Publications by authors named "Amit Dhingra"

53 Publications

Fruit crops in the era of genome editing: closing the regulatory gap.

Plant Cell Rep 2021 Jan 30. Epub 2021 Jan 30.

Department of Plant Production and Forestry Science, University of Lleida-Agrotecnio Center, Lleida, Spain.

The conventional breeding of fruits and fruit trees has led to the improvement of consumer-driven traits such as fruit size, yield, nutritional properties, aroma and taste, as well as the introduction of agronomic properties such as disease resistance. However, even with the assistance of modern molecular approaches such as marker-assisted selection, the improvement of fruit varieties by conventional breeding takes considerable time and effort. The advent of genetic engineering led to the rapid development of new varieties by allowing the direct introduction of genes into elite lines. In this review article, we discuss three such case studies: the Arctic apple, the Pinkglow pineapple and the SunUp/Rainbow papaya. We consider these events in the light of global regulations for the commercialization of genetically modified organisms (GMOs), focusing on the differences between product-related systems (the USA/Canada comparative safety assessment) and process-related systems (the EU "precautionary principle" model). More recently, genome editing has provided an efficient way to introduce precise mutations in plants, including fruits and fruit trees, replicating conventional breeding outcomes without the extensive backcrossing and selection typically necessary to introgress new traits. Some jurisdictions have reacted by amending the regulations governing GMOs to provide exemptions for crops that would be indistinguishable from conventional varieties based on product comparison. This has revealed the deficiencies of current process-related regulatory frameworks, particularly in the EU, which now stands against the rest of the world as a unique example of inflexible and dogmatic governance based on political expediency and activism rather than rigorous scientific evidence.
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http://dx.doi.org/10.1007/s00299-021-02664-xDOI Listing
January 2021

Beyond Ethylene: New Insights Regarding the Role of Alternative Oxidase in the Respiratory Climacteric.

Front Plant Sci 2020 27;11:543958. Epub 2020 Oct 27.

Molecular Plant Sciences Program, Washington State University, Pullman, WA, United States.

Climacteric fruits are characterized by a dramatic increase in autocatalytic ethylene production that is accompanied by a spike in respiration at the onset of ripening. The change in the mode of ethylene production from autoinhibitory to autostimulatory is known as the System 1 (S1) to System 2 (S2) transition. Existing physiological models explain the basic and overarching genetic, hormonal, and transcriptional regulatory mechanisms governing the S1 to S2 transition of climacteric fruit. However, the links between ethylene and respiration, the two main factors that characterize the respiratory climacteric, have not been examined in detail at the molecular level. Results of recent studies indicate that the alternative oxidase (AOX) respiratory pathway may play an essential role in mediating cross-talk between ethylene response, carbon metabolism, ATP production, and ROS signaling during climacteric ripening. New genomic, metabolic, and epigenetic information sheds light on the interconnectedness of ripening metabolic pathways, necessitating an expansion of the current, ethylene-centric physiological models. Understanding points at which ripening responses can be manipulated may reveal key, species- and cultivar-specific targets for regulation of ripening, enabling superior strategies for reducing postharvest wastage.
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http://dx.doi.org/10.3389/fpls.2020.543958DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7652990PMC
October 2020

Identification of f. sp. () Responsive Genes in .

Front Genet 2020 18;11:950. Epub 2020 Aug 18.

Molecular Plant Sciences, Washington State University, Pullman, WA, United States.

(pea) is rapidly emerging as an inexpensive and significant contributor to the plant-derived protein market. Due to its nitrogen-fixation capability, short life cycle, and low water usage, pea is a useful cover-and-break crop that requires minimal external inputs. It is critical for sustainable agriculture and indispensable for future food security. Root rot in pea, caused by the fungal pathogen f. sp. (), can result in a 15-60% reduction in yield. It is urgent to understand the molecular basis of interaction in pea to develop root rot tolerant cultivars. A complementary genetics and gene expression approach was undertaken in this study to identify -responsive genes in four tolerant and four susceptible pea genotypes. Time course RNAseq was performed on both sets of genotypes after the challenge. Analysis of the transcriptome data resulted in the identification of 42,905 differentially expressed contigs (DECs). Interestingly, the vast majority of DECs were overexpressed in the susceptible genotypes at all sampling time points, rather than in the tolerant genotypes. Gene expression and GO enrichment analyses revealed genes coding for receptor-mediated endocytosis, sugar transporters, salicylic acid synthesis, and signaling, and cell death were overexpressed in the susceptible genotypes. In the tolerant genotypes, genes involved in exocytosis, and secretion by cell, the anthocyanin synthesis pathway, as well as the DRR230 gene, a pathogenesis-related (PR) gene, were overexpressed. The complementary genetic and RNAseq approach has yielded a set of potential genes that could be targeted for improved tolerance against root rot in . challenge produced a futile transcriptomic response in the susceptible genotypes. This type of response is hypothesized to be related to the speed at which the pathogen infestation advances in the susceptible genotypes and the preexisting level of disease-preparedness in the tolerant genotypes.
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http://dx.doi.org/10.3389/fgene.2020.00950DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7461991PMC
August 2020

