Floral and Nursery Plants Research Unit

West Ocean City, MD, United States

Floral and Nursery Plants Research Unit

West Ocean City, MD, United States

Time filter

Source Type

Natarajan S.S.,U.S. Department of Agriculture | Xu C.,Rutgers University | Garrett W.M.,Beltsville Agricultural Research Center | Lakshman D.,Floral and Nursery Plants Research Unit | Bae H.,Yeungnam University
Journal of Plant Biochemistry and Biotechnology | Year: 2012

Using two-dimensional polyacrylamide gel electrophoresis and mass spectrometry, we investigated the distribution of the low abundant proteins that are involved in soybean seed development in four wild and 12 cultivated soybean genotypes. We found proteomic variation of low abundant proteins involved in soybean seed metabolism within and between groups. The major proteomic variation among these 16 genotypes was observed in the seed maturation proteins, which consisted of 4-6 protein spots. All genotypes showed 3 spots of sucrose-binding protein except one wild genotype which had 2 spots. Two protein spots were detected for a triacylglycerol (TAG) accumulation factor protein in 13 genotypes, while one spot was detected in one ancestral and one wild genotype, and no spot was detected in one of the wild genotypes. All genotypes showed 3 spots of alcohol dehydrogenase except one Asian landrace and one wild genotype that had only one spot. Minor proteomic variation was detected in 16 genotypes for an elongation factor (EF2) and formate dehydrogenase, with apparent absence of EF2 in one landrace and formate dehydrogenase in another landrace genotype. No differences in the proteomic distribution of dehydrin-like protein, seed biotin-containing protein, glyceraldehyde 3-phosphate dehydrogenase, and fructose bisphosphate aldolase were detected. This information will be useful in selecting genotypes for breeding programs, and forms a baseline to which variation in transgenic varieties can be compared. © 2011 Society for Plant Biochemistry and Biotechnology.


Merewitz E.B.,Rutgers University | Belanger F.C.,Rutgers University | Warnke S.E.,Floral and Nursery Plants Research Unit | Huang B.,Rutgers University
Crop Science | Year: 2012

Identification of quantitative trait loci (QTL) for drought tolerance will allow for detection of important genomic regions associated with specifi c drought tolerance traits. This study aimed to identify QTL for drought tolerance traits in a colonial bentgrass (Agrostis capillaris L.) × creeping bentgrass (Agrostis stolonifera L.) hybrid backcross population. The traits included relative water content (RWC), turf quality (TQ), electrolyte leakage (EL), chlorophyll content (CHL), normalized difference vegetation index (NDVI), and canopy temperature depression (CTD). A colonial × creeping bentgrass hybrid backcross population segregating for drought tolerance was exposed to drought stress by withholding irrigation in three different locations or environmental conditions (two greenhouse studies in two different years, 2009 and 2010, and a growth chamber study in 2010). Phenotypic trait data were collected in these studies. Significant variation in the parents and the progenies occurred for phenotypic traits and the broad-sense heritability values indicated that the traits were polygenic in nature. A total of 32 potential QTL of varying effects (31 major and 1 minor) were detected on seven chromosomes. Significant overlap of QTL was found, particularly for CHL and CTD on 1A1, CTD, CHL, EL, and NDVI on linkage group 2A1, CTD and TQ on 2A2, TQ and RWC on 5A1 and 5A2, and TQ and CHL on 5A2. The QTL with the strongest effect for each trait (highest likelihood of the odds [LOD] and percent of phenotypic variance explained by the QTL) were CTD (4.19, 18.8%), CHL (4.23, 18.9%), EL (3.25, 14.9%), and NDVI (4.12, 22.4%) on group 2A1, RWC (3.27, 15.7%) on group 5A1, and TQ (4.38, 19.5%) on group 5A2. The analysis of potential genes in the QTL regions for these physiological traits indicate that the QTL may be linked to metabolic factors involved in N metabolism and energy metabolism such as photosynthesis and respiration. The QTL regions identified here could contain important genetic factors conferring drought tolerance in bentgrass species. © Crop Science Society of America.


PubMed | Floral and Nursery Plants Research Unit, Chungnam National University and Korea Research Institute of Bioscience and Biotechnology
Type: Journal Article | Journal: Archives of virology | Year: 2016

The complete genomic sequence of a novel putative member of the genus Potyvirus was detected from Callistephus chinensis (China aster) in South Korea. The genomic RNA consists of 9,859 nucleotides (excluding the 3 poly(A) tail) and contains the typical open reading frame of potyviruses, encoding a putative large polyprotein of 3,154 amino acids. The Callistephus virus is most closely related to plum pox virus and members of the ApVY subgroup which showed 50-52% polyprotein amino acid sequence identity. These results suggest that the Callistephus virus is a novel member of the genus Potyvirus, tentatively named callistephus mottle virus (CalMV).


