Renée S Arias

Oregon State University, Corvallis, OR, United States

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Publications (19)61.67 Total impact

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    ABSTRACT: Aspergillus flavus accumulates carcinogenic aflatoxins in peanuts, mainly in immature kernels during drought. Aspergillus flavus invasion induces accumulation of phytoalexins, mostly stilbenoids in peanut, as a plant defence mechanism. Because fungal laccases are often related to pathogenicity and can degrade stilbenoids, this study reports for the first time the expression of A. flavus laccases in the presence of kernels, hulls and low water potential in relation to the accumulation of phytoalexins in peanut kernels. Packed-cell volume (PCV) of A. flavus biomass was significantly higher (P ≤ 0·01) in the presence of mature kernels, dead kernels, and mature and immature peanut hulls than the control. The presence of kernels and hulls lowered the level of expression of three A. flavus laccases by 4–6-fold (P < 0·01), whereas 3% sucrose up-regulated them by 35–304-fold, and low water potential (−1·1 MPa) up-regulated them by 85–248-fold (P < 0·01). Phytoalexins that accumulated in peanut kernels in the presence of A. flavus and were quantified by HPLC-DAD-MS were primarily the stilbenoids: 3′-isopentadienyl-3,5,4′-trihydroxystilbene (IPD), chiricanine-A, arachidin-2, arachidin-3 and arahypin-1. Apparent degradation of phytoalexins was observed when using a priori induction of phytoalexins in seeds in combination with a priori induction of laccases in A. flavus. The up-regulation of laccase expression observed at −1·1 MPa and at high sucrose concentration could be contributing to peanut invasion in immature kernels under drought conditions.
    Plant Pathology 04/2014; 63(2). · 2.73 Impact Factor
  • V. S. Sobolev, V. A. Orner, R. S. Arias
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    ABSTRACT: Background and Aims The role and linkage of endophytic bacteria to resistance of peanut seeds to biotic stress is poorly understood. The aims of the present study were to survey the experimental (axenic) and control (conventional) peanut plants for the predominant endophytic bacteria, and to characterize isolates with activity against selected A. flavus strains. Methods Young axenic plants were grown from presumably bacteria-free embryos in the lab, and then they were grown in a field. Endophytic bacterial species were identified by the analysis of DNA sequences of their 16S-ribosomal RNA gene. DNA extracted from soil was also analyzed for predominant bacteria. Results Mature seeds from the experimental and control plants contained several species of nonpathogenic endophytic bacteria. Among the eight bacterial species isolated from seeds, and DNA sequences detected in soil, Bacillus thuringiensis was dominant. All B. amyloliquefaciens isolates, the second abundant species in seeds demonstrated activity against A. flavus. This effect was not observed with any other bacterial isolates. There was no significant difference in number and relative occurrence of the two major bacterial species between the experimental and conventionally grown control seeds. Conclusion Endophytic bacterial colonization derives from local soil and not from the seed source, and the peanut plant accommodates only selected species of bacteria from diverse soil populations. Some bacterial isolates showed antibiosis against A. flavus.
    Plant and Soil 01/2013; · 3.24 Impact Factor
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    ABSTRACT: Arias RS, Molin WT, Ray JD, Peel MD & Scheffler BE (2011). Isolation and characterisation of the first microsatellite markers for Cyperus rotundus. Weed Research51, 451–460.SummaryThis is the first report of microsatellite markers for Cyperus rotundus. A total of 191 sequence-specific microsatellite markers were isolated and used to screen 12 accessions of C. rotundus and one accession of Cyperus esculentus collected from 10 different countries. Polymorphisms were observed in 49% of the markers tested, 22% of the markers were monomorphic and 29% had weak or no amplification. The best 57 markers are reported, and cluster analysis was used to analyse their resolving power. BLASTx screening of the contig sequences was also performed. Multiallelic loci over all samples ranged from 24% to 60%. The maximum number of alleles detected by the markers suggests a polyploidy nature of all C. rotundus accessions tested, except for the sample N25-Brazil. Chromosome number was determined for N12-Taiwan and used as an internal flow cytometry standard to estimate the amount of DNA within haploid nuclei of the remaining material. Chromosome numbers estimated for C. rotundus were 16 and 24. The markers identified in this study can be used for the identification of biotypes and detection of potential crosses of C. rotundus, to implement management practices for the effective control of this weed.