Plastid transit peptides-where do they come from and where do they all belong? Multi-genome and pan-genomic assessment of chloroplast transit peptide evolution.

PeerJ 2020 27;8:e9772. Epub 2020 Aug 27.

Molecular Plant Sciences, Washington State University, Pullman, WA, USA.

Subcellular relocalization of proteins determines an organism's metabolic repertoire and thereby its survival in unique evolutionary niches. In plants, the plastid and its various morphotypes import a large and varied number of nuclear-encoded proteins to orchestrate vital biochemical reactions in a spatiotemporal context. Recent comparative genomics analysis and high-throughput shotgun proteomics data indicate that there are a large number of plastid-targeted proteins that are either semi-conserved or non-conserved across different lineages. This implies that homologs are differentially targeted across different species, which is feasible only if proteins have gained or lost plastid targeting peptides during evolution. In this study, a broad, multi-genome analysis of 15 phylogenetically diverse genera and in-depth analyses of pangenomes from Arabidopsis and Brachypodium were performed to address the question of how proteins acquire or lose plastid targeting peptides. The analysis revealed that random insertions or deletions were the dominant mechanism by which novel transit peptides are gained by proteins. While gene duplication was not a strict requirement for the acquisition of novel subcellular targeting, 40% of novel plastid-targeted genes were found to be most closely related to a sequence within the same genome, and of these, 30.5% resulted from alternative transcription or translation initiation sites. Interestingly, analysis of the distribution of amino acids in the transit peptides of known and predicted chloroplast-targeted proteins revealed monocot and eudicot-specific preferences in residue distribution.
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http://dx.doi.org/10.7717/peerj.9772DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7456531PMC
August 2020

Methods of analysis of chloroplast genomes of C, Kranz type C and Single Cell C photosynthetic members of Chenopodiaceae.

Plant Methods 2020 31;16:119. Epub 2020 Aug 31.

Department of Horticulture, Washington State University, Pullman, WA 99164 USA.

Background: Chloroplast genome information is critical to understanding forms of photosynthesis in the plant kingdom. During the evolutionary process, plants have developed different photosynthetic strategies that are accompanied by complementary biochemical and anatomical features. Members of family Chenopodiaceae have species with C photosynthesis, and variations of C photosynthesis in which photorespiration is reduced by concentrating CO around Rubisco through dual coordinated functioning of dimorphic chloroplasts. Among dicots, the family has the largest number of C species, and greatest structural and biochemical diversity in forms of C including the canonical dual-cell Kranz anatomy, and the recently identified single cell C with the presence of dimorphic chloroplasts separated by a vacuole. This is the first comparative analysis of chloroplast genomes in species representative of photosynthetic types in the family.

Results: Methodology with high throughput sequencing complemented with Sanger sequencing of selected loci provided high quality and complete chloroplast genomes of seven species in the family and one species in the closely related Amaranthaceae family, representing C, Kranz type C and single cell C (SSC) photosynthesis six of the eight chloroplast genomes are new, while two are improved versions of previously published genomes. The depth of coverage obtained using high-throughput sequencing complemented with targeted resequencing of certain loci enabled superior resolution of the border junctions, directionality and repeat region sequences. Comparison of the chloroplast genomes with previously sequenced plastid genomes revealed similar genome organization, gene order and content with a few revisions. High-quality complete chloroplast genome sequences resulted in correcting the orientation the LSC region of the published chloroplast genome, identification of stop codons in the rpl23 gene in and , and identifying an instance of IR expansion in the inverted repeat sequence. The rare observation of a mitochondria-to-chloroplast inter-organellar gene transfer event was identified in family Chenopodiaceae.

