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

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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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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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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Genome-wide screening and identification of Nuclear Factor-Y family genes and exploration their function on regulating abiotic and biotic stress in potato (Solanum tuberosum)

Gene ◽

10.1016/j.gene.2021.146089 ◽

2021 ◽

pp. 146089

Author(s):

Guochao Xuanyuan ◽

Qun Lian ◽

Ruifang Jia ◽

Miru Du ◽

Liru Kang ◽

...

Keyword(s):

Solanum Tuberosum ◽

Biotic Stress ◽

Nuclear Factor ◽

Abiotic And Biotic Stress ◽

Nuclear Factor Y ◽

Genome Wide ◽

Screening And Identification ◽

Y Family

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

PLoS ONE ◽

10.1371/journal.pone.0222203 ◽

2019 ◽

Vol 14 (9) ◽

pp. e0222203 ◽

Cited By ~ 4

Author(s):

P. Maheshwari ◽

Divya Kummari ◽

Sudhakar Reddy Palakolanu ◽

U. Nagasai Tejaswi ◽

M. Nagaraju ◽

...

Keyword(s):

Sorghum Bicolor ◽

Expression Profile ◽

Profile Analysis ◽

Nuclear Factor ◽

Nuclear Factor Y ◽

Expression Profile Analysis ◽

Genome Wide ◽

Y Family ◽

Sorghum Bicolor L

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Three Homologous Genes Encoding sn-Glycerol-3-Phosphate Acyltransferase 4 Exhibit Different Expression Patterns and Functional Divergence in Brassica napus

PLANT PHYSIOLOGY ◽

10.1104/pp.110.169482 ◽

2010 ◽

Vol 155 (2) ◽

pp. 851-865 ◽

Cited By ~ 37

Author(s):

Xue Chen ◽

Martin Truksa ◽

Crystal L. Snyder ◽

Aliaa El-Mezawy ◽

Saleh Shah ◽

...

Keyword(s):

Brassica Napus ◽

Functional Divergence ◽

Expression Patterns ◽

Homologous Genes ◽

Genes Encoding

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

Agronomy ◽

10.3390/agronomy10020236 ◽

2020 ◽

Vol 10 (2) ◽

pp. 236 ◽

Cited By ~ 1

Author(s):

Lianghai Chen ◽

Yong Zhou ◽

Wei Lai ◽

Lifang Hu ◽

Lunwei Jiang ◽

...

Keyword(s):

Transcription Factors ◽

Crop Improvement ◽

Nuclear Factor ◽

Rna Seq ◽

Abiotic Stress Response ◽

Promoter Regions ◽

Nuclear Factor Y ◽

Cucumber Genome ◽

Drought And Salt Stress ◽

Gene Structures

The nuclear factor Y (NF-Y) transcription factors (TFs) play vital regulatory roles in diverse developmental processes and responses to abiotic stresses in plants. However, the NF-Y genes remain largely unknown in cucumber. In this study, based on phylogenetic and protein structure analyses, we identified 27 CsaNF-Y members of this gene family in the cucumber genome, including 7 NF-YAs, 13 NF-YBs, and 7 NF-YCs. Their chromosome locations, gene structures, conserved domains, gene duplication, and promoter regions containing stress- and hormone-responsive cis-elements were also analyzed. As reported earlier, RNA-seq data showed that the expression of some CsaNF-Y genes was tissue-specific and varied during fruit development. The qRT-PCR results showed that all the detected CsaNF-Y genes were differentially regulated by drought and salt stress. Taken together, our findings provide a comprehensive understanding of CsaNF-Y genes in the development and abiotic stress response of cucumber and lay the foundation for future crop improvement.

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Genome-Wide Analysis of Myeloblastosis-Related Genes in Brassica napus L. and Positive Modulation of Osmotic Tolerance by BnMRD107

Frontiers in Plant Science ◽

10.3389/fpls.2021.678202 ◽

2021 ◽

Vol 12 ◽

Author(s):

Jian Li ◽

Keyun Lin ◽

Shuai Zhang ◽

Jian Wu ◽

Yujie Fang ◽

...

Keyword(s):

Transcription Factors ◽

Brassica Napus ◽

Expression Profiles ◽

Expression Patterns ◽

Regulatory Elements ◽

Functional Study ◽

Evolutionary Analysis ◽

Genome Wide Analysis ◽

Genome Wide ◽

A Genome

Myeloblastosis (MYB)-related transcription factors comprise a large subfamily of the MYB family. They play significant roles in plant development and in stress responses. However, MYB-related proteins have not been comprehensively investigated in rapeseed (Brassica napus L.). In the present study, a genome-wide analysis of MYB-related transcription factors was performed in rapeseed. We identified 251 Brassica napus MYB (BnMYB)-related members, which were divided phylogenetically into five clades. Evolutionary analysis suggested that whole genome duplication and segmental duplication events have played a significant role in the expansion of BnMYB-related gene family. Selective pressure of BnMYB-related genes was estimated using the Ka/Ks ratio, which indicated that BnMYB-related genes underwent strong purifying selection during evolution. In silico analysis showed that various development-associated, phytohormone-responsive, and stress-related cis-acting regulatory elements were enriched in the promoter regions of BnMYB-related genes. Furthermore, MYB-related genes with tissue or organ-specific, stress-responsive expression patterns were identified in B. napus based on temporospatial and abiotic stress expression profiles. Among the stress-responsive MYB-related genes, BnMRD107 was strongly induced by drought stress, and was therefore selected for functional study. Rapeseed seedlings overexpressing BnMRD107 showed improved resistance to osmotic stress. Our findings not only lay a foundation for further functional characterization of BnMYB-related genes, but also provide valuable clues to determine candidate genes for future genetic improvement of B. napus.

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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

International Journal of Molecular Sciences ◽

10.3390/ijms19113290 ◽

2018 ◽

Vol 19 (11) ◽

pp. 3290 ◽

Cited By ~ 7

Author(s):

Ha Chu ◽

Kien Nguyen ◽

Yasuko Watanabe ◽

Dung Le ◽

Thu Pham ◽

...

Keyword(s):

Abscisic Acid ◽

In Silico ◽

Major Gene ◽

Expression Patterns ◽

Dependent Manner ◽

Nuclear Factor ◽

Nuclear Factor Y ◽

Fundamental Information ◽

Close Relationship ◽

In Silico Analyses

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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