An Assessment of the Genetic Diversity in a Field Population of Phytophthora nicotianae with a Changing Race Structure

One hundred fifty-three isolates of Phytophthora nicotianae that were collected over a 4-year period from a single field were subjected to amplified fragment length polymorphism (AFLP) analysis to investigate the effect of different types of resistance in tobacco (Nicotiana tabacum) on genetic diversity in the pathogen population. No race 1 isolates were detected in the field prior to initiating the study, but the race was present in multiple plots by the end of the 4-year period. There were 102 race 0 isolates and 51 race 1 isolates characterized. Seventy-six of the 153 isolates had a unique AFLP profile, whereas the remaining 77 isolates were represented by 27 AFLP profiles shared by at least two isolates. Isolates of both races were found in both the unique and shared AFLP profile groups. Twenty-three of the AFLP profiles were detected in multiple years, indicating a clonal component to the pathogen population. Race 1 isolates that were detected over multiple years were always obtained from the same plot. No race 1 profile was found in more than one plot, confirming the hypothesis that the multiple occurrences of the race throughout the field were the result of independent events and not pathogen spread. Three identical race 0 AFLP profiles occurred in noncontiguous plots, and in each case, the plots contained the same partially resistant variety. Cluster analysis provided a high level of bootstrap support for 41 isolates in 19 clusters that grouped primarily by race and rotation treatment. Estimates of genetic diversity ranged from 0.365 to 0.831 and varied depending on tobacco cultivar planted and race. When averaged over all treatments, diversity in race 1 isolates was lower than in race 0 isolates at the end of each season. Deployment of single-gene resistance initially decreased genetic diversity of the population, but the diversity increased each year, indicating the pathogen was adapting to the host genotypes deployed in the field.

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Genetic Diversity Among Garlic Clones as Revealed by Aflp, Phenotypic Descriptors and S-Amino Acids Level

Vegetable Crops Research Bulletin ◽

10.2478/v10032-007-0013-9 ◽

2007 ◽

Vol 66 (1) ◽

pp. 105-116 ◽

Cited By ~ 4

Author(s):

Jaroslava Ovesná ◽

Ladislav Kučera ◽

Jana Králová ◽

Leona Leišová ◽

Helena Stavělíková ◽

...

Keyword(s):

Genetic Diversity ◽

Amino Acids ◽

Czech Republic ◽

Soviet Union ◽

Former Soviet Union ◽

Allium Sativum ◽

Health Benefit ◽

Biologically Active ◽

Aflp Analysis ◽

High Level

Genetic Diversity Among Garlic Clones as Revealed by Aflp, Phenotypic Descriptors andS-Amino Acids LevelGarlic (Allium sativumL.) belongs to well known vegetables. Garlic is considered a valuable source of health benefit compounds.S-amino acids, namelyS-alk(en)yl-L-cysteine sulfoxides, are one of the major garlic constituents. We evaluated a set of garlic genetics resources representing namely valuable germplasm from Czech Republic, Slovakia, Poland and former Soviet Union. We showed that differences exist among analysed genotypes inS-amino acids (alliin/methiin) level and donors of high level of alliin/methiin can be identified. High alliin/methiin level was found within genetic resources and registered cultivars under the use. Level of alliin and isoalliin did not correlate with measured level of methiin. Donors of high methiin level were found within accessions marked as being "wild" in EVIGEZ database. Sufficient variability was found by AFLP analysis as well. Accessions were divided by PCA basically into two categories: hardnecks (Ophioscorodongroup,Longicuspisgroup) and softneck (sativum group). Presented work showes possibility to find suitable donors of biologically active compounds in garlic.

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Virulence and Molecular Diversity in the Kabatiella zeae Population Causing Maize Eyespot in China

Plant Disease ◽

10.1094/pdis-03-20-0509-re ◽

2020 ◽

Vol 104 (12) ◽

pp. 3197-3206

Author(s):

Nan Chen ◽

Shuqin Xiao ◽

Jiaying Sun ◽

Lu He ◽

Miaomiao Liu ◽

...