Conclusions: This study reports complete chloroplast genomes from seven Chenopodiaceae and one Amaranthaceae species. The depth of coverage obtained using high-throughput sequencing complemented with targeted resequencing of certain loci enabled superior resolution of the border junctions, directionality, and repeat region sequences. Therefore, the use of high throughput and Sanger sequencing, in a hybrid method, reaffirms to be rapid, efficient, and reliable for chloroplast genome sequencing.
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http://dx.doi.org/10.1186/s13007-020-00662-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7457496PMC
August 2020

Evidence for the Involvement of Vernalization-related Genes in the Regulation of Cold-induced Ripening in 'D'Anjou' and 'Bartlett' Pear Fruit.

Sci Rep 2020 05 21;10(1):8478. Epub 2020 May 21.

Molecular Plant Sciences, Washington State University, Pullman, Washington, USA.

European pear (Pyrus communis L.) cultivars require a genetically pre-determined duration of cold-temperature exposure to induce autocatalytic system 2 ethylene biosynthesis and subsequent fruit ripening. The physiological responses of pear to cold-temperature-induced ripening have been well characterized, but the molecular mechanisms underlying this phenomenon continue to be elucidated. This study employed previously established cold temperature conditioning treatments for ripening of two pear cultivars, 'D'Anjou' and 'Bartlett'. Using a time-course transcriptomics approach, global gene expression responses of each cultivar were assessed at four stages of developmental during the cold conditioning process. Differential expression, functional annotation, and gene ontology enrichment analyses were performed. Interestingly, evidence for the involvement of cold-induced, vernalization-related genes and repressors of endodormancy release was found. These genes have not previously been described to play a role in fruit during the ripening transition. The resulting data provide insight into cultivar-specific mechanisms of cold-induced transcriptional regulation of ripening in European pear, as well as a unique comparative analysis of the two cultivars with very different cold conditioning requirements.
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http://dx.doi.org/10.1038/s41598-020-65275-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7242362PMC
May 2020

Genome-Scale Characterization of Predicted Plastid-Targeted Proteomes in Higher Plants.

Sci Rep 2020 05 19;10(1):8281. Epub 2020 May 19.

Department of Horticulture, Washington State University, Pullman, WA, USA.

Plastids are morphologically and functionally diverse organelles that are dependent on nuclear-encoded, plastid-targeted proteins for all biochemical and regulatory functions. However, how plastid proteomes vary temporally, spatially, and taxonomically has been historically difficult to analyze at a genome-wide scale using experimental methods. A bioinformatics workflow was developed and evaluated using a combination of fast and user-friendly subcellular prediction programs to maximize performance and accuracy for chloroplast transit peptides and demonstrate this technique on the predicted proteomes of 15 sequenced plant genomes. Gene family grouping was then performed in parallel using modified approaches of reciprocal best BLAST hits (RBH) and UCLUST. A total of 628 protein families were found to have conserved plastid targeting across angiosperm species using RBH, and 828 using UCLUST. However, thousands of clusters were also detected where only one species had predicted plastid targeting, most notably in Panicum virgatum which had 1,458 proteins with species-unique targeting. An average of 45% overlap was found in plastid-targeted protein-coding gene families compared with Arabidopsis, but an additional 20% of proteins matched against the full Arabidopsis proteome, indicating a unique evolution of plastid targeting. Neofunctionalization through subcellular relocalization is known to impart novel biological functions but has not been described before on a genome-wide scale for the plastid proteome. Further work to correlate these predicted novel plastid-targeted proteins to transcript abundance and high-throughput proteomics will uncover unique aspects of plastid biology and shed light on how the plastid proteome has evolved to influence plastid morphology and biochemistry.
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http://dx.doi.org/10.1038/s41598-020-64670-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7237471PMC
May 2020

Glyoxylic acid overcomes 1-MCP-induced blockage of fruit ripening in Pyrus communis L. var. 'D'Anjou'.

Sci Rep 2020 04 27;10(1):7084. Epub 2020 Apr 27.

Molecular Plant Sciences Graduate Program, Washington State University, Pullman, WA, USA.

