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Downy mildews caused by obligate biotrophic oomycetes result in severe crop losses worldwide. Among these pathogens, Pseudoperonospora cubensis and P. humuli, two closely related oomycetes, adversely affect cucurbits and hop, respectively. Discordant hypotheses concerning their taxonomic relationships have been proposed based on host–pathogen interactions and specificity evidence and gene sequences of a few individuals, but population genetics evidence supporting these scenarios is missing. Furthermore, nuclear and mitochondrial regions of both pathogens have been analyzed using microsatellites and phylogenetically informative molecular markers, but extensive comparative population genetics research has not been done. Here, we genotyped 138 current and historical herbarium specimens of those two taxa using microsatellites (SSRs). Our goals were to assess genetic diversity and spatial distribution, to infer the evolutionary history of P. cubensis and P. humuli, and to visualize genome-scale organizational relationship between both pathogens. High genetic diversity, modest gene flow, and presence of population structure, particularly in P. cubensis, were observed. When tested for cross-amplification, 20 out of 27 P. cubensis-derived gSSRs cross-amplified DNA of P. humuli individuals, but few amplified DNA of downy mildew pathogens from related genera. Collectively, our analyses provided a definite argument for the hypothesis that both pathogens are distinct species, and suggested further speciation in the P. cubensis complex.
Marcin Nowicki; Denita Hadziabdic; Robert N. Trigiano; Sarah L. Boggess; Loukas Kanetis; Phillip A. Wadl; Peter S. Ojiambo; Marc A. Cubeta; Otmar Spring; Marco Thines; Fabian Runge; Brian E. Scheffler. “Jumping Jack”: Genomic Microsatellites Underscore the Distinctiveness of Closely Related Pseudoperonospora cubensis and Pseudoperonospora humuli and Provide New Insights Into Their Evolutionary Past. Frontiers in Microbiology 2021, 12, 1 .
AMA StyleMarcin Nowicki, Denita Hadziabdic, Robert N. Trigiano, Sarah L. Boggess, Loukas Kanetis, Phillip A. Wadl, Peter S. Ojiambo, Marc A. Cubeta, Otmar Spring, Marco Thines, Fabian Runge, Brian E. Scheffler. “Jumping Jack”: Genomic Microsatellites Underscore the Distinctiveness of Closely Related Pseudoperonospora cubensis and Pseudoperonospora humuli and Provide New Insights Into Their Evolutionary Past. Frontiers in Microbiology. 2021; 12 ():1.
Chicago/Turabian StyleMarcin Nowicki; Denita Hadziabdic; Robert N. Trigiano; Sarah L. Boggess; Loukas Kanetis; Phillip A. Wadl; Peter S. Ojiambo; Marc A. Cubeta; Otmar Spring; Marco Thines; Fabian Runge; Brian E. Scheffler. 2021. "“Jumping Jack”: Genomic Microsatellites Underscore the Distinctiveness of Closely Related Pseudoperonospora cubensis and Pseudoperonospora humuli and Provide New Insights Into Their Evolutionary Past." Frontiers in Microbiology 12, no. : 1.
Pyrus calleryana Decne. (Callery pear) includes cultivars that in the United States are popular ornamentals in commercial and residential landscapes. Last few decades, this species has increasingly naturalized across portions of the eastern and southern US. However, the mechanisms behind this plant’s spread are not well understood. The genetic relationship of present-day P.calleryana trees with their Asian P. calleryana forebears (native trees from China, Japan, and Korea) and the original specimens of US cultivars are unknown. We developed and used 18 microsatellite markers to analyze 147 Pyrus source samples and to articulate the status of genetic diversity within Asian P. calleryana and US cultivars. We hypothesized that Asian P. calleryana specimens and US cultivars would be genetically diverse and would show genetic relatedness. Our data revealed high genetic diversity, high gene flow, and presence of population structure in P. calleryana, potentially relating to the highly invasive capability of this species. Strong evidence for genetic relatedness between Asian P. calleryana specimens and US cultivars was also demonstrated. Our data suggest the source for P. calleryana that have become naturalized in US was China. These results will help understand the genetic complexity of invasive P. calleryana when developing management for escaped populations: In follow-up studies, we use the gSSRs developed here to analyze P. calleryana escape populations from across US.
Shiwani Sapkota; Sarah Boggess; Robert Trigiano; William Klingeman; Denita Hadziabdic; David Coyle; Bode Olukolu; Ryan Kuster; Marcin Nowicki. Microsatellite Loci Reveal Genetic Diversity of Asian Callery Pear (Pyrus calleryana) in the Species Native Range and in the North American Cultivars. Life 2021, 11, 531 .
AMA StyleShiwani Sapkota, Sarah Boggess, Robert Trigiano, William Klingeman, Denita Hadziabdic, David Coyle, Bode Olukolu, Ryan Kuster, Marcin Nowicki. Microsatellite Loci Reveal Genetic Diversity of Asian Callery Pear (Pyrus calleryana) in the Species Native Range and in the North American Cultivars. Life. 2021; 11 (6):531.
Chicago/Turabian StyleShiwani Sapkota; Sarah Boggess; Robert Trigiano; William Klingeman; Denita Hadziabdic; David Coyle; Bode Olukolu; Ryan Kuster; Marcin Nowicki. 2021. "Microsatellite Loci Reveal Genetic Diversity of Asian Callery Pear (Pyrus calleryana) in the Species Native Range and in the North American Cultivars." Life 11, no. 6: 531.
