Renée S Arias

Oregon State University, Corvallis, OR, United States

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Publications (24)62.65 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). · 2.97 Impact Factor
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    ABSTRACT: The feasibility of genotyping Spodoptera frugiperda (J. E. Smith) crosses between Bt resistant and susceptible populations using SSRs was assessed. Parents and their corresponding progeny (five resistant, five susceptible phenotype) were genotyped using 192 SSRs on three reciprocate crosses of Bt-susceptible and Bt-resistant populations. Oviposition, mortality and fecundity were evaluated for five pairs of each of the crosses. Cluster analysis, heterozygosity and phenotype marker association were analyzed. Also a multi-allele discrimination of isofamilies by markers associated to insect behavior is reported.
    Entomological Society of America Annual Meeting 2013; 11/2013
  • 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. · 2.97 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: This is the first report of sequence-specific microsatellite markers (SSRs) of Spodoptera frugiperda (Smith) (Lepidoptera: Noctuidae), an economically important pest of the American continent. We developed 178 microsatellite markers using pyrosequencing, and screened 15 individuals from 8 colonies collected from three geographical areas, Puerto Rico (PR), Texas (TX) and Mississippi (MS), including Bacillus thuringiensis (Bt) resistant and susceptible colonies. Cluster analysis was performed to determine the potential use of these SSRs in discriminating populations. SSR polymorphism grouped individuals of each colony together with a reliability of 100% estimated by bootstrap. In this analysis, colonies from TX grouped away from those from PR, but the two MS colonies grouped with TX and PR separately. Genetic distance between individuals of the same colony ranged between 0.22 and 0.56, whereas minimum genetic distance between colonies was 0.83. Unique pattern informative combination (UPIC) scores were calculated, and the 80 SSR markers that had UPIC scores of 1 or higher are listed according to their discriminating potential. UPIC scores allow choosing combinations of few highly informative markers for future studies. Heterozygosity of S. frugiperda individuals, estimated as the percentage of multiallelic loci based on 120 SSR markers, ranged between 35 and 59 %, with a difference of 2-15% between individuals of the same population. The markers reported here effectively identified the eight colonies of S. frugiperda tested. In addition, they could be used for monitoring migration of populations, in the development of biocontrol agents, in breeding programs, and for management practices in general.
    Entomological Society of America Annual Meeting 2010; 12/2010
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    ABSTRACT: El gusano cogollero, Spodoptere frugiperde (J. E. Smith), es una de las plagas más importantes del continente Americano. Su control se basa principalmente en multiples aplicaciones de insecticidas que pueden llegar a acumular 1,000 gramos de ingrediente activo por hectárea en algunos de los 30 cultivos que este insecto ataca. El uso de cultivos genéticamente modificados que expresan toxinas de Becillus thuringiensis Berliner (Bt), como el maíz Bt, Zee meys L. y el algodonero Bt Gossypium hirsutum L., son otra forma de controlar a esta plaga. Sin embargo, S. frugiperde es una de las especies con menor susceptibilidad a las proteínas Bt, y un caso de alta tolerancia a maíz Bt ya ha sido reportado. En este estudio encontramos que la susceptibilidad a las proteínas Cry1Ac y Cry1F en 133 isofamilias provenientes de cinco regiones de tres países, fue similar a la obtenida en dos colonias susceptibles de laboratorio. Cuatro de estas familias de Puerto Rico mostraron una elevada tolerancia a Cry1F y en menor grado a Cry1Ac. Dos de estas cuatro isofamilias se cruzaron con una familia de laboratorio susceptible y la progenie fue tan susceptible a ambas proteínas como lo fue la colonia susceptible, indicando que la resistencia en estas isofamilias es una condición genética recesiva.
    Southwestern Entomologist 11/2010; · 0.50 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: Redbud (Cercis spp.) are popular ornamental small trees or shrubs, valued commercially for their showy early spring bloom, heart-shaped glossy leaves, and adaptability to diverse environmental conditions. The genus Cercis (Fabaceae) contains seven to thirteen species or sub-species that occur in North America, Europe, and Asia. Species range in size from small shrubs to trees, tolerate full sun to shade, and are hardy in USDA Zones 4-9. At least 12 cultivars of redbud have been introduced in the past decade with variations in foliage characteristics, flower color, or plant habit. We developed SSR markers for C. canadensis and other species and used them to analyze 20 cultivars. We also tested the inheritance of these markers by analyzing parents and progeny from controlled hybridizations. These markers successfully differentiated among all the cultivars tested, and were useful in estimating genetic distances between cultivars. We are currently investigating the relationship between genetic associations revealed by SSR markers and various horticultural and adaptability traits in the landscape.
    2009 ASHS Annual Conference; 07/2009
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    ABSTRACT: Chionanthus is a genus of the Oleaceae family along with Olea, Fraxinus and Forsythia. Albeit being used as ornamental and commercialized as a natural product, the genetic information of Chionanthus spp. is negligible. We have created microsatellite-enriched libraries of C. retusus, assembled 1072 contigs, and detected 1010 repeats. The frequency of the repeats decreased exponentially with the increase in repeat length, and the most abundant motives were: AG, AC, AAG, ACC, AT and ACTC. We have screened 384 markers on 12 Chionanthus related taxa, characterized 57 microsatellite loci across four species of Oleaceae and characterized 195 within the species C. retusus, most of these being polymorphic. Polymorphic information content (PIC) values varied from zero to 0.85, and the percentage of heterozygous loci was in a range from 24.6 to 68.4%. The SSR markers developed here could assist in the botanical characterization for breeding programs and in the industry for the quality control and authentication of varieties of these medicinal plants.
    2009 ASHS Annual Conference; 07/2009
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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.