Molecular Profiling and Precise Diagnosis of Pratylenchus penetrans Infestation in Soil: A qPCR-Based Molecular Approach.

IF 2.5 3区 农林科学 Q2 PLANT SCIENCES
Karthi Natesan, Byeong-Yong Park, Hyoung-Rai Ko, Eunhwa Kim, Sohee Park, Sekeun Park
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Abstract

Pratylenchus penetrans, an important soil pathogen, has been reported on various crops in the temperate regions of South Korea. In concern, there is an urgent need for a precise, species-specific quantitative polymerase chain reaction (qPCR) kit to detect and quantify root lesion nematodes for early pest management and to controls yield losses. The present study focuses on D2-D3 region, a known marker for molecular profiling of Pratylenchus sp. A primer set mined from the highly conserved D2-D3 region of P. penetrans was used in a SYBR green based qPCR assay. Initial examination identified P. penetrans from infested soil samples using morphological and phylogenetic analyses. The DPp7F12R primer set demonstrated significant specificity in identifying P. penetrants by both conventional polymerase chain reaction (PCR) and qPCR assays. Linear regression of serially diluted DNA from nematode and nematode inoculated soil revealed a limit of quantification of 2 picograms (r² = 0.984), while also highlighting the impact of soil inhibitors. The qPCR using the DNA from varying densities of P. penetrans inoculated in soil demonstrated a robust correlation (r² = 0.98), indicating the limit of detection down to single nematode. Primer specificity evaluation with field soil sample precisely detected only P. penetrants. Species-specific DPp7F12R facilitate the direct detection of P. penetrants from soil DNA in very shorter time. Reliability of PCR was confirmed using BLAST algorithm, which identified partial sequence of PCR amplicon (300 bp) as P. penetrants. Finally, PCR assay using DPp7F12R is crucial for early detection of P. penetrans infestations, helping improve the plant health.

基于qpcr的土壤渗透叶青虫侵染分子分析与精确诊断
渗透扇叶虫是一种重要的土壤病原菌,在韩国温带地区的多种作物上都有报道。令人担忧的是,迫切需要一种精确的、物种特异性的定量聚合酶链反应(qPCR)试剂盒来检测和量化根损线虫,用于早期害虫管理和控制产量损失。本研究的重点是Pratylenchus sp.的D2-D3区域,这是一个已知的分子分析标记。从P. penetrans高度保守的D2-D3区域中挖掘的引物集用于基于SYBR绿色的qPCR检测。初步检查通过形态学和系统发育分析从侵染土壤样品中鉴定出穿透假单胞菌。DPp7F12R引物组在常规聚合酶链反应(PCR)和qPCR检测中均表现出显著的特异性。对连续稀释的线虫DNA和接种线虫的土壤DNA进行线性回归,定量限为2 picograms (r²= 0.984),同时也突出了土壤抑制剂的影响。利用不同密度接种土壤的穿透线虫DNA进行qPCR,结果显示出较强的相关性(r²= 0.98),表明其检测范围仅限于单个线虫。利用田间土壤样品进行引物特异性评价,准确地检测出磷渗透物。DPp7F12R具有物种特异性,可以在很短的时间内从土壤DNA中直接检测到渗透菌。利用BLAST算法对PCR扩增子的部分序列(300 bp)进行鉴定,验证了PCR的可靠性。最后,利用DPp7F12R进行PCR检测对于早期发现穿透性假单胞菌侵染至关重要,有助于改善植物的健康状况。
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来源期刊
Plant Pathology Journal
Plant Pathology Journal 生物-植物科学
CiteScore
4.90
自引率
4.30%
发文量
71
审稿时长
12 months
期刊介绍: Information not localized
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