scholarly journals Diversity of Epidemic Populations of Gibberella zeae from Small Quadrats in Kansas and North Dakota

2003 ◽  
Vol 93 (7) ◽  
pp. 874-880 ◽  
Author(s):  
Kurt A. Zeller ◽  
Robert L. Bowden ◽  
John F. Leslie
Keyword(s):  
North Dakota ◽  
The United States ◽  
Gibberella Zeae ◽  
Group Method ◽  
Head Blight ◽  
Arithmetic Means ◽  
Vegetative Compatibility Groups ◽  
Initial Inoculum ◽  
Population Sampling ◽  
Pair Group

Gibberella zeae (anamorph Fusarium graminearum) causes Fusarium head blight (FHB) of wheat and barley and has been responsible for several billion dollars of losses in the United States since the early 1990s. We isolated G. zeae from the top, middle, and bottom positions of wheat spikes collected from 0.25-m2 quadrats during severe FHB epidemics in a single Kansas (KS) field (1993) and in a single North Dakota (ND) field (1994). Three amplified fragment length polymorphism (AFLP) primer pairs were used to resolve 94 polymorphic loci from 253 isolates. Members of a subset of 26 isolates also were tested for vegetative compatibility groups (VCGs). Both methods indicated high levels of genotypic variability and identified the same sets of isolates as probable clones. The mean number of AFLP multilocus haplotypes per head was approximately 1.8 in each population, but this value probably underestimates the true mean due to the small number of samples taken from each head. Isolates with the same AFLP haplotype often were recovered from different positions in a single head, but only rarely were such apparently clonal isolates recovered from more than one head within a quadrat, a pattern that is consistent with a genetically diverse initial inoculum and limited secondary spread. The KS and ND samples had no common AFLP haplotypes. All G. zeae isolates had high AFLP fingerprint similarity (>70%, unweighted pair group method with arithmetic means similarity) to reference isolates of G. zeae lineage 7. The genetic identity between the KS and ND populations was >99% and the estimated effective migration rate was high (Nm ≈70). Tests for linkage disequilibrium provide little evidence for nonrandom associations between loci. Our results suggest that these populations are parts of a single, panmictic population that experiences frequent recombination. Our results also suggest that a variety of population sampling designs may be satisfactory for assessing diversity in this fungus.

scholarly journals Detection of DNA and Ploidy Variation within Vegetatively Propagated Zoysiagrass Cultivars

2014 ◽  
Vol 139 (5) ◽  
pp. 547-552 ◽  
Author(s):  
Karen R. Harris-Shultz ◽  
Susana Milla-Lewis ◽  
Aaron J. Patton ◽  
Kevin Kenworthy ◽  
Ambika Chandra ◽  
...  
Keyword(s):  
Genetic Variability ◽  
Reference Sample ◽  
Warm Season ◽  
The United States ◽  
Group Method ◽  
Group Iii ◽  
Climatic Regions ◽  
Pair Group ◽  
Group I ◽  
Two Samples

