中国南方八省（自治区）水稻纹枯病菌群体遗传结构的SSR分析

【目的】明确中国南方水稻纹枯病菌不同地理群体的遗传结构，为研究该病害的流行规律提供信息。【方法】采用8个SSR荧光标记对收集自中国南方8省（自治区）的188个水稻纹枯病菌进行检测。利用POPGENE version 1.31软件计算各项遗传多样性参数，近交系数由FSTAT 2.9.3软件估算。基于马尔可夫链模型，采用GENEPOP 4.2软件以卡方检验估计Hardy-Weinberg平衡。应用Arlequin 3.1软件进行分子方差变异分析，并通过遗传分化系数计算基因流。基于Nei’s遗传距离，利用MEGA5.0软件构建UPGMA树状图。使用STRUCTURE 2.3.3软件的贝叶斯聚类法进行群体遗传结构分析，并估计群体间遗传混杂程度。采用Mantel test检测遗传距离与地理距离的相关性。【结果】8个地理群体的平均观测等位基因数和有效等位基因数分别为4.025和2.071。Shannon’s信息指数为0.659-1.088，平均为0.859。等位基因丰富度为2.500-5.152，平均为3.858。观测杂合度为0.425-0.619，平均为0.506。期望杂合度为0.399-0.546，平均为0.472。总群体水平的近交系数（F_IS = -0.069）为负值，表明总群体内杂合子过剩（纯合子缺失）。Hardy-Weinberg平衡检验表明，在6个群体中存在因杂合子的缺失或过剩引起的平衡偏离，暗示了水稻纹枯病菌同时具有克隆生长和有性繁殖，两种繁殖方式间的平衡因群体而异。AMOVA分析结果显示，有88.14%的遗传变异来自群体内部的个体间，表明遗传变异主要发生在群体内。Mantel检测发现，遗传距离与其地理距离之间呈显著正相关（r=0.422，P=0.025）。UPGMA聚类表明，所有群体可被划分为遗传分化明显的两个亚群（F_ST =0.209-0.624），其中位于珠江沿岸的广宁和长塘群体为一个组群，而位于长江沿岸的6个群体为另一组群，与遗传结构分析结果一致。位于长江沿岸的群体遗传混杂明显，基因交流水平高（Nm=2.525-8.447），群体分化程度较低（F_ST=0.029-0.094）。【结论】中国南方水稻纹枯病菌分布范围广泛、可能的混合繁殖模式以及菌核或菌丝具有远距离传播特性，是导致其遗传多样性水平较高的原因。长江亚群内部个体在不同群体之间的迁移所形成的基因流动，在一定程度上阻止了群体间的遗传分化。而长江亚群和珠江亚群之间存在明显的遗传分化，推测病原菌有限的长距离迁移可能是群体遗传变异空间结构形成的主要原因。

SSR Analysis of Population Genetic Structure of Rice Sheath Blight Causing Agent Rhizoctonia solani AG1-IA Collected from Eight Provinces (Autonomous Region) in Southern China

【Objective】The objectives of this study are to investigate genetic structure of Rhizoctonia solani AG1-IA among different geographic populations from southern China, and to provide valuable information for the epidemiology of sheath blight disease on rice.【Method】R. solani AG1-IA population containing 188 isolates collected from 8 provinces (autonomous region) in southern China were genetically assessed using 8 fluorescence-labeled SSR markers. Genetic diversity parameters were calculated using POPGENE version 1.31, and inbreeding coefficient (F_IS) was generated with the computer program FSTAT 2.9.3. Deviation from Hardy-Weinberg equilibrium (HWE) was tested by the Markov chain model with chi-square test implemented in the GENEPOP 4.2. Analysis of molecular variance (AMOVA) was carried out in the software Arlequin 3.1, and gene flow (Nm) was estimated according to population differentiation index (F_ST). To illustrate genetic relationships based on their pairwise Nei’s genetic distances, UPGMA dendrogram was constructed with MEGA 5.0. Bayesian clustering analysis was undertaken to determine the population structure and the degrees of genetic admixture using the STRUCTURE program version 2.3.3. Correlation between genetic and geographic distances between populations was assessed with a Mantel test. 【Result】 For populations of R. solani AG1-IA, the mean observed and effective number of alleles were 4.025 and 2.071, respectively. Shannon’s information index ranged from 0.659 to 1.088 with an average of 0.859. Allele richness varied from 2.500 to 5.152 with a mean of 3.858. Observed heterozygosity ranged from 0.425 to 0.619 with an average of 0.506, and the expected heterozygosity ranged from 0.399 to 0.546 with an average of 0.472. The negative value of inbreeding coefficient (F_IS=-0.069) indicated excess of heterozygotes (or deficiency of homozygotes) in the total population. Six of the eight populations significantly deviated from Hardy-Weinberg equilibrium due to heterozygote excess ordeficiency, supporting the evidence for a mixed reproductive system in populations, including both asexual and sexual reproduction, while the balance between asexual and sexual reproduction was population dependent. AMOVA attributed about 88.14% of the variance to individuals within populations, indicating that the main genetic variation existed within populations. A positive correlation (r=0.422, P=0.025) was detected between genetic and geographical distances of populations by Mantel test. UPGMA dendrogram indicated that all populations were separated into two genetically differentiated subgroups (F_ST =0.209-0.624), the first included two populations (GN and CT) located along the Pearl River was significantly distinct from the second made up of six populations located along the Yangtze River, which in agreement with STRUCTURE-based analysis. Extensive genetic admixture was observed in the Yangtze River populations, and high levels of gene exchange occurring within the subgroup (Nm = 2.525-8.447) were indicated by low population differentiation (F_ST=0.029-0.094). 【Conclusion】 R. solani AG1-IA with a wide distribution, a mixed reproductive mode, and long-distance dispersal via sclerotia or mycelium, these characteristics could account for the relatively high level of genetic diversity among populations in southern China. The migration of R. solani AG1-IA, to some extent, to prevent genetic divergence of pathogen populations to ensure that high levels of gene flow occured in populations located in the Yangtze River tributary region. Significant population subdivision was evident between the Yangtze River populations and the Pearl River populations, suggesting that restricted long-distance migration of R. solani AG1-IA was a plausible explanation for the spatial structures of genetic variation of pathogen populations.