Keyword(s):

Genetic Diversity ◽

Molecular Diversity ◽

Fragment Length Polymorphism ◽

Genotypic Diversity ◽

Limiting Factor ◽

Aflp Analysis ◽

Limited Information ◽

Pathogen Population ◽

Nomenclature System ◽

Differential Hosts

Maize eyespot, caused by Kabatiella zeae, has become a major yield-limiting factor in maize planting areas in northeast China. Limited information is available on pathotypes, virulence, and the genetic diversity of the K. zeae population. We analyzed virulence and genetic diversity of 103 K. zeae isolates collected from six provinces in China with differential hosts and the amplified fragment length polymorphism (AFLP) technique, respectively. To evaluate the virulence, 103 isolates were inoculated on nine differential hosts (maize inbred lines)—E28, Shen137, Qi319, B73, Danhuang34, Zi330, Mo17, Huangzaosi, and CN165—and grouped into 23 pathotypes and three virulence groups according to the coded triplet nomenclature system on differential hosts. AFLP analysis resolved the set of isolates into four genetic diversity clusters (DICE similarity values of 76%). Genetic variation of K. zeae among and between pathotypes revealed that the pathogen population had a high genotypic diversity. The correlation between pathotypes, virulence, and genetic diversity grouping was low. A correlation between AFLP groups and geographic locations was detected.

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Adaptation of Phytophthora nicotianae to multiple sources of partial-resistance in tobacco.

Plant Disease ◽

10.1094/pdis-06-21-1241-re ◽

2021 ◽

Author(s):

Jing Jin ◽

Kestrel Lannon McCorkle ◽

Vicki Cornish ◽

Ignazio Carbone ◽

Ramsey Lewis ◽

...

Keyword(s):

Partial Resistance ◽

Single Gene ◽

Field Studies ◽

Phytophthora Nicotianae ◽

Multiple Sources ◽

Rapid Loss ◽

Sources Of Resistance ◽

Black Shank ◽

Race 1

Host resistance is an important tool in the management of black shank disease of tobacco. While race development leads to rapid loss of single-gene resistance, the adaptation by Phytophthora nicotianae to sources of partial resistance from Beinhart 1000, Florida 301, and the Wz gene region introgressed from Nicotiana rustica is poorly characterized. In greenhouse environments, host genotypes with QTLs conferring resistance from multiple sources were initially inoculated with an aggressive isolate of race 0 or race 1 of P. nicotianae. The most aggressive isolate was selected after each of six host generations to inoculate the next generation of plants. The race 0 isolate demonstrated a continuous gradual increase in disease severity and percent root rot on all sources of resistance except the genotype K 326 Wz/--, where a large increase in both was observed between generations two and three. Adaptation by the race 0 isolate on Beinhart 1000 represents the first report of adaptation to this genotype by P. nicotianae. The race 1 isolate did not exhibit significant increases in aggressiveness over generations, but also exhibited a large increase in aggressiveness on K 326 Wz/-- between generations 3 and 4. Molecular characterization of isolates recovered during selection was completed using ddRADseq, but no polymorphisms were associated with the observed changes in aggressiveness. The rapid adaptation to Wz resistance and the gradual adaptation to other QTLs highlights the need to study the nature of Wz resistance and for conducting field studies on efficacy of resistance-gene rotation for disease management.

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Genetic Diversity in Colletotrichum gloeosporioides from Stylosanthes spp. at Centers of Origin and Utilization

Phytopathology ◽

10.1094/phyto.2003.93.2.176 ◽

2003 ◽

Vol 93 (2) ◽

pp. 176-185 ◽

Cited By ~ 21

Author(s):

P. L. Weeds ◽

S. Chakraborty ◽

C. D. Fernandes ◽

M. J. d'A. Charchar ◽

C. R. Ramesh ◽

...

