苹果黑星病菌遗传多样性的SSR分析

 Apple scab caused by Venturia inaequalis has a tendency to spread and threatens the development of apple production in recent years in China. The genetic diversity and population structure were investigated by using simple sequence repeat (SSR) markers. 51 strains were classified into 3 groups by UPGMA method as Xunyi, Xingping and U. K. population, each of them mainly including strains from its original place. A relatively high level of genetic diversity was revealed:H=0.425 3, I=0.675 8, PPL=66.67% (at species level); H=0.149 1, I=0.228 0, PPL=44.44% (at population level). A high level of genetic differentia-tion was detected among/within populations with Nei's Gst analysis and AMOVA. Molecular genetic variance within populations was greater than that among populations. Genetic variance among populations might result from barriers to gene flow (Nm=0.675 8). Genetic variance within populations might result from sexual propagation of V. inaequalis.     

Population genetic structure of four regional populations of the barley pathogen Pyrenophora teres f. maculata in Iran is characterized by high genetic diversity and sexual recombination

The leaf spot form of the barley disease net blotch, caused by the fungus Pyrenophora teres f. maculata (PTM), is an increasingly important foliar disease of barley. Studies of population genetic structure and reproductive mode are necessary to make predictions of the evolutionary potential of the pathogen. Sources of resistance to PTM have been found in Iranian landraces, which may have the potential to improve plant breeding efforts. However, little is known about the population genetic structure of this fungus in Iran. In this study, we analysed the frequency of the mating type genes to assess the potential for sexual mating of PTM collected from four provinces—Khuzestan, Hamadan, Golestan, and East Azerbaijan—and we investigated the population genetic structure using seven simple sequence repeat markers. High genotype diversity, linkage equilibrium, and equal ratios of mating types frequencies in the PTM populations at Khuzestan and Hamadan support the occurrence of sexual reproduction in these populations, while in Golestan and East Azerbaijan populations, significant gametic disequilibrium and relatively low genotype diversity suggest a higher incidence of clonality or different demographic histories. Unequal mating type frequencies in Golestan confirm a predominance of asexual reproduction. Finally, we found significant evidence for strong population structure with most of the genetic variation represented within regional populations (89%). Overall, our study provides evidence for high genetic variation in Iranian PTM populations, which may be the basis for rapid adaptive evolution in this pathosystem. This highlights the need for integrated efforts to control the disease.     

Population structure,genetic diversity,and sexual state of the rice brown spot pathogen Bipolaris oryzae from three Asian countries

Bipolaris oryzae causes brown spot in rice (Oryza sativa) inflicting substantial grain yield losses worldwide. Knowledge of the population structure, genetic diversity and sexual recombination of the fungal pathogen can help to implement effective disease management strategies. In this study, B. oryzae isolates sampled from Iran, the Philippines and Japan were analysed with 12 simple‐sequence repeat (SSR) markers, newly developed from the genome sequence of the fungus. Among the 288 B. oryzae isolates genotyped, 278 unique haplotypes were identified. High genotype numbers (richness) with even distribution (evenness) were found within the collection sites. Both mating types, MAT1‐1 and MAT1‐2, were present in each collection area, and the sexual state was induced under controlled conditions with production of viable ascospores. However, the tests of linkage disequilibrium rejected of the hypothesis of random mating. Discriminant analysis of principal components (DAPC) revealed that the B. oryzae collection formed three clusters, each consisting of isolates from different collection sites. Analysis of molecular variance (amova ) showed that genetic variation among clusters was 18.7%, with the rest of the variation distributed within clusters (R_ST = 0.187, P < 0.001). Statistically significant pairwise genetic differentiation was found between the clusters. These results show that Asian B. oryzae isolates are genetically diverse, and, overall, distributed in three groups. These findings will be helpful in managing the disease and guide the use of representative isolates needed for selection of resistant rice varieties.     

