Haplotype associated RNA expression (HARE) improves prediction of complex traits in maize.

Genomic prediction typically relies on associations between single-site polymorphisms and traits of interest. This representation of genomic variability has been successful for predicting many complex traits. However, it usually cannot capture the combination of alleles in haplotypes and it has gene...

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Autores principales:	Anju Giri, Merritt Khaipho-Burch, Edward S Buckler, Guillaume P Ramstein
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Genetics QH426-470
Acceso en línea:	https://doaj.org/article/bbb11d5873334253b6aafcae1c0155dd
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spelling	oai:doaj.org-article:bbb11d5873334253b6aafcae1c0155dd2021-12-02T20:03:33ZHaplotype associated RNA expression (HARE) improves prediction of complex traits in maize.1553-73901553-740410.1371/journal.pgen.1009568https://doaj.org/article/bbb11d5873334253b6aafcae1c0155dd2021-10-01T00:00:00Zhttps://doi.org/10.1371/journal.pgen.1009568https://doaj.org/toc/1553-7390https://doaj.org/toc/1553-7404Genomic prediction typically relies on associations between single-site polymorphisms and traits of interest. This representation of genomic variability has been successful for predicting many complex traits. However, it usually cannot capture the combination of alleles in haplotypes and it has generated little insight about the biological function of polymorphisms. Here we present a novel and cost-effective method for imputing cis haplotype associated RNA expression (HARE), studied their transferability across tissues, and evaluated genomic prediction models within and across populations. HARE focuses on tightly linked cis acting causal variants in the immediate vicinity of the gene, while excluding trans effects from diffusion and metabolism. Therefore, HARE estimates were more transferrable across different tissues and populations compared to measured transcript expression. We also showed that HARE estimates captured one-third of the variation in gene expression. HARE estimates were used in genomic prediction models evaluated within and across two diverse maize panels-a diverse association panel (Goodman Association panel) and a large half-sib panel (Nested Association Mapping panel)-for predicting 26 complex traits. HARE resulted in up to 15% higher prediction accuracy than control approaches that preserved haplotype structure, suggesting that HARE carried functional information in addition to information about haplotype structure. The largest increase was observed when the model was trained in the Nested Association Mapping panel and tested in the Goodman Association panel. Additionally, HARE yielded higher within-population prediction accuracy as compared to measured expression values. The accuracy achieved by measured expression was variable across tissues, whereas accuracy by HARE was more stable across tissues. Therefore, imputing RNA expression of genes by haplotype is stable, cost-effective, and transferable across populations.Anju GiriMerritt Khaipho-BurchEdward S BucklerGuillaume P RamsteinPublic Library of Science (PLoS)articleGeneticsQH426-470ENPLoS Genetics, Vol 17, Iss 10, p e1009568 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Genetics QH426-470
spellingShingle	Genetics QH426-470 Anju Giri Merritt Khaipho-Burch Edward S Buckler Guillaume P Ramstein Haplotype associated RNA expression (HARE) improves prediction of complex traits in maize.
description	Genomic prediction typically relies on associations between single-site polymorphisms and traits of interest. This representation of genomic variability has been successful for predicting many complex traits. However, it usually cannot capture the combination of alleles in haplotypes and it has generated little insight about the biological function of polymorphisms. Here we present a novel and cost-effective method for imputing cis haplotype associated RNA expression (HARE), studied their transferability across tissues, and evaluated genomic prediction models within and across populations. HARE focuses on tightly linked cis acting causal variants in the immediate vicinity of the gene, while excluding trans effects from diffusion and metabolism. Therefore, HARE estimates were more transferrable across different tissues and populations compared to measured transcript expression. We also showed that HARE estimates captured one-third of the variation in gene expression. HARE estimates were used in genomic prediction models evaluated within and across two diverse maize panels-a diverse association panel (Goodman Association panel) and a large half-sib panel (Nested Association Mapping panel)-for predicting 26 complex traits. HARE resulted in up to 15% higher prediction accuracy than control approaches that preserved haplotype structure, suggesting that HARE carried functional information in addition to information about haplotype structure. The largest increase was observed when the model was trained in the Nested Association Mapping panel and tested in the Goodman Association panel. Additionally, HARE yielded higher within-population prediction accuracy as compared to measured expression values. The accuracy achieved by measured expression was variable across tissues, whereas accuracy by HARE was more stable across tissues. Therefore, imputing RNA expression of genes by haplotype is stable, cost-effective, and transferable across populations.
format	article
author	Anju Giri Merritt Khaipho-Burch Edward S Buckler Guillaume P Ramstein
author_facet	Anju Giri Merritt Khaipho-Burch Edward S Buckler Guillaume P Ramstein
author_sort	Anju Giri
title	Haplotype associated RNA expression (HARE) improves prediction of complex traits in maize.
title_short	Haplotype associated RNA expression (HARE) improves prediction of complex traits in maize.
title_full	Haplotype associated RNA expression (HARE) improves prediction of complex traits in maize.
title_fullStr	Haplotype associated RNA expression (HARE) improves prediction of complex traits in maize.
title_full_unstemmed	Haplotype associated RNA expression (HARE) improves prediction of complex traits in maize.
title_sort	haplotype associated rna expression (hare) improves prediction of complex traits in maize.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/bbb11d5873334253b6aafcae1c0155dd
work_keys_str_mv	AT anjugiri haplotypeassociatedrnaexpressionhareimprovespredictionofcomplextraitsinmaize AT merrittkhaiphoburch haplotypeassociatedrnaexpressionhareimprovespredictionofcomplextraitsinmaize AT edwardsbuckler haplotypeassociatedrnaexpressionhareimprovespredictionofcomplextraitsinmaize AT guillaumepramstein haplotypeassociatedrnaexpressionhareimprovespredictionofcomplextraitsinmaize
_version_	1718375682940076032

Haplotype associated RNA expression (HARE) improves prediction of complex traits in maize.

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