PubMed | Floral and Nursery Plants Research Unit, Chinese Academy of Agricultural Sciences, Instituto Agronomico Mediterraneo and U.S. Department of Agriculture
Type: Journal Article | Journal: PloS one | Year: 2015

Xylella fastidiosa causes bacterial leaf scorch in many landscape trees including elm, oak, sycamore and mulberry, but methods for specific identification of a particular tree host species-limited strain or differentiation of tree-specific strains are lacking. It is also unknown whether a particular landscape tree-infecting X. fastidiosa strain is capable of infecting multiple landscape tree species in an urban environment. We developed two PCR primers specific for mulberry-infecting strains of X. fastidiosa based on the nucleotide sequence of a unique open reading frame identified only in mulberry-infecting strains among all the North and South American strains of X. fastidiosa sequenced to date. PCR using the primers allowed for detection and identification of mulberry-infecting X. fastidiosa strains in cultures and in samples collected from naturally infected mulberry trees. In addition, no mixed infections with or non-specific detections of the mulberry-infecting strains of X. fastidiosa were found in naturally X. fastidiosa-infected oak, elm and sycamore trees growing in the same region where naturally infected mulberry trees were grown. This genotype-specific PCR assay will be valuable for disease diagnosis, studies of strain-specific infections in insects and plant hosts, and management of diseases caused by X. fastidiosa. Unexpectedly but interestingly, the unique open reading frame conserved in the mulberry-infecting strains in the U. S. was also identified in the recently sequenced olive-associated strain CoDiRO isolated in Italy. When the primer set was tested against naturally infected olive plant samples collected in Italy, it allowed for detection of olive-associated strains of X. fastidiosa in Italy. This PCR assay, therefore, will also be useful for detection and identification of the Italian group of X. fastidiosa strains to aid understanding of the occurrence, evolution and biology of this new group of X. fastidiosa strains.


Ozel C.A.,Gazi University | Kamo K.,Floral and Nursery Plants Research Unit
Acta Horticulturae | Year: 2013

Conditions were optimized for transient transformation of Lilium longiflorum 'Nellie White' using Agrobacterium tumefaciens. Bulb scale and basal meristem explants were inoculated with A. tumefaciens strain AGL1 containing the binary vector pCAMBIA 2301 which has the uidA gene that codes for/7-glucuronidase, GUS expression. Transformed bulb scales showed transient GUS expression when they had been precultured 11 days on Murashige and Skoog's (MS) medium supplemented with 2 mg/L dicamba. The outer, larger-sized bulb scales were not infected nearly as well as the inner, smaller bulb scales. Maximum GUS expression occurred when bulb scales had been obtained from plants that had been grown in the dark for at least 2 months rather than in the light indicating the importance of growing plants in the dark for Agrobacterium- mediated transient transformation of bulb scales. Basal meristems taken from plants grown 4 months in the dark showed 3 times as much GUS expression as basal meristems from plants grown in a 12 h light photoperiod. The frequency of transient GUS expression achieved in this study indicated that it should be possible to achieve stable transformation of 'Nellie White' which is the cultivar that dominates the US market of Easter lilies. Experiments for stable transformation are in progress.


Stulberg M.J.,Floral and Nursery Plants Research Unit | Stulberg M.J.,Oak Ridge Institute for Science and Education | Huang Q.,Floral and Nursery Plants Research Unit
PLoS ONE | Year: 2015

Ralstonia solanacearum race 3 biovar 2 strains belonging to phylotype IIB, sequevars 1 and 2 (IIB-1&2) cause brown rot of potato in temperate climates, and are quarantined pathogens in Canada and Europe. Since these strains are not established in the U.S. and because of their potential risk to the potato industry, the U.S. government has listed them as select agents. Cultivated geraniums are also a host and have the potential to spread the pathogen through trade, and its extracts strongly inhibits DNA-based detection methods. We designed four primer and probe sets for an improved qPCR method that targets stable regions of DNA. RsSA1 and RsSA2 recognize IIB-1&2 strains, RsII recognizes the current phylotype II (the newly proposed R. solanacearum species) strains (and a non-plant associated R. mannitolilytica), and Cox1 recognizes eight plant species including major hosts of R. solanacearum such as potato, tomato and cultivated geranium as an internal plant control. We multiplexed the RsSA2 with the RsII and Cox1 sets to provide two layers of detection of a positive IIB-1&2 sample, and to validate plant extracts and qPCR reactions. The TaqMan-based uniplex and multiplex qPCR assays correctly identified 34 IIB-1&2 and 52 phylotype II strains out of 90 R. solanacearum species complex strains. Additionally, the multiplex qPCR assay was validated successfully using 169 artificially inoculated symptomatic and asymptomatic plant samples from multiple plant hosts including geranium. Furthermore, we developed an extraction buffer that allowed for a quick and easy DNA extraction from infected plants including geraniumfor detection of R. solanacearumby qPCR. Our multiplex qPCR assay, especially when coupled with the quick extraction buffer method, allows for quick, easy and reliable detection and differentiation of the IIB-1&2 strains of R. solanacearum.