Peronospora tabacina is an obligate parasite that causes blue mold of tobacco. The pathogen reproduces primarily asexually by sporangia, and sexual oospores are a rarely observed form of propagation. A collection of 122 isolates of P. tabacina was genotyped using nine microsatellites to assess the population structure of individuals from subpopulations collected from Central, Southern, and Eastern Europe, the Middle East, Central and North America, and Australia. Genetic variation among the six subpopulations accounted for about 8% of total variation with moderate levels of genetic differentiation, high gene flow among these subpopulations, and a positive correlation between geographic and genetic distance (r = 0.225; P<0.001). Evidence of linkage disequilibrium (P<0.001) showed that populations contained partially clonal subpopulations, except subpopulations from Australia and Mediterranean Europe. High genetic variation and population structure among samples could be explained by continuous gene flow across continents via infected transplant exchange and/or long-distance dispersal of sporangia via wind currents. This study analyzed the most numerous P. tabacina collection to date and allowed conclusions on the migration, mutation, and evolutionary history of this obligate biotrophic oomycete. The evidence pointed to the species origin in Australia and identified intra- and inter-continental migration patterns of this important pathogen.
Marcin Nowicki; Denita Hadziabdic Guerry; Robert N Trigiano; Fabian Runge; Marco Thines; Sarah L Boggess; Jean B. Ristaino; Otmar Spring. Microsatellite markers from Peronospora tabacina, the cause of blue mold of tobacco, reveal species origin, population structure, and high gene flow. Phytopathology® 2021, 1 .
AMA StyleMarcin Nowicki, Denita Hadziabdic Guerry, Robert N Trigiano, Fabian Runge, Marco Thines, Sarah L Boggess, Jean B. Ristaino, Otmar Spring. Microsatellite markers from Peronospora tabacina, the cause of blue mold of tobacco, reveal species origin, population structure, and high gene flow. Phytopathology®. 2021; ():1.
Chicago/Turabian StyleMarcin Nowicki; Denita Hadziabdic Guerry; Robert N Trigiano; Fabian Runge; Marco Thines; Sarah L Boggess; Jean B. Ristaino; Otmar Spring. 2021. "Microsatellite markers from Peronospora tabacina, the cause of blue mold of tobacco, reveal species origin, population structure, and high gene flow." Phytopathology® , no. : 1.
The Viburnum genus is of particular interest to horticulturalists, phylogeneticists, and biogeographers. Despite its popularity, there are few existing molecular markers to investigate genetic diversity in this large genus, which includes over 160 species. There are also few polymorphic molecular tools that can delineate closely related species within the genus. Viburnum farreri, a member of the Solenotinus subclade and one of the centers of diversity for Viburnum, was selected for DNA sequencing and development of genomic simple sequence repeats (gSSRs). In this study, 15 polymorphic gSSRs were developed and characterized for a collection of 19 V. farreri samples. Number of alleles per locus ranged from two- to- eight and nine loci had four or more alleles. Observed heterozygosity ranged from 0 to 0.84 and expected heterozygosity ranged from 0.10 to 0.80 for the 15 loci. Shannon diversity index values across these loci ranged from 0.21 to 1.62. The markers developed in this study add to the existing molecular toolkit for the genus and will be used in future studies investigating cross-transferability, genetic variation, and species and cultivar delimitation in the Viburnum genus and closely allied genera in the Adoxaceae and Caprifoliaceae.
Trinity Hamm; Marcin Nowicki; Sarah Boggess; William Klingeman; Denita Hadziabdic; Matthew Huff; Margaret Staton; Robert Trigiano. Development and Characterization of 15 Novel Genomic SSRs for Viburnum farreri. Plants 2021, 10, 487 .
AMA StyleTrinity Hamm, Marcin Nowicki, Sarah Boggess, William Klingeman, Denita Hadziabdic, Matthew Huff, Margaret Staton, Robert Trigiano. Development and Characterization of 15 Novel Genomic SSRs for Viburnum farreri. Plants. 2021; 10 (3):487.
Chicago/Turabian StyleTrinity Hamm; Marcin Nowicki; Sarah Boggess; William Klingeman; Denita Hadziabdic; Matthew Huff; Margaret Staton; Robert Trigiano. 2021. "Development and Characterization of 15 Novel Genomic SSRs for Viburnum farreri." Plants 10, no. 3: 487.
Cornus kousa (Asian dogwood), an East Asia native tree, is the most economically important species of the dogwood genus, owing to its desirable horticultural traits and ability to hybridize with North America‐native dogwoods. To assess the species genetic diversity and to better inform the ongoing and future breeding efforts, we assembled an herbarium and arboretum collection of 131 noncultivated C. kousa specimens. Genotyping and capillary electrophoresis analyses of our C. kousa collection with the newly developed genic and published nuclear genomic microsatellites permitted assessment of genetic diversity and evolutionary history of the species. Regardless of the microsatellite type used, the study yielded generally similar insights into the C. kousa diversity with subtle differences deriving from and underlining the marker used. The accrued evidence pointed to the species distinct genetic pools related to the plant country of origin. This can be helpful in the development of the commercial cultivars for this important ornamental crop with increased pyramided utility traits. Analyses of the C. kousa evolutionary history using the accrued genotyping datasets pointed to an unsampled ancestor population, possibly now extinct, as per the phylogeography of the region. To our knowledge, there are few studies utilizing the same gDNA collection to compare performance of genomic and genic microsatellites. This is the first detailed report on C. kousa species diversity and evolutionary history inference.
Marcin Nowicki; Logan C. Houston; Sarah L. Boggess; Anthony S. Aiello; Miriam Payá‐Milans; Margaret E. Staton; Mitsuhiro Hayashida; Masahiro Yamanaka; Shigetoshi Eda; Robert N. Trigiano. Species diversity and phylogeography ofCornus kousa(Asian dogwood) captured by genomic and genic microsatellites. Ecology and Evolution 2020, 10, 8299 -8312.