Keyword(s):

Genetic Diversity ◽

Colletotrichum Gloeosporioides ◽

Host Population ◽

South American ◽

Pathogen Population ◽

Center Of Origin ◽

China And India ◽

Wild Host ◽

Exotic Pathogen ◽

High Level

Using molecular markers, this work compares the genetic diversity in Colletotrichum gloeosporioides infecting species of the tropical forage legume Stylosanthes at the center of origin in Brazil and Colombia with that of Australia, China, and India, where Stylosanthes spp. have been introduced for commercial use. There was extensive diversity in the pathogen population from Brazil, Colombia, China, and India. The Australian pathogen population was least diverse probably due to its geographical isolation and effective quarantine. The extensive diversity in China and India means that threats from exotic pathogen races to Stylosanthes pastures can potentially come from countries outside the South American center of origin. In Brazil and India, both with native Stylosanthes populations, a high level of genetic differentiation in the pathogen population was associated with sites where native or naturalized host population was widely distributed. There was limited genetic diversity at germplasm evaluation sites, with a large proportion of isolates having identical haplotypes. This contrasts recent pathogenicity results for 78 of the Brazilian isolates that show hot spots of complex races are more common around research stations where host germplasm are tested, but few are found at sites containing wild host populations. For a pathogen in which the same races arise convergently from different genetic backgrounds, this study highlights the importance of using both virulence and selectively neutral markers to understand pathogen population structure.

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AFLP Fingerprinting Analysis of Citrus Cultivars and Wild Accessions from Oman Suggests the Presence of Six Distinct Cultivars

Agriculture (Pol nohospodárstvo) ◽

10.2478/agri-2018-0018 ◽

2018 ◽

Vol 64 (4) ◽

pp. 173-182

Author(s):

Hamed Al-Nadabi ◽

Mumtaz Khan ◽

Rashid Abdullah Al-Yahyai ◽

Abdullah Mohammed Al-Sadi

Keyword(s):

Genetic Diversity ◽

Genetic Similarity ◽

Genetic Relatedness ◽

Aflp Analysis ◽

Aflp Fingerprinting ◽

The Past ◽

Low Genetic Diversity ◽

The World ◽

Wild Accessions ◽

High Level

Abstract A study was conducted to evaluate genetic relatedness of 27 citrus cultivars and 6 wild citrus accessions using AFLP fingerprinting. The 27 citrus cultivars belonged to Citrus sinensis, C. aurantifolia, C. aurantium, C. paradise, C. reticulata, C. limon, C. latifolia, C. maxima, C. limettoides, C. limetta, C. medica and C. Jambhiri. The wild cultivars were obtained from Oman while the other cultivars originated from Oman and other countries. AFLP analysis using 4 primer pair combinations resolved 910 polymorphic alleles. All citrus cultivars and accessions had low genetic diversity (H = 0.0281 to 0.1300), with the percent polymorphic loci ranging from 8 to 35%. Populations of the six wild citrus accessions showed a very low level of genetic diversity (< 0.0700). Cluster analysis of the 33 cultivars and accessions showed that they share a high level of genetic similarity (81‒99%; mean = 92%). The six wild accessions clustered into two main clusters, with the analysis indicating that the six wild accessions may make up six distinct cultivars. The study provides information on the phylogeny of citrus cultivars and citrus diversity in Oman, a country through which citrus moved in the past from Asia to different African and European countries. In addition, it shows that some distinct citrus cultivars are present in this part of the world.

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Genetic and Pathogenic Variability of Mycogone perniciosa Isolates Causing Wet Bubble Disease on Agaricus bisporus in China

Pathogens ◽

10.3390/pathogens8040179 ◽

2019 ◽

Vol 8 (4) ◽

pp. 179

Author(s):

Dan Li ◽

Frederick Leo Sossah ◽

Yang Yang ◽

Zhenghui Liu ◽

Yueting Dai ◽

...

Keyword(s):

Genetic Diversity ◽

Agaricus Bisporus ◽

Aflp Analysis ◽

Disease Management Strategy ◽

Key Factor ◽

Colony Color ◽

Resistant Strains ◽

Pathogenic Variability ◽

Different Strains ◽

High Level

Wet bubble disease, caused by Mycogone perniciosa, is a major threat to Agaricus bisporus production in China. In order to understand the variability of in genetic, pathogenicity, morphology, and symptom production of the fungus, 18 isolates of the pathogen were collected from diseased A. bisporus in different provinces in China. The isolates were characterized by a combination of morphological, cultural, and molecular pathogenicity testing on different strains of A. bisporus and amplified fragment length polymorphism (AFLP) analysis. The 18 isolates were identified by Koch’s postulate and confirmed different pathogenic variability among them. The yellow to brown isolates were more virulent than the white isolates. AFLP markers clustered the isolates into two distinct groups based on their colony color, with a high level of polymorphism of Jaccard similarities ranges from 0.39% to 0.64%. However, there was no evidence of an association between the genetic diversity and the geographical origin of the isolates. Through knowledge of the genetic diversity, phenotypic virulence of M. perniciosa is a key factor for successful breeding of resistant strains of A. bisporus and developing of an integrated disease management strategy to manage wet bubble disease of A. bisporus.