Stulberg M.J.,Floral and Nursery Plants Research Unit | Stulberg M.J.,Oak Ridge Institute for Science and Education | Huang Q.,Floral and Nursery Plants Research Unit
Journal of Microbiological Methods | Year: 2016

The phytopathogen Ralstonia solanacearum is a species complex that contains race 3 biovar 2 strains belonging to phylotype IIB sequevars 1 and 2 that are quarantined or select agent pathogens. Recently, the R. solanacearum species complex strains have been reclassified into three genospecies: R. solanacearum, Ralstonia pseudosolanacearum and Ralstonia syzygii. An unidentified R. solanacearum strain is considered a select agent in the US until proven to be a non-race 3 biovar 2 (non-phylotype IIB sequevars 1&2). Currently, sequevars of R. solanacearum species complex strains can only be determined by phylogenetic analysis of a partial endoglucanase (egl) sequence of approximately 700-bp in length. Such analysis, however, requires expert knowledge to properly trim the sequence, to include the correct reference strains, and to interpret the results. By comparing GenBank egl sequences of representative R. solanacearum species-complex strains, we identified genospecies- and sequevar 1 and 2-specific single nucleotide polymorphisms (SNPs). We also designed primers to amplify a shorter, 526-bp, egl fragment from R. solanacearum species complex strains for easy sequencing of the amplicon, and to facilitate direct and specific amplification of egl from R. solanacearum-infected plant samples without the need of bacterial isolation. We wrote a computer program (Ralstonia solanacearum typing program) that analyzes a minimum 400-bp user-input egl sequence from a R. solanacearum strain for egl homology and SNP content to determine 1) whether it belongs to the R. solanacearum species complex, 2) if so, to which genospecies, and 3) whether it is of the sequevar type (sequevars 1 and 2) associated with the select agent/quarantined R. solanacearum strain. The program correctly typed all 371 tested egl sequences with known sequevars, obtained either from GenBank or through personal communication. Additionally, the program successfully typed 25 R. solanacearum strains in our collection with no prior sequevar information, as well as 4 strains in infected plant samples, using their partial egl sequences amplified and sequenced with primers designed in this study. The Ralstonia solanacearum typing program does not require expertise or specific knowledge to use, gives results in seconds, and provides data interpretation for the user. The program and primers can help expert or non-expert users to quickly type an unknown R. solanacearum species-complex strain and determine whether it is a highly regulated R. solanacearum strain. The program can also serve as a confirmation method, since it is the only method that can easily and directly determine whether the strain in question is a sequevar 1 or 2 strain of R. solanacearum. © 2016 .


PubMed | Floral and Nursery Plants Research Unit and Oak Ridge Institute for Science and Education
Type: Journal Article | Journal: PloS one | Year: 2015

Ralstonia solanacearum race 3 biovar 2 strains belonging to phylotype IIB, sequevars 1 and 2 (IIB-1&2) cause brown rot of potato in temperate climates, and are quarantined pathogens in Canada and Europe. Since these strains are not established in the U.S. and because of their potential risk to the potato industry, the U.S. government has listed them as select agents. Cultivated geraniums are also a host and have the potential to spread the pathogen through trade, and its extracts strongly inhibits DNA-based detection methods. We designed four primer and probe sets for an improved qPCR method that targets stable regions of DNA. RsSA1 and RsSA2 recognize IIB-1&2 strains, RsII recognizes the current phylotype II (the newly proposed R. solanacearum species) strains (and a non-plant associated R. mannitolilytica), and Cox1 recognizes eight plant species including major hosts of R. solanacearum such as potato, tomato and cultivated geranium as an internal plant control. We multiplexed the RsSA2 with the RsII and Cox1 sets to provide two layers of detection of a positive IIB-1&2 sample, and to validate plant extracts and qPCR reactions. The TaqMan-based uniplex and multiplex qPCR assays correctly identified 34 IIB-1&2 and 52 phylotype II strains out of 90 R. solanacearum species complex strains. Additionally, the multiplex qPCR assay was validated successfully using 169 artificially inoculated symptomatic and asymptomatic plant samples from multiple plant hosts including geranium. Furthermore, we developed an extraction buffer that allowed for a quick and easy DNA extraction from infected plants including geranium for detection of R. solanacearum by qPCR. Our multiplex qPCR assay, especially when coupled with the quick extraction buffer method, allows for quick, easy and reliable detection and differentiation of the IIB-1&2 strains of R. solanacearum.