AMA StyleMarcin Nowicki, Logan C. Houston, Sarah L. Boggess, Anthony S. Aiello, Miriam Payá‐Milans, Margaret E. Staton, Mitsuhiro Hayashida, Masahiro Yamanaka, Shigetoshi Eda, Robert N. Trigiano. Species diversity and phylogeography ofCornus kousa(Asian dogwood) captured by genomic and genic microsatellites. Ecology and Evolution. 2020; 10 (15):8299-8312.
Chicago/Turabian StyleMarcin Nowicki; Logan C. Houston; Sarah L. Boggess; Anthony S. Aiello; Miriam Payá‐Milans; Margaret E. Staton; Mitsuhiro Hayashida; Masahiro Yamanaka; Shigetoshi Eda; Robert N. Trigiano. 2020. "Species diversity and phylogeography ofCornus kousa(Asian dogwood) captured by genomic and genic microsatellites." Ecology and Evolution 10, no. 15: 8299-8312.
Helianthus verticillatus (Asteraceae), whorled sunflower, is a perennial species restricted to a few locations in the Southeastern United States. Habitat loss has caused H. verticillatus to become rare, and since 2014, it has been federally listed as an endangered species. As a part of the recovery plan for the restoration and protection of H. verticillatus, an efficient micropropagation protocol based on axillary shoot proliferation was developed. Various concentrations of 6-benzylaminopurine (BAP; 0 to 4.44 µM) were examined for their morphogenetic potential in the regeneration of six genotypes of H. verticillatus from the nodal explants derived from greenhouse-grown plants. Both the BAP concentration and genotype had significant effects on the regeneration capacity of H. verticillatus. Although the induced buds were observed on ½-strength Murashige and Skoog medium without plant growth regulators, a higher rate of induction and bud development were achieved on media with either 0.88 or 2.22 µM BAP, regardless of the genotype. Successful rooting of the induced shoots was achieved within four weeks after the transfer from the induction medium to the fresh ½-strength MS medium, but the rooting efficiency was dependent on the plant’s genetic background. Regenerated plantlets, with well-developed shoots and roots, were acclimatized successfully to greenhouse conditions with a 97% survival rate. Simple sequence repeats (SSRs) markers were employed to assess the genetic uniformity of the micropropagated plants of H. verticillatus. No extraneous bands were detected between regenerants and their respective donor plants, confirming the genetic fidelity and stability of regenerated plants. To our knowledge, the protocol developed in this study is the first such report for this endangered species.
Marzena Nowakowska; Žaklina Pavlović; Marcin Nowicki; Sarah L. Boggess; Robert N. Trigiano. In Vitro Propagation of an Endangered Helianthus verticillatus by Axillary Bud Proliferation. Plants 2020, 9, 1 .
AMA StyleMarzena Nowakowska, Žaklina Pavlović, Marcin Nowicki, Sarah L. Boggess, Robert N. Trigiano. In Vitro Propagation of an Endangered Helianthus verticillatus by Axillary Bud Proliferation. Plants. 2020; 9 (6):1.
Chicago/Turabian StyleMarzena Nowakowska; Žaklina Pavlović; Marcin Nowicki; Sarah L. Boggess; Robert N. Trigiano. 2020. "In Vitro Propagation of an Endangered Helianthus verticillatus by Axillary Bud Proliferation." Plants 9, no. 6: 1.
Seed treatments help reduce the pathogen load and thus improve the condition of plants from their earliest developmental stages, but they can have impacts beyond their basic fungicide protection role. In this study, we investigated how seven spring barley seed treatments affected the plants’ physiological state. The tested seed treatments differed significantly in their impacts on the vigor parameters of barley seeds and on the physiological state of seedlings under drought stress and after regeneration. Seed treatments based on substances from the succinate-dehydrogenase-inhibitors (SDHI) group did not cause inhibition of seedling growth and also display by the highest vigor index values. Using the analysis of photosynthesis-related parameters, we showed that seed treatments from the SDHI group provided a superior tolerance of the imposed drought in spring barley than other treatments. In addition to protection against abiotic stress, SDHI treatments also rendered a higher efficiency of photochemical reactions in the treated plants.
Dominika Radzikowska; Monika Grzanka; Przemysław Łukasz Kowalczewski; Romana Głowicka-Wołoszyn; Andrzej Blecharczyk; Marcin Nowicki; Zuzanna Sawinska. Influence of SDHI Seed Treatment on the Physiological Conditions of Spring Barley Seedlings under Drought Stress. Agronomy 2020, 10, 731 .
AMA StyleDominika Radzikowska, Monika Grzanka, Przemysław Łukasz Kowalczewski, Romana Głowicka-Wołoszyn, Andrzej Blecharczyk, Marcin Nowicki, Zuzanna Sawinska. Influence of SDHI Seed Treatment on the Physiological Conditions of Spring Barley Seedlings under Drought Stress. Agronomy. 2020; 10 (5):731.
Chicago/Turabian StyleDominika Radzikowska; Monika Grzanka; Przemysław Łukasz Kowalczewski; Romana Głowicka-Wołoszyn; Andrzej Blecharczyk; Marcin Nowicki; Zuzanna Sawinska. 2020. "Influence of SDHI Seed Treatment on the Physiological Conditions of Spring Barley Seedlings under Drought Stress." Agronomy 10, no. 5: 731.