油茶暹罗刺盘孢菌群体遗传结构分析

暹罗刺盘孢菌是油茶炭疽病病原之一,在我国多个油茶产区均有分布。研究油茶暹罗刺盘孢菌群体遗传结构可为全面、有效防治油茶炭疽病害提供理论依据。本研究对分离自海南、江西、湖南、广西4省(自治区)6个地区暹罗刺盘孢菌菌株的ITS、CAL和GAPDH 3个基因的序列进行群体遗传结构分析。根据拼接的上述3个基因的序列,57个暹罗刺盘孢菌菌株可定义为13个单倍型,其中单倍型H7为主要单倍型,分布于本研究所涉及的所有地区。病菌不同地理种群间的遗传分化较大,AMOVA分析显示,遗传变异主要发生在种群内,病菌未经历过大规模的种群扩张。研究结果表明油茶炭疽病原暹罗刺盘孢菌种群具有丰富的遗传多样性。     

北京市及河北省小麦赤霉病菌群体遗传结构及生物学特性

本文分析了北京市与河北省小麦赤霉病菌群体遗传结构以及基础生物学特性。结果表明所有菌株均为禾谷镰刀菌(Fusarium graminearum),属于一个大的单一群体,群体内具有较高的遗传多样性。毒素化学型测定表明,北京与河北地区小麦真菌毒素污染的主要风险为DON与15ADON毒素。表型测定显示,与F.asiaticum群体相比,F.graminearum具有较高的产孢能力,而生长速率和产毒能力较低。该群体对主要杀菌剂多菌灵、戊唑醇和氰烯菌酯均无抗药性。     

西藏小麦条锈菌群体结构与遗传多样性

为查明西藏小麦条锈菌Puccinia striiformis f. sp. tritici群体结构和遗传多样性,采用中国鉴别寄主和近等基因系鉴别寄主,以及竞争性等位基因特异性PCR-单核苷酸多态性（kompetitive al-lele specific PCR-single nucleotide polymorphism,KASP-SNP）分子标记对2017年采自西藏的150个小麦条锈菌菌系分别进行表型分析和基因型分析。表型分析结果显示,中国鉴别寄主将150个菌系区分为 12 个已知小种、6 个已知致病类型和 13 个未知致病类型,所有菌系均不能侵染中四和Triticum spelta album鉴别寄主。近等基因系鉴别寄主将150个菌系区分为88个毒性类型,这些毒性类型均不侵染携带抗性基因Yr5、Yr10或Yr15的品种。基因型分析结果显示,26对引物将150个菌系划分为73个基因型,表明西藏小麦条锈菌群体基因型丰富。基因流分析结果表明,波密县与洛扎县小麦条锈菌亚群体之间的基因流N_m最高,达5.86,米林县西部与波密县、洛扎县、巴宜县、米林县东部条锈菌亚群体之间的N_m较低,分别为0.25、0.34、0.42和0.67,表明西藏不同地区条锈菌群体之间基因交流强度差异较大。说明西藏作为我国小麦条锈病的独立流行区,条锈菌群体毒性结构复杂,遗传多样性高。     

福建省马铃薯黑胫病病原菌的鉴定及其遗传多样性分析

为明确福建省马铃薯黑胫病病原菌的种类、分布情况及群体遗传特性,通过16S rDNA序列分析法对分离自福建省各马铃薯产区的90株黑胫病病原菌进行鉴定,并利用细菌基因组重复序列PCR(repetitive sequence-PCR,Rep-PCR)方法分析福建省不同地区的马铃薯黑胫病病原菌群体的遗传变异情况。结果表明,经16S rDNA序列分析鉴定,引起福建省马铃薯黑胫病的病原菌包括黑腐果胶杆菌Pectobacterium atrosepticum、胡萝卜果胶杆菌巴西亚种P. carotovorum subsp. brasiliense、胡萝卜果胶杆菌胡萝卜亚种P. carotovorum subsp. carotovorum、帕曼蒂氏果胶杆菌P. parmentieri、P. polaris和达旦提狄基氏菌Dickeya dadantii。对90株菌株的Rep-PCR检测得到47多态性条带条,多态性比率为100.00%。按采集地区将菌株划分为8个群体,其等位基因数平均为1.48,有效等位基数平均为1.30,Nei’s基因多样性指数平均为0.17,Shannon信息指数平均为0.26,多态...     

山西玉米丝黑穗病菌SSR遗传多样性与群体结构分析

为明确山西省玉米丝黑穗病菌群体的遗传结构,为该病害的综合防控提供理论依据.采用SSR标记方法对山西省不同地区玉米丝黑穗病菌进行检测.结果显示,12个SSR分子标记在118株玉米丝黑穗病菌中共检测出30个等位基因,平均等位基因数(Na)、有效等位基因数(Ne)、Shannon's信息指数(I)、等位基因丰度(Ar)分别为...     

