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Genome-wide identification and analysis of Catharanthus roseus RLK1-like kinases in rice

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Abstract

Main conclusion

A genome-wide survey of Catharanthus roseus receptor-like kinase1-like kinases (CrRLK1Ls) in rice revealed that the pattern of expression by some CrRLK1Ls is controlled by drought or circadian rhythms. This is probably accomplished through the functioning of Gigantea ( OsGI ). Such findings provide a novel angle for using CrRLK1Ls to study the drought-stress response and circadian regulation.

Abstract

The 17 CrRLK1L members of a novel RLK family have been identified in Arabidopsis. Each carries a putative extracellular carbohydrate-binding malectin-like domain. However, their roles in rice, a widely consumed staple food, are not well understood. To investigate the functions of CrRLK1Ls in rice, we utilized phylogenomics data obtained through anatomical and diurnal meta-expression analyses. This information was integrated with a large set of public microarray data within the context of the rice CrRLK1L family phylogenic tree. Chromosomal locations indicated that 3 of 16 genes were tandem-duplicated, suggesting possible functional redundancy within this family. However, integrated diurnal expression showed functional divergence between two of three genes, i.e., peak expression was detected during the day for OsCrRLK1L2, but during the night for OsCrRLK1L3. We found it interesting that OsCrRLK1L2 expression was repressed in osgigantea (osgi) mutants, which suggests that it could function downstream of OsGI. Network analysis associated with OsCrRLK1L2 and OsGI suggested a novel circadian regulation mechanism mediated by OsGI. In addition, two of five OsCrRLK1Ls preferentially expressed in the roots were stimulated by drought, suggesting a potential role for this family in water-use efficiency. This preliminary identification of CrRLK1Ls and study of their expression in rice will facilitate further functional classifications and applications in plant production.

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Abbreviations

DAT:

Days after treatment

GO:

Gene ontology

RGAP:

Rice Genome Annotation Project

RLK:

Receptor-like kinase

TAIR:

The Arabidopsis Information Resource

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Acknowledgments

This work was supported by the Cooperative Research Program for Agriculture Science and Technology Development (Project title: Systematic Identification of Key Genes in Rice for Increasing Yield Using Integrating Omics Technology; Project No. PJ00911002 and Project title: Construction of rice signalom network for regulating hormone biosynthesis and metabolism and the identification of the key regulator for enhancing crop yield, SSAC, Project No.PJ00951405).

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Authors and Affiliations

  1. Department of Plant Molecular Systems Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 446-701, Korea

    Quynh-Nga Nguyen, Yang-Seok Lee, Lae-Hyeon Cho, Hee-Jeong Jeong, Gynheung An & Ki-Hong Jung

  2. Graduate School of Biotechnology, Kyung Hee University, Yongin, 446-701, Korea

    Gynheung An & Ki-Hong Jung

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  1. Quynh-Nga Nguyen
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Correspondence to Ki-Hong Jung.

Electronic supplementary material

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425_2014_2203_MOESM1_ESM.jpg

Supplementary material 1 Fig. S1 CrRLK1L mapping on rice chromosomes. Red box indicates tandem-duplicated genes. Chromosome numbers are shown at top of each bar. (JPEG 862 kb)

425_2014_2203_MOESM2_ESM.jpg

Supplementary material 2 Fig. S2 CrRLK1L rice family phylogenomics with GO and ortholog information in Arabidopsis. Each Locus id and gene name is defined from RGAP. Pale-orange box, Group I; pale-green box,Group II; pale-yellow box, Group III. (JPEG 1373 kb)

425_2014_2203_MOESM3_ESM.jpg

Supplementary material 3 Fig. S3 Circadian expression of 17 Arabidopsis CrRLK1L members. Heat map was generated using Affymetrix Arabidopsis ATH1 genome array data sets (GSE3416) that contain expression information from 3 biological replicates of diurnal time series (4-h intervals for 24 h). Yellow, high expression; blue, low expression. (JPEG 1212 kb)

425_2014_2203_MOESM4_ESM.jpg

Supplementary material 4 Fig. S4 Effect of drought stress on morphology of WT rice. Plants were initially well-watered for 30 d, then exposed to either water-deficit or control (well-watered) conditions for 3 or 4 d. Length of white bar = 5 cm. (JPEG 3229 kb)

425_2014_2203_MOESM5_ESM.jpg

Supplementary material 5 Fig. S5 Primary structures of Arabidopsis and rice CrRLK1L family members. Proteins contain extracellular carbohydrate-binding malectin-like domain(s) (red box) and transmembrane domain (yellow box), plus protein kinase domain (blue box) that shares catalytic functions found in serine/threonine-protein kinases, tyrosine-protein kinases, and dual-specificity protein kinases. (JPEG 1772 kb)

Supplementary material 6 Table S1 Detailed information for rice CrRLK1L family members. (DOCX 21 kb)

Supplementary material 7 Table S2 Primer sequences used for RT-PCR and real-time PCR analyses. (DOCX 22 kb)

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Nguyen, QN., Lee, YS., Cho, LH. et al. Genome-wide identification and analysis of Catharanthus roseus RLK1-like kinases in rice. Planta 241, 603–613 (2015). https://doi.org/10.1007/s00425-014-2203-2

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