A metagenetic approach to determine the diversity and distribution of cyst nematodes at the level of the country, the field and the individual.
A metagenetic approach to determine the diversity and distribution of cyst nematodes at the level of the country, the field and the individual.
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DOI：
10.1111/mec.13434
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发表时间：
2015-12
影响因子：
4.9
通讯作者：
Blok VC
中科院分区：
文献类型：
--
作者：
Eves-van den Akker S;Lilley CJ;Reid A;Pickup J;Anderson E;Cock PJ;Blaxter M;Urwin PE;Jones JT;Blok VC
英国存在马铃薯胞囊线虫 (PCN) Globodera pallida 的不同种群，它们克服各种抗性来源的能力不同。区分种群的有效方法将使田间能够根据病原体选择品种。苏格兰农业科学与咨询 (SASA) 每年都会进行国家 DNA 诊断测试，通过从土壤浮游物中提取 DNA 来确定马铃薯种子和仓库中是否存在多氯化萘。这些 DNA 样本为监测 PCN 的分布和进一步探究物种内的多样性提供了独特的资源。我们确定了描述英国境内三个主要 G. pallida 类群的线粒体 DNA 区域，并采用宏遗传学方法同时对所有 SASA 样本进行测序和分析。使用这种方法，我们以现场尺度分辨率描述了 G. pallida 线粒体型在苏格兰的分布。大多数领域包含单一有丝分裂型，五分之一包含多种有丝分裂型的混合，不到 3% 包含所有三种有丝分裂型。在混合领域中，我们能够在一个数量级上量化每种有丝分裂型的相对丰度。混合领域内的局部区域以某些线粒体型为主，并表明存在复杂的潜在“病理景观”。最后，我们评估个体囊肿水平的有丝分裂型分布，并提供“杂交”的证据。这项研究提供了一种同时对多达 1000 个领域进行准确、定量和高通量分型的方法，同时揭示了对一种具有重要经济意义的植物寄生虫的国家遗传变异性的新见解。
Distinct populations of the potato cyst nematode (PCN) Globodera pallida exist in the UK that differ in their ability to overcome various sources of resistance. An efficient method for distinguishing between populations would enable pathogen‐informed cultivar choice in the field. Science and Advice for Scottish Agriculture (SASA) annually undertake national DNA diagnostic tests to determine the presence of PCN in potato seed and ware land by extracting DNA from soil floats. These DNA samples provide a unique resource for monitoring the distribution of PCN and further interrogation of the diversity within species. We identify a region of mitochondrial DNA descriptive of three main groups of G. pallida present in the UK and adopt a metagenetic approach to the sequencing and analysis of all SASA samples simultaneously. Using this approach, we describe the distribution of G. pallida mitotypes across Scotland with field‐scale resolution. Most fields contain a single mitotype, one‐fifth contain a mix of mitotypes, and less than 3% contain all three mitotypes. Within mixed fields, we were able to quantify the relative abundance of each mitotype across an order of magnitude. Local areas within mixed fields are dominated by certain mitotypes and indicate towards a complex underlying ‘pathoscape’. Finally, we assess mitotype distribution at the level of the individual cyst and provide evidence of ‘hybrids’. This study provides a method for accurate, quantitative and high‐throughput typing of up to one thousand fields simultaneously, while revealing novel insights into the national genetic variability of an economically important plant parasite.