Genetic diversity and population structure analysis of isolates of the rice false smut pathogen Ustilaginoidea virens in India

Genetic diversity assessment and population structure analysis are essential for characterization of pathogens and their isolates. Markers are essential tools for exploring genetic variation among the isolates. False smut of rice caused by Ustilaginoidea virens, formerly Villosiclava virens, is a major emerging disease of rice in India. A high level of variability is observed at the field level, but no information is available from India on genetic diversity and population structure. This is the first report of genetic diversity and population structure of U. virens from India that included 63 isolates distributed across the vast geographical area of eastern and north-eastern India (18.9 to 26.7°N and 82.6 to 94.2°E). Seventeen RAPDs and 14 SSRs were identified as polymorphic and a total of 140 alleles were detected across the populations. The average number of alleles per locus for each primer was 4.5. All the isolates were grouped into two major clusters, with partial geographical segregation that was supported by principal coordinate analysis. Mantel test suggested genetic distance within the isolates increased with increasing geographical distance. Analysis of molecular variation showed more genetic variation within populations and less among populations. This outcome will help in understanding genetic diversity of U. virens from eastern and north-eastern India and in planning effective management strategies.     

Genetic diversity of Phytophthora pluvialis,a pathogen of conifers,in New Zealand and the west coast of the United States of America

Phytophthora pluvialis is the causal agent of red needle cast on Pinus radiata in New Zealand. It was first isolated in 2008 but had previously been recovered from tanoak (Notholithocarpus densiflorus) and Douglas‐fir (Pseudotsuga menziesii) trees in Oregon, USA in 2002. Phytophthora pluvialis was subsequently described as a new species in 2013 and classified as a clade III Phytophthora species. The aim of this study was to gain a better understanding of the genetic diversity, population structure and origin of this pathogen. A total of 360 P. pluvialis isolates were collected from the USA and New Zealand. The genome sequences of two P. pluvialis isolates were used to identify 27 single nucleotide polymorphism (SNP) markers that were then used to genotype the two populations. The genotypic data showed that the USA population of P. pluvialis had twice the genetic diversity and a greater number of multilocus genotypes (MLGs) compared to the New Zealand population, with 126 and 24 MLGs, respectively. The majority of the subpopulations within the USA and New Zealand showed linkage disequilibrium. All subpopulations had a negative fixation index, indicating that clonal reproduction is prevalent in both countries. A minimum spanning network (MSN) showed two unique clusters of isolates in the New Zealand population, suggesting two potential introductions of P. pluvialis into New Zealand from the USA. There was no significant structure within the New Zealand or USA populations. This study provides novel insight into the genetic structure of P. pluvialis in New Zealand and the USA.     

不同栽培模式下葡萄霜霉病菌遗传结构的时间动态分析

为明确不同栽培模式下葡萄霜霉病菌Plasmopara viticola的遗传结构、遗传多样性及遗传分化水平,于2014-2015年定期采集露地和避雨2种栽培模式下的葡萄霜霉病菌菌株,利用6对SSR引物对该病菌基因型、遗传多样性及遗传分化进行对比分析。结果表明,露地和避雨栽培模式下葡萄霜霉病菌群体的Nei’s基因多样性指数大于0.14,香农多样性指数大于0.31,2种栽培模式下群体具有丰富的遗传多样性,但避雨栽培模式可显著降低群体等位基因数和等位基因频率。露地栽培模式下该病菌群体的流行模式呈现中等水平无性繁殖,2年初侵染和再侵染对病害流行的贡献率分别约占26.1%和73.9%;避雨栽培模式下葡萄霜霉病菌群体的流行模式则呈现高等水平无性繁殖,初侵染和再侵染对病害流行的贡献率分别约占4.3%和95.7%。卵孢子的形成对于葡萄霜霉病菌种群遗传变异和有效越冬起着关键的作用。2014-2015年露地栽培模式下葡萄霜霉病菌群体的主效流行基因型对病害流行的贡献率分别为44.5%和51.8%;而其在避雨栽培模式下葡萄霜霉病菌群体的贡献率分别可达84.2%和87.1%。同一年份的露地和避雨栽培模式下葡萄霜霉病菌群体的主效基因型种类相同,2个群体间的等位基因频率呈现显著正相关性,且二者之间存在频繁的基因交流,推测避雨栽培模式下葡萄霜霉病的初侵染源自于避雨设施附近的露地栽培病株上再侵染形成的飞散传播孢子囊。     