Zoysiagrass (Zoysia sp.) is used as a warm-season turfgrass for lawns, parks, and golf courses in the warm, humid and transitional climatic regions of the United States. Zoysiagrass is an allotetraploid species (2n = 4x = 40) and some cultivars are known to easily self- and cross-pollinate. Previous studies showed that genetic variability in the clonal cultivars Emerald and Diamond was likely the result of contamination (seed production or mechanical transfer) or mislabeling. To determine the extent of genetic variability of vegetatively propagated zoysiagrass cultivars, samples were collected from six commercially available zoysiagrass cultivars (Diamond, Emerald, Empire, JaMur, Meyer, Zeon) from five states (Arkansas, Florida, Georgia, North Carolina, Texas). Two of the newest cultivar releases (Geo and Atlantic) were to serve as outgroups. Where available, one sample from university research plots and two samples from sod farms were collected for each cultivar per state. Forty zoysiagrass simple sequence repeat (SSR) markers and flow cytometry were used to compare genetic and ploidy variation of each collected sample to a reference sample. Seventy-five samples were genotyped and an unweighted pair group method with arithmetic mean clustering revealed four groups. Group I (Z. japonica) included samples of ‘Meyer’ and Empire11 (‘Empire’ sample at location #11), Group II (Z. japonica × Z. pacifica) included samples of ‘Emerald’ and ‘Geo’, Group III (Z. matrella) included samples of ‘Diamond’ and ‘Zeon’, and Group IV (Z. japonica) consisted of samples from ‘Empire’, ‘JaMur’, ‘Atlantic’, and Meyer3 (‘Meyer’ at sample location #3). Samples of ‘Empire’, ‘Atlantic’, and ‘JaMur’ were indistinguishable with the markers used. Four samples were found to have alleles different from the respective reference cultivar, including two samples of ‘Meyer’, one sample of ‘Empire’, and one sample of ‘Emerald’. Three of these samples were from Texas and one of these samples was from Florida. Three of the four samples that were different from the reference cultivar were university samples. In addition, one sample, Empire11, was found to be an octoploid (2n = 8x = 80). For those samples that had a fingerprint different from the reference cultivar, contamination, selfing, and/or hybridization with other zoysiagrasses may have occurred.

scholarly journals Comparative Mycotoxin Profiles of Gibberella zeae Populations from Barley, Wheat, Potatoes, and Sugar Beets

2008 ◽  
Vol 74 (21) ◽  
pp. 6513-6520 ◽  
Author(s):  
Rishi R. Burlakoti ◽  
Shaukat Ali ◽  
Gary A. Secor ◽  
Stephen M. Neate ◽  
Marcia P. McMullen ◽  
...  
Keyword(s):  
Genetic Relationships ◽  
Sampling Site ◽  
Management Strategies ◽  
The United States ◽  
Gibberella Zeae ◽  
Gas Chromatography Mass Spectrometry ◽  
Head Blight ◽  
Sugar Beets ◽  
Biosynthesis Gene ◽  
Pcr Assays

ABSTRACT Gibberella zeae is one of the most devastating pathogens of barley and wheat in the United States. The fungus also infects noncereal crops, such as potatoes and sugar beets, and the genetic relationships among barley, wheat, potato, and sugar beet isolates indicate high levels of similarity. However, little is known about the toxigenic potential of G. zeae isolates from potatoes and sugar beets. A total of 336 isolates of G. zeae from barley, wheat, potatoes, and sugar beets were collected and analyzed by TRI (trichothecene biosynthesis gene)-based PCR assays. To verify the TRI-based PCR detection of genetic markers by chemical analysis, 45 representative isolates were grown in rice cultures for 28 days and 15 trichothecenes and 2 zearalenone (ZEA) analogs were quantified using gas chromatography-mass spectrometry. TRI-based PCR assays revealed that all isolates had the deoxynivalenol (DON) marker. The frequencies of isolates with the 15-acetyl-deoxynivalenol (15-ADON) marker were higher than those of isolates with the 3-acetyl-deoxynivalenol (3-ADON) marker among isolates from all four crops. Fusarium head blight (FHB)-resistant wheat cultivars had little or no influence on the diversity of isolates associated with the 3-ADON and 15-ADON markers. However, the frequency of isolates with the 3-ADON marker among isolates from the Langdon, ND, sampling site was higher than those among isolates from the Carrington and Minot, ND, sites. In chemical analyses, DON, 3-ADON, 15-ADON, b-ZEA, and ZEA were detected. All isolates produced DON (1 to 782 μg/g) and ZEA (1 to 623 μg/g). These findings may be useful for monitoring mycotoxin contamination and for formulating FHB management strategies for these crops.

scholarly journals Genetic Diversity of Gibberella zeae Isolates from Manitoba

Plant Disease ◽  
2006 ◽  
Vol 90 (10) ◽  
pp. 1337-1342 ◽  
Author(s):  
W. G. D. Fernando ◽  
J. X. Zhang ◽  
M. Dusabenyagasani ◽  
X. W. Guo ◽  
H. Ahmed ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Significant Proportion ◽  
Geographic Origin ◽  
Geographic Location ◽  
Principal Component ◽  
Vegetative Compatibility ◽  
Gibberella Zeae ◽  
Srap Marker ◽  
Head Blight ◽  
Vegetative Compatibility Groups