    Weed Research 09/2011; 51(5):451 - 460. · 2.05 Impact Factor
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    ABSTRACT: One hundred and eighty-two microsatellites or simple-sequence-repeat (SSR) markers for Macrophomina phaseolina were developed. These were tested on 24 isolates of M. phaseolina obtained from seven plant species, and the genetic variation of isolates was studied in relation to potential biological processes that could be affected in this fungus. A total of 120 SSR markers were polymorphic, amplifying >90% of the 24 isolates tested. Thirty percent of the markers showed multiple alleles on individual samples. A large number of markers showed unique alleles in isolates collected from pumpkin and snap bean. DNA sequences corresponding to 43 markers had significant hits on blastx and/or blast2go, and the polymorphism of 36 of those markers showed specific allele patterns for one or more plant host origin of the isolates. Additional tests on growth rate and copper resistance of the isolates identified markers that could be related to those traits. In addition, 27 markers were monomorphic and amplified all 24 isolates. Whereas polymorphic markers can be used for population genetics studies of M. phaseolina, the group of 27 monomorphic markers could help in the fast identification of this species in clinical specimens. The SSR markers developed here will enrich the limited molecular marker resource in M. phaseolina and could be used as the basis for more in-depth studies of the host-pathogen interactions of M. phaseolina.
    Plant Pathology 07/2011; 60(4):709 - 718. · 2.73 Impact Factor
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    Renée S. Arias
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    ABSTRACT: Esta es la primera publicación de microsatelites de Spodoptera frugiperda (J.E. Smith) (Lepidoptera: Noctuidae), una plaga importante del continente Americano. Hemos aislado 192 marcadores de microsatelites usando un pyrosequenciador, y analizamos 15 individuos de eight isofamilias colectadas de tres áreas geográficas, Puerto Rico (PR), Texas (TX) y Mississippi (MS), incluyendo isofamilias resistentes y susceptibles a Bacillus thuringiensis (Berliner) (Bacillales: Bacillaceae). Análisis de cluster SE realizó con el propósito de determinar el potencial discriminatorio de los microsatélites. Este agrupo las isofamilias de TX distantes de las isofamilias de PR, mientras que las de MS SE agruparon con TX y con PR separadamente. La distancia genética dentro de isofamilias fue de 0.22 a 0.56, mientras que la distancia mínima entre isofamilias fue 0.83. Un total de 80 marcadores que tuvieron valores de UPIC ≥1 como potencial discriminante son presentados. Valores de UPIC permiten reducir costos y elegir marcadores que brindan la máxima variabilidad genética en estudios posteriores. Los marcadores listados pueden contribuir significativamente al n-mero de marcadores moleculares disponibles para S. frugiperda. De los mejores 125 markers, 103 presentaron un máximo de two alelos por muestra, lo que los hace buenos candidatos para estudios de genética poblacional. Resultados de BLAST indicarían potencial significado biológico del polimorfismo. El porcentaje de alelos compartidos por las tres regiones geográficas fue 14%. Además, estos marcadores podrían ser usados para monitorear migración de poblaciones, en el desarrollo de agentes de control biológico, en programas de mejoramiento, y para prácticas de manejo en general.
    Annals of the Entomological Society of America 05/2011; · 1.20 Impact Factor
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    Electronic Journal of Biotechnology 05/2011; 14(3):14-14. · 0.83 Impact Factor
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    ABSTRACT: We studied the effects on plant growth from insertion of five cisgenes that encode proteins involved in gibberellin metabolism or signalling. Intact genomic copies of PtGA20ox7, PtGA2ox2,Pt RGL1_1, PtRGL1_2 and PtGAI1 genes from the genome-sequenced Populus trichocarpa clone Nisqually-1 were transformed into Populus tremula × alba (clone INRA 717-1B4), and growth, morphology and xylem cell size characterized in the greenhouse. Each cisgene encompassed 1-2 kb of 5' and 1 kb of 3' flanking DNA, as well as all native exons and introns. Large numbers of independent insertion events per cisgene (19-38), including empty vector controls, were studied. Three of the cisgenic modifications had significant effects on plant growth rate, morphology or wood properties. The PtGA20ox7 cisgene increased rate of shoot regeneration in vitro, accelerated early growth, and variation in growth rate was correlated with PtGA20ox7 gene expression. PtRGL1_1 and PtGA2ox2 caused reduced growth, while PtRGL1_2 gave rise to plants that grew normally but had significantly longer xylem fibres. RT-PCR studies suggested that the lack of growth inhibition observed in PtRGL1_2 cisgenic plants was a result of co-suppression. PtGAI1 slowed regeneration rate and both PtGAI1 and PtGA20ox7 gave rise to increased variance among events for early diameter and volume index, respectively. Our work suggests that cisgenic insertion of additional copies of native genes involved in growth regulation may provide tools to help modify plant architecture, expand the genetic variance in plant architecture available to breeders and accelerate transfer of alleles between difficult-to-cross species.
