Understanding pathogen population structure and virulence variation for efficient resistance breeding to control cucurbit powdery mildews

2021 ◽  
Author(s):  
A. Lebeda ◽  
B. Sedláková ◽  
E. Křístková ◽  
M.P. Widrlechner ◽  
E. Kosman
Keyword(s):  
Population Structure ◽  
Resistance Breeding ◽  
Pathogen Population ◽  
Powdery Mildews ◽  
Virulence Variation

Genetic diversity and population structure of the rice false smut pathogen Ustilaginoidea virens in Sichuan-Chongqing region

Plant Disease ◽  
2021 ◽  
Author(s):  
Anfei Fang ◽  
Zhuangyuan Fu ◽  
Zexiong Wang ◽  
Yuhang Fu ◽  
Yubao Qin ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
Genetic Recombination ◽  
Resistance Breeding ◽  
Ustilaginoidea Virens ◽  
Breeding Lines ◽  
Rice False Smut ◽  
Geographical Populations ◽  
False Smut

Rice false smut caused by Ustilaginoidea virens is currently one of the most devastating fungal diseases of rice panicles worldwide. In this study, two novel molecular markers derived from SNP-rich genomic DNA fragments and a previously reported molecular marker were used for analyzing the genetic diversity and population structure of 167 U. virens isolates collected from nine areas in Sichuan-Chongqing region, China. A total of 62 haplotypes were identified, and a few haplotypes with high frequency were found and distributed in two to three areas, suggesting gene flow among different geographical populations. All isolates were divided into six genetic groups. The groups Ⅰ and Ⅵ were the largest including 61 and 48 isolates, respectively. The pairwise FST values showed significant genetic differentiation among all compared geographical populations. AMOVA showed that intergroup genetic variation accounted for 40.17% of the total genetic variation, while 59.83% of genetic variation came from intragroup. The UPGMA dendrogram and population structure revealed that the genetic composition of isolates collected from ST (Santai), NC (Nanchong), YC (Yongchuan), and WS (Wansheng) dominated by the same genetic subgroup was different from those collected from other areas. In addition, genetic recombination was found in a few isolates. These findings will help to improve the strategies for rice false smut management and resistance breeding, such as evaluating breeding lines with different isolates or haplotypes at different elevations and landforms.

scholarly journals Mycelial Compatibility Grouping and Aggressiveness of Sclerotinia sclerotiorum

Plant Disease ◽  
2004 ◽  
Vol 88 (4) ◽  
pp. 325-332 ◽  
Author(s):  
L. S. Kull ◽  
W. L. Pedersen ◽  
D. Palmquist ◽  
G. L. Hartman
Keyword(s):  
Population Structure ◽  
Disease Management ◽  
Sclerotinia Sclerotiorum ◽  
Stem Rot ◽  
Management Systems ◽  
Sclerotinia Stem Rot ◽  
Pathogen Population ◽  
Causal Organism ◽  
Soybean Field ◽  
Mycelial Compatibility

Population variability of Sclerotinia sclerotiorum, the causal organism of Sclerotinia stem rot of soybean, was determined by mycelial compatibility grouping (MCG) and isolate aggressiveness comparisons. MCG and aggressiveness of S. sclerotiorum isolates from diverse hosts and geographic locations (Diverse Set, 24 isolates), from a soybean field in Argentina (Argentine Set, 21 isolates), and from soybean fields in DeKalb and Watseka, Illinois (DeKalb Set, 124 isolates, and Watseka Set, 130 isolates) were assessed. Among 299 isolates tested, 42 MCGs were identified, and 61% were represented by single isolates observed at single locations. Within the Diverse Set, 17 MCGs were identified; 1 MCG consisted of six isolates, and 16 MCGs consisted of one isolate each. Nine MCGs were identified within the Argentine field with two MCGs composed of either five or six isolates, two MCGs composed of two isolates, and the remaining composed of one isolate each. Each Illinois field was a mosaic of MCGs, but MCG frequencies differed between the two fields. Common MCGs were identified among the Diverse, DeKalb, and Watseka Sets, but no MCGs within the Argentine Set were observed with other sets. MCG 8 was the most frequently sampled and widely dispersed MCG and occurred at a frequency of 29, 36, and 62% in the Diverse, DeKalb, and Watseka Sets, respectively. Variation in isolate aggressiveness was assessed using a limited-term, plug inoculation technique. Isolate aggressiveness varied (P = 0.001) within the Diverse, Argentine, DeKalb, and Watseka Sets. Within widely dispersed MCGs, isolate aggressiveness varied (P ≤ 0.10); however, within locally observed MCGs detected only in single fields, isolate aggressiveness did not vary. Additionally, individual MCGs within the DeKalb and Watseka Sets differed in isolate aggressiveness. Using six soybean cultivars and six S. sclerotiorum isolates, no cultivar-isolate interaction was detected, but resistant and susceptible cultivars performed similarly when inoculated with either less or highly aggressive isolates. Pathogen population structure and variability in isolate aggressiveness may be important considerations in disease management systems.