1-methylcyclopropene (1-MCP) in an ethylene receptor antagonist that blocks ethylene perception and downstream ripening responses in climacteric fruit imparting a longer shelf life. However, in European pear, the application of 1-MCP irreversibly obstructs the onset of system 2 ethylene production resulting in perpetually unripe fruit with undesirable quality. Application of exogenous ethylene, carbon dioxide and treatment to high temperatures is not able to reverse the blockage in ripening. We recently reported that during cold conditioning, activation of alternative oxidase (AOX) occurs pre-climacterically. In this study, we report that activation of AOX via exposure of 1-MCP treated 'D'Anjou' pear fruit to glyoxylic acid triggers an accelerated ripening response. Time course physiological analysis revealed that ripening is evident from decreased fruit firmness and increased internal ethylene. Transcriptomic and functional enrichment analyses revealed genes and ontologies implicated in glyoxylic acid-mediated ripening, including AOX, TCA cycle, fatty acid metabolism, amino acid metabolism, organic acid metabolism, and ethylene-responsive pathways. These observations implicate the glyoxylate cycle as a biochemical hub linking multiple metabolic pathways to stimulate ripening through an alternate mechanism. The results provide information regarding how blockage caused by 1-MCP may be circumvented at the metabolic level, thus opening avenues for consistent ripening in pear and possibly other fruit.
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http://dx.doi.org/10.1038/s41598-020-63642-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7184741PMC
April 2020

Concomitant phytonutrient and transcriptome analysis of mature fruit and leaf tissues of tomato (Solanum lycopersicum L. cv. Oregon Spring) grown using organic and conventional fertilizer.

PLoS One 2020 13;15(1):e0227429. Epub 2020 Jan 13.

Department of Horticulture, Washington State University,Pullman, WA, United States of America.

Enhanced levels of antioxidants, phenolic compounds, carotenoids and vitamin C have been reported for several crops grown under organic fertilizer, albeit with yield penalties. As organic agricultural practices continue to grow and find favor it is critical to gain an understanding of the molecular underpinnings of the factors that limit the yields in organically farmed crops. Concomitant phytochemical and transcriptomic analysis was performed on mature fruit and leaf tissues derived from Solanum lycopersicum L. 'Oregon Spring' grown under organic and conventional fertilizer conditions to evaluate the following hypotheses. 1. Organic soil fertilizer management results in greater allocation of photosynthetically derived resources to the synthesis of secondary metabolites than to plant growth, and 2. Genes involved in changes in the accumulation of phytonutrients under organic fertilizer regime will exhibit differential expression, and that the growth under different fertilizer treatments will elicit a differential response from the tomato genome. Both these hypotheses were supported, suggesting an adjustment of the metabolic and genomic activity of the plant in response to different fertilizers. Organic fertilizer treatment showed an activation of photoinhibitory processes through differential activation of nitrogen transport and assimilation genes resulting in higher accumulation of phytonutrients. This information can be used to identify alleles for breeding crops that allow for efficient utilization of organic inputs.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0227429PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6957345PMC
April 2020

Evidence for pre-climacteric activation of AOX transcription during cold-induced conditioning to ripen in European pear (Pyrus communis L.).

PLoS One 2019 4;14(12):e0225886. Epub 2019 Dec 4.

Department of Horticulture, Washington State University, Pullman, WA, United States of America.

European pears (Pyrus communis L.) require a range of cold-temperature exposure to induce ethylene biosynthesis and fruit ripening. Physiological and hormonal responses to cold temperature storage in pear have been well characterized, but the molecular underpinnings of these phenomena remain unclear. An established low-temperature conditioning model was used to induce ripening of 'D'Anjou' and 'Bartlett' pear cultivars and quantify the expression of key genes representing ripening-related metabolic pathways in comparison to non-conditioned fruit. Physiological indicators of pear ripening were recorded, and fruit peel tissue sampled in parallel, during the cold-conditioning and ripening time-course experiment to correlate gene expression to ontogeny. Two complementary approaches, Nonparametric Multi-Dimensional Scaling and efficiency-corrected 2-(ΔΔCt), were used to identify genes exhibiting the most variability in expression. Interestingly, the enhanced alternative oxidase (AOX) transcript abundance at the pre-climacteric stage in 'Bartlett' and 'D'Anjou' at the peak of the conditioning treatments suggests that AOX may play a key and a novel role in the achievement of ripening competency. There were indications that cold-sensing and signaling elements from ABA and auxin pathways modulate the S1-S2 ethylene transition in European pears, and that the S1-S2 ethylene biosynthesis transition is more pronounced in 'Bartlett' as compared to 'D'Anjou' pear. This information has implications in preventing post-harvest losses of this important crop.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0225886PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6892529PMC
March 2020

CRISPR-associated nucleases: the Dawn of a new age of efficient crop improvement.

