GENOME-WIDE IDENTIFICATION, CHARACTERIZATION AND EXPRESSION ANALYSIS OF NPR1-LIKE IN ORYZA SATIVA GENOTYPES UNDER PATHOGEN STRESS

T NAZISH; M SHAFIQ; MR ASHRAF; Z ALI; MA ZUHAIB; Q HAYYAT

doi:10.64013/bbasr.v2026i1.123

Authors

T NAZISH Department of Horticulture, Faculty of Agriculture Sciences, University of the Punjab, Lahore, 54590, Pakistan
M SHAFIQ Department of Horticulture, Faculty of Agriculture Sciences, University of the Punjab, Lahore, 54590, Pakistan
MR ASHRAF Department of Botany, Faculty of Sciences, The Superior University Lahore, Pakistan
Z ALI Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, P.O BOX. 54590, Lahore, Pakistan
MA ZUHAIB Department of Agronomy, Faculty of Agriculture Sciences, University of Punjab, Lahore, 54590, Pakistan
Q HAYYAT Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, P.O BOX. 54590, Lahore, Pakistan

DOI:

https://doi.org/10.64013/bbasr.v2026i1.123

Keywords:

Oryza sativa, Non-expressor of Pathogenesis-Related genes 1, transcriptional regulation, miRNA, salicylic acid

Abstract

Rice (Oryza sativa) is the main food source in many countries and its production is continuously threatened by various pathogens and harsh environmental conditions. The family of NPR1 (Non-expressor of Pathogenesis-Related genes 1) proteins play a central role not only in signaling and plant immunity but also in tolerance to various types of stresses. In the present study, a systematic search and investigation of the functional relevance of OsNPR1 members, taking Arabidopsis NPR1 as the standard, were carried out. Five genes similar to NPR1 (OsNPR1-1 to OsNPR1-5) were identified in the rice genome by the use of Phytozome. Observations of gene structures showed variations in the arrangements of exon-intron, while chromosome mapping displayed that these genes were unevenly located on chromosomes 1 and 3; also some of these genes were absent on several other chromosomes. Physicochemical features revealed that proteins had lengths from 582 to 635 amino acids; they also displayed different isoelectric points. A phylogenetic tree was drawn and showed 5 distinct groups, revealing the evolutionary relationships established by conserved nodes. The search of conserved motifs through MEME substantiated the presence of NPR1-like motifs and this suggests functional conservation. Based on subcellular localization prediction, majority of OsNPR1 proteins may be present in the nucleus and this supports their involvement in transcriptional regulation. Ka/Ks analysis showed that while segmental duplications have led to a gene expansion, purifying selection has been keeping the genes stable throughout evolution. Analysis of synteny between OsNPR genes and other plants showed that OsNPR1-4 had strong collinearity mainly with Arabidopsis. Examination of the gene promoter regions revealed the presence of cis-elements related to hormone, stress, and light responses. Also, by predicting the miRNA-target, post-transcriptional regulation of OsNPR1-1 by several conserved miRNA families was suggested. As per GO annotation, OsNPR1-1, OsNPR1-2, and OsNPR1-5 participate in salicylic acid response which enhances defense. They have organic acid-binding capacity and get localized to the cytoplasmic INA complex, thereby elevating disease resistance of Oryza sativa. Expression profiling in response to nitrogen fertilizer and Pyricularia oryzae infection showed OsNPR1-1 as the gene having highest level of mRNA. That finding was statistically significant for biotic and abiotic stress conditions. Results indicate that OsNPR1-1 is essential in defense and nutrient signaling pathways in rice. This detailed characterization establishes a basis for upcoming functional studies and genetic enhancement initiatives focused on improving rice stress resilience via NPR1-mediated signaling.

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