Gibberella zeae (anamorph Fusarium graminearum) causes Fusarium head blight, one of the most important diseases of cereals in the Canadian prairies for the last decade. In 2002, 60 isolates of G. zeae were collected and single spored from naturally infected spikes of wheat from Carman and Winnipeg in Manitoba. These isolates were compared using vegetative compatibility analysis and polymerase chain reaction (PCR)-based sequence related amplified polymorphisms (SRAP). Sixteen vegetative compatibility groups (VCG) were found among the 50 isolates tested. Five VCGs were found in the two locations, five in Carman and six in Winnipeg. Eight SRAP primer pairs amplified 90 polymorphic DNA fragments from 60 isolates and identified 59 distinct haplotypes. Among seven pairs of isolates, each pair from a distinct spike, four had isolates with different VCGs and six comprised different SRAP haplotypes. Principal component analysis and UPGMA separated the dataset into two main groups, each with isolates from both locations. The analysis of molecular variance also revealed that 75 and 20% of the variance was associated with differences among individual isolates and varieties sampled, respectively. Geographic location was not a significant source of variation at P = 0.05 and accounted for only 4% of total variance. A low correlation between VCG and SRAP marker data was detected. This study showed that, although genetic diversity is high among G. zeae isolates, Carman and Winnipeg collections have a similar genetic makeup and are likely part of the same population. The significant proportion of variance accounted by the variety compared with the geographic origin of isolates suggests that seedborne inoculum might have contributed to the genetic diversity within the G. zeae collection under study.

scholarly journals SSR Markers Reveal the Genetic Diversity of Asian Cercis Taxa at the U.S. National Arboretum

HortScience ◽  
2017 ◽  
Vol 52 (4) ◽  
pp. 498-502 ◽  
Author(s):  
Chandra S. Thammina ◽  
David L. Kidwell-Slak ◽  
Stefan Lura ◽  
Margaret R. Pooler
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
The United States ◽  
Group Method ◽  
Cercis Canadensis ◽  
Landscape Plant ◽  
Pair Group ◽  
Upgma Cluster Analysis ◽  
Eastern Redbud ◽  
The U.S

The redbud (Cercis L. species) is a popular landscape plant grown widely in the United States. There are more than 20 cultivars of eastern redbud (Cercis canadensis L.) and at least three cultivars of Asian taxa (primarily Cercis chinensis Bunge) in the trade. The U.S. National Arboretum (USNA) has a diverse collection of Cercis germplasm collected in North America and Asia. Fourteen genomic simple sequence repeat (genomic-SSR) markers were used to analyze the genetic diversity of 53 accessions of Asian Cercis taxa from our collection, including C. chinensis, Cercis chingii Chun, Cercis gigantea ined., Cercis glabra Pamp., Cercis racemosa Oliv., and Cercis yunnanensis Hu and W. C. Cheng. SSR markers detected an average of 5.7 alleles per locus with a range of two to nine alleles. A dendrogram was generated by unweighted pair group method with arithmetic mean (UPGMA) cluster analysis using the Jaccard similarity coefficient. Four major clusters were identified. Accessions tended to group by taxa or provenance, but with some notable exceptions caused either by misidentification or nomenclatural confusion in the species. This information will be used for collection management and for making decisions in the breeding program to maximize genetic diversity of cultivated Cercis.

scholarly journals Blueberry Cultivar Identification Using Random Amplified Polymorphic DNA and Sequence-characterized Amplified Region Markers

