Genome-wide analysis of AP2/ERF transcription factors family in Brassica napus

Ghorbani, Razieh; Zakipour, Zahra; Alemzadeh, Abbas; Razi, Hooman

doi:10.1007/s12298-020-00832-z

Cited by 28 publications

(20 citation statements)

References 44 publications

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“…There’s a possibility of deletion of some of the pre-existing genes or newly generated genes during the process of cotton evolution. Collinearity and chromosomal locations showed the significant role of segmental duplications in ERF genes expansion in cotton which was following the results reported in rice, B. napus , A. thaliana and other plants [ 10 , 42 , 51 , 52 ]. The synteny analysis results could be used to reveal the evolutional and functional connections among the cotton species.…”

Section: Discussionsupporting

confidence: 84%

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Genome-wide characterization and expression analysis of Erf gene family in cotton

et al. 2022

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Background AP2/ERF transcription factors are important in a variety of biological activities, including plant growth, development, and responses to biotic and abiotic stressors. However, little study has been done on cotton’s AP2/ERF genes, although cotton is an essential fibre crop. We were able to examine the tissue and expression patterns of AP2/ERF genes in cotton on a genome-wide basis because of the recently published whole genome sequence of cotton. Genome-wide analysis of ERF gene family within two diploid species (G. arboreum & G. raimondii) and two tetraploid species (G. barbadense, G. hirsutum) was performed. Results A total of 118, 120, 213, 220 genes containing the sequence of single AP2 domain were identified in G. arboreum, G. raimondii, G. barbadense and G. hirsutum respectively. The identified genes were unevenly distributed across 13/26 chromosomes of A and D genomes of cotton. Synteny and collinearity analysis revealed that segmental duplications may have played crucial roles in the expansion of the cotton ERF gene family, as well as tandem duplications played a minor role. Cis-acting elements of the promoter sites of Ghi-ERFs genes predict the involvement in multiple hormone responses and abiotic stresses. Transcriptome and qRT-PCR analysis revealed that Ghi-ERF-2D.6, Ghi-ERF-12D.13, Ghi-ERF-6D.1, Ghi-ERF-7A.6 and Ghi-ERF-11D.5 are candidate genes against salinity tolerance in upland cotton. Conclusion Overwhelmingly, the present study paves the way to better understand the evolution of cotton ERF genes and lays a foundation for future investigation of ERF genes in improving salinity stress tolerance in cotton.

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Section: Discussionsupporting

confidence: 84%

“…Due to their coordinating ability with multiple signaling and hormonal pathways, ERFs are considered excellent entities for engineering biotic/abiotic stress tolerance in plants [ 9 ]. Several studies have shown the involvement of ERF gene expression under different stress tolerance conditions and tissues in plants [ 10 – 12 ].…”

Section: Introductionmentioning

confidence: 99%

Genome-wide characterization and expression analysis of Erf gene family in cotton

et al. 2022

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“…Different TF families have been identified in plants such as AP2/ERF, MYB, HSP, bZIP, NAC, DOF, MADS-box, etc. ( Ghorbani et al, 2020 ; Table 1 ). In a recent study, Wang et al (2018) identified 2,167 TFs belonging to five different families in B. napus with 7.6% identified as novel and unique to B. napus .…”

Section: Plant Response Mechanisms To Heat Stressmentioning

confidence: 99%

Genetic and Physiological Responses to Heat Stress in Brassica napus

et al. 2022

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Given the current rise in global temperatures, heat stress has become a major abiotic challenge affecting the growth and development of various crops and reducing their productivity. Brassica napus, the second largest source of vegetable oil worldwide, experiences a drastic reduction in seed yield and quality in response to heat. This review outlines the latest research that explores the genetic and physiological impact of heat stress on different developmental stages of B. napus with a special attention to the reproductive stages of floral progression, organogenesis, and post flowering. Several studies have shown that extreme temperature fluctuations during these crucial periods have detrimental effects on the plant and often leading to impaired growth and reduced seed production. The underlying mechanisms of heat stress adaptations and associated key regulatory genes are discussed. Furthermore, an overview and the implications of the polyploidy nature of B. napus and the regulatory role of alternative splicing in forming a priming-induced heat-stress memory are presented. New insights into the dynamics of epigenetic modifications during heat stress are discussed. Interestingly, while such studies are scarce in B. napus, opposite trends in expression of key genetic and epigenetic components have been identified in different species and in cultivars within the same species under various abiotic stresses, suggesting a complex role of these genes and their regulation in heat stress tolerance mechanisms. Additionally, omics-based studies are discussed with emphasis on the transcriptome, proteome and metabolome of B. napus, to gain a systems level understanding of how heat stress alters its yield and quality traits. The combination of omics approaches has revealed crucial interactions and regulatory networks taking part in the complex machinery of heat stress tolerance. We identify key knowledge gaps regarding the impact of heat stress on B. napus during its yield determining reproductive stages, where in-depth analysis of this subject is still needed. A deeper knowledge of heat stress response components and mechanisms in tissue specific models would serve as a stepping-stone to gaining insights into the regulation of thermotolerance that takes place in this important crop species and support future breeding of heat tolerant crops.

