading date of individual plants can be determined via direct phenotyping, which has a time and labour cost. It can also be inferred from family means, although the spread in days to heading within families demands roguing in first generation synthetics. Another option is to predict heading date from molecular markers. In this study we used a large training population consisting of individual plants to develop equations to predict heading date from marker genotypes. Using permutation-based variable selection measures we reduced the marker set from 217,563 to 50 without impacting the predictive ability. Opportunities exist to develop a cheap assay to sequence a small number of regions in linkage disequilibrium with heading date QTL in thousands of samples. Simultaneous use of these markers in non-linkage based marker-assisted selection approaches, such as paternity testing, should enhance the utility of such an approach.
format	article
author	Stephen L. Byrne Patrick Conaghan Susanne Barth Sai Krishna Arojju Michael Casler Thibauld Michel Janaki Velmurugan Dan Milbourne
author_facet	Stephen L. Byrne Patrick Conaghan Susanne Barth Sai Krishna Arojju Michael Casler Thibauld Michel Janaki Velmurugan Dan Milbourne
author_sort	Stephen L. Byrne
title	Using variable importance measures to identify a small set of SNPs to predict heading date in perennial ryegrass
title_short	Using variable importance measures to identify a small set of SNPs to predict heading date in perennial ryegrass
title_full	Using variable importance measures to identify a small set of SNPs to predict heading date in perennial ryegrass
title_fullStr	Using variable importance measures to identify a small set of SNPs to predict heading date in perennial ryegrass
title_full_unstemmed	Using variable importance measures to identify a small set of SNPs to predict heading date in perennial ryegrass
title_sort	using variable importance measures to identify a small set of snps to predict heading date in perennial ryegrass
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/f10d2c0d5f0a41799d4096bc29d285d7
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Using variable importance measures to identify a small set of SNPs to predict heading date in perennial ryegrass

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