PubMed | Floral and Nursery Plants Research Unit and Oak Ridge Institute for Science and Education
Type: | Journal: Journal of microbiological methods | Year: 2016

The phytopathogen Ralstonia solanacearum is a species complex that contains race 3 biovar 2 strains belonging to phylotype IIB sequevars 1 and 2 that are quarantined or select agent pathogens. Recently, the R. solanacearum species complex strains have been reclassified into three genospecies: R. solanacearum, Ralstonia pseudosolanacearum and Ralstonia syzygii. An unidentified R. solanacearum strain is considered a select agent in the US until proven to be a non-race 3 biovar 2 (non-phylotype IIB sequevars 1&2). Currently, sequevars of R. solanacearum species complex strains can only be determined by phylogenetic analysis of a partial endoglucanase (egl) sequence of approximately 700-bp in length. Such analysis, however, requires expert knowledge to properly trim the sequence, to include the correct reference strains, and to interpret the results. By comparing GenBank egl sequences of representative R. solanacearum species-complex strains, we identified genospecies- and sequevar 1 and 2-specific single nucleotide polymorphisms (SNPs). We also designed primers to amplify a shorter, 526-bp, egl fragment from R. solanacearum species complex strains for easy sequencing of the amplicon, and to facilitate direct and specific amplification of egl from R. solanacearum-infected plant samples without the need of bacterial isolation. We wrote a computer program (Ralstonia solanacearum typing program) that analyzes a minimum 400-bp user-input egl sequence from a R. solanacearum strain for egl homology and SNP content to determine 1) whether it belongs to the R. solanacearum species complex, 2) if so, to which genospecies, and 3) whether it is of the sequevar type (sequevars 1 and 2) associated with the select agent/quarantined R. solanacearum strain. The program correctly typed all 371 tested egl sequences with known sequevars, obtained either from GenBank or through personal communication. Additionally, the program successfully typed 25 R. solanacearum strains in our collection with no prior sequevar information, as well as 4 strains in infected plant samples, using their partial egl sequences amplified and sequenced with primers designed in this study. The Ralstonia solanacearum typing program does not require expertise or specific knowledge to use, gives results in seconds, and provides data interpretation for the user. The program and primers can help expert or non-expert users to quickly type an unknown R. solanacearum species-complex strain and determine whether it is a highly regulated R. solanacearum strain. The program can also serve as a confirmation method, since it is the only method that can easily and directly determine whether the strain in question is a sequevar 1 or 2 strain of R. solanacearum.


PubMed | Center for Plant Health Science and Technology and Floral and Nursery Plants Research Unit
Type: Journal Article | Journal: Current microbiology | Year: 2016

Bacterial wilt caused by Ralstonia solanacearum is destructive to many plant species worldwide. The race 3 biovar 2 (r3b2) strains of R. solanacearum infect potatoes in temperate climates and are listed as select agents by the U.S. government. TaqMan-based real-time quantitative PCR (qPCR) is commonly used in federal and state diagnostic laboratories over conventional PCR due to its speed and sensitivity. We developed the Rs16S primers and probe set and compared it with a widely used set (RS) for detecting R. solanacearum species complex strains. We also developed the RsSA3 primers and probe set and compared it with the previously published B2 and RsSA2 sets for specific detection of r3b2 strains. Both comparisons were done under standardized qPCR master mix and cycling conditions. The Rs16S and RS assays detected all 90 R. solanacearum species complex strains and none of the five outgroups, but the former was more sensitive than the latter. For r3b2 strain detection, the RsSA2 and RsSA3 sets specifically detected the 34 r3b2 strains and none of the 56 R. solanacearum non-r3b2 strains or out-group strains. The B2 set, however, detected five non-r3b2 R. solanacearum strains and was less sensitive than the other two sets under the same testing conditions. We conclude that the Rs16S, RsSA2, and RsSA3 sets are best suited under the standardized conditions for the detection of R. solanacearum species complex and r3b2 strains by TaqMan-based qPCR assays.

Loading Floral and Nursery Plants Research Unit collaborators
Loading Floral and Nursery Plants Research Unit collaborators