Transgenic Res 2020 02 1;29(1):1-35. Epub 2019 Nov 1.

Washington State University, Pullman, USA.

The world stands at a new threshold today. As a planet, we face various challenges, and the key one is how to continue to produce enough food, feed, fiber, and fuel to support the burgeoning population. In the past, plant breeding and the ability to genetically engineer crops contributed to increasing food production. However, both approaches rely on random mixing or integration of genes, and the process can be unpredictable and time-consuming. Given the challenge of limited availability of natural resources and changing environmental conditions, the need to rapidly and precisely improve crops has become urgent. The discovery of CRISPR-associated endonucleases offers a precise yet versatile platform for rapid crop improvement. This review summarizes a brief history of the discovery of CRISPR-associated nucleases and their application in genome editing of various plant species. Also provided is an overview of several new endonucleases reported recently, which can be utilized for editing of specific genes in plants through various forms of DNA sequence alteration. Genome editing, with its ever-expanding toolset, increased efficiency, and its potential integration with the emerging synthetic biology approaches hold promise for efficient crop improvement to meet the challenge of supporting the needs of future generations.
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http://dx.doi.org/10.1007/s11248-019-00181-yDOI Listing
February 2020

Transposons played a major role in the diversification between the closely related almond and peach genomes: results from the almond genome sequence.

Plant J 2020 01 22;101(2):455-472. Epub 2019 Oct 22.

IRTA, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193, Barcelona, Spain.

We sequenced the genome of the highly heterozygous almond Prunus dulcis cv. Texas combining short- and long-read sequencing. We obtained a genome assembly totaling 227.6 Mb of the estimated almond genome size of 238 Mb, of which 91% is anchored to eight pseudomolecules corresponding to its haploid chromosome complement, and annotated 27 969 protein-coding genes and 6747 non-coding transcripts. By phylogenomic comparison with the genomes of 16 additional close and distant species we estimated that almond and peach (Prunus persica) diverged around 5.88 million years ago. These two genomes are highly syntenic and show a high degree of sequence conservation (20 nucleotide substitutions per kb). However, they also exhibit a high number of presence/absence variants, many attributable to the movement of transposable elements (TEs). Transposable elements have generated an important number of presence/absence variants between almond and peach, and we show that the recent history of TE movement seems markedly different between them. Transposable elements may also be at the origin of important phenotypic differences between both species, and in particular for the sweet kernel phenotype, a key agronomic and domestication character for almond. Here we show that in sweet almond cultivars, highly methylated TE insertions surround a gene involved in the biosynthesis of amygdalin, whose reduced expression has been correlated with the sweet almond phenotype. Altogether, our results suggest a key role of TEs in the recent history and diversification of almond and its close relative peach.
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http://dx.doi.org/10.1111/tpj.14538DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7004133PMC
January 2020

Neuropeptides and peptide hormones identified in codling moth, Cydia pomonella (Lepidoptera: Tortricidae).

Arch Insect Biochem Physiol 2019 Aug;101(4):e21587

Horticultural Crops Research Unit, USDA-ARS, Corvallis, Oregon.

The codling moth, Cydia pomonella, is a worldwide pest of pome fruits. Neuropeptides regulate most physiological functions in insects and represent new targets for the development of control agents. The only neuropeptides reported from the codling moth to date are the allatostatin A family peptides. To identify other neuropeptides and peptide hormones from codling moth, we analyzed head transcriptomes, identified 50 transcripts, and predicted 120 prepropeptides for the codling moth neuropeptides and peptide hormones. All transcripts were amplified, and these sequences were verified. One of the notable findings in this study is that diapause hormones (DHs) reported from Tortricid moths, including the codling moth, do not have the WFGPRL sequence in C-terminal ends in the pban genes. The C-terminal motif is critical to characterize insect DH peptides, and always conserved in pban/dh genes in Lepidoptera and many insect orders. Interestingly, the WFGPRL sequence was produced only from the capa gene in the codling moth. The allatostatin A-family encoding transcript predicted nine peptides, seven of which, as expected, are identical to those previously isolated from the moth. We also identified new codling moth orthologs of insect neuropeptides including CCHamides, allatostatin CC, RYamides, and natalisins. The information provided in this study will benefit future codling moth investigations using peptidoproteomics to determine peptide presence and functions.
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http://dx.doi.org/10.1002/arch.21587DOI Listing
August 2019

Development of a highly efficient Axiom™ 70 K SNP array for Pyrus and evaluation for high-density mapping and germplasm characterization.

