Unraveling regulatory divergence, heterotic malleability, and allelic imbalance switching in rice due to drought stress

Abstract The indica ecotypes, IR64, an elite drought-susceptible variety adapted to irrigated ecosystem, and Apo (IR55423-01 or NSIC RC9), a moderate drought-tolerant upland genotype together with their hybrid (IR64 × Apo) were exposed to non- and water-stress conditions. By sequencing (RNA-seq) the...

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Autores principales:	Nelzo C. Ereful, Antonio Laurena, Li-Yu Liu, Shu-Min Kao, Eric Tsai, Andy Greenland, Wayne Powell, Ian Mackay, Hei Leung
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/7b68091ed81144fe9c94bafbdebe9967
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spelling	oai:doaj.org-article:7b68091ed81144fe9c94bafbdebe99672021-12-02T14:33:57ZUnraveling regulatory divergence, heterotic malleability, and allelic imbalance switching in rice due to drought stress10.1038/s41598-021-92938-x2045-2322https://doaj.org/article/7b68091ed81144fe9c94bafbdebe99672021-06-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-92938-xhttps://doaj.org/toc/2045-2322Abstract The indica ecotypes, IR64, an elite drought-susceptible variety adapted to irrigated ecosystem, and Apo (IR55423-01 or NSIC RC9), a moderate drought-tolerant upland genotype together with their hybrid (IR64 × Apo) were exposed to non- and water-stress conditions. By sequencing (RNA-seq) these genotypes, we were able to map genes diverging in cis and/or trans factors. Under non-stress condition, cis dominantly explains (11.2%) regulatory differences, followed by trans (8.9%). Further analysis showed that water-limiting condition largely affects trans and cis + trans factors. On the molecular level, cis and/or trans regulatory divergence explains their genotypic differences and differential drought response. Between the two parental genotypes, Apo appears to exhibit more photosynthetic efficiency even under water-limiting condition and is ascribed to trans. Statistical analyses showed that regulatory divergence is significantly influenced by environmental conditions. Likewise, the mode of parental expression inheritance which drives heterosis (HET) is significantly affected by environmental conditions indicating the malleability of heterosis to external factors. Further analysis revealed that the HET class, dominance, was significantly enriched under water-stress condition. We also identified allelic imbalance switching in which several genes prefer IR64- (or Apo-) specific allele under non-stress condition but switched to Apo- (or IR64-) specific allele when exposed to water-stress condition.Nelzo C. ErefulAntonio LaurenaLi-Yu LiuShu-Min KaoEric TsaiAndy GreenlandWayne PowellIan MackayHei LeungNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-13 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Nelzo C. Ereful Antonio Laurena Li-Yu Liu Shu-Min Kao Eric Tsai Andy Greenland Wayne Powell Ian Mackay Hei Leung Unraveling regulatory divergence, heterotic malleability, and allelic imbalance switching in rice due to drought stress
description	Abstract The indica ecotypes, IR64, an elite drought-susceptible variety adapted to irrigated ecosystem, and Apo (IR55423-01 or NSIC RC9), a moderate drought-tolerant upland genotype together with their hybrid (IR64 × Apo) were exposed to non- and water-stress conditions. By sequencing (RNA-seq) these genotypes, we were able to map genes diverging in cis and/or trans factors. Under non-stress condition, cis dominantly explains (11.2%) regulatory differences, followed by trans (8.9%). Further analysis showed that water-limiting condition largely affects trans and cis + trans factors. On the molecular level, cis and/or trans regulatory divergence explains their genotypic differences and differential drought response. Between the two parental genotypes, Apo appears to exhibit more photosynthetic efficiency even under water-limiting condition and is ascribed to trans. Statistical analyses showed that regulatory divergence is significantly influenced by environmental conditions. Likewise, the mode of parental expression inheritance which drives heterosis (HET) is significantly affected by environmental conditions indicating the malleability of heterosis to external factors. Further analysis revealed that the HET class, dominance, was significantly enriched under water-stress condition. We also identified allelic imbalance switching in which several genes prefer IR64- (or Apo-) specific allele under non-stress condition but switched to Apo- (or IR64-) specific allele when exposed to water-stress condition.
format	article
author	Nelzo C. Ereful Antonio Laurena Li-Yu Liu Shu-Min Kao Eric Tsai Andy Greenland Wayne Powell Ian Mackay Hei Leung
author_facet	Nelzo C. Ereful Antonio Laurena Li-Yu Liu Shu-Min Kao Eric Tsai Andy Greenland Wayne Powell Ian Mackay Hei Leung
author_sort	Nelzo C. Ereful
title	Unraveling regulatory divergence, heterotic malleability, and allelic imbalance switching in rice due to drought stress
title_short	Unraveling regulatory divergence, heterotic malleability, and allelic imbalance switching in rice due to drought stress
title_full	Unraveling regulatory divergence, heterotic malleability, and allelic imbalance switching in rice due to drought stress
title_fullStr	Unraveling regulatory divergence, heterotic malleability, and allelic imbalance switching in rice due to drought stress
title_full_unstemmed	Unraveling regulatory divergence, heterotic malleability, and allelic imbalance switching in rice due to drought stress
title_sort	unraveling regulatory divergence, heterotic malleability, and allelic imbalance switching in rice due to drought stress
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/7b68091ed81144fe9c94bafbdebe9967
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Unraveling regulatory divergence, heterotic malleability, and allelic imbalance switching in rice due to drought stress

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