Forest fragmentation may negatively affect plants through reduced genetic diversity and increased population structure due to habitat isolation, decreased population size, and disturbance of pollen‐seed dispersal mechanisms. However, in the case of tree species, effective pollen‐seed dispersal, mating system, and ecological dynamics may help the species overcome the negative effect of forest fragmentation. A fine‐scale population genetics study can shed light on the postfragmentation genetic diversity and structure of a species. Here, we present the genetic diversity and population structure of Cercis canadensis L. (eastern redbud) wild populations on a fine scale within fragmented areas centered around the borders of Georgia–Tennessee, USA. We hypothesized high genetic diversity among the collections of C. canadensis distributed across smaller geographical ranges. Fifteen microsatellite loci were used to genotype 172 individuals from 18 unmanaged and naturally occurring collection sites. Our results indicated presence of population structure, overall high genetic diversity (HE = 0.63, HO = 0.34), and moderate genetic differentiation (FST = 0.14) among the collection sites. Two major genetic clusters within the smaller geographical distribution were revealed by STRUCTURE. Our data suggest that native C. canadensis populations in the fragmented area around the Georgia–Tennessee border were able to maintain high levels of genetic diversity, despite the presence of considerable spatial genetic structure. As habitat isolation may negatively affect gene flow of outcrossing species across time, consequences of habitat fragmentation should be regularly monitored for this and other forest species. This study also has important implications for habitat management efforts and future breeding programs.
Meher A. Ony; Marcin Nowicki; Sarah L. Boggess; William E. Klingeman; John M. Zobel; Robert N. Trigiano; Denita Hadziabdic. Habitat fragmentation influences genetic diversity and differentiation: Fine‐scale population structure of Cercis canadensis (eastern redbud). Ecology and Evolution 2020, 10, 3655 -3670.
AMA StyleMeher A. Ony, Marcin Nowicki, Sarah L. Boggess, William E. Klingeman, John M. Zobel, Robert N. Trigiano, Denita Hadziabdic. Habitat fragmentation influences genetic diversity and differentiation: Fine‐scale population structure of Cercis canadensis (eastern redbud). Ecology and Evolution. 2020; 10 (8):3655-3670.
Chicago/Turabian StyleMeher A. Ony; Marcin Nowicki; Sarah L. Boggess; William E. Klingeman; John M. Zobel; Robert N. Trigiano; Denita Hadziabdic. 2020. "Habitat fragmentation influences genetic diversity and differentiation: Fine‐scale population structure of Cercis canadensis (eastern redbud)." Ecology and Evolution 10, no. 8: 3655-3670.
Potato juice (PJ), commonly considered a burdensome waste, is rich in various compounds with bioactive properties. It has long been considered a remedy for gastric problems in traditional folk medicine. If valorization of PJ through implementation in the production of functional foods is to be considered, stabilization methods must be developed to allow long-term storage of this seasonal product. It is important that such methods are chosen with regard to their effect on the bioactive value of the obtained product. In this study, the impact of four stabilization methods on the antioxidant and cytotoxic activities of PJ was investigated. Elevated temperatures were used in thermal deproteinization used to obtain DPJW (deproteinated potato juice water) and spray-drying of FPJ (fresh potato juice) that resulted in SDPJ. Freeze drying and cryoconcentration were the low temperature processing methods that yielded PJL (potato juice lyophilisate) and CPJ (cryocorncentrated potato juice), respectively. All processed materials were characterized chemically and compared with raw materials in terms of phenolic compounds content, antioxidant activity as well as cytotoxicity to human tumor cells isolated from the gastric mucosa (Hs476T cell line), colon (Caco-2 and HT-29 cell lines), and normal cells isolated from the small intestine and colon epithelium (IEC-6 and NCM460 cell lines). It was stated that high-temperature processes – thermal deproteinization and spray-drying – yielded products with increased antioxidant potential (TEAC) that also showed increased cytotoxic activity towards intestinal cancer cells. At the same time the cytotoxicity towards normal cells remained on par with that of fresh PJ (IEC-6 cells) or decreased (NCM460 cells). Thermal deproteinization significantly decreased the content of glycoalcaloids in the juice, while spray drying did not have such an effect. The two low-temperature processes investigated – cryoconcentration and freeze drying – did not affect the PJ cytotoxic activity towards any of the cell lines used in the tests, whereas they did affect the antioxidant properties and glycoalcaloids content of PJ.
Przemysław Łukasz Kowalczewski; Anna Olejnik; Wojciech Białas; Piotr Kubiak; Aleksander Siger; Marcin Nowicki; Grażyna Lewandowicz. Effect of Thermal Processing on Antioxidant Activity and Cytotoxicity of Waste Potato Juice. Open Life Sciences 2019, 14, 150 -157.
AMA StylePrzemysław Łukasz Kowalczewski, Anna Olejnik, Wojciech Białas, Piotr Kubiak, Aleksander Siger, Marcin Nowicki, Grażyna Lewandowicz. Effect of Thermal Processing on Antioxidant Activity and Cytotoxicity of Waste Potato Juice. Open Life Sciences. 2019; 14 (1):150-157.
Chicago/Turabian StylePrzemysław Łukasz Kowalczewski; Anna Olejnik; Wojciech Białas; Piotr Kubiak; Aleksander Siger; Marcin Nowicki; Grażyna Lewandowicz. 2019. "Effect of Thermal Processing on Antioxidant Activity and Cytotoxicity of Waste Potato Juice." Open Life Sciences 14, no. 1: 150-157.
