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Transcriptomics of nine-cis-epoxycarotenoid dioxygenase 6 induction in imbibed seeds reveals feedback mechanisms and long non-coding RNAs

Published online by Cambridge University Press:  11 September 2017

Khadidiatou Sall ,
David Hendrix ,
Taira Sekine ,
Yoshihiko Katsuragawa ,
Ryosuke Koyari  and
Hiroyuki Nonogaki
Khadidiatou Sall
Affiliation:
Department of Horticulture, Oregon State University, Corvallis, OR 97331, USA
David Hendrix
Affiliation:
Department of Biochemistry and Biophysics and School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR 97331, USA
Taira Sekine
Affiliation:
Department of Horticulture, Oregon State University, Corvallis, OR 97331, USA
Yoshihiko Katsuragawa
Affiliation:
Department of Horticulture, Oregon State University, Corvallis, OR 97331, USA
Ryosuke Koyari
Affiliation:
Department of Horticulture, Oregon State University, Corvallis, OR 97331, USA
Hiroyuki Nonogaki*
Affiliation:
Department of Horticulture, Oregon State University, Corvallis, OR 97331, USA
*
*Correspondence Email: hiro.nonogaki@oregonstate.edu
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Abstract

Induction of nine-cis-epoxycarotenoid dioxygenase 6 (NCED6), an abscisic acid (ABA) biosynthesis gene, alone is sufficient to suspend germination in testa-ruptured seeds, which are at the final step of germination. Molecular consequences of NCED6 induction in imbibed seeds were investigated by RNA sequencing. The analysis identified many unknown and uncharacterized genes that were up-regulated by NCED6 induction, in addition to the major regulators of ABA signalling. Interestingly, other NCEDs were up-regulated by NCED6 induction, suggesting that the major rate-limiting enzymes in the ABA biosynthesis pathway are subject to positive-feedback regulation. ZEAXANTHIN EPOXIDASE and ABSCISIC ALDEHYDE OXIDASE3, which function upstream and downstream of NCED, were also up-regulated in seeds by NCED6 induction, which suggests that the distinct layers of positive feedback loops are coordinately operating in the NCED6-induced seeds. SOMNUS (SOM), which was also up-regulated by NCED6 induction, was the major mediator of enhanced ABA signalling in NCED6-induced seeds. SOM exerted negative effects on GA biosynthesis, which also contributes to a high ABA–GA ratio and reinforces the suppressive state of germination. Besides these coding genes, long intergenic non-coding RNAs (lincRNAs) were also up-regulated upon NCED6 induction (termed N6LINCRs). Conditional expression of N6LINCR1 altered gene expression profiles in seeds. Twenty-six genes were up-regulated and 66 genes were down-regulated by the induction of N6LINCR1. These results suggest that some of N6LINCRs have a regulatory role in gene expression in seeds, which potentially contributes to the regulation of germination by ABA.

Keywords

ABAArabidopsislong non-coding RNANCEDpositive feedback
Type
Research Papers
Information
Seed Science Research , Volume 27 , Issue 4 , December 2017 , pp. 251 - 261
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Copyright
Copyright © Cambridge University Press 2017 

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