BMC Genomics 2019 May 2;20(1):331. Epub 2019 May 2.

Department of Plant Sciences, University of California, Davis, CA, USA.

Background: Both a source of diversity and the development of genomic tools, such as reference genomes and molecular markers, are equally important to enable faster progress in plant breeding. Pear (Pyrus spp.) lags far behind other fruit and nut crops in terms of employment of available genetic resources for new cultivar development. To address this gap, we designed a high-density, high-efficiency and robust single nucleotide polymorphism (SNP) array for pear, with the main objectives of conducting genetic diversity and genome-wide association studies.

Results: By applying a two-step design process, which consisted of the construction of a first 'draft' array for the screening of a small subset of samples, we were able to identify the most robust and informative SNPs to include in the Applied Biosystems™ Axiom™ Pear 70 K Genotyping Array, currently the densest SNP array for pear. Preliminary evaluation of this 70 K array in 1416 diverse pear accessions from the USDA National Clonal Germplasm Repository (NCGR) in Corvallis, OR identified 66,616 SNPs (93% of all the tiled SNPs) as high quality and polymorphic (PolyHighResolution). We further used the Axiom Pear 70 K Genotyping Array to construct high-density linkage maps in a bi-parental population, and to make a direct comparison with available genotyping-by-sequencing (GBS) data, which suggested that the SNP array is a more robust method of screening for SNPs than restriction enzyme reduced representation sequence-based genotyping.

Conclusions: The Axiom Pear 70 K Genotyping Array, with its high efficiency in a widely diverse panel of Pyrus species and cultivars, represents a valuable resource for a multitude of molecular studies in pear. The characterization of the USDA-NCGR collection with this array will provide important information for pear geneticists and breeders, as well as for the optimization of conservation strategies for Pyrus.
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http://dx.doi.org/10.1186/s12864-019-5712-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6498479PMC
May 2019

Transcriptome datasets from leaves and fruits of the sweet cherry cultivars 'Bing', 'Lapins' and 'Rainier'.

Data Brief 2019 Apr 22;23:103696. Epub 2019 Jan 22.

Universidad de Chile, Facultad de Ciencias Agronómicas, Departamento de Producción Agrícola, Laboratorio de Genómica Funcional, & Bioinformática, 820808 La Pintana, Santiago, Chile.

Sweet cherry fruits from different cultivars have different pre- and post-harvest qualities. Here we present the transcriptome profile datasets of leaves and mature fruits of three sweet cherry cultivars ('Bing', 'Lapin' and 'Rainier'). Using 454 GS-FLX technology (454 Life Sciences, Roche), transcriptomes of leaves and mature fruits were obtained from these cultivars. These transcriptome data sets are reported here.
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http://dx.doi.org/10.1016/j.dib.2019.01.044DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6369327PMC
April 2019

Identification of water use efficiency related genes in 'Garnem' almond-peach rootstock using time-course transcriptome analysis.

PLoS One 2018 11;13(10):e0205493. Epub 2018 Oct 11.

Hortofruticulture Department. Agrifood Research and Technology Centre of Aragon (CITA), Zaragoza, Spain.

Drought is one of the main abiotic stresses with far-reaching ecological and socioeconomic impacts, especially in perennial food crops such as Prunus. There is an urgent need to identify drought resilient rootstocks that can adapt to changes in water availability. In this study, we tested the hypothesis that PEG-induced water limitation stress will simulate drought conditions and drought-related genes, including transcription factors (TFs), will be differentially expressed in response to this stress. 'Garnem' genotype, an almond × peach hybrid [P. amygdalus Batsch, syn P. dulcis (Mill.) x P. persica (L.) Batsch] was exposed to PEG-6000 solution, and a time-course transcriptome analysis of drought-stressed roots was performed at 0, 2 and 24 h time points post-stress. Transcriptome analysis resulted in the identification of 12,693 unique differentially expressed contigs (DECs) at the 2 h time point, and 7,705 unique DECs at the 24 h time point after initiation of the drought treatment. Interestingly, three drought-induced genes, directly related to water use efficiency (WUE) namely, ERF023 TF; LRR receptor-like serine/threonine-kinase ERECTA; and NF-YB3 TF, were found induced under stress. The RNAseq results were validated with quantitative RT-PCR analysis of eighteen randomly selected differentially expressed contigs (DECs). Pathway analysis in the present study provides valuable information regarding metabolic events that occur during stress-induced signalling in 'Garnem' roots. This information is expected to be useful in understanding the potential mechanisms underlying drought stress responses and drought adaptation strategies in Prunus species.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0205493PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6181374PMC
April 2019