Virulence variation of cucurbit powdery mildews in the Czech Republic – population approach

2018 ◽  
Vol 152 (2) ◽  
pp. 309-326 ◽  
Author(s):  
Aleš Lebeda ◽  
Eva Křístková ◽  
Božena Sedláková ◽  
James D. McCreight ◽  
Evsey Kosman
Keyword(s):  
Czech Republic ◽  
Population Approach ◽  
The Czech Republic ◽  
Powdery Mildews ◽  
Virulence Variation

Leptosphaeria maculans isolates reveal their allele frequency in western Canada

Plant Disease ◽  
2020 ◽  
Author(s):  
Fei Liu ◽  
Zhongwei Zou ◽  
Gary Peng ◽  
W. G. Dilantha Fernando
Keyword(s):  
Leptosphaeria Maculans ◽  
Resistance Breeding ◽  
Western Canada ◽  
R Genes ◽  
Pathogen Population ◽  
Pcr Assay ◽  
Differential Host ◽  
Resistant Varieties ◽  
Disease Resistance Breeding ◽  
Avr Genes

Blackleg, caused by Leptosphaeria maculans, is a major disease of canola in Canada, Australia, and Europe. For effective deployment of resistant varieties and disease management, it is crucial to understand the population structure of L. maculans. In this study, we analyze L. maculans isolates from commercial fields in western Canada from 2014 to 2016 for the presence and frequency of avirulence (Avr) genes. A total of 1, 584 isolates was examined for the presence of Avr genes AvrLm1, AvrLm2, AvrLm3, AvrLm4, AvrLm6, AvrLm7, AvrLm9, AvrLepR1, AvrLepR2, and AvrLmS using a set of differential host genotypes carrying known resistance genes and a PCR assay. Several Avr genes showed a higher frequency in the pathogen population, such as AvrLm6 and AvrLm7, which were present in >90% of isolates; while AvrLm3, AvrLm9 and AvrLepR2 showed frequencies of <10%. A total of 189 races (different combinations of Avr genes) were detected, with Avr-2-4-6-7-S, Avr-1-4-6-7 and Avr-2-4-6-7 as the three predominant races. When the effect of crop rotation was assessed, only a three-year rotation showed a significantly higher frequency of AvrLm2, relative to shorter rotations. This study provides the information for producers to select effective canola varieties for blackleg management, and for breeders to deploy new R genes in disease resistance breeding in the western Canada region.

scholarly journals Genomics-Enabled Novel Insight Into the Pathovar-Specific Population Structure of the Bacterial Leaf Streak Pathogen Xanthomonas translucens in Small Grain Cereals

2021 ◽  
Vol 12 ◽  
Author(s):  
Syed Mashab Ali Shah ◽  
Moein Khojasteh ◽  
Qi Wang ◽  
S. Mohsen Taghavi ◽  
Zhengyin Xu ◽  
...  
Keyword(s):  
Population Structure ◽  
Resistance Breeding ◽  
Effector Genes ◽  
C Terminus ◽  
Wide Range ◽  
Complete Genomes ◽  
Species Population ◽  
Xanthomonas Translucens ◽  
Disease Resistance Breeding ◽  
Insight Into