Taraxacum kok-saghyz (TKS) carries great potential as alternative natural rubber source. To better inform future breeding efforts with TKS and gain a deeper understanding of its genetic diversity, we utilized de novo sequencing to generate novel genomic simple sequence repeats markers (gSSRs). We utilized 25 gSSRs on a collection of genomic DNA (gDNA) samples from germplasm bank, and two gDNA samples from historical herbarium specimens. PCR coupled with capillary electrophoresis and an array of population genetics tools were employed to analyze the dataset of our study as well as a dataset of the recently published genic SSRs (eSSRs) generated on the same germplasm. Our results using both gSSRs and eSSRs revealed that TKS has low- to- moderate genetic diversity with most of it partitioned to the individuals and individuals within populations, whereas the species lacked population structure. Nineteen of the 25 gSSR markers cross-amplified to other Taraxacum spp. collected from Southeastern United States and identified as T. officinale by ITS sequencing. We used a subset of 14 gSSRs to estimate the genetic diversity of the T. officinale gDNA collection. In contrast to the obligatory outcrossing TKS, T. officinale presented evidence for population structure and clonal reproduction, which agreed with the species biology. We mapped the molecular markers sequences from this study and several others to the well-annotated sunflower genome. Our gSSRs present a functional tool for the biodiversity analyses in Taraxacum, but also in the related genera, as well as in the closely related tribes of the Asteraceae.
Marcin Nowicki; Yichen Zhao; Sarah L. Boggess; Helge Fluess; Miriam Payá-Milans; Margaret E. Staton; Logan Houston; Denita Hadziabdic; Robert N. Trigiano. Taraxacum kok-saghyz (rubber dandelion) genomic microsatellite loci reveal modest genetic diversity and cross-amplify broadly to related species. Scientific Reports 2019, 9, 1 -17.
AMA StyleMarcin Nowicki, Yichen Zhao, Sarah L. Boggess, Helge Fluess, Miriam Payá-Milans, Margaret E. Staton, Logan Houston, Denita Hadziabdic, Robert N. Trigiano. Taraxacum kok-saghyz (rubber dandelion) genomic microsatellite loci reveal modest genetic diversity and cross-amplify broadly to related species. Scientific Reports. 2019; 9 (1):1-17.
Chicago/Turabian StyleMarcin Nowicki; Yichen Zhao; Sarah L. Boggess; Helge Fluess; Miriam Payá-Milans; Margaret E. Staton; Logan Houston; Denita Hadziabdic; Robert N. Trigiano. 2019. "Taraxacum kok-saghyz (rubber dandelion) genomic microsatellite loci reveal modest genetic diversity and cross-amplify broadly to related species." Scientific Reports 9, no. 1: 1-17.
The genus Chrysogonum is native to the eastern United States. Three entities have been recognized—either as three varieties of Chrysogonum virginianum or as two species, one of them with two varieties. The current study suggests that a fourth entity should be recognized. Several forms of the complex are in commercial trade as ornamentals. As very limited molecular information on Chrysogonum is available, we developed a set of genic simple sequence repeat markers (eSSRs) from de novo transcriptome sequencing. We tested a set of 17 eSSRs on a collection of C. virginianum genomic DNA samples from the three botanical varieties, and a new putative type observed in Tennessee, dubbed “Ocoee-type” for its geographic origin. The polymerase chain reaction and capillary electrophoresis analyses with downstream population genetics tools verified the usefulness of the eSSRs. By applying this approach, we showed recognizable variation within Chrysogonum, although it did not correspond exactly to previous infraspecific classifications. Finally, as demonstrated for the commercial cultivar Pierre included in the study, the eSSRs can be used for enhancing the future breeding or hybridization efforts of this ornamental plant.
Marcin Nowicki; Edward E. Schilling; Sarah L. Boggess; Logan Houston; Matthew L. Huff; Margaret E. Staton; Jayne A. Lampley; Robert N. Trigiano. Development and Characterization of Genic Microsatellites for the Ornamental Plant Green and Gold (Chrysogonum virginianum). HortScience 2019, 54, 395 -400.
AMA StyleMarcin Nowicki, Edward E. Schilling, Sarah L. Boggess, Logan Houston, Matthew L. Huff, Margaret E. Staton, Jayne A. Lampley, Robert N. Trigiano. Development and Characterization of Genic Microsatellites for the Ornamental Plant Green and Gold (Chrysogonum virginianum). HortScience. 2019; 54 (2):395-400.
Chicago/Turabian StyleMarcin Nowicki; Edward E. Schilling; Sarah L. Boggess; Logan Houston; Matthew L. Huff; Margaret E. Staton; Jayne A. Lampley; Robert N. Trigiano. 2019. "Development and Characterization of Genic Microsatellites for the Ornamental Plant Green and Gold (Chrysogonum virginianum)." HortScience 54, no. 2: 395-400.
Chloroplast DNA is a part of plant non-nuclear genome, and is of particular interest for lineage studies. Moreover, the non-coding regions of cpDNA display higher mutation rates than the conserved coding cpDNA, which has been employed for phylogenetic and population research. We analyzed the cpDNA of 332 gDNA samples from collections of Cornus florida and C. kousa (commercial cultivars, breeding selections, and wild kousa accessions from Asia), using the chlorotyping system developed on North America-native, wild accessions of C. florida. Our results indicated significant differences in chlorotype frequencies between the two species. Cornus florida samples were represented by all major chlorotypes previously described, whereas all C. kousa samples analyzed had only one of the chlorotype patterns shown by C. florida. The chlorotyping analytic panel was then expanded by sequencing the targeted three non-coding cpDNA regions. Results indicated a major difference in the maternally-inherited cpDNA between the two closely related Big-Bracted Cornus species. Chlorotype diversity and differences in the proportion of informative sites in the cpDNA regions of focus emphasized the importance of proper loci choice for cpDNA-based comparative studies between the closely related dogwood species. Phylogenetic analyses of the retrieved sequences for the other species of Cornus provided information on the relative utility of the cpDNA regions studied and helped delineate the groups (Big-Bracted, Cornelian Cherries, Blue/White-Fruited) within the genus. Genealogical relationships based on the cpDNA sequences and the inferred chlorotype networks indicated the need for continued analyses across further non-coding cpDNA regions to improve the phylogenetic resolution of dogwoods.
