Genome-wide analysis of NPR1-like genes in citrus species and expression analysis in response to citrus canker (Xanthomonas axonopodis pv. citri)

Mobeen Ali; Muhammad Shafiq; Muhammad Zeshan Haider; Adnan Sami; Pravej Alam; Thamir Albalawi; Zuha Kamran; Saleh Sadiq; Mujahid Hussain; Muhammad Adnan Shahid; Mouna Jeridi; Ghulam Abbas Ashraf; Muhammad Aamir Manzoor; Irfan Ali Sabir

doi:10.3389/fpls.2024.1333286

Genome-wide analysis of NPR1-like genes in citrus species and expression analysis in response to citrus canker (Xanthomonas axonopodis pv. citri)

Front Plant Sci. 2024 Mar 25:15:1333286. doi: 10.3389/fpls.2024.1333286. eCollection 2024.

Affiliations

¹ Department of Horticulture, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan.
² Department of Plant Breeding & Genetics, Faculty of Agriculture Sciences, University of the Punjab, Lahore, Pakistan.
³ Department of Biology, College of Science and Humanities in Al-Kharj, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia.
⁴ Horticultural Science Department University of Florida-Institute of Food and Agricultural Sciences (IFAS) North Florida Research and Education Center, Gainesville FL, United States.
⁵ Biology Department, College of Science, King Khalid University, Abha, Saudi Arabia.
⁶ College of Environment, Hohai University, Nanjing, China.
⁷ School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China.
⁸ College of Horticulture, South China Agricultural University, Guangzhou, China.

Abstract

Citrus fruits, revered for their nutritional value, face significant threats from diseases like citrus canker, particularly impacting global citrus cultivation, notably in Pakistan. This study delves into the critical role of NPR1-like genes, the true receptors for salicylic acid (SA), in the defense mechanisms of citrus against Xanthomonas axonopodis pv. citri (Xcc). By conducting a comprehensive genome-wide analysis and phylogenetic study, the evolutionary dynamics of Citrus limon genes across diverse citrus cultivars are elucidated. Structural predictions unveil conserved domains, such as the BTB domain and ankyrin repeat domains, crucial for the defense mechanism. Motif analysis reveals essential conserved patterns, while cis-regulatory elements indicate their involvement in transcription, growth, response to phytohormones, and stress. The predominantly cytoplasmic and nuclear localization of NPR1-like genes underscores their pivotal role in conferring resistance to various citrus species. Analysis of the Ks/Ka ratio indicates a purifying selection of NPR1-like genes, emphasizing their importance in different species. Synteny and chromosomal mapping provide insights into duplication events and orthologous links among citrus species. Notably, Xac infection stimulates the expression of NPR1-like genes, revealing their responsiveness to pathogenic challenges. Interestingly, qRT-PCR profiling post-Xac infection reveals cultivar-specific alterations in expression within susceptible and resistant citrus varieties. Beyond genetic factors, physiological parameters like peroxidase, total soluble protein, and secondary metabolites respond to SA-dependent PR genes, influencing plant characteristics. Examining the impact of defense genes (NPR1) and plant characteristics on disease resistance in citrus, this study marks the inaugural investigation into the correlation between NPR1-associated genes and various plant traits in both susceptible and resistant citrus varieties to citrus bacterial canker.

Keywords: biotic stress; citrus; expression profile of NPR1; phylogenetic analysis; salicylic acid.

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. The authors extend their appreciation to the Deanship of Scientific Research at King Khalid University, Saudi Arabia for funding this work through Large Groups Project under Grant Number (RGP.2/176/44).