Evolutionary insights and expression dynamics of the CaNFYB transcription factor gene family in pepper (Capsicum annuum) under salinity stress

Diaa Abd El Moneim; Hassan Mansour; Rana M Alshegaihi; Fatmah Ahmed Safhi; Khairiah Mubarak Alwutayd; Rahma Alshamrani; Amnah Alamri; Wessam Felembam; Amani Omar Abuzaid; Mahmoud Magdy

doi:10.3389/fgene.2023.1288453

Evolutionary insights and expression dynamics of the CaNFYB transcription factor gene family in pepper (Capsicum annuum) under salinity stress

Front Genet. 2023 Nov 2:14:1288453. doi: 10.3389/fgene.2023.1288453. eCollection 2023.

Authors

Diaa Abd El Moneim^#¹, Hassan Mansour^{2

3}, Rana M Alshegaihi⁴, Fatmah Ahmed Safhi⁵, Khairiah Mubarak Alwutayd⁵, Rahma Alshamrani⁶, Amnah Alamri⁶, Wessam Felembam^{6

7}, Amani Omar Abuzaid⁶, Mahmoud Magdy^#⁸

Affiliations

¹ Department of Plant Production (Genetic Branch), Faculty of Environmental Agricultural Sciences, Arish University, El-Arish, Egypt.
² Department of Biological Sciences, Faculty of Science & Arts, King Abdulaziz University, Rabigh, Saudi Arabia.
³ Department of Botany and Microbiology, Faculty of Science, Suez Canal University, Ismailia, Egypt.
⁴ Department of Biology, College of Science, University of Jeddah, Jeddah, Saudi Arabia.
⁵ Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia.
⁶ Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.
⁷ Immunology Unit, King Fahad Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia.
⁸ Department of Genetics, Faculty of Agriculture, Ain Shams University, Cairo, Egypt.

^# Contributed equally.

Abstract

Introduction: The Capsicum annuum nuclear factor Y subunit B (CaNFYB) gene family plays a significant role in diverse biological processes, including plant responses to abiotic stressors such as salinity. Methods: In this study, we provide a comprehensive analysis of the CaNFYB gene family in pepper, encompassing their identification, structural details, evolutionary relationships, regulatory elements in promoter regions, and expression profiles under salinity stress. Results and discussion: A total of 19 CaNFYB genes were identified and subsequently characterized based on their secondary protein structures, revealing conserved domains essential for their functionality. Chromosomal distribution showed a non-random localization of these genes, suggesting potential clusters or hotspots for NFYB genes on specific chromosomes. The evolutionary analysis focused on pepper and comparison with other plant species indicated a complex tapestry of relationships with distinct evolutionary events, including gene duplication. Moreover, promoter cis-element analysis highlighted potential regulatory intricacies, with notable occurrences of light-responsive and stress-responsive binding sites. In response to salinity stress, several CaNFYB genes demonstrated significant temporal expression variations, particularly in the roots, elucidating their role in stress adaptation. Particularly CaNFYB01, CaNFYB18, and CaNFYB19, play a pivotal role in early salinity stress response, potentially through specific regulatory mechanisms elucidated by their cis-elements. Their evolutionary clustering with other Solanaceae family members suggests conserved ancestral functions vital for the family's survival under stress. This study provides foundational knowledge on the CaNFYB gene family in C. annuum, paving the way for further research to understand their functional implications in pepper plants and relative species and their potential utilization in breeding programs to enhance salinity tolerance.

Keywords: CaNFYB transcription factor; Capsicum annum; expression analysis; gene structure; phylogenetic analysis; salinity stress.

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. Princess Nourah bint Abdulrahman University Researchers Supporting Project number (PNURSP2023R318), Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia.