scholarly journals Genetic Divergence and Diversity in Himalayan Puccinia striiformis Populations from Bhutan, Nepal, and Pakistan

2019 ◽  
Vol 109 (10) ◽  
pp. 1793-1800 ◽  
Author(s):  
Muhammad Rameez Khan ◽  
Zia-ur Rehman ◽  
Sidra Noreen Nazir ◽  
Sangay Tshewang ◽  
Suraj Baidya ◽  
...  
Keyword(s):  
Puccinia Striiformis ◽  
Gene Diversity ◽  
Genotypic Diversity ◽  
Himalayan Region ◽  
Population Subdivision ◽  
Aerial Dispersal ◽  
Western Himalayan Region ◽  
Nonsignificant Difference ◽  
Limited Gene Flow ◽  
High Level

The western Himalayan region in Pakistan has been shown to be the center of diversity of Puccinia striiformis; however, little is known about its genetic relations with the eastern part of the Himalayas. We studied the genetic structure of P. striiformis from Nepal (35 isolates) and Bhutan (31 isolates) in comparison with 81 Pakistani samples collected during 2015 and 2016, through microsatellite genotyping. Genetic analyses revealed a recombinant and highly diverse population structure in Pakistan, Bhutan, and Nepal. A high level of genotypic diversity (>0.90) was observed for the three countries of Pakistan (0.96), Bhutan (0.96), and Nepal (0.91) with the detection of 108 distinct multilocus genotypes (MLGs) in the overall population; 59 for Pakistan, 27 for Bhutan, and 26 for Nepal. Mean number of alleles per locus and gene diversity were higher in Nepal (3.19 and 0.458, respectively) than Bhutan (3.12 and 0.458, respectively). A nonsignificant difference between the observed and the expected heterozygosity in all populations further confirmed the recombinant structure. A clear population subdivision between the Himalayan region of Nepal, Bhutan, and Pakistan was evident, as revealed by FST values (ranging between 0.111 to 0.198), discriminant analysis of principal components, and resampling of MLGs. Limited gene flow could be present between Nepal and Bhutan, while the population from Pakistan was clearly distinct, and no divergence was present between two populations from Pakistan (Bajaur and Malakand). The overall high diversity and recombination signature suggested the potential role of recombination in the eastern Himalayan region (Nepal and Bhutan), which needs to be considered during host resistance deployment and in the context of aerial dispersal of the pathogen. Further surveillance should be made in the Himalayan region for disease management in the region and in the context of worldwide invasions. [Formula: see text] Copyright © 2019 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .

scholarly journals Population Structure Among and Within Iowa, Missouri, Ohio, and South Dakota Populations of Phytophthora sojae

Plant Disease ◽  
2016 ◽  
Vol 100 (2) ◽  
pp. 367-379 ◽  
Author(s):  
S. Stewart ◽  
A. E. Robertson ◽  
D. Wickramasinghe ◽  
M. A. Draper ◽  
A. Michel ◽  
...  
Keyword(s):  
Gene Flow ◽  
South Dakota ◽  
Genotypic Diversity ◽  
Phytophthora Sojae ◽  
Field Variation ◽  
Limited Gene Flow ◽  
Rps Gene ◽  
Pathogen Populations ◽  
High Level ◽  
Important Disease

Phytophthora root and stem rot, caused by Phytophthora sojae, is an economically important disease of soybean throughout the Midwestern United States. This disease has been successfully managed with resistance (Rps) genes; however, pathogen populations throughout the Midwest have developed virulence to many Rps genes, including those that have not been deployed. To gain a better understanding of the processes that influence P. sojae evolution, the population genetic structure was compared among populations using one isolate collected from 17, 33, and 20 fields in Iowa, Ohio, and South Dakota, respectively, as well as multiple isolates from individual fields in Iowa, Ohio, and Missouri. Genotypic diversity was measured using 21 polymorphic microsatellite (simple-sequence repeat) markers. and pathotype diversity using 15 soybean differentials. For all but three of the populations with low sample size, there was a high level of pathotype diversity and a low to moderate level of genotypic diversity among the populations for both comparisons between states and within-field variation. None of the Rps-gene differentials were resistant to all of the isolates. There were 103 unique multilocus genotypes identified in this study and only 2 were identified from the same field. Although no clones were identified in more than one field, pairwise FST indicated that some gene flow within neighboring fields does occur but not across the region, including fields from neighboring states. These results suggest that there is a strong probability that each state may have their own or several regional populations, as well as provide further evidence of high diversity within this homothallic pathogen which may be due, in part, to limited gene flow, mutation, or outcrossing, and this likely affects the success of deployment of resistance.

scholarly journals Population Structure of Rhizoctonia oryzae-sativae in California Rice Fields

2010 ◽  
Vol 100 (5) ◽  
pp. 502-510 ◽  
Author(s):  
Patcharavipa Chaijuckam ◽  
Jong-Min Baek ◽  
Christopher A. Greer ◽  
Robert K. Webster ◽  
R. Michael Davis
Keyword(s):  
Population Structure ◽  
Gene Flow ◽  
Genotypic Diversity ◽  
Fixation Index ◽  
Population Subdivision ◽  
Microsatellite Primers ◽  
Rhizoctonia Oryzae ◽  
Sexual Recombination ◽  
Hierarchical Levels ◽  
High Level