    Plant Biotechnology Journal 02/2011; 9(2):162-78. · 6.28 Impact Factor
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    ABSTRACT: The construction of microsatellite-enriched libraries is an indispensable tool to search for molecular markers as complete genome sequences are still not available for the majority of species of interest. Numerous protocols are available in the literature for the construction of these libraries; however, sometimes their low efficiency or lack of optimization in the protocols can restrict their efficacy. We have designed and tested various adapters and ligation methods; we also tested oligo-repeat combinations and hybridization temperatures, and created libraries with this new protocol for four organisms: Ipomoea batatas (L.) Lam, Chionanthus retusus Lindley & Paxton, Rotylenchulus reniformis Linford & Olivera and Puccinia kuehnii W. Krüger. The number of microsatellites detected for these species ranged from 2494 to 3919 per Mb of nonredundant sequence, that was 0.86 and 1.53 microsatellites per contig, with 37-66% of di-nucleotide motifs and 21-49% of tri- to octa-nucleotide repeats combined. A simplified protocol is provided for the successful generation of SSR-enriched libraries.
    Molecular Ecology Resources 05/2010; 10(3):508-15. · 7.43 Impact Factor
  • Plant Biotechnol. J. 01/2010;
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    ABSTRACT: Rotylenchulus reniformis is the predominant parasitic nematode of cotton in the Mid South area of the United States. Although variable levels of infection and morphological differences have been reported for this nematode, genetic variability has been more elusive. We developed microsatellite-enriched libraries for R. reniformis, produced 1152 clones, assembled 694 contigs, detected 783 simple sequence repeats (SSR) and designed 192 SSR-markers. The markers were tested on six R. reniformis cultures from four states, Texas, Louisiana, Mississippi and Georgia, in the USA. Based on performance we selected 156 SSR markers for R. reniformis from which 88 were polymorphic across the six reniform nematode populations, showing as the most frequent motif the dinucleotide AG. The polymorphic information content of the markers ranged from 0.00 to 0.82, and the percentage of multiallelic loci of the isolates was between 40.9 and 45.1%. An interesting finding in this study was the genetic variability detected among the three Mississippi isolates, for which 22 SSR markers were polymorphic. We also tested the level of infection of these isolates on six cotton genotypes, where significant differences were found between the Texas and Georgia isolates. Coincidentally, 62 polymorphic markers were able to distinguish these two populations. Further studies will be necessary to establish possible connections, if any, between markers and level of pathogenicity of the nematode. The SSR markers developed here will be useful in the assessment of the genetic diversity of this nematode, could assist in management practices for control of reniform nematode, be used in breeding programs for crop resistance, and help in detecting the origin and spread of this nematode in the United States.
    Journal of nematology 06/2009; 41(2):146-56. · 0.52 Impact Factor
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    ABSTRACT: We describe the development of a reporter system for monitoring meristem initiation in poplar using promoters of poplar homologs to the meristem-active regulatory genes WUSCHEL (WUS) and SHOOTMERISTEMLESS (STM). When ~3 kb of the 5' flanking regions of close homologs were used to drive expression of the GUSPlus gene, 50-60% of the transgenic events showed expression in apical and axillary meristems. However, expression was also common in other organs, including in leaf veins (40 and 46% of WUS and STM transgenic events, respectively) and hydathodes (56% of WUS transgenic events). Histochemical GUS staining of explants during callogenesis and shoot regeneration using in vitro stems as explants showed that expression was detectable prior to visible shoot development, starting 3-15 days after explants were placed onto callus inducing medium. A minority of WUS and STM events also showed expression in the cambium, phloem, or xylem of regenerated, greenhouse grown plants undergoing secondary growth. Based on microarray gene expression data, a paralog of poplar WUS was detectably up-regulated during shoot initiation, but the other paralog was not. Both paralogs of poplar STM were down-regulated threefold to sixfold during early callus initiation. We identified 15-35 copies of cytokinin response regulator binding motifs (ARR1AT) and one copy of the auxin response element (AuxRE) in both promoters. Several of the events recovered may be useful for studying the process of primary and secondary meristem development, including treatments intended to stimulate meristem development to promote clonal propagation and genetic transformation.