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Managing the Race Structure of Phytophthora parasitica var. nicotianae with Cultivar Rotation

Plant Disease ◽

10.1094/pd-89-1285 ◽

2005 ◽

Vol 89 (12) ◽

pp. 1285-1294 ◽

Cited By ~ 33

Author(s):

M. J. Sullivan ◽

T. A. Melton ◽

H. D. Shew

Keyword(s):

Partial Resistance ◽

Disease Incidence ◽

Single Gene ◽

Growing Season ◽

Phytophthora Parasitica ◽

Black Shank ◽

Complete Resistance ◽

Race 1 ◽

High Level ◽

Different Levels

Deployment of tobacco cultivars with single-gene, complete resistance to race 0 of the tobacco black shank pathogen, Phytophthora parasitica var. nicotianae, has resulted in a rapid increase in the occurrence of race 1 of the pathogen in North Carolina. Cultivar-rotation studies were conducted in three fields to assess how different levels and types of resistance affected the race structure and population dynamics of the pathogen when deployed in fields initially containing single or mixed races of the pathogen. In a field with both races present, a high level of partial resistance in cv. K 346 was most effective in reducing disease and decreasing the proportion of race 1 in the pathogen population. The deployment of complete resistance in cv. NC 71 resulted in intermediate levels of disease control and race 1 became the predominate race. The cv. K 326, with a low level of partial resistance, had the highest levels of disease, and race 0 was the dominant race recovered. In a field where no race 1 was detected initially, disease incidence was high with the use of partial resistance. Complete resistance was very effective in suppressing disease, but race 1 was recovered after only one growing season. By the end of the third growing season, race 1 was recovered from most treatments where single-gene resistance was deployed. A high level of partial resistance was most effective in suppressing disease in a field where race 1 initially was the predominant race. A rotation between cultivars with single-gene resistance and cultivars with a high level of partial resistance should provide the most effective approach to black shank management. This rotation will reduce disease incidence and minimize race shifts in the pathogen and, over time, should prolong the usefulness of the Ph gene for black shank control in commercial production of tobacco.

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Components of aggressiveness in Phytophthora nicotianae during adaptation to multiple sources of partial resistance in tobacco

Plant Disease ◽

10.1094/pdis-09-20-1929-re ◽

2020 ◽

Author(s):

Jing Jin ◽

H. David Shew

Keyword(s):

Partial Resistance ◽

Single Gene ◽

Phytophthora Nicotianae ◽

Root Tip ◽

Multiple Sources ◽

Root Tips ◽

Black Shank ◽

Resistance Sources ◽

Infected Root ◽

Race 1

Black shank is a devastating disease of tobacco caused by Phytophthora nicotianae. Host resistance has been an integral part of black shank management, but after the loss of Php single-gene resistance following its widespread deployment in the 1990s, growers have relied on varieties with varying levels of partial resistance. Partial resistance is effective in suppressing disease, but continued exposure can result in an increase in pathogen aggressiveness that threatens durability of the resistance to P. nicotianae. Aggressiveness components in P. nicotianae were characterized following adaptation on two sources of partial resistance, Fla 301 and the Wz gene from Nicotiana rustica. An aggressive isolate of the two major races of P. nicotianae, race 0 and race 1, were adapted for either ‘one/two’ or ‘five/six’ generations on the two resistance sources, giving four sets of isolates based on race, number of generations of adaptation, and source of resistance. Across the four sets of isolates, adapted isolates infected higher proportions of root tips, produced more sporangia per infected root tip, and caused larger lesions than their respective non-adapted isolates of the same race and from the same resistance source. Adapted isolates also produced more aggressive zoospore progeny than the non-adapted isolates. Adaptation to partial resistance involves multiple aggressiveness components that results in the increased aggressiveness observed for P. nicotianae. These results improve our knowledge on the nature of P. nicotianae adaptation to partial resistance in tobacco and indicate that different resistance sources are likely to select for similar aggressiveness components in the pathogen.

