Atallah Zahi K, Subbarao Krishna V
Department of Plant Pathology, University of California, Davis, CA, USA.
Methods Mol Biol. 2012;835:333-63. doi: 10.1007/978-1-61779-501-5_20.
Studies of the population genetics of fungal and oomycetous phytopathogens are essential to clarifying the disease epidemiology and devising management strategies. Factors commonly associated with higher organisms such as migration, natural selection, or recombination, are critical for the building of a clearer picture of the pathogen in the landscape. In this chapter, we focus on a limited number of experimental and analytical methods that are commonly applied in population genetics. At first, we present different types of qualitative and quantitative traits that could be identified morphologically (phenotype). Subsequently, we describe several molecular methods based on dominant and codominant markers, and we provide our assessment of the advantages and shortfalls of these methods. Third, we discuss various analytical methods, which include phylogenies, summary statistics as well as coalescent-based methods, and we elaborate on the benefits associated with each approach. Last, we develop a case study in which we investigate the population structure of the fungal phytopathogen Verticillium dahliae in coastal California, and assess the hypotheses of transcontinental gene flow and recombination in a fungus that is described as asexual.
对真菌和卵菌植物病原体的群体遗传学进行研究，对于阐明疾病流行病学和制定管理策略至关重要。与高等生物相关的常见因素，如迁移、自然选择或重组，对于更清晰地描绘病原体在环境中的情况至关重要。在本章中，我们重点关注群体遗传学中常用的一些实验和分析方法。首先，我们介绍可以通过形态学（表型）识别的不同类型的定性和定量性状。随后，我们描述几种基于显性和共显性标记的分子方法，并对这些方法的优缺点进行评估。第三，我们讨论各种分析方法，包括系统发育、汇总统计以及基于溯祖的方法，并详细阐述每种方法的优点。最后，我们开展一个案例研究，调查加利福尼亚沿海地区真菌植物病原体大丽轮枝菌的群体结构，并评估一种被描述为无性的真菌中跨大陆基因流动和重组的假设。
