Genome-Wide Characterization and Analysis of CIPK Gene Family in Two Cultivated Allopolyploid Cotton Species: Sequence Variation, Association with Seed Oil Content, and the Role of GhCIPK6.

Yupeng Cui,Ying Su,Bing Jia,Man Wu,Jiwen Yu,Jinfa Zhang,Wenfeng Pei,Junjuan Wang

doi:10.3390/ijms21030863

Abstract

Calcineurin B-like protein-interacting protein kinases (CIPKs), as key regulators, play an important role in plant growth and development and the response to various stresses. In the present study, we identified 80 and 78 CIPK genes in the Gossypium hirsutum and G. barbadense, respectively. The phylogenetic and gene structure analysis divided the cotton CIPK genes into five groups which were classified into an exon-rich clade and an exon-poor clade. A synteny analysis showed that segmental duplication contributed to the expansion of Gossypium CIPK gene family, and purifying selection played a major role in the evolution of the gene family in cotton. Analyses of expression profiles showed that GhCIPK genes had temporal and spatial specificity and could be induced by various abiotic stresses. Fourteen GhCIPK genes were found to contain 17 non-synonymous single nucleotide polymorphisms (SNPs) and co-localized with oil or protein content quantitative trait loci (QTLs). Additionally, five SNPs from four GhCIPKs were found to be significantly associated with oil content in one of the three field tests. Although most GhCIPK genes were not associated with natural variations in cotton oil content, the overexpression of the GhCIPK6 gene reduced the oil content and increased C18:1 and C18:1+C18:1d6 in transgenic cotton as compared to wild-type plants. In addition, we predicted the potential molecular regulatory mechanisms of the GhCIPK genes. In brief, these results enhance our understanding of the roles of CIPK genes in oil synthesis and stress responses.

Highlights

Calcium, as a secondary messenger, plays an important role in plant growth and development and plant responses to environmental stresses [1]
The two steps resulted in 80 calcineurin B-like protein (CBL)-interacting protein kinases (CIPKs) genes from G. hirsutum Nanjing Agricultural University (NAU) version, 79 CIPK genes from G. hirsutum Zhejiang University (ZJU) version, and 79 CIPK genes from G. hirsutum Huazhong Agricultural University (HAU) version (Table S2)
80 GhCIPKs from G. hirsutum NAU version and 78 GbCIPKs from G. barbadense HAU version were analyzed in the subsequent research

Summary

Introduction

As a secondary messenger, plays an important role in plant growth and development and plant responses to environmental stresses [1]. There are four major calcium ion sensors in plants, including calmodulin, calmodulin-like protein, calcium-dependent protein kinase, and calcineurin B-like protein (CBL), which sense and decode the changes of calcium ion concentration in response to various stimuli [2]. Among the four calcium sensors, CBL decodes calcium transients by interacting with and modulating the activity of CBL-interacting protein kinases (CIPKs) in higher plants [3]. The N-terminal domain of CIPKs is similar with the protein structures of SNF1 kinase and AMO-dependent protein kinase. A conserved NAF domain within the C-terminus of CIPKs is required for interacting with CBLs, which activate the catalytic activity of CIPKs, and the activated CIPKs can transfer perceived calcium signals by phosphorylating target downstream signaling components [6,7]. A protein phosphatase interaction (PPI) domain in the C-terminus of CIPKs can interact with specific members of protein phosphatase 2C (PP2C) [8]

Methods

Results

Discussion

Conclusion