Identification, Structural Characterization and Gene Expression Analysis of Members of the Nuclear Factor-Y Family in Chickpea (Cicer arietinum L.) under Dehydration and Abscisic Acid Treatments.

Ha Chu,Dung Le,Lam-Son Tran,Thu Pham,Keiichi Mochida,Kien Nguyen,Yasuko Watanabe

doi:10.3390/ijms19113290

Abstract

In plants, the Nuclear Factor-Y (NF-Y) transcription factors (TFs), which include three distinct types of NF-YA, NF-YB, and NF-YC TFs, have been identified to play key roles in the regulation of various plant growth and developmental processes under both normal and environmental stress conditions. In this work, a total of 40 CaNF-Y-encoding genes, including eight CaNF-YAs, 21 CaNF-YBs, and 11 CaNF-YCs, were identified in chickpea, and their major gene and protein characteristics were subsequently obtained using various web-based tools. Of our interest, a phylogenetically-based analysis predicted 18 CaNF-Ys (eight CaNF-YAs, seven CaNF-YBs, and three CaNF-YCs) that potentially play roles in chickpea responses to dehydration according to their close relationship with the well-characterized GmNF-Ys in soybean. These results were in good agreement with the enrichment of drought-responsive cis-regulatory motifs and expression patterns obtained from in silico analyses using publically available transcriptome data. Most of the phylogenetically predicted drought-responsive CaNF-Y genes (15 of 18) were quantitatively validated to significantly respond to dehydration treatment in leaves and/or roots, further supporting the results of in silico analyses. Among these CaNF-Y genes, the transcript levels of CaNF-YA01 and CaNF-YC10 were the most highly accumulated in leaves (by approximately eight-fold) and roots (by approximately 18-fold), respectively, by dehydration. Furthermore, 12 of the 18 CaNF-Y genes were found to be responsive to the most well-known stress hormone, namely abscisic acid (ABA), in leaves and/or roots, suggesting that these genes may act in chickpea response to dehydration in ABA-dependent manner. Taken together, our study has provided a comprehensive and fundamental information for further functional analyses of selected CaNF-Y candidate genes, ultimately leading to the improvement of chickpea growth under water-limited conditions.

Highlights

Chickpea (Cicer arietinum L.) has been identified as a native leguminous crop of the Mediterranean region, especially in the Afro-Asian countries [1]
To obtain all potential genes encoding CaNF-Y transcription factors (TFs), an intensive search was conducted in the two major TF databases, namely the iTAK (Plant Transcription factors & Protein Kinase Identifier and Classifier) [37] and the PlantTFDB (Plant Transcription Factor Database) [38], which predicted the CaNF-Y TFs in the ‘kabuli’ chickpea [35]
As for hormone-related cis-motifs, we found that ABRE was distributed in the promoters of eight CaNF-Y genes (Table S2), among which there were five phylogenetically predicted drought-related genes, namely CaNF-YA01, CaNF-YA04, CaNF-YB10, CaNF-YC04, and CaNF-YC10 (Figure 2; Table S2), suggesting that these CaNF-Y genes might be implied in regulation of plant response to drought/dehydration through abscisic acid (ABA)-dependent pathway

Summary

Introduction

Chickpea (Cicer arietinum L.) has been identified as a native leguminous crop of the Mediterranean region, especially in the Afro-Asian countries [1]. To develop strategies for development of improved drought-tolerant chickpea, a great effort has been made to identify and characterize drought-responsible genes, those encoding transcription factors (TFs), from this legume species [8,9,10]. We have made an effort to identify all putative members (referred to as CaNF-Y TFs) of the NF-Y family in chickpea and provide comprehensive information on their structural characteristics. A list of putative dehydration-responsive CaNF-Y genes was proposed using phylogenetic analysis. Screening of the hormone- and/or stress-related cis-acting motifs in the putative promoter sequences of the identified CaNF-Y genes was performed to increase the confidence of the phylogenetic analysis-based prediction. To precisely identify the CaNF-Y genes with potential functions in regulation of chickpea responses to dehydration, quantitative PCR (qPCR) was used to separately examine the expression of the identified CaNF-Y genes in roots and leaves of chickpea plants exposed to dehydration or abscisic acid (ABA) treatment

Identification and Annotation of the CaNF-Y Genes in Chickpea

Protein Features and Gene Organization of the CaNF-Ys

Prediction of the Stress- and Hormone-Related Cis-Regulatory Elements

Transcript Patterns of the CaNF-Y Genes in Different Organs

Expression Analysis of CaNF-Y Genes by qPCR

Conclusions