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Molecular caracterization of a corn core collection–landraces subgroup

Revista Agro mbiente On-line ◽

10.18227/1982-8470ragro.v12i1.4641 ◽

2017 ◽

Vol 12 (1) ◽

pp. 11

Author(s):

Ronaldo Rodrigues Coimbra ◽

Glauco Vieira Miranda ◽

Newton Portilho Carneiro ◽

Cláudia Teixeira Guimarães ◽

Derly José Henriques da Silva ◽

...

Keyword(s):

Genetic Diversity ◽

Core Collection ◽

Jaccard Index ◽

Aflp Analysis ◽

Diversity Analysis ◽

The Core ◽

Germplasm Collections ◽

Molecular Information ◽

High Level ◽

Landrace Accessions

The efficient use of genetic resources- stored in germplasm collections can be maximized if morphoagronomic and molecular information on the accessions is made available. To achieve this, a collection that is well-structured, well-curated and easily accessible (the core collection) is required. Consequently, the objective of the current study was to characterize 80 landrace accessions from the maize core collection of the Federal University of Viçosa (UFV), and assay thenngenetic diversity of the various landraces, considering grain type and ecogeographic origin. For this, AFLP analysis was performed using 12 primer combinations. Genetic diversity of the collection was quantified with the UPGMA method, using the Jaccard Index to quantify dissimilarity. The core collection was divided into four sub-populations by grain type, and into six sub-populations based on ecogeographic origin. Genetic diversity analysis was performed both within and between sub-populations. A high level of genetic variability was found among the landrace accessions of UFV Core Collection, principally among those accessions with dentate type grains.Classification by grain type and ecogeographic origin allowed genetically divergent groups to be distinguished.

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Diversity of Meloidogyne arenaria using morphological, cytological and molecular approaches

Nematology ◽

10.1163/156854108786161526 ◽

2008 ◽

Vol 10 (6) ◽

pp. 819-834 ◽

Cited By ~ 23

Author(s):

Maria Ritta Almeida ◽

Regina Carneiro ◽

Marcilene dos Santos ◽

Myrian Tigano ◽

Ana Cristina Gomes ◽

...

Keyword(s):

Bootstrap Support ◽

Meloidogyne Arenaria ◽

Molecular Approaches ◽

Morphological Studies ◽

Race 1 ◽

Unidentified Species ◽

High Bootstrap ◽

Race 2 ◽

Species Specific ◽

High Level

AbstractThirteen Meloidogyne arenaria isolates representing two cytological types (3n = 51-56, 2n = 42-48) and four enzymatic phenotypes (esterase and malate dehydrogenase: A3N1, A2N1, A1N1, A2N3) were studied using different approaches. The analysis of molecular markers showed a high level of polymorphism among the isolates. The trees obtained with RAPD or ISSR polymorphisms showed concordant results and agree with morphological studies. By considering morphometrical and morphological features, it was possible to conclude that the isolate with enzymatic phenotype A2N3 race 1 was the M. arenaria described in 1949 by Chitwood and appearing clearly separated in the trees, as well as in the outgroups. The seven isolates with phenotype A2N1 from different localities and isolate A1N1 can be considered morphometrically typical of M. arenaria race 2 and they were apparently clustered by geographical origin. Morphologically, they differed from isolate A2N3 race 1. The two isolates with phenotype A3N1 appeared to be closely related to the isolate of M. morocciensis and, considering all of the features described for this species, were identified as such. The two isolates A2N3 race 2 were identified either as an atypical M. arenaria or an unidentified species (females and males having atypical stylets), and clustered together and separated from other M. arenaria isolates with high bootstrap support. The same M. arenaria isolates were tested with the species-specific molecular marker, type SCAR. A fragment of 420 bp was obtained for ten isolates of M. arenaria, including the atypical A2N3 race 2 and M. morocciensis. This fragment was not amplified for three typical A2N1 isolates of M. arenaria.

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