Cucumber mosaic virus (CMV) is a major production constraint in black pepper causing stunted disease. Resistant varieties are unavailable and control measures are not effective till now. Recently, RNA interference (RNAi) is the most promising strategy for combating virus infection in plants but the effectiveness depends on sequence specificity between the transgene and the targeting virus. This study was undertaken to design the most suitable region for double stranded RNA synthesis with maximum specificity and minimized off–targets for all the five genes of CMV from black pepper. A 400 bp off–target minimized region identified from each of the five genes was subjected to sequence polymorphism study with selected CMV subgroup IB strains and common ‘siRNAs’ were designed in silico. As 3b gene had the least variations (of 17%) with four common and potential siRNAs designed from this region in silico, a hairpin construct was assembled using this region in Agrobacterium that can be used for developing black pepper resistant to selected CMV subgroup IB strains.

中文翻译：

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黄瓜花叶病毒IB亚群各种靶基因的siRNA设计

黄瓜花叶病毒（CMV）是黑胡椒中导致发育不良疾病的主要生产限制。目前尚无抗性品种，而且控制措施尚未生效。最近，RNA干扰（RNAi）是对抗植物中病毒感染的最有希望的策略，但有效性取决于转基因和靶向病毒之间的序列特异性。这项研究的目的是为双链RNA合成设计最合适的区域，该区域具有最大的特异性，并使黑胡椒CMV的所有五个基因的脱靶目标最小化。从五个基因的每一个中识别出一个400 bp的脱靶最小化区域，并与选定的CMV亚组IB菌株进行序列多态性研究，并在计算机上设计了常见的“ siRNA”。由于3b基因在计算机上从该区域设计的四个常见和潜在siRNA的变异最小（为17％），因此在农杆菌中使用该区域组装了发夹构建体，可用于开发对选定的CMV亚组IB菌株产生抗性的黑胡椒。