Marcin Nowicki; Sarah L. Boggess; Arnold M. Saxton; Denita Hadziabdic; Qiu-Yun Jenny Xiang; Thomas Molnar; Matthew L. Huff; Margaret E. Staton; Yichen Zhao; Robert N. Trigiano. Haplotyping of Cornus florida and C. kousa chloroplasts: Insights into species-level differences and patterns of plastic DNA variation in cultivars. PLOS ONE 2018, 13, e0205407 .
AMA StyleMarcin Nowicki, Sarah L. Boggess, Arnold M. Saxton, Denita Hadziabdic, Qiu-Yun Jenny Xiang, Thomas Molnar, Matthew L. Huff, Margaret E. Staton, Yichen Zhao, Robert N. Trigiano. Haplotyping of Cornus florida and C. kousa chloroplasts: Insights into species-level differences and patterns of plastic DNA variation in cultivars. PLOS ONE. 2018; 13 (10):e0205407.
Chicago/Turabian StyleMarcin Nowicki; Sarah L. Boggess; Arnold M. Saxton; Denita Hadziabdic; Qiu-Yun Jenny Xiang; Thomas Molnar; Matthew L. Huff; Margaret E. Staton; Yichen Zhao; Robert N. Trigiano. 2018. "Haplotyping of Cornus florida and C. kousa chloroplasts: Insights into species-level differences and patterns of plastic DNA variation in cultivars." PLOS ONE 13, no. 10: e0205407.
Heavy losses incited yearly by Alternaria brassicicola on the vegetable Brassicaceae have prompted our search for sources of genetic resistance against the pathogen and the resultant disease, dark leaf spot. We optimized several parameters to test the performance of the plants under artificial inoculations with this pathogen, including leaf age and position, inoculum concentration, and incubation temperature. Using these optimized conditions, we screened a collection of 38 Brassicaceae cultigens with two methods (detached leaf and seedlings). Our results show that either method can be used for the A. brassicicola resistance breeding, and that the plant genotype was crucial in determining its response to the pathogen. The bio-assays for A. brassicicola resistance were run under more stringent lab conditions than the field tests (natural epidemics), resulting in identification of two interspecific hybrids that might be used in breeding programs. Based on the results of the biochemical analyses, reactive oxygen species and red-ox enzymes interplay has been suggested to determine the outcome of the plant-A. brassicicola interplay. Confocal microscopy analyses of the leaf samples provided data on the pathogen mode of infection: Direct epidermal infection or stomatal attack were related to plant resistance level against A. brassicicola among the cultigens tested. Further, the microscopic analyses suggested rapid actin network activation of the host cells around the papillas deposited under the pathogen appressorium.
Marzena Nowakowska; Małgorzata Wrzesińska; Piotr Kamiński; Wojciech Szczechura; Małgorzata Lichocka; Małgorzata Tartanus; Elżbieta U. Kozik; Marcin Nowicki. Alternaria brassicicola – Brassicaceae pathosystem: insights into the infection process and resistance mechanisms under optimized artificial bio-assay. European Journal of Plant Pathology 2018, 153, 131 -151.
AMA StyleMarzena Nowakowska, Małgorzata Wrzesińska, Piotr Kamiński, Wojciech Szczechura, Małgorzata Lichocka, Małgorzata Tartanus, Elżbieta U. Kozik, Marcin Nowicki. Alternaria brassicicola – Brassicaceae pathosystem: insights into the infection process and resistance mechanisms under optimized artificial bio-assay. European Journal of Plant Pathology. 2018; 153 (1):131-151.
Chicago/Turabian StyleMarzena Nowakowska; Małgorzata Wrzesińska; Piotr Kamiński; Wojciech Szczechura; Małgorzata Lichocka; Małgorzata Tartanus; Elżbieta U. Kozik; Marcin Nowicki. 2018. "Alternaria brassicicola – Brassicaceae pathosystem: insights into the infection process and resistance mechanisms under optimized artificial bio-assay." European Journal of Plant Pathology 153, no. 1: 131-151.
Heavy losses incited yearly by Alternaria brassicicola on the vegetable Brassicaceae – have prompted our search for sources of genetic resistance against the pathogen and the resultant disease, dark leaf spot. We optimized several parameters to test the performance of the plants under controlled conditions to this disease, including leaf age and position, inoculum concentration, and incubation temperature. Using these optimized conditions, we screened a collection of 38 Brassicaceae cultigens with two methods (detached leaf and seedlings). Our results show, that either method can be used for the A. brassicicola resistance breeding, while the plant’s genotype was crucial in determining its response to the pathogen. The laboartory bio-assays for A. brassicicola resistance were run under more stringent conditions than the field tests, and resulted in identification of two interspecific hybrids that might be used in breeding programs. Confocal microscopy analyses of the leaf samples provided data into the pathogen mode of infection: Direct epidermal infection or stomatal attack were related to plants’ resistance against A. brassicicola among the cultigens tested. Further, the actin network of the host cells reorganized around the papillas deposited under the pathogen’s appressorium.
Marzena Nowakowska; Małgorzata Wrzesińska; Piotr Kamiński; Marcin Nowicki; Małgorzata Lichocka; Michał Tartanus; Elżbieta U Kozik. Screening for Alternaria brassicicola resistance in the Brassicaceae: Bio-assay optimization and confocal microscopy insights into the infection process. 2016, 1 .
