Table_1_Genome wide identification of the NPR1 gene family in plant defense mechanisms against biotic stress in chili (Capsicum annuum L.).XLSX

Chili pepper cultivation in the Indian subcontinent is severely affected by viral diseases, prompting the need for environmentally friendly disease control methods. To achieve this, it is essential to understand the molecular mechanisms of viral resistance in chili pepper. The NONEXPRESSOR OF PATHOGENESIS-RELATED GENES 1 (NPR1) genes are known to provide broad-spectrum resistance to various phytopathogens by activating systemic acquired resistance (SAR). An in-depth understanding of NPR1 gene expression during begomovirus infection and its correlation with different biochemical and physiological parameters is crucial for enhancing resistance against begomoviruses in chili pepper. Nevertheless, limited information on chili CaNPR genes and their role in biotic stress constrains their potential in breeding for biotic stress resistance. By employing bioinformatics for genome mining, we identify 5 CaNPR genes in chili. The promoter regions of 1,500 bp of CaNPR genes contained cis-elements associated with biotic stress responses, signifying their involvement in biotic stress responses. Furthermore, these gene promoters harbored components linked to light, development, and hormone responsiveness, suggesting their roles in plant hormone responses and development. MicroRNAs played a vital role in regulating these five CaNPR genes, highlighting their significance in the regulation of chili genes. Inoculation with the begomovirus “cotton leaf curl Khokhran virus (CLCuKV)” had a detrimental effect on chili plant growth, resulting in stunted development, fibrous roots, and evident virus symptoms. The qRT-PCR analysis of two local chili varieties inoculated with CLCuKV, one resistant (V1) and the other susceptible (V2) to begomoviruses, indicated that CaNPR1 likely provides extended resistance and plays a role in chili plant defense mechanisms, while the remaining genes are activated during the early stages of infection. These findings shed light on the function of chili’s CaNPR in biotic stress responses and identify potential genes for biotic stress-resistant breeding. However, further research, including gene cloning and functional analysis, is needed to confirm the role of these genes in various physiological and biological processes. This in-silico analysis enhances our genome-wide understanding of how chili CaNPR genes respond during begomovirus infection.

印度次大陆的辣椒栽培深受病毒病害的严重为害，亟需研发环境友好型的病害防控手段。为此，解析辣椒抗病毒的分子机制至关重要。病程相关基因非表达子1（NPR1，全称NONEXPRESSOR OF PATHOGENESIS-RELATED GENES 1）可通过激活系统获得性抗性（systemic acquired resistance, SAR），赋予植物对多种植物病原菌的广谱抗性。深入解析双生病毒（begomovirus）侵染过程中NPR1基因的表达模式，及其与不同生化、生理参数的关联，对于提升辣椒对双生病毒的抗性至关重要。然而，目前关于辣椒CaNPR基因及其在生物胁迫中的功能相关信息匮乏，限制了其在生物胁迫抗性育种中的应用潜力。本研究通过生物信息学手段开展全基因组挖掘，在辣椒中鉴定出5个CaNPR基因。CaNPR基因上游1500碱基对（bp）的启动子区域含有与生物胁迫响应相关的顺式作用元件，表明这些基因参与生物胁迫响应过程。此外，这些基因的启动子还包含与光照、生长发育及激素响应相关的调控元件，提示它们在植物激素响应与生长发育过程中发挥作用。微小RNA（microRNA, miRNA）在这5个CaNPR基因的调控中发挥关键作用，凸显了其对辣椒基因调控的重要性。接种双生病毒——棉花卷叶Khokhran病毒（cotton leaf curl Khokhran virus, CLCuKV）会对辣椒植株生长产生不利影响，导致植株矮化、根系纤维化，并出现明显的病毒病症。对两个分别抗（V1）、感（V2）双生病毒的当地辣椒品种接种CLCuKV后的实时荧光定量聚合酶链反应（qRT-PCR）分析显示，CaNPR1可能赋予辣椒持久抗性并参与植株防御机制，而其余基因则在侵染早期被激活。本研究结果阐明了辣椒CaNPR基因在生物胁迫响应中的功能，并为生物胁迫抗性育种筛选出了潜在的目标基因。不过，仍需开展包括基因克隆与功能分析在内的后续研究，以验证这些基因在不同生理与生物学过程中的具体功能。本次硅基分析（in-silico analysis）加深了我们对辣椒CaNPR基因在双生病毒侵染过程中全基因组响应模式的理解。