玉米抗南方锈病种质标记基因型鉴定与遗传多样性分析

为阐明玉米抗南方锈病种质的标记基因型和遗传背景,利用7个与玉米抗南方锈病3个基因连锁的SSR标记鉴定了38份抗病玉米种质的标记基因型,并采用40个多态性SSR标记对39份抗南方锈病的玉米自交系和6个标准测验种进行了遗传多样性研究。结果表明,7个与抗病基因连锁的SSR标记将38份抗病种质鉴定为17种标记基因型,表明可能存在多样的抗性基因组合方式;辽2204等9份种质仅扩增出齐319的标记基因型,沈136和W456仅扩增出W2D的标记基因型;种质LO932未扩增出与齐319、P25和W2D相同的标记,可能携带新的抗南方锈病基因;相近遗传背景的抗性种质分属不同的标记基因型,表明抗病种质可能携带的抗南方锈病基因在育种选择中发生了分离。40对多态性SSR引物在45份自交系中共检测出115个等位基因变异,平均每对引物检测到2.88个等位基因,变异范围为2~4;平均多态性信息含量为0.4649,变化范围为0.1258~0.6951;通过UPGMA聚类分析,39份抗病材料被划分到以标准测验种为代表的6个杂种优势亚群中,与系谱分析基本一致,这为在育种中合理利用抗源提供了信息。     

陕西省小麦条锈菌群体遗传结构分析

 利用TP-M13-SSR自动荧光检测技术,对陕西省小麦条锈菌群体遗传结构进行了分析。研究结果显示,在物种水平上,陕西省小麦条锈菌群体Nei’s基因多样性指数（H）为0.18、Shannon 信息指数（I）为0.29,表明该省条锈菌群体遗传多样性较为丰富。同时,条锈菌群体遗传多样性在地区之间也存在明显的差异,在7个条锈菌群体中,宁强种群遗传多样性相对较高（H为0.18,I为0.28）。AMOVA分析显示,陕西省小麦条锈菌在地区间、种群间和群体内的遗传分化分别为：12.26%、10.88%和76.86%,表明陕西省小麦条锈菌群体存在一定的遗传分化,但遗传变异主要发生在群体内部。     

甘肃中部及周边地区小麦条锈菌种群的遗传结构分析

为明确甘肃中部与周边地区小麦条锈菌种群的遗传结构及关系,利用SSR分子标记技术对采自甘肃、陕南、青海及新疆等7个地区共369份小麦条锈病菌标样的群体遗传结构进行了分析。结果表明,小麦条锈菌群体Nei’s基因多样性指数为0.39、Shannon信息指数为0.57,各地区条锈菌群体遗传多样性较为丰富,且在不同地区之间存在明显差异,7个条锈菌群体中以天水种群的遗传多样性相对较高,其Nei’s基因多样性指数为0.42、Shannon信息指数为0.61。该地区小麦条锈菌群体间和群体内都存在着一定的遗传分化,群体间遗传变异占总变异的2.24%,群体内遗传变异占总变异的97.76%。表明甘肃中部及周边地区小麦条锈菌群体存在一定的遗传分化,但遗传变异主要发生在群体内部;甘肃中部、陇南及陕南3地的小麦条锈菌种群遗传相似度较高,菌源交流密切。     

Low genetic diversity and strong geographic structure in introduced populations of the Eucalyptus foliar pathogen Teratosphaeria destructans

The aggressive Eucalyptus leaf pathogen, Teratosphaeria destructans, causes widespread damage in tropical and subtropical Eucalyptus-growing regions of Indonesia, China, Thailand, East Timor, Vietnam, Lao, and South Africa. Little is known regarding the origin, pathways of dispersal, or reproductive biology of this pathogen. The aim of this study was to investigate the genetic structure of a global collection of T. destructans isolates. This was achieved by developing and using polymorphic microsatellite markers. Low genotypic diversity and a limited number of private alleles were found in all investigated populations, with the highest maximum diversity of 10.7% in isolates from South Sumatra. This supports the hypothesis that T. destructans was introduced to these regions. High levels of clonality were common in all populations, especially in isolates sampled from the recent disease outbreak in South Africa, which were all identical. The global collection of isolates grouped into three distinct clusters, corresponding largely to their sampled regions. Low levels of genotypic diversity, high levels of clonality, and strong geographic structure suggest independent introductions into all the sampled areas from an unknown source. The results imply that strict biosecurity measures are needed to avoid introductions of additional genotypes in these areas.     

