Comparative transcriptomics and network analysis define gene coexpression modules that control maize aleurone development and auxin signaling

Abstract The naked endosperm1 (nkd1), naked endosperm2 (nkd2), and thick aleurone1 (thk1) genes are important regulators of maize (Zea mays L.) endosperm development. Double mutants of nkd1 and nkd2 (nkd1,2) show multiple aleurone (AL) cell layers with disrupted AL cell differentiation, whereas muta...

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Autores principales:	Hao Wu, Philip W. Becraft
Formato:	article
Lenguaje:	EN
Publicado:	Wiley 2021
Materias:	Plant culture SB1-1110 Genetics QH426-470
Acceso en línea:	https://doaj.org/article/9b4f1306c6c54fccb39a4b3d24f85959
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spelling	oai:doaj.org-article:9b4f1306c6c54fccb39a4b3d24f859592021-12-05T07:50:12ZComparative transcriptomics and network analysis define gene coexpression modules that control maize aleurone development and auxin signaling1940-337210.1002/tpg2.20126https://doaj.org/article/9b4f1306c6c54fccb39a4b3d24f859592021-11-01T00:00:00Zhttps://doi.org/10.1002/tpg2.20126https://doaj.org/toc/1940-3372Abstract The naked endosperm1 (nkd1), naked endosperm2 (nkd2), and thick aleurone1 (thk1) genes are important regulators of maize (Zea mays L.) endosperm development. Double mutants of nkd1 and nkd2 (nkd1,2) show multiple aleurone (AL) cell layers with disrupted AL cell differentiation, whereas mutants of thk1 cause multiple cell layers of fully differentiated AL cells. Here, we conducted a comparative analysis of nkd1,2 and thk1 mutant endosperm transcriptomes to study how these factors regulate gene networks to control AL layer specification and cell differentiation. Weighted gene coexpression network analysis was incorporated with published laser capture microdissected transcriptome datasets to identify a coexpression module associated with AL development. In this module, both Nkd1,2+ and Thk1+ appear to regulate cell cycle and division, whereas Nkd1,2+, but not Thk1+, regulate auxin signaling. Further investigation of nkd1,2 differentially expressed genes combined with published putative targets of auxin response factors (ARFs) identified 61 AL‐preferential genes that may be directly activated by NKD‐modulated ARFs. All 61 genes were upregulated in nkd1,2 mutant and the enriched Gene Ontology terms suggested that they are associated with hormone crosstalk, lipid metabolism, and developmental growth. Expression of a transgenic DR5–red fluorescent protein auxin reporter was significantly higher in nkd1,2 mutant endosperm than in wild type, supporting the prediction that Nkd1,2+ negatively regulate auxin signaling in developing AL. Overall, these results suggest that Nkd1,2+ and Thk1+ may normally restrict AL development to a single cell layer by limiting cell division, and that Nkd1,2+ restrict auxin signaling in the AL to maintain normal cell patterning and differentiation processes.Hao WuPhilip W. BecraftWileyarticlePlant cultureSB1-1110GeneticsQH426-470ENThe Plant Genome, Vol 14, Iss 3, Pp n/a-n/a (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Plant culture SB1-1110 Genetics QH426-470
spellingShingle	Plant culture SB1-1110 Genetics QH426-470 Hao Wu Philip W. Becraft Comparative transcriptomics and network analysis define gene coexpression modules that control maize aleurone development and auxin signaling
description	Abstract The naked endosperm1 (nkd1), naked endosperm2 (nkd2), and thick aleurone1 (thk1) genes are important regulators of maize (Zea mays L.) endosperm development. Double mutants of nkd1 and nkd2 (nkd1,2) show multiple aleurone (AL) cell layers with disrupted AL cell differentiation, whereas mutants of thk1 cause multiple cell layers of fully differentiated AL cells. Here, we conducted a comparative analysis of nkd1,2 and thk1 mutant endosperm transcriptomes to study how these factors regulate gene networks to control AL layer specification and cell differentiation. Weighted gene coexpression network analysis was incorporated with published laser capture microdissected transcriptome datasets to identify a coexpression module associated with AL development. In this module, both Nkd1,2+ and Thk1+ appear to regulate cell cycle and division, whereas Nkd1,2+, but not Thk1+, regulate auxin signaling. Further investigation of nkd1,2 differentially expressed genes combined with published putative targets of auxin response factors (ARFs) identified 61 AL‐preferential genes that may be directly activated by NKD‐modulated ARFs. All 61 genes were upregulated in nkd1,2 mutant and the enriched Gene Ontology terms suggested that they are associated with hormone crosstalk, lipid metabolism, and developmental growth. Expression of a transgenic DR5–red fluorescent protein auxin reporter was significantly higher in nkd1,2 mutant endosperm than in wild type, supporting the prediction that Nkd1,2+ negatively regulate auxin signaling in developing AL. Overall, these results suggest that Nkd1,2+ and Thk1+ may normally restrict AL development to a single cell layer by limiting cell division, and that Nkd1,2+ restrict auxin signaling in the AL to maintain normal cell patterning and differentiation processes.
format	article
author	Hao Wu Philip W. Becraft
author_facet	Hao Wu Philip W. Becraft
author_sort	Hao Wu
title	Comparative transcriptomics and network analysis define gene coexpression modules that control maize aleurone development and auxin signaling
title_short	Comparative transcriptomics and network analysis define gene coexpression modules that control maize aleurone development and auxin signaling
title_full	Comparative transcriptomics and network analysis define gene coexpression modules that control maize aleurone development and auxin signaling
title_fullStr	Comparative transcriptomics and network analysis define gene coexpression modules that control maize aleurone development and auxin signaling
title_full_unstemmed	Comparative transcriptomics and network analysis define gene coexpression modules that control maize aleurone development and auxin signaling
title_sort	comparative transcriptomics and network analysis define gene coexpression modules that control maize aleurone development and auxin signaling
publisher	Wiley
publishDate	2021
url	https://doaj.org/article/9b4f1306c6c54fccb39a4b3d24f85959
work_keys_str_mv	AT haowu comparativetranscriptomicsandnetworkanalysisdefinegenecoexpressionmodulesthatcontrolmaizealeuronedevelopmentandauxinsignaling AT philipwbecraft comparativetranscriptomicsandnetworkanalysisdefinegenecoexpressionmodulesthatcontrolmaizealeuronedevelopmentandauxinsignaling
_version_	1718372571396702208

Comparative transcriptomics and network analysis define gene coexpression modules that control maize aleurone development and auxin signaling

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