The Gram-negative bacterium Xanthomonas translucens infects a wide range of gramineous plants with a notable impact on small grain cereals. However, genomics-informed intra-species population structure and virulence repertories of the pathogen have rarely been investigated. In this study, the complete genome sequences of seven X. translucens strains representing an entire set of genetic diversity of two pathovars X. translucens pv. undulosa and X. translucens pv. translucens is provided and compared with those of seven publicly available complete genomes of the pathogen. Organization of the 25 type III secretion system genes in all the 14 X. translucens strains was exactly the same, while TAL effector genes localized singly or in clusters across four loci in X. translucens pv. translucens and five to six loci in X. translucens pv. undulosa. Beside two previously unreported endogenous plasmids in X. translucens pv. undulosa, and variations in repeat variable diresidue (RVD) of the 14 strains, tal1a of X. translucens pv. translucens strain XtKm8 encode the new RVDs HE and YI which have not previously been reported in xanthomonads. Further, a number of truncated tal genes were predicted among the 14 genomes lacking conserved BamHI site at N-terminus and SphI site at C-terminus. Our data have doubled the number of complete genomes of X. translucens clarifying the population structure and genomics of the pathogen to pave the way in the small grain cereals industry for disease resistance breeding in the 21st century’s agriculture.

scholarly journals The host brain is permissive to colonization by Toxoplasma gondii

2020 ◽  
Author(s):  
CJ. Wincott ◽  
G. Sritharan ◽  
M. Bunyan ◽  
E. Alves ◽  
HJ. Benns ◽  
...  
Keyword(s):  
Population Structure ◽  
Toxoplasma Gondii ◽  
Cell Types ◽  
Intervention Strategies ◽  
Evolutionary Strategy ◽  
Pathogen Population ◽  
Persister Cells ◽  
Host Blood ◽  
Cellular Barcoding ◽  
Host Brain

SummaryPathogenic infections and the diseases they cause are defined by invasion and colonization of distinct host cell types and tissue niches. In the case of viruses and bacteria, molecular and cellular barcoding has shaped our understanding of within-host pathogen population dynamics, and informed therapeutic intervention strategies. Host brain colonization is a clinically untreatable feature of persistent infection by the eukaryotic pathogen Toxoplasma gondii, and the process remains poorly understood. The host blood-brain barrier is expected to physically restrict parasite colonization of this tissue niche and force the infection through a selection bottleneck, however tools and technologies to test this hypothesis have not been available. Here, we have developed a simple CRISPR-based method to barcode Toxoplasma parasites, and then used complex libraries of barcoded parasites to define how the different phases of an infection shape the pathogen population structure. Unexpectedly, we have discovered that the murine host brain does not restrict parasite colonization, with the population structure predominantly shaped by a bottleneck experienced during the acute phase of infection. These data support an evolutionary strategy to maximize genetic diversity of parasite persister cells within the intermediate host brain for subsequent transmission into the definitive feline host.

scholarly journals Vaccination can drive an increase in frequencies of antibiotic resistance among nonvaccine serotypes of Streptococcus pneumoniae

2018 ◽  
Vol 115 (12) ◽  
pp. 3102-3107 ◽  
Author(s):  
Uri Obolski ◽  
José Lourenço ◽  
Craig Thompson ◽  
Robin Thompson ◽  
Andrea Gori ◽  
...  
Keyword(s):  
Public Health ◽  
Antibiotic Resistance ◽  
Population Structure ◽  
Streptococcus Pneumoniae ◽  
Bacterial Pathogen ◽  
Epidemiological Studies ◽  
Theoretical Framework ◽  
Health Concern ◽  
Public Health Concern ◽  
Pathogen Population

The bacterial pathogen Streptococcus pneumoniae is a major public health concern, being responsible for more than 1.5 million deaths annually through pneumonia, meningitis, and septicemia. Available vaccines target only a subset of serotypes, so vaccination is often accompanied by a rise in the frequency of nonvaccine serotypes. Epidemiological studies suggest that such a change in serotype frequencies is often coupled with an increase of antibiotic resistance among nonvaccine serotypes. Building on previous multilocus models for bacterial pathogen population structure, we have developed a theoretical framework incorporating variation of serotype and antibiotic resistance to examine how their associations may be affected by vaccination. Using this framework, we find that vaccination can result in a rapid increase in the frequency of preexisting resistant variants of nonvaccine serotypes due to the removal of competition from vaccine serotypes.

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