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

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.

In Silico Identification and Expression Analysis of Nuclear Factor Y (Nf-Y) Transcription Factors in Cucumber

“…In this study, CsaNF-YA genes contained 2-5 introns, and multiple intron/exon organizations were observed for NF-YB and NF-YC genes (Figure 4), which is in agreement with previous studies, revealing the conserved features of the evolution of these subunits in plants. In addition, the CsaNF-YBs (7/13) and CsaNF-YCs (3/7) were prevalently lack of introns (Figure 4), which is a universal feature of NF-YB and NF-YC genes in other plant species, such as peach, in which 6 out of 12 NF-YBs and 4 out of 6 NF-YCs have no introns [14]; tea plant, in which 7 out of 15 NF-YBs and 6 out of 10 NF-YCs have no introns [16]; castor bean, in which 8 out of 12 NF-YBs and 3 out of 7 NF-YCs have no introns [15]; chickpea, in which 11 out of 21 NF-YBs and 7 out of 11 NF-YCs have no introns [43]; and banana, in which 12 out of 16 NF-YBs and 12 out of 14 NF-YCs have no introns [18]. The similar conserved domain arrangements and intron/exon organizations in each subunit indicate that NF-Y genes are highly conserved during the evolution of plants, which may contribute to their crucial biological functions.…”

Genome-wide identification and expression profile analysis of nuclear factor Y family genes in Sorghum bicolor L. (Moench)

“…Chen et al [59] reported that most of the NF-YB contained only one exon, and the genes from the same clade displayed a similar motif pattern in Gossypium hirsuyum . Chu et al [60] reported 5 exons and 4 introns (6 genes) or 6 exons and 5 introns (2 genes) in CaNF-YA gene family members in Cicer arietinum . Further, they noticed 1 to 6 exons in CaNF-YB family, and 7 intronless out of 11 members in the CaNF-YC family.…”

“…Further, several members of the NF-YB and NF-YC have been found without any introns like in S . bicolor [55], Ricinus cummunis [34] and chickpea [60]. Introns are essential parts of all eukaryotic genes.…”

Genome-wide analysis of the NF-Y gene family in peach (Prunus persica L.)

“…In castor bean, 25 RcNF-Y genes have been identified across the genome and their expression changes were investigated under four types of abiotic stresses (drought, cold, heat and salt stresses) [44, 45]. In chickpea, a total of 40 CaNF-Y genes have been identified and some CaNF-Y genes were found to be responsive to dehydration and abscisic acid treatments [9].…”