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“…With more draft genomic information of plants released, AP2/ERF superfamily members have been identified and characterized in eudicots, i.e., Arabidopsis ( Sakuma et al, 2002 ; Nakano et al, 2006 ), grapevine ( Licausi et al, 2010 ), cucumber ( Hu and Liu, 2011 ), Chinese plum ( Du et al, 2013 ), apple ( Girardi et al, 2013 ), sweet orange ( Ito et al, 2014 ), pineapple ( Huang et al, 2020 ), canola ( Ghorbani et al, 2020 ), Chinese cherry ( Zhu et al, 2021 ), and dark jute ( Kabir et al, 2021 ), and in monocots, i.e., rice ( Sharoni et al, 2011 ), common wheat ( Zhuang et al, 2011 ), sugarcane ( Li et al, 2020 ), maize ( Liu et al, 2013 ), barley ( Guo et al, 2016 ), and foxtail millet ( Lata et al, 2014 ). In general, AP2 TFs have been found to regulate various developmental processes, such as the development of floral organs ( Irish and Sussex, 1990 ; Jofuku et al, 1994 ; Chuck et al, 1998 and, 2008 ; Maes et al, 2001 ; Aukerman and Sakai, 2003 ) and embryo and seed growth ( Boutilier et al, 2002 ; Jofuku et al, 2005 ; Krizek and Beth, 2009 ).…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Identification and Expression Analysis of AP2/ERF Transcription Factor Related to Drought Stress in Cultivated Peanut (Arachis hypogaea L.)

et al. 2021

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APETALA2/ethylene response element-binding factor (AP2/ERF) transcription factors (TFs) have been found to regulate plant growth and development and response to various abiotic stresses. However, detailed information of AP2/ERF genes in peanut against drought has not yet been performed. Herein, 185 AP2/ERF TF members were identified from the cultivated peanut (A. hypogaea cv. Tifrunner) genome, clustered into five subfamilies: AP2 (APETALA2), ERF (ethylene-responsive-element-binding), DREB (dehydration-responsive-element-binding), RAV (related to ABI3/VP), and Soloist (few unclassified factors)). Subsequently, the phylogenetic relationship, intron–exon structure, and chromosomal location of AhAP2/ERF were further characterized. All of these AhAP2/ERF genes were distributed unevenly across the 20 chromosomes, and 14 tandem and 85 segmental duplicated gene pairs were identified which originated from ancient duplication events. Gene evolution analysis showed that A. hypogaea cv. Tifrunner were separated 64.07 and 66.44 Mya from Medicago truncatula L. and Glycine max L., respectively. Promoter analysis discovered many cis-acting elements related to light, hormones, tissues, and stress responsiveness process. The protein interaction network predicted the exitance of functional interaction among families or subgroups. Expression profiles showed that genes from AP2, ERF, and dehydration-responsive-element-binding subfamilies were significantly upregulated under drought stress conditions. Our study laid a foundation and provided a panel of candidate AP2/ERF TFs for further functional validation to uplift breeding programs of drought-resistant peanut cultivars.

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Genome-wide analysis of AP2/ERF transcription factors family in Brassica napus

Cited by 28 publications

References 44 publications

Genome-wide characterization and expression analysis of Erf gene family in cotton

Genome-wide characterization and expression analysis of Erf gene family in cotton

Genetic and Physiological Responses to Heat Stress in Brassica napus

Genome-Wide Identification and Expression Analysis of AP2/ERF Transcription Factor Related to Drought Stress in Cultivated Peanut (Arachis hypogaea L.)

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