Genome-wide gene phylogeny of CIPK family in cassava and expression analysis of partial drought-induced genes

Abstract

Cassava is an important food and potential biofuel crop that is tolerant to multiple abiotic stressors. The mechanisms underlying these tolerances are currently less known. CBL-interacting protein kinases (CIPKs) have been shown to play crucial roles in plant developmental processes, hormone signaling transduction, and in the response to abiotic stress. However, no data is currently available about the CPK family in cassava. In this study, a total of 25 CIPK genes were identified from cassava genome based on our previous genome sequencing data. Phylogenetic analysis suggested that 25 MeCIPKs could be classified into four subfamilies, which was supported by exon-intron organizations and the architectures of conserved protein motifs. Transcriptomic analysis of a wild subspecies and two cultivated varieties showed that most MeCIPKs had different expression patterns between wild subspecies and cultivatars in different tissues or in response to drought stress. Some orthologous genes involved in CIPK interaction networks were identified between Arabidopsis and cassava. The interaction networks and co-expression patterns of these orthologous genes revealed that the crucial pathways controlled by CIPK networks may be involved in the differential response to drought stress in different accessions of cassava. Nine MeCIPK genes were selected to investigate their transcriptional response to various stimuli and the results showed the comprehensive response of the tested MeCIPK genes to osmotic, salt, cold, oxidative stressors, and ABA signaling. The identification and expression analysis of CIPK family suggested that CIPK genes are important components of development and multiple signal transduction pathways in cassava. The findings of this study will help lay a foundation for the functional characterization of the CIPK gene family and provide an improved understanding of abiotic stress responses and signaling transduction in cassava.

Physiological adaptations to osmotic stress and characterization of a polyethylene glycol-responsive gene in Braya humilis

“…However, different expression patterns also have been observed. MeCIPK12 expression did not show obvious trend during osmotic treatment in cassava [56]. Altogether, these results suggest that Bh-CIPK12 might have an important role in B. humilis plants exposed to osmotic stress or drought.…”

Rooting for cassava: insights into photosynthesis and associated physiology as a route to improve yield potential

“…Application of high-throughput phenotyping capabilities will be critical to making full use of the rapidly advancing genomic information for cassava (Lopez et al, 2005;Prochnik et al, 2012;Hu et al, 2015Hu et al, , 2016Wei et al, 2016). Development or application of high-throughput phenotyping facilities such as those developed for the major grain crops will accelerate realization of the traits outlined in this review in cassava (Trachsel et al, 2011;Winterhalter et al, 2011;Okogbenin et al, 2013;Yang et al, 2013;Kipp et al, 2014;Grosskinsky et al, 2015;Haghighattalab et al, 2016).…”

“…One of the most studied environmental stresses acting on cassava is drought (El‐Sharkawy et al ., b; El‐Sharkawy, ; Sundaresan & Sudhakaran, ; Lokko et al ., ; Okogbenin et al ., ; Vandegeer et al ., ; Hu et al ., ). Water stress impacts cassava physiology and yield, even though it is generally better adapted to extended periods of drought than most crops.…”

The ERF transcription factor family in cassava: genome-wide characterization and expression analyses against drought stress

“…Then, cDNA libraries of each sample were constructed with 3 μg of total RNA following the Illumina manufacture protocol, and sequenced by Illumina GAII. Data analysis was carried out by previously described65. The generated transcriptomic data has been submitted to NCBI as supplied in Supplementary Table S6.…”