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

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.

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Genomic Organization, Phylogenetic Comparison, and Differential Expression of the Nuclear Factor-Y Gene Family in Apple (Malus Domestica)

Plants ◽

10.3390/plants10010016 ◽

2020 ◽

Vol 10 (1) ◽

pp. 16

Author(s):

Yanjie Qu ◽

Yaping Wang ◽

Jun Zhu ◽

Yugang Zhang ◽

Hongmin Hou

Keyword(s):

Abiotic Stress ◽

Malus Domestica ◽

Growth And Development ◽

Expression Patterns ◽

Specific Response ◽

Nuclear Factor ◽

Element Analysis ◽

Nuclear Factor Y ◽

Gene Structures ◽

Y Family

The nuclear factor Y (NF-Y) as a transcription factor plays an important role in plants growth and development, and response to stress. However, few genome-wide analyzes and functional research of the NF-Y family has been undertaken in apple (Malus domestica Borkh.) so far. In this study, we comprehensively identified the 43 MdNF-Y genes in apple, which dispersedly distributed among the three subgroups based on their sequence alignment analysis, including 11 MdNF-YAs, 22 MdNF-YBs and 10 MdNF-YCs. The members in the same subgroups had similar evolution relationships, gene structures, and conserved motifs. The gene duplication analysis suggested that all the genes were dispersed followed by 27 segmental duplication. Moreover, based on synteny analysis of MdNF-Ys with eight plant species results suggested that some ortholog genes were preserved during the evolution of these species. Cis-element analysis showed potential functions of MdNF-Ys in apple growth and development and responded to abiotic stress. Furthermore, the interaction among MdNF-Ys protein were investigated in yeast two-hybrid assays. The expression patterns of MdNF-Ys in tissue-specific response reveled divergence and might play important role in apple growth and development. Subsequently, whole MdNF-Y genes family was carried out for RT-PCR in response to five abiotic stress (ABA, drought, heat, cold, and salinity) to identify their expression patterns. Taken together, our study will provide a foundation for the further study to the molecular mechanism of apple in growing development and response to abiotic stresses.

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NUCLEAR FACTOR Y, subunit A (NF-YA) proteins positively regulate flowering and act through FLOWERING LOCUS T

10.1101/066399 ◽

2016 ◽

Author(s):

Chamindika L. Siriwardana ◽

Nerina Gnesutta ◽

Roderick W. Kumimoto ◽

Daniel S. Jones ◽

Zachary A. Myers ◽

...

Keyword(s):

Reproductive Success ◽

Plant Species ◽

Strong Support ◽

Day Length ◽

Dependent Manner ◽

Nuclear Factor ◽

Flowering Locus T ◽

Nuclear Factor Y ◽

Timing Mechanisms ◽

Flowering Locus

AbstractPhotoperiod dependent flowering is one of several mechanisms used by plants to initiate the developmental transition from vegetative growth to reproductive growth. The NUCLEAR FACTOR Y (NF-Y) transcription factors are heterotrimeric complexes composed of NF-YA and histone-fold domain (HFD) containing NF-YB/NF-YC, that initiate photoperiod-dependent flowering by cooperatively interacting with CONSTANS (CO) to drive the expression of FLOWERING LOCUS T (FT). This involves NF-Y and CO binding at distal CCAAT and proximal “CORE” elements, respectively, in the FT promoter. While this is well established for the HFD subunits, there remains some question over the potential role of NF-YA as either positive or negative regulators of this process. Here we provide strong support, in the form of genetic and biochemical analyses, that NF-YA, in complex with NF-YB/NF-YC proteins, can directly bind the distal CCAAT box in the FT promoter and are positive regulators of flowering in an FT-dependent manner.Author SummaryFor plants to have reproductive success, they must time their flowering with the most beneficial biotic and abiotic environmental conditions - after all, reproductive success would likely be low if flowers developed when pollinators were not present or freezing temperatures were on the horizon. Proper timing mechanisms for flowering vary significantly between different species, but can be connected to a variety of environmental cues, including water availability, temperature, and day length. Numerous labs have studied the molecular aspects of these timing mechanisms and discovered that many of these pathways converge on the gene FLOWERING LOCUS T (FT). This means that understanding precisely how this gene is regulated can teach us a lot about many plant species in both natural and agricultural settings. In the current study, we focus on day length as an essential cue for flowering in the plant species Arabidopsis thaliana. We further unravel the complexity of FT regulation by clarifying the roles of NUCLEAR FACTOR Y genes in day length perception.

