Genome-wide association study and gene network analyses reveal potential candidate genes for high night temperature tolerance in rice

Abstract High night temperatures (HNT) are shown to significantly reduce rice (Oryza sativa L.) yield and quality. A better understanding of the genetic architecture of HNT tolerance will help rice breeders to develop varieties adapted to future warmer climates. In this study, a diverse indica rice...

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Autores principales:	Raju Bheemanahalli, Montana Knight, Cherryl Quinones, Colleen J. Doherty, S. V. Krishna Jagadish
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/30033ae224024338a9e2aee8176974a0
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spelling	oai:doaj.org-article:30033ae224024338a9e2aee8176974a02021-12-02T11:45:03ZGenome-wide association study and gene network analyses reveal potential candidate genes for high night temperature tolerance in rice10.1038/s41598-021-85921-z2045-2322https://doaj.org/article/30033ae224024338a9e2aee8176974a02021-03-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-85921-zhttps://doaj.org/toc/2045-2322Abstract High night temperatures (HNT) are shown to significantly reduce rice (Oryza sativa L.) yield and quality. A better understanding of the genetic architecture of HNT tolerance will help rice breeders to develop varieties adapted to future warmer climates. In this study, a diverse indica rice panel displayed a wide range of phenotypic variability in yield and quality traits under control night (24 °C) and higher night (29 °C) temperatures. Genome-wide association analysis revealed 38 genetic loci associated across treatments (18 for control and 20 for HNT). Nineteen loci were detected with the relative changes in the traits between control and HNT. Positive phenotypic correlations and co-located genetic loci with previously cloned grain size genes revealed common genetic regulation between control and HNT, particularly grain size. Network-based predictive models prioritized 20 causal genes at the genetic loci based on known gene/s expression under HNT in rice. Our study provides important insights for future candidate gene validation and molecular marker development to enhance HNT tolerance in rice. Integrated physiological, genomic, and gene network-informed approaches indicate that the candidate genes for stay-green trait may be relevant to minimizing HNT-induced yield and quality losses during grain filling in rice by optimizing source-sink relationships.Raju BheemanahalliMontana KnightCherryl QuinonesColleen J. DohertyS. V. Krishna JagadishNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-17 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Raju Bheemanahalli Montana Knight Cherryl Quinones Colleen J. Doherty S. V. Krishna Jagadish Genome-wide association study and gene network analyses reveal potential candidate genes for high night temperature tolerance in rice
description	Abstract High night temperatures (HNT) are shown to significantly reduce rice (Oryza sativa L.) yield and quality. A better understanding of the genetic architecture of HNT tolerance will help rice breeders to develop varieties adapted to future warmer climates. In this study, a diverse indica rice panel displayed a wide range of phenotypic variability in yield and quality traits under control night (24 °C) and higher night (29 °C) temperatures. Genome-wide association analysis revealed 38 genetic loci associated across treatments (18 for control and 20 for HNT). Nineteen loci were detected with the relative changes in the traits between control and HNT. Positive phenotypic correlations and co-located genetic loci with previously cloned grain size genes revealed common genetic regulation between control and HNT, particularly grain size. Network-based predictive models prioritized 20 causal genes at the genetic loci based on known gene/s expression under HNT in rice. Our study provides important insights for future candidate gene validation and molecular marker development to enhance HNT tolerance in rice. Integrated physiological, genomic, and gene network-informed approaches indicate that the candidate genes for stay-green trait may be relevant to minimizing HNT-induced yield and quality losses during grain filling in rice by optimizing source-sink relationships.
format	article
author	Raju Bheemanahalli Montana Knight Cherryl Quinones Colleen J. Doherty S. V. Krishna Jagadish
author_facet	Raju Bheemanahalli Montana Knight Cherryl Quinones Colleen J. Doherty S. V. Krishna Jagadish
author_sort	Raju Bheemanahalli
title	Genome-wide association study and gene network analyses reveal potential candidate genes for high night temperature tolerance in rice
title_short	Genome-wide association study and gene network analyses reveal potential candidate genes for high night temperature tolerance in rice
title_full	Genome-wide association study and gene network analyses reveal potential candidate genes for high night temperature tolerance in rice
title_fullStr	Genome-wide association study and gene network analyses reveal potential candidate genes for high night temperature tolerance in rice
title_full_unstemmed	Genome-wide association study and gene network analyses reveal potential candidate genes for high night temperature tolerance in rice
title_sort	genome-wide association study and gene network analyses reveal potential candidate genes for high night temperature tolerance in rice
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/30033ae224024338a9e2aee8176974a0
work_keys_str_mv	AT rajubheemanahalli genomewideassociationstudyandgenenetworkanalysesrevealpotentialcandidategenesforhighnighttemperaturetoleranceinrice AT montanaknight genomewideassociationstudyandgenenetworkanalysesrevealpotentialcandidategenesforhighnighttemperaturetoleranceinrice AT cherrylquinones genomewideassociationstudyandgenenetworkanalysesrevealpotentialcandidategenesforhighnighttemperaturetoleranceinrice AT colleenjdoherty genomewideassociationstudyandgenenetworkanalysesrevealpotentialcandidategenesforhighnighttemperaturetoleranceinrice AT svkrishnajagadish genomewideassociationstudyandgenenetworkanalysesrevealpotentialcandidategenesforhighnighttemperaturetoleranceinrice
_version_	1718395272647671808

Genome-wide association study and gene network analyses reveal potential candidate genes for high night temperature tolerance in rice

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