Kashyap Prem Lal, Kumar Sudheer, Kumar Ravi Shekhar, Tripathi Rahul, Sharma Palika, Sharma Anju, Jasrotia Poonam, Singh Gyanendra Pratap
ICAR - Indian Institute of Wheat and Barley Research, Karnal, India.
Front Microbiol. 2020 Jan 15;10:2929. doi: 10.3389/fmicb.2019.02929. eCollection 2019.
Barley covered smut (CS) pathogen genome was mined for microsatellite distribution and their application in defining population structure and genetic variation. To dissect the molecular variation and genetic structure of , 59 fungal isolates representing two distinct agro-ecological zones of India were analyzed by employing simple sequence repeats (SSRs). Using bioinformatic approaches, a total of 100,239 and 137,442 microsatellites were identified from 20.13 and 26.94 Mb of assembled genomic sequences of Uh364 and Uh4857-4 isolates of , respectively. Penta-nucleotides (31.29 and 29.75%) followed by tri-nucleotide (28.27 and 29.88%) were most prevalent in both the genomes. Out of them, 15 polymorphic microsatellites showing conservancies in both the genomes were selected for exploring population genetic structure of . An average of two alleles per microsatellite marker was generated with band size ranging from 180 to 850 bp. Polymorphic information content (PIC) varied between 0.095 and 0.37. Fifty-nine isolates were distributed in two distinct groups with about 65% genetic similarity according to UPGMA clustering and population structure analysis ( = 2). Gene flow analysis (Nm = 1.009) reflected moderate gene flow among the analyzed population. An analysis of molecular variance (AMOVA) displayed high level of genetic variation within population (87%) and low variation among populations (13%). Linkage disequilibrium (LD) analysis indicated positively significant but relatively low standardized index of association (SIA) value in both the population sets (SIA = 0.181), advocating a state of LD with epidemic population structure. In conclusion, the newly developed neutral SSR markers are highly polymorphic within and will be useful for revealing evolutionary history and providing deep insight into the population dynamics of in India as well as facilitating developing management strategies for CS of barley.
对大麦坚黑穗病菌（CS）病原体基因组进行微卫星分布挖掘及其在定义群体结构和遗传变异中的应用研究。为剖析该病菌的分子变异和遗传结构，采用简单序列重复（SSR）对代表印度两个不同农业生态区的59个真菌分离株进行了分析。利用生物信息学方法，分别从病菌Uh364和Uh4857 - 4分离株组装的20.13 Mb和26.94 Mb基因组序列中鉴定出总共分别为100239个和137442个微卫星。五核苷酸（分别为31.29%和29.75%）之后是三核苷酸（分别为28.27%和29.88%）在两个基因组中最为普遍。其中，选择了15个在两个基因组中均显示保守性的多态性微卫星来探究该病菌的群体遗传结构。每个微卫星标记平均产生两个等位基因，条带大小范围为180至850 bp。多态信息含量（PIC）在0.095至0.37之间变化。根据UPGMA聚类和群体结构分析（K = 2），59个分离株分为两个不同的组，遗传相似性约为65%。基因流分析（Nm = 1.009）反映了分析群体间的中等基因流。分子方差分析（AMOVA）显示群体内高水平的遗传变异（87%）和群体间低水平的变异（13%）。连锁不平衡（LD）分析表明，在两个群体中标准化关联指数（SIA）值均呈正显著但相对较低（SIA = 0.181），表明处于具有流行群体结构的LD状态。总之，新开发的中性SSR标记在该病菌内具有高度多态性，将有助于揭示其进化历史，深入了解印度该病菌的群体动态，并促进制定大麦坚黑穗病的管理策略。