HortScience ◽  
2017 ◽  
Vol 52 (11) ◽  
pp. 1483-1489 ◽  
Author(s):  
Kang Hee Cho ◽  
Seo Jun Park ◽  
Su Jin Kim ◽  
Se Hee Kim ◽  
Han Chan Lee ◽  
...  
Keyword(s):  
Random Amplified Polymorphic Dna ◽  
The United States ◽  
Morphological Characters ◽  
Polymorphic Band ◽  
Group Method ◽  
Highbush Blueberry ◽  
United States Department ◽  
Scar Markers ◽  
Sequence Characterized Amplified Region ◽  
Pair Group

Blueberry cultivars have traditionally been identified based on the evaluation of sets of morphological characters; however, distinguishing closely related cultivars remains difficult. In the present study, we developed DNA markers for the genetic fingerprinting of 45 blueberry cultivars, including 31 cultivars introduced from the United States Department of Agriculture. We obtained 210 random amplified of polymorphic DNA (RAPD) markers using 43 different primers. The number of polymorphic bands ranged from three (OPG-10 and OPQ-04) to eight (OPR-16), with an average of five. A cluster analysis performed with the unweighted pair group method using arithmetic averages produced genetic similarity values among the blueberry cultivars ranging from 0.53 to 0.85, with an average similarity of 0.68. A dendrogram clustered the 45 blueberry cultivars into two main clusters, with a similarity value of 0.65. Cluster I consisted of four rabbiteye cultivars (Pink Lemonade, Alapaha, Titan, and Vernon) and the Ashworth northern highbush cultivar. Cluster II consisted of 31 northern highbush cultivars, eight southern highbush blueberry cultivars, and Northland half-highbush blueberry cultivar. Fifty five RAPD fragments selected were sequenced to develop sequence-characterized amplified region (SCAR) markers, resulting in the successful conversion of 16 of 55 fragments into SCAR markers. An amplified polymorphic band has the same size as the RAPD fragment or smaller according to the primer combinations in the 16 SCAR markers. Among these markers, a combination of 11 SCAR markers provided sufficient polymorphisms to distinguish the blueberry cultivars investigated in this study. These newly developed markers could be a fast and reliable tool to identify blueberry cultivars.

Genetic diversity and differentiation in populations of Japanese stone pine (Pinuspumila) in Japan

1996 ◽  
Vol 26 (8) ◽  
pp. 1454-1462 ◽  
Author(s):  
Naoki Tani ◽  
Nobuhiro Tomaru ◽  
Masayuki Araki ◽  
Kihachiro Ohba
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Differentiation ◽  
Phylogenetic Trees ◽  
Genetic Relationships ◽  
Natural Populations ◽  
Group Method ◽  
Stone Pine ◽  
Arithmetic Means ◽  
Pair Group

Japanese stone pine (Pinuspumila Regel) is a dominant species characteristic of alpine zones of high mountains. Eighteen natural populations of P. pumila were studied in an effort to determine the extent and distribution of genetic diversity. The extent of genetic diversity within this species was high (HT = 0.271), and the genetic differentiation among populations was also high (GST = 0.170) compared with those of other conifers. In previous studies of P. pumila in Russia, the genetic variation within the species was also high, but the genetic differentiation among populations was low. We infer that this difference originates from differences in geographic distribution and ecological differences between the two countries. The genetic variation within each population tended, as a whole, to be smaller within marginal southern populations than within northern populations. Genetic relationships among populations reflect the geographic locations, as shown by unweighted pair-group method with arithmetic means and neighbor-joining phylogenetic trees.

scholarly journals Trichothecene Profiling and Population Genetic Analysis of Gibberella zeae from Barley in North Dakota and Minnesota

2011 ◽  
Vol 101 (6) ◽  
pp. 687-695 ◽  
Author(s):  
Rishi R. Burlakoti ◽  
Stephen M. Neate ◽  
Tika B. Adhikari ◽  
Sanjaya Gyawali ◽  
Bacilio Salas ◽  
...  
Keyword(s):  
United States ◽  
Spatial Structure ◽  
North Dakota ◽  
Population Genetic ◽  
The United States ◽  
Gibberella Zeae ◽  
Upper Midwest ◽  
High Gene ◽  
Pcr Assays ◽  
Made In