AMA StyleMarzena Nowakowska, Małgorzata Wrzesińska, Piotr Kamiński, Marcin Nowicki, Małgorzata Lichocka, Michał Tartanus, Elżbieta U Kozik. Screening for Alternaria brassicicola resistance in the Brassicaceae: Bio-assay optimization and confocal microscopy insights into the infection process. . 2016; ():1.
Chicago/Turabian StyleMarzena Nowakowska; Małgorzata Wrzesińska; Piotr Kamiński; Marcin Nowicki; Małgorzata Lichocka; Michał Tartanus; Elżbieta U Kozik. 2016. "Screening for Alternaria brassicicola resistance in the Brassicaceae: Bio-assay optimization and confocal microscopy insights into the infection process." , no. : 1.
Heavy losses incited yearly by Alternaria brassicicola on the vegetable Brassicaceae – have prompted our search for sources of genetic resistance against the pathogen and the resultant disease, dark leaf spot. We optimized several parameters to test the performance of the plants under controlled conditions to this disease, including leaf age and position, inoculum concentration, and incubation temperature. Using these optimized conditions, we screened a collection of 38 Brassicaceae cultigens with two methods (detached leaf and seedlings). Our results show, that either method can be used for the A. brassicicola resistance breeding, while the plant’s genotype was crucial in determining its response to the pathogen. The laboartory bio-assays for A. brassicicola resistance were run under more stringent conditions than the field tests, and resulted in identification of two interspecific hybrids that might be used in breeding programs. Confocal microscopy analyses of the leaf samples provided data into the pathogen mode of infection: Direct epidermal infection or stomatal attack were related to plants’ resistance against A. brassicicola among the cultigens tested. Further, the actin network of the host cells reorganized around the papillas deposited under the pathogen’s appressorium.
Marzena Nowakowska; Małgorzata Wrzesińska; Piotr Kamiński; Marcin Nowicki; Małgorzata Lichocka; Michał Tartanus; Elżbieta U. Kozik. Screening for Alternaria brassicicola resistance in the Brassicaceae: Bio-assay optimization and confocal microscopy insights into the infection process. 2016, 1 .
AMA StyleMarzena Nowakowska, Małgorzata Wrzesińska, Piotr Kamiński, Marcin Nowicki, Małgorzata Lichocka, Michał Tartanus, Elżbieta U. Kozik. Screening for Alternaria brassicicola resistance in the Brassicaceae: Bio-assay optimization and confocal microscopy insights into the infection process. . 2016; ():1.
Chicago/Turabian StyleMarzena Nowakowska; Małgorzata Wrzesińska; Piotr Kamiński; Marcin Nowicki; Małgorzata Lichocka; Michał Tartanus; Elżbieta U. Kozik. 2016. "Screening for Alternaria brassicicola resistance in the Brassicaceae: Bio-assay optimization and confocal microscopy insights into the infection process." , no. : 1.
We developed the LAMP-HRM assay for detection of P. infestans in a RealTime PCR machine. Specific pathogen detection was achieved in the 18th minute of the reaction, which, in comparison with other diagnostic methods, shortens the analysis time. For instance, first late blight symptoms after inoculation of tomato plants with P. infestans are manifested only 4-5 dpi. We applied the downstream HRM analyses to estimate the variablility of 96 pathogen isolates, collected from symptomatic tomatoes all over Poland, in the years 2009-2012.
Marcin Nowicki; Marzena Nowakowska; Małgorzata Wrzesińska; Elżbieta Kozik. Development of LAMP-HRM for sensitive and specific detection of Phytophthora infestans. EuroBlight workshop 10-13 May, 2015 http://euroblight.net/euroblight-workshop-10-13-may-2015/about-the-workshop/ 2015, 1 .
AMA StyleMarcin Nowicki, Marzena Nowakowska, Małgorzata Wrzesińska, Elżbieta Kozik. Development of LAMP-HRM for sensitive and specific detection of Phytophthora infestans. EuroBlight workshop 10-13 May, 2015 http://euroblight.net/euroblight-workshop-10-13-may-2015/about-the-workshop/. 2015; ():1.
Chicago/Turabian StyleMarcin Nowicki; Marzena Nowakowska; Małgorzata Wrzesińska; Elżbieta Kozik. 2015. "Development of LAMP-HRM for sensitive and specific detection of Phytophthora infestans." EuroBlight workshop 10-13 May, 2015 http://euroblight.net/euroblight-workshop-10-13-may-2015/about-the-workshop/ , no. : 1.
Late blight (LB) caused by the oomycete Phytophthora infestans continues to thwart global tomato production, while only few resistant cultivars have been introduced locally. In order to gain from the released tomato germplasm with LB resistance, we compared the 5-year field performance of LB resistance in several tomato cultigens, with the results of controlled conditions testing (i.e., detached leaflet/leaf, whole plant). In case of these artificial screening techniques, the effects of plant age and inoculum concentration were additionally considered. In the field trials, LA 1033, L 3707, L 3708 displayed the highest LB resistance, and could be used for cultivar development under Polish conditions. Of the three methods using controlled conditions, the detached leaf and the whole plant tests had the highest correlation with thefield experiments. The plant age effect on LB resistance in tomato reported here, irrespective of the cultigen tested or inoculum concentration used, makes it important to standardize the test parameters when screening for resistance. Our results help show why other reports disagree on LB resistance in tomato.