Six pairs of single-locus microsatellite primers were developed to study the population structure of Rhizoctonia oryzae-sativae, the cause of aggregate sheath spot disease of rice, among and within three rice-growing areas in California over a 3-year period. A high level of gene flow among growing areas was indicated by low population subdivision according to analysis of molecular variance and moderate to no population differentiation between pairs of populations based on the fixation index (FST). Gametic equilibrium of most pairs of microsatellite loci, high numbers of unique multilocus genotypes, and high genotypic diversity indicated extensive sexual recombination within growing areas. Because there was little differentiation among populations in all hierarchical levels, including among growing areas within sampling years, fields within growing areas, and corners within individual fields, a high level of gene flow was revealed in all levels. Basidiospores were likely the main vehicle of gene flow among populations, including short and long distances. Asexual inocula (sclerotia and mycelia) probably overwinter because a few clones were detected over a 2-year period within the same field. A few clones were shared among fields but were not commonly shared among growing areas.

Population structure of Sclerotinia sclerotiorum in an Australian canola field at flowering and stem-infection stages of the disease cycle

Genome ◽  
2006 ◽  
Vol 49 (11) ◽  
pp. 1408-1415 ◽  
Author(s):  
Adrienne C. Sexton ◽  
Athol R. Whitten ◽  
Barbara J. Howlett
Keyword(s):  
Sclerotinia Sclerotiorum ◽  
Gene Diversity ◽  
Genotypic Diversity ◽  
Population Subdivision ◽  
Analysis Of Molecular Variance ◽  
Molecular Variance ◽  
Stem Infection ◽  
Fixation Indices ◽  
Stem Lesions ◽  
Genotypic Disequilibrium

Populations of the ascomycete pathogen Sclerotinia sclerotiorum sampled from a canola field were analysed using microsatellite markers. Fifty isolates were collected from ascospore-infested canola petals and, later in the season, another 55 isolates were obtained from stem lesions; these isolates were used to compare inoculum and disease-causing populations. Fifty-five unique haplotypes were identified, with gene diversity ranging from 0.40 to 0.71. Genotypic diversity was higher in the inoculum population than it had been in the previous year, but analysis of molecular variance (AMOVA) showed that less than 10% of the variation was attributable to differences between the 2 years. Genotypic disequilibrium measures were consistent with the occurrence of both clonal reproduction and out-crossing. There was no significant population subdivision between the ascospore and stem-lesion populations, as measured with fixation indices (RST = 0.015, p = 0.90) and AMOVA, suggesting that there are no genetically defined subgroups of isolates more likely to proceed from petal colonization to cause stem infection. This might be because S. sclerotiorum possesses wide-ranging pathogenicity mechanisms that account for the lack of host specificity observed to date.

Molecular Characterization and Genetic Diversity Study in F3 Population of Rice

2013 ◽  
Vol 20 (1-2) ◽  
pp. 1-8
Author(s):  
MM Rahman ◽  
L Rahman ◽  
SN Begum ◽  
F Nur
Keyword(s):  
Genetic Distance ◽  
Gene Diversity ◽  
Random Amplified Polymorphic Dna ◽  
Molecular Genetic ◽  
Molecular Genetic Analysis ◽  
Polymorphic Loci ◽  
Rice Genotypes ◽  
High Level ◽  
Genetic Diversity Study ◽  
Diversity Study

Random Amplified Polymorphic DNA (RAPD) assay was initiated for molecular genetic analysis among 13 F3 rice lines and their parents. Four out of 15 decamer random primers were used to amplify genomic DNA and the primers yielded a total of 41 RAPD markers of which 37 were considered as polymorphic with a mean of 9.25 bands per primer. The percentage of polymorphic loci was 90.24. The highest percentage of polymorphic loci (14.63) and gene diversity (0.0714) was observed in 05-6 F3 line and the lowest polymorphic loci (0.00) and gene diversity (0.00) was found in 05-12 and 05-15 F3 lines. So, relatively high level of genetic variation was found in 05-6 F3 line and it was genetically more diverse compared to others. The average co-efficient of gene differentiation (GST) and gene flow (Nm) values across all the loci were 0.8689 and 0.0755, respectively. The UPGMA dendrogram based on the Nei’s genetic distance differentiated the rice genotypes into two main clusters: PNR-519, 05-19, 05-14, 05-12 and 05-17 grouped in cluster 1. On the other hand, Baradhan, 05-9, 05-13, 05-11, 05-5, 05-6, 05-1, 05-4, 05-15 and 05-25 were grouped in cluster 2. The highest genetic distance (0.586) was found between 05-4 and 05-17 F3 lines and they remain in different cluster.DOI: http://dx.doi.org/10.3329/pa.v20i1-2.16839 Progress. Agric. 20(1 & 2): 1 – 8, 2009