Gibberella zeae, the principal cause of Fusarium head blight (FHB) of barley, contaminates grains with several mycotoxins, which creates a serious problem for the malting barley industry in the United States, China, and Europe. However, limited studies have been conducted on the trichothecene profiles and population genetic structure of G. zeae isolates collected from barley in the United States. Trichothecene biosynthesis gene (TRI)-based polymerase chain reaction (PCR) assays and 10 variable number tandem repeat (VNTR) markers were used to determine the genetic diversity and compare the trichothecene profiles of an older population (n = 115 isolates) of G. zeae collected in 1997 to 2000 with a newer population (n = 147 isolates) collected in 2008. Samples were from across the major barley-growing regions in North Dakota and Minnesota. The results of TRI-based PCR assays were further validated using a subset of 32 and 28 isolates of G. zeae by sequence analysis and gas chromatography, respectively. TRI-based PCR assays revealed that all the G. zeae isolates in both populations had markers for deoxynivalenol (DON), and the frequencies of isolates with a 3-acetyldeoxynivalenol (3-ADON) marker in the newer population were ≈11-fold higher than those among isolates in the older population. G. zeae populations from barley in the Midwest of the United States showed no spatial structure, and all the isolates were solidly in clade 7 of G. zeae, which is quite different from other barley-growing areas of world, where multiple species of G. zeae are commonly found in close proximity and display spatial structure. VNTR analysis showed high gene diversity (H = 0.82 to 0.83) and genotypic diversity but low linkage disequilibrium (LD = 0.02 to 0.07) in both populations. Low genetic differentiation (FST = 0.013) and high gene flow (Nm = 36.84) was observed between the two populations and among subpopulations within the same population (Nm = 12.77 to 29.97), suggesting that temporal and spatial variations had little influence on population differentiation in the Upper Midwest. Similarly, low FST (0.02) was observed between 3-ADON and 15-acetyldeoxynivalenol populations, indicating minor influence of the chemotype of G. zeae isolates on population subdivision, although there was a rapid increase in the frequencies of isolates with the 3-ADON marker in the Upper Midwest between the older collection made in 1997 to 2000 and the newer collection made in 2008. This study provides information to barley-breeding programs for their selection of isolates of G. zeae for evaluating barley genotypes for resistance to FHB and DON accumulation.

scholarly journals Genetic Variation of ‘Candidatus Liberibacter solanacearum’ Haplotype C and Identification of a Novel Haplotype from Trioza urticae and Stinging Nettle

2018 ◽  
Vol 108 (8) ◽  
pp. 925-934 ◽  
Author(s):  
M. Haapalainen ◽  
J. Wang ◽  
S. Latvala ◽  
M. T. Lehtonen ◽  
M. Pirhonen ◽  
...  
Keyword(s):  
Wild Plants ◽  
Cultivated Plants ◽  
Group Method ◽  
Stinging Nettle ◽  
Arithmetic Means ◽  
Candidatus Liberibacter Solanacearum ◽  
Pair Group ◽  
Carrot Seed ◽  
Candidatus Liberibacter ◽  
Different Strains

‘Candidatus Liberibacter solanacearum’ (CLso) haplotype C is associated with disease in carrots and transmitted by the carrot psyllid Trioza apicalis. To identify possible other sources and vectors of this pathogen in Finland, samples were taken of wild plants within and near the carrot fields, the psyllids feeding on these plants, parsnips growing next to carrots, and carrot seeds. For analyzing the genotype of the CLso-positive samples, a multilocus sequence typing (MLST) scheme was developed. CLso haplotype C was detected in 11% of the T. anthrisci samples, in 35% of the Anthriscus sylvestris plants with discoloration, and in parsnips showing leaf discoloration. MLST revealed that the CLso in T. anthrisci and most A. sylvestris plants represent different strains than the bacteria found in T. apicalis and the cultivated plants. CLso haplotype D was detected in 2 of the 34 carrot seed lots tested, but was not detected in the plants grown from these seeds. Phylogenetic analysis by unweighted-pair group method with arithmetic means clustering suggested that haplotype D is more closely related to haplotype A than to C. A novel, sixth haplotype of CLso, most closely related to A and D, was found in the psyllid T. urticae and stinging nettle (Urtica dioica, Urticaceae), and named haplotype U.