Marzena Nowakowska; Marcin Nowicki; Urszula Kłosińska; Robert Maciorowski; Elżbieta U. Kozik. Appraisal of Artificial Screening Techniques of Tomato to Accurately Reflect Field Performance of the Late Blight Resistance. PLOS ONE 2014, 9, e109328 .
AMA StyleMarzena Nowakowska, Marcin Nowicki, Urszula Kłosińska, Robert Maciorowski, Elżbieta U. Kozik. Appraisal of Artificial Screening Techniques of Tomato to Accurately Reflect Field Performance of the Late Blight Resistance. PLOS ONE. 2014; 9 (10):e109328.
Chicago/Turabian StyleMarzena Nowakowska; Marcin Nowicki; Urszula Kłosińska; Robert Maciorowski; Elżbieta U. Kozik. 2014. "Appraisal of Artificial Screening Techniques of Tomato to Accurately Reflect Field Performance of the Late Blight Resistance." PLOS ONE 9, no. 10: e109328.
Cucumber (Cucumis sativus L.) germinates in an optimal temperature ranging from 24 to 28 °C. In order to develop cultivars with low temperature germination ability, knowledge regarding its genetic basis is needed. In our earlier study, we identified the accession PI 390953 as chilling tolerant and a good cold germinator. The objective of our present study was to compare cold germinability of cold tolerant breeding line B 5669 with PI 390953, and to measure the inheritance of this trait. At 13 °C, both tested cultigens (B 5669, PI 390953) showed the highest germinability and we found no significant differences between them regarding the rate of germination, days to germination (DTG), or germination index (GI). We also observed differences in the germination ability at 13 °C among seven hybrid populations of cucumber, derived from the cross between good cold germinator B 5669 (P1) and B 6115 (P2) lacking cold-germination ability. The fastest low temperature germination and the highest low temperature germination percentages were observed in B 5669 (P1) with germination of 78 and 100% on the 6th and 10th day of the test, respectively. In addition, the cultigen B 5669 exhibited the fastest germination, reaching on average of DTG = 5.7. B 6115 (P2) and BC1P2 proved unable to germinate at 13 °C even within 21 days. The seed germinability of F2 population fits a three-recessive gene model. Cucumber cultigens B 5669, PI 390953, and PI 246903 showed low temperature tolerance, but of them B 5669 may become the most desirable to breeders since it exhibits cold germinability combined with good fruit quality traits.
Urszula Kłosińska; Elżbieta U. Kozik; Marcin Nowicki; Todd C. Wehner. Low temperature seed germination of cucumber: genetic basis of the tolerance trait. Journal of Horticultural Research 2013, 21, 125 -130.
AMA StyleUrszula Kłosińska, Elżbieta U. Kozik, Marcin Nowicki, Todd C. Wehner. Low temperature seed germination of cucumber: genetic basis of the tolerance trait. Journal of Horticultural Research. 2013; 21 (2):125-130.
Chicago/Turabian StyleUrszula Kłosińska; Elżbieta U. Kozik; Marcin Nowicki; Todd C. Wehner. 2013. "Low temperature seed germination of cucumber: genetic basis of the tolerance trait." Journal of Horticultural Research 21, no. 2: 125-130.
Marcin Nowicki; Elzbieta U. Kozik; Majid R. Foolad. Late Blight of Tomato. Translational Genomics for Crop Breeding 2013, 241 -265.
AMA StyleMarcin Nowicki, Elzbieta U. Kozik, Majid R. Foolad. Late Blight of Tomato. Translational Genomics for Crop Breeding. 2013; ():241-265.
Chicago/Turabian StyleMarcin Nowicki; Elzbieta U. Kozik; Majid R. Foolad. 2013. "Late Blight of Tomato." Translational Genomics for Crop Breeding , no. : 241-265.
Summary Dramatic increase in confocal microscopy observation output has been gained by optimization of a simple trypan blue and aniline blue dual-stain and its application to two model pathosystems: Pseudoperonospora cubensiscucumber and Phytophthora infestans-tomato. Comparison of two dual-stain methods for confocal microscopy studies of P. cubensis-challenged cucumber leaves indicated the 'mild' approach most successful. This methodology provides simultaneous detection of different pathogen structures layered with the plant defense reactions. Moreover, ImageJ-assisted quantification of plant defense responses renders this method useful for addressing the host plant resistance reactions, as well as investigating the given isolate's pathogenicity. Application of this method for the P. infestans-challenged tomato leaf samples resulted in detection of several fungal infection structures, along with plant defense responses. The dual-stain also enabled detection of a peculiar aniline blue-sensitive material in the pathogen cell walls at the area of its hyphae emerging through the leaf stomata. Results presented herein indicate this method is applicable for detailed (possibly quantitative) investigations of multiple plant-fungal pathosystems.
Marcin Nowicki; Małgorzata Lichocka; Marzena Nowakowska; Urszula Kłosińska; Elżbieta U. Kozik. A Simple Dual Stain for Detailed Investigations of Plant-Fungal Pathogen Interactions. Vegetable Crops Research Bulletin 2012, 77, 61 -74.
AMA StyleMarcin Nowicki, Małgorzata Lichocka, Marzena Nowakowska, Urszula Kłosińska, Elżbieta U. Kozik. A Simple Dual Stain for Detailed Investigations of Plant-Fungal Pathogen Interactions. Vegetable Crops Research Bulletin. 2012; 77 (1):61-74.
Chicago/Turabian StyleMarcin Nowicki; Małgorzata Lichocka; Marzena Nowakowska; Urszula Kłosińska; Elżbieta U. Kozik. 2012. "A Simple Dual Stain for Detailed Investigations of Plant-Fungal Pathogen Interactions." Vegetable Crops Research Bulletin 77, no. 1: 61-74.