A case study of a thermally ducted undular mesospheric bore accompanied by ripples over the western Himalayan region

2021 ◽  
Author(s):  
S. Mondal ◽  
M. Sivakandan ◽  
S. Sarkhel ◽  
M.V. Sunil Krishna ◽  
Martin G. Mlynczak ◽  
...  
Keyword(s):  
Himalayan Region ◽  
Western Himalayan Region

Molecular Characterization of Morchella Species from the Western Himalayan Region of India

2010 ◽  
Vol 62 (4) ◽  
pp. 1245-1252 ◽  
Author(s):  
Harpreet Kaur Kanwal ◽  
Karan Acharya ◽  
G. Ramesh ◽  
M. Sudhakara Reddy
Keyword(s):  
Molecular Characterization ◽  
Himalayan Region ◽  
Western Himalayan Region

scholarly journals Population Genetic Analysis Corroborates Dispersal of Fusarium oxysporum f. sp. radicis-lycopersici from Florida to Europe

1999 ◽  
Vol 89 (8) ◽  
pp. 623-630 ◽  
Author(s):  
U. Liane Rosewich ◽  
R. E. Pettway ◽  
Talma Katan ◽  
H. C. Kistler
Keyword(s):  
Fusarium Oxysporum ◽  
Gene Diversity ◽  
Population Subdivision ◽  
Founder Population ◽  
Palm Beach County ◽  
Population Genetic Analysis ◽  
Low Frequencies ◽  
The United Kingdom ◽  
Crown And Root Rot ◽  
Southern Florida

Fusarium oxysporum isolates from tomato plants displaying crown and root rot symptoms were collected in central and southern Florida and analyzed using vegetative compatibility grouping (VCG) and nuclear restriction fragment length polymorphism (RFLP) data. VCG 0094 of F. oxysporum f. sp. radicis-lycopersici, previously known only from northwestern Europe, was predominant among 387 isolates assessed. In addition, two newly described VCGs (0098 and 0099) were detected at low frequencies. Floridian VCG 0094 isolates displayed a continuum of compatibilities, which is in contrast to the three distinct subgroups previously identified among European VCG 0094 isolates. RFLP haplotypes were constructed using one repetitive and three low-copy probes. Population subdivision of VCG 0094 from various Floridian counties and from northwestern Europe (Belgium, the Netherlands, and the United Kingdom) was evaluated by analysis of molecular variance. A “natural” population structure was revealed, differentiating populations from the east and west coasts of Florida. In addition, isolates from Europe were statistically indistinguishable from the Palm Beach County, FL, population. Furthermore, gene diversity among Palm Beach County VCG 0094 isolates was more than five times greater than among European isolates. Results from both VCG and RFLP analyses strongly support the inference that the European VCG 0094 constitutes a founder population that resulted from intercontinental migration of a few isolates from Palm Beach County, FL.

scholarly journals Performance of CMIP3 and CMIP5 GCMs to Simulate Observed Rainfall Characteristics over the Western Himalayan Region

2017 ◽  
Vol 30 (19) ◽  
pp. 7777-7799 ◽  
Author(s):  
Jitendra Kumar Meher ◽  
Lalu Das ◽  
Javed Akhter ◽  
Rasmus E. Benestad ◽  
Abdelkader Mezghani
Keyword(s):  
Interannual Variability ◽  
Annual Cycle ◽  
Climate Models ◽  
Global Climate ◽  
India Meteorological Department ◽  
Rain Gauge ◽  
Global Climate Models ◽  
Himalayan Region ◽  
Western Himalayan Region ◽  
Cmip5 Gcms

Abstract The western Himalayan region (WHR) was subject to a significant negative trend in the annual and monsoon rainfall during 1902–2005. Annual and seasonal rainfall change over the WHR of India was estimated using 22 rain gauge station rainfall data from the India Meteorological Department. The performance of 13 global climate models (GCMs) from phase 3 of the Coupled Model Intercomparison Project (CMIP3) and 42 GCMs from CMIP5 was evaluated through multiple analysis: the evaluation of the mean annual cycle, annual cycles of interannual variability, spatial patterns, trends, and signal-to-noise ratio. In general, CMIP5 GCMs were more skillful in terms of simulating the annual cycle of interannual variability compared to CMIP3 GCMs. The CMIP3 GCMs failed to reproduce the observed trend, whereas approximately 50% of the CMIP5 GCMs reproduced the statistical distribution of short-term (30 yr) trend estimates than for the longer-term (99 yr) trends from CMIP5 GCMs. GCMs from both CMIP3 and CMIP5 were able to simulate the spatial distribution of observed rainfall in premonsoon and winter months. Based on performance, each model of CMIP3 and CMIP5 was given an overall rank, which puts the high-resolution version of the MIROC3.2 model [MIROC3.2 (hires)] and MIROC5 at the top in CMIP3 and CMIP5, respectively. Robustness of the ranking was judged through a sensitivity analysis, which indicated that ranks were independent during the process of adding or removing any individual method. It also revealed that trend analysis was not a robust method of judging performances of the models as compared to other methods.

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