    Plant Cell Reports 04/2009; 28(6):947-62. · 2.94 Impact Factor
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    ABSTRACT: We introduce here the concept of Unique Pattern Informative Combinations (UPIC), a decision tool for the cost-effective design of DNA fingerprinting/genotyping experiments using simple-sequence/tandem repeat (SSR/STR) markers. After the first screening of SSR-markers tested on a subset of DNA samples, the user can apply UPIC to find marker combinations that maximize the genetic information obtained by a minimum or desirable number of markers. This allows a cost-effective planning of future experiments. We have developed Perl scripts to calculate all possible subset combinations of SSR markers, and determine based on unique patterns or alleles, which combinations can discriminate among all DNA samples included in a test. This makes UPIC an essential tool for optimizing resources when working with microsatellites. An example using real data from eight markers and 12 genotypes shows that UPIC detected groups of as few as three markers sufficient to discriminate all 12- DNA samples. Should markers for future experiments be chosen based only on polymorphism-information content (PIC), the necessary number of markers for discrimination of all samples cannot be determined. We also show that choosing markers using UPIC, an informative combination of four markers can provide similar information as using a combination of six markers (23 vs. 25 patterns, respectively), granting a more efficient planning of experiments. Perl scripts with documentation are also included to calculate the percentage of heterozygous loci on the DNA samples tested and to calculate three PIC values depending on the type of fertilization and allele frequency of the organism. AVAILABILITY: Perl scripts are freely available for download from http://www.ars.usda.gov/msa/jwdsrc/gbru.
    Bioinformation 02/2009; 3(8):352-60. · 0.50 Impact Factor
  • Plant Cell Rep. 01/2009; 28:947-962.
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    ABSTRACT: We investigated the efficiency of RNA interference (RNAi) in Arabidopsis using transitive and homologous inverted repeat (hIR) vectors. hIR constructs carry self-complementary intron-spliced fragments of the target gene whereas transitive vectors have the target sequence fragment adjacent to an intron-spliced, inverted repeat of heterologous origin. Both transitive and hIR constructs facilitated specific and heritable silencing in the three genes studied (AP1, ETTIN and TTG1). Both types of vectors produced a phenotypic series that phenocopied reduction of function mutants for the respective target gene. The hIR yielded up to fourfold higher proportions of events with strongly manifested reduction of function phenotypes compared to transitive RNAi. We further investigated the efficiency and potential off-target effects of AP1 silencing by both types of vectors using genome-scale microarrays and quantitative RT-PCR. The depletion of AP1 transcripts coincided with reduction of function phenotypic changes among both hIR and transitive lines and also showed similar expression patterns among differentially regulated genes. We did not detect significant silencing directed against homologous potential off-target genes when constructs were designed with minimal sequence similarity. Both hIR and transitive methods are useful tools in plant biotechnology and genomics. The choice of vector will depend on specific objectives such as cloning throughput, number of events and degree of suppression required.
    Plant Biotechnology Journal 10/2007; 5(5):615-26. · 6.28 Impact Factor
  • Plant Biotechnology. 01/2007; 5:615-626.
