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Functional genomics of the protein kinase superfamily from wheat

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Abstract

Protein kinases (PKs) belonging to a large superfamily play vital roles in plant development and stress tolerance, whereas only a small number of PKs have been functionally studied in wheat. Genome-wide survey and characterization of wheat PK genes (TaPKs) will be valuable in future genetic improvement program. In this study, we performed genome-wide identification of PK in wheat, containing phylogenetic evolution, gene expression pattern, and functional prediction analysis, and to explore structure–function relationship, the secondary and tertiary structures of wheat OST1 were visualized. Totally, 4479 TaPKs composed of 4446 Ser/Thr/Tyr (TaPK1 to TaPK4446) and 33 His PKs (TaHPK1 to TaHPK33) were identified in the TGACv1 assembly. According to phylogenetic analysis, wheat Ser/Thr/Tyr PKs were categorized into eight groups with 57 families and 64 subfamilies, and His PKs were classified into three families. The genes contained on average 5.07 introns, ranging from 0 to 31, and about 54.68% TaPKs exhibited relatively simpler exon–intron organization (0–4 introns). RNA-seq analysis showed 324 TaPKs were significantly differentially expressed after exposure to drought, 372 TaPKs were significantly differentially expressed after inoculation with Puccinia striiformis f. sp. tritici (Pst) and Blumeria graminis f. sp. tritici (Bgt), and a large number of TaPKs exhibited stage- or organ-specific expression patterns. Co-expression analysis showed that 1388 TaPKs were distributed in 19 modules, while 9 modules with 511 TaPKs had the most obvious tissue- or stress-specific expression trends. A suite of sexual reproduction related genes were identified in magenta module where TaPK960, TaPK707–3708, TaPK4243, and TaPK4249 were related to polarized pollen tube growth, TaPK627 and TaPK629 to pollen tube guidance, and TaPK4226–4228 to flowering time regulation. Finally, 12 TaPKs were selected to validate their expression level through qRT-PCR. Our findings obtained will offer a clue to elaborate the roles of PKs in wheat growth and stress resistance for agricultural improvement.

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Abbreviations

ABA :

abscisic acid

Bgt :

Blumeria graminis f. sp. tritici

BRs :

brassinosteroids

CKs :

cytokinins

CV :

coefficient of variation

DEG :

differentially expressed genes

dpi :

day post-inoculation

DS1h :

in drought stress after 1 h

DS6h :

in drought stress after 6 h

ET :

ethylene

FF1 :

fruit at whole plant fruit formation stage 30 to 50%

FF2 :

Fruit at whole plant fruit formation stage 70% to final size

FR :

fruit at whole plant fruit ripening stage

GA :

gibberellin

GO :

Gene Ontology

IFL.02 :

inflorescence at 1/2 of flowers open stage

ISE.02 :

inflorescence at two nodes or internodes visible stage

ISE.99 :

inflorescence at maximum stem length reached stage

JA :

jasmonic acid

KEGG :

Kyoto Encyclopedia of Genes and Genomes

L3N :

leaf at main shoot and axillary shoots visible at three nodes stage

LCE :

leaf at cotyledon emergence stage

LF1 :

leaf at whole plant fruit formation stage 30 to 50%

PK :

protein kinase

Pst :

Puccinia striiformis f. sp. tritici

RCE :

root at cotyledon emergence stage

RLP.03 :

root at three leaves visible stage

RSE.99 :

root at maximum stem length reached stage

SA :

salicylic acid

SFL.02 :

stem at 1/2 of flowers open stage

SSE.00 :

stem at stem elongation begins stage

SSE.02 :

stem at two nodes or internodes visible stage

TaPK :

wheat protein kinase

WGCNA :

weighted gene co-expression network analysis

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Acknowledgments

We are grateful to the providers who submitted the RNA-seq data to the public expression databases which can be applied freely. We sincerely thank Cui Yin (Shanghai Majorbio Bio-pharm Technology Co., Ltd.) for her great contribution to the data analysis. We also thank Wei Zhang in our laboratory for useful discussions.

Funding

The project was supported by the Science and Technology Cooperation Project of Fujian Province, China (Grant No. 2015I0006). The funding institutions had no direct role in the study design, sample collection, analysis, and interpretation of data, nor in manuscript writing. Annual reports were submitted to the funding institutions tracking the progress of the projects.

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  1. These authors have contributed equally to this work.

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  1. School of Biological Sciences and Biotechnology, Minnan Normal University, 36 Xian-Qian-Zhi Street, Zhangzhou, 363000, Fujian, China

    Kaifa Wei & YiXuan Li

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  1. Kaifa Wei
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Correspondence to Kaifa Wei.

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Wei, K., Li, Y. Functional genomics of the protein kinase superfamily from wheat. Mol Breeding 39, 141 (2019). https://doi.org/10.1007/s11032-019-1045-9

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