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Identification of fasciclin-like arabinogalactan proteins in textile hemp (Cannabis sativa L.): in silico analyses and gene expression patterns in different tissues

BMC Genomics ◽

10.1186/s12864-017-3970-5 ◽

2017 ◽

Vol 18 (1) ◽

Cited By ~ 18

Author(s):

Gea Guerriero ◽

Lauralie Mangeot-Peter ◽

Sylvain Legay ◽

Marc Behr ◽

Stanley Lutts ◽

...

Keyword(s):

Gene Expression ◽

In Silico ◽

Cannabis Sativa ◽

Expression Patterns ◽

Arabinogalactan Proteins ◽

Gene Expression Patterns ◽

In Silico Analyses ◽

Different Tissues

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NF-YB-Mediated Active Responses of Plant Growth under Salt and Temperature Stress in Eucalyptus grandis

Plants ◽

10.3390/plants10061107 ◽

2021 ◽

Vol 10 (6) ◽

pp. 1107

Author(s):

Jia-Hao Dai ◽

An-Qi Hu ◽

Jia-Shuo Zhang ◽

Wen-Hai Liao ◽

Hua-Yan Ma ◽

...

Keyword(s):

Plant Growth ◽

Stress Responses ◽

Expression Profiles ◽

Expression Patterns ◽

Eucalyptus Grandis ◽

Nuclear Factor ◽

Nuclear Factor Y ◽

Gene Structures ◽

Genetic Structures ◽

Y Family

The transcription factor NF-YB (nuclear factor-YB) family is a subfamily of the nuclear factor Y (NF-Y), which plays an important role in regulating plant growth, development and participates in various stress responses. Although the NF-Y family has been studied in many species, it is still obscure in Eucalyptus grandis. In this study, 23 EgNF-YB genes in eucalyptus were identified and unevenly distributed on 11 chromosomes. Phylogenetic analysis showed the EgNF-YB genes were divided into two clades, LEC-1 type and non-LEC1 type. The evolution of distinct clades was relatively conservative, the gene structures were analogous, and the differences of genetic structures among clades were small. The expression profiles showed that the distinct EgNF-YB genes were highly expressed in diverse tissues, and EgNF-YB4/6/13/19/23 functioned in response to salinity, heat and cold stresses. Our study characterized the phylogenetic relationship, gene structures and expression patterns of EgNF-YB gene family and investigated their potential roles in abiotic stress responses, which provides solid foundations for further functional analysis of NF-YB genes in eucalyptus.

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Identification and Comprehensive Analysis of the Nuclear Factor-Y Family Genes Reveal Their Multiple Roles in Response to Nutrient Deficiencies in Brassica napus

International Journal of Molecular Sciences ◽

10.3390/ijms221910354 ◽

2021 ◽

Vol 22 (19) ◽

pp. 10354

Author(s):

Xinrui Zheng ◽

Hao Zhang ◽

Limei Zhang ◽

Fangsen Xu ◽

Lei Shi ◽

...

Keyword(s):

Brassica Napus ◽

Expression Patterns ◽

Multiple Roles ◽

Functional Study ◽

Nuclear Factor ◽

Nutrient Deficiencies ◽

Abiotic Stress Response ◽

Nuclear Factor Y ◽

Homologous Genes ◽

Y Family

Nuclear Factor-Y (NF-Y) transcription factors play vital roles in plant abiotic stress response. Here, the NF-Y family in Brassica napus, which is hyper-sensitive to nitrogen (N) deprivation, was comprehensively identified and systematically characterized. A total of 108 NF-Y family members were identified in B. napus and categorized into three subfamilies (38 NF-YA, 46 NF-YB and 24 NF-YC; part of the Arabidopsis NF-YC homologous genes had been lost during B. napus evolution). In addition, the expansion of the NF-Y family in B. napus was driven by whole-genome duplication and segmental duplication. Differed expression patterns of BnaNF-Ys were observed in response to multiple nutrient starvations. Thirty-four genes were regulated only in one nutrient deficient condition. Moreover, more BnaNF-YA genes were differentially expressed under nutrient limited environments compared to the BnaNF-YB and BnaNF-YC subfamilies. Sixteen hub genes responded diversely to N deprivation in five rapeseed tissues. In summary, our results laid a theoretical foundation for the follow-up functional study of the key NF-Y genes in B. napus in regulating nutrient homeostasis, especially N.

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