scholarly journals Characterization of Induced Sugarcane Somaclones and their Sources Varieties Using Random Amplified Polymorphic DNA

2016 ◽  
Vol 25 (2) ◽  
pp. 223-229 ◽  
Author(s):  
Kuasha Mahmud ◽  
KM Nasiruddin ◽  
MA Hossain ◽  
L Hassan
Keyword(s):  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Group Method ◽  
Arithmetic Means ◽  
Sugarcane Varieties ◽  
Main Cluster ◽  
Pair Group ◽  
The Relationship ◽  
Linkage Distance

Sugarcane somaclones and their sources varieties were analyzed by RAPD molecular markers to check the variation at molecular level based on 1.4% agarose gel electrophoresis (AGE). Six RAPD primers generated 237 bands with average 39.5 varied from 15 to 63 with size ranging 145 - 1000 bp among the four sugarcane varieties and their 12 somaclones. Genetic diversity or polymorphism information content (PIC) value ranged from 0.39 to 0.50 for all loci across the 4 varieties and their 12 somaclones based on RAPD markers. Dendrogram based on linkage distance using unweighted pair group method of arithmetic means (UPGMA) based on 6 RAPD primers indicated segregation of the 4 sugarcane varieties and their somaclones into two main clusters at linkage distance 36. Variety Isd 39 was observed in main cluster C1 while its (Isd 39) somaclones and other varieties (Isd 37, Isd 38 and Isd 40) and also their somaclones were found in main cluster C2 having different sub-clusters. Theirfore, it may be concluded that RAPD markers can be used for identification of somaclonal variation and the relationship between sources varieties and their somaclones.Plant Tissue Cult. & Biotech. 25(2): 223-229, 2015 (December)

A native QTL for Fusarium head blight resistance in North American barley (Hordeum vulgareL.) independent of height, maturity, and spike type loci

Genome ◽  
2010 ◽  
Vol 53 (2) ◽  
pp. 111-118 ◽  
Author(s):  
G. T. Yu ◽  
J. D. Franckowiak ◽  
S. M. Neate ◽  
B. Zhang ◽  
R. D. Horsley
Keyword(s):  
North Dakota ◽  
Fusarium Head Blight ◽  
North American ◽  
Eastern China ◽  
Heading Date ◽  
Fusarium Head Blight Resistance ◽  
Gibberella Zeae ◽  
Head Blight ◽  
Hordeum Vulgare L ◽  
Fhb Resistance

Fusarium head blight (FHB), caused by Fusarium graminearum Schwabe (teleomorph Gibberella zeae (Schwein.) Petch), is one of the major diseases of barley (Hordeum vulgare L.) in eastern China, the Upper Midwest of the USA, and the eastern Prairie Provinces of Canada. To identify quantitative trait loci (QTL) controlling FHB resistance, a recombinant inbred line population (F6:7) was developed from the cross Zhenongda 7/PI 643302. The population was phenotyped for resistance to FHB in two experiments in China and four experiments in North Dakota. Accumulation of the mycotoxin deoxynivalenol was determined in one experiment in China and two in North Dakota. Simplified composite interval mapping was performed on the whole genome level using the software MQTL. The QTL FHB-2 from PI 643302 for FHB resistance was found on the distal portion of chromosome 2HL in all six FHB screening environments. This QTL accounted for 14% of phenotypic variation over six environments and was not associated with heading date or plant height. The FHB resistance QTL FHB-2 detected near the end of chromosome 2HL is in a different location from those found previously and is therefore probably unique. Because the QTL was not contributed by the Chinese cultivar Zhenongda 7, it is likely a native QTL present in North American barley. The QTL FHB-2 represents the first reported QTL for native FHB resistance in North American germ plasm and has been given the provisional name Qrgz-2H-14. This QTL should be considered for pyramiding with other FHB QTL previously mapped.

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