基于CP基因的中国云南省烟草TMV群体遗传多样性分析

为探明云南烟草上烟草花叶病毒(tobacco mosaic virus, TMV)的群体遗传多样性特征, 本研究使用TMV外壳蛋白(coat protein, CP)基因的特异性引物对采自云南各烟区的疑似烟草花叶病样品进行检测, 通过克隆测序获得138个TMV CP基因序列, 对其进行了一致性比对, 及系统发育、错配分布、遗传变异、群体多样性等分析。变异分析显示, 138条CP基因序列共有变异位点数122个, 占总位点数的25.42%, 变异类型只有核苷酸替换, 核酸多样性为0.018, 单倍型多样性为0.970;一致性比对结果显示, 138条序列的核苷酸和氨基酸序列一致性均为96%～100%; 重组分析未检测到重组信号;对来自云南烟草, NCBI上其他地区烟草及云南地区其他寄主的TMV分离物的CP基因进行系统发育分析, 结果显示, 所有TMV分离物在进化上可分为4个组, 本试验获得的分离物分布在1、2、3组, 其中只有来源昭通地区的分离物倾向于聚成簇, 表明云南烟草TMV分离物的适应性进化受地理适应性所驱动, 与寄主适应性基本无关;错配分布分析显示, 云南烟草TMV群体呈多峰分布, 表明该群体近期未经历群体扩张事件; 群体间遗传分化分析结果表明, 除昭通和曲靖烟草TMV群体与其他TMV群体之间很容易发生遗传漂变促使群体发生遗传分化外, 其余大部分TMV群体之间的基因流都可以抵制遗传漂变。本研究首次报道了云南各烟区TMV分离物群体遗传变异情况, 研究结果可为TMV的抗病育种和制定更为有效的防治策略提供重要参考。     

Genetic variation,vegetative compatibility,and aggressiveness diversity of Diplodia bulgarica isolates from apple orchards in West Azarbaijan province of Iran

This study investigated inter-simple sequence repeat (ISSR), vegetative compatibility, and aggressiveness diversity in 101 isolates of Diplodia bulgarica recovered from apple trees displaying symptoms of canker and decline in West Azarbaijan province of Iran. Marker analyses revealed high within population diversity, low genetic differentiation, high gene flow, and sharing of multilocus genotypes (MLGs) among geographic populations. Moreover, clustering and multivariate analyses identified two highly differentiated genetic clusters with limited admixture between them. These findings may suggest that the pathogen has been introduced from two genetically divergent sources and has been moved within the region through infected materials. The large number of MLGs, low clonal fraction, and absence of a widely distributed dominant genotype may explain the occurrence of recombination in this pathogen. However, significant linkage disequilibrium in the populations and limited admixture between genetic clusters may indicate the rare occurrence of recombination in D. bulgarica populations in West Azarbaijan, and that the pathogen has not been in the province long enough to reach equilibrium. Vegetative compatibility analyses revealed the occurrence of anastomosis between nonself pairings and high vegetative compatibility group diversity within populations. All studied MLGs produced necrotic lesions on detached shoots of Red Delicious apple but differed in their aggressiveness levels. Our results provide new insights into genetic and phenotypic variation of D. bulgarica that can assist in developing management strategies. Our findings also highlight the vital need for quarantine measures and the production of healthy plant materials to prevent the introduction and spread of the pathogen in Iran.     

Genetic Variability and Population Structure of the Wheat Foot Rot Fungus, Fusarium culmorum, in Tunisia

The random amplified polymorphic DNA (RAPD) method was used to investigate the genetic variability and population structure of Fusarium culmorum isolated from wheat stem bases. A total of 108 isolates, representing seven geographically distinct populations, was collected from five climatic regions in Tunisia. Pseudo-allelic frequencies were estimated at each of the 25 putative RAPD loci analyzed by scoring for the presence or absence of amplified fragments; 92 haplotypes were found among the 108 strains. The analysis of the population structure did not reveal any trend with regard to geographic origin. Total gene diversity (H_T ^* = 0.318) was mostly attributable to diversity within populations (H_S ^* = 0.308). Analysis of molecular variance confirmed that most of the genetic variability was within populations. Genetic differentiation among populations was low to moderate (G_ST ^* ranged from 0 to 0.190 and averaged 0.041 over all loci). Cluster analysis with UPGMA using genetic distances did not reveal any spatial clustering of the isolates collected from the different geographic regions. Based on these results, we conclude that the F. culmorum isolates recovered from different regions in Tunisia might be part of a single population pool.