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    ABSTRACT: Three natural somatic mutations at codon 304 of the phytoene desaturase gene (pds) of Hydrilla verticillata (L. f. Royle) have been reported to provide resistance to the herbicide fluridone. We substituted the arginine 304 present in the wild-type H. verticillata phytoene desaturase (PDS) with all 19 other natural amino acids and tested PDS against fluridone. In in vitro assays, the threonine (Thr), cysteine (Cys), alanine (Ala) and glutamine (Gln) mutations imparted the highest resistance to fluridone. Thr, the three natural mutations [Cys, serine (Ser), histidine (His)] and the wild-type PDS protein were tested in vitro against seven inhibitors of PDS representing several classes of herbicides. These mutations conferred cross-resistance to norflurazon and overall negative cross-resistance to beflubutamid, picolinafen and diflufenican. The T3 generation of transgenic Arabidopsis thaliana plants harbouring the four selected mutations and wild-type pds had similar patterns of cross-resistance to the herbicides as observed in the in vitro assays. The Thr304 Hydrilla pds mutant proved to be an excellent marker for the selection of transgenic plants. Seedlings harbouring Thr304 pds had a maximum resistance to sensitivity (R/S) ratio of 57 and 14 times higher than that of the wild-type for treatments with norflurazon and fluridone, respectively. These plants exhibited normal growth and development, even after long-term exposure to herbicide. As Thr304 pds is of plant origin, it could become more acceptable than other selectable markers for use in genetically modified food.
    Plant Biotechnology Journal 04/2006; 4(2):263-73. · 6.28 Impact Factor
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    ABSTRACT: Genetic transformation and regeneration of transgenic plants remains unfeasible for the majority of plant species. We propose that inducible expression and/or suppression of the genes that control the cell cycle and development, by altering chromatin structure and exerting epigenetic control of gene expression, might substantially improve competence for transformation and/or regeneration. Transformation efficiency was higher in cells with nuclei at the S and G2 phases, and manipulating the genes whose activation or silencing promote the G1-S transition has increased both transient and stable transformation. Controlling the cell cycle directly, using RBR and VIP1, or indirectly, through hormone regulation using IPT and ESR1, has improved rates of stable transformation. Other target genes that might promote incorporation of DNA and/or pluripotency of cells include HP1, CycD3 and CycD1. The availability of large EST databanks, complete plant-genome sequences and/or inducible gene expression systems create opportunities for testing homologous genes to increase competence of transformation and regeneration.
    Trends in Biotechnology 01/2006; 24:267-273. · 9.66 Impact Factor
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    ABSTRACT: Hydrilla [Hydrilla verticillata (Lf) Royle] is one of the most serious invasive aquatic weed problems in the USA. This plant possesses numerous mechanisms of vegetative reproduction that enable it to spread very rapidly. Management of this weed has been achieved by the systemic treatment of water bodies with the herbicide fluridone. At least three dioecious fluridone-resistant biotypes of hydrilla with two- to fivefold higher resistance to the herbicide than the wild-type have been identified. Resistance is the result of one of three independent somatic mutations at the arginine 304 codon of the gene encoding phytoene desaturase, the molecular target site of fluridone. The specific activities of the three purified phytoene desaturase variants are similar to the wild-type enzyme. The appearance of these herbicide-resistant biotypes may jeopardize the ability to control the spread of this non-indigenous species to other water bodies in the southern USA. The objective of this paper is to provide general information about the biology and physiology of this aquatic weed in relation to its recent development of resistance to the herbicide fluridone, and to discuss how this discovery might lead to a new generation of herbicide-resistant crops.
    Pest Management Science 04/2005; 61(3):258-68. · 2.74 Impact Factor
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    ABSTRACT: Hydrilla (Hydrilla verticillata L.f. Royle) was introduced to the surface water of Florida in the 1950s and is today one of the most serious aquatic weed problems in the USA. As a result of concerns associated with the applications of pesticides to aquatic systems, fluridone is the only USEPA-approved chemical that provides systemic control of hydrilla. After a decrease in fluridone's efficacy at controlling hydrilla, 200 Florida water bodies were sampled to determine the extent of the problem and the biological basis for the reduced efficacy. Our studies revealed that hydrilla phenotypes with two- to six-fold higher fluridone resistance were present in 20 water bodies. Since fluridone is an inhibitor of the enzyme phytoene desaturase (PDS), the gene for PDS (pds) was cloned from herbicide-susceptible and -resistant hydrilla plants. We report for the first time in higher plants three independent herbicide-resistant hydrilla biotypes arising from the selection of somatic mutations at the arginine 304 codon of pds. The three PDS variants had specific activities similar to the wild-type enzyme but were two to five times less sensitive to fluridone. In vitro activity levels of the enzymes correlated with in vivo resistance of the corresponding biotypes. As hydrilla spread rapidly to lakes across the southern United States in the past, the expansion of resistant biotypes is likely to pose significant environmental challenges in the future.
    Molecular Ecology 11/2004; 13(10):3229-37. · 6.28 Impact Factor