Assessing consumers' preferences and willingness to pay for novel sliced packed fresh pears: A latent class approach.

Agribusiness (N Y N Y) 2018 19;34(2):321-337. Epub 2017 Nov 19.

Molecular PlantSciences,Washington State University, PO Box 646414, Pullman,WA99164, USA.

The North American fresh pear industry faces marketing challenges that could jeopardize its' long-term economic profitability. The production of sliced fresh pears is a promising alternative to overcome the lack of supplying consistently a product with superior quality with added convenience, potentially able to increase domestic consumption. In this paper, we used sensory evaluation and a Vickrey experimental auction to elicit consumers' preferences and willingness to pay for sliced packed fresh pears treated with SmartFresh (1-methylcyclopropene)and subsequently with a ripening compound (RC) in the form of glyoxylic acid at different concentration levels (1%, 2%, 3%, and control). Panelists were willing to pay a price premium equivalent to $0.119/2 oz packet for the 2% RC sample, $0.055/2 oz packet for the 3% RC sample, and $0.025/2 oz packet for the 1% RC sample compared to the control sample. Results from a market segmentation analyses indicate the presence of two groups in the panelist sample. The group that liked sliced pears assigned higher importance to locally grown fruit and price, shopped at conventional retailer grocery stores, had fewer children in the household, and were younger compared to the group that disliked sliced pears.
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http://dx.doi.org/10.1002/agr.21532DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6660009PMC
November 2017

Population structure and genetic diversity of within the small grain production region of the Pacific Northwest.

Ecol Evol 2017 10 7;7(20):8316-8328. Epub 2017 Sep 7.

Department of Crop and Soil Sciences Washington State University Pullman WA USA.

L. is an invasive winter annual grass naturalized across the United States. Numerous studies have investigated population structure and genetics in the context of as an ecological invader of natural areas and rangeland. Despite the wealth of information regarding , previous studies have not focused on, or made comparisons to, as it persists in individual agroecosystems. The objectives of this study were to assess the genetic diversity and structure, the occurrence of generalist and specialist genotypes, and the influence of climate on distribution of sourced exclusively from within small grain production regions of the Pacific Northwest. Genetic diversity of sourced from agronomic fields was found to be similar to what has been observed from other land use histories. Six distinct genetic clusters of were identified, with no evidence to indicate that any of the genetic clusters were better adapted to a particular geographical area or climate within the region. Given the apparent random spatial distribution of genetic clusters at the spatial scale of this analysis, unique genotypes may be well mixed within region, similar to what was reported for other inbreeding weedy grass species.
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http://dx.doi.org/10.1002/ece3.3386DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5648657PMC
October 2017

The Role of Light-Dark Regulation of the Chloroplast ATP Synthase.

Front Plant Sci 2017 24;8:1248. Epub 2017 Jul 24.

Department of Energy Plant Research Laboratory, Michigan State University, East LansingMI, United States.

The chloroplast ATP synthase catalyzes the light-driven synthesis of ATP and is activated in the light and inactivated in the dark by redox-modulation through the thioredoxin system. It has been proposed that this down-regulation is important for preventing wasteful hydrolysis of ATP in the dark. To test this proposal, we compared the effects of extended dark exposure in Arabidopsis lines expressing the wild-type and mutant forms of ATP synthase that are redox regulated or constitutively active. In contrast to the predictions of the model, we observed that plants with wild-type redox regulation lost photosynthetic capacity rapidly in darkness, whereas those expressing redox-insensitive form were far more stable. To explain these results, we propose that in wild-type plants, down-regulation of ATP synthase inhibits ATP hydrolysis, leading to dissipation of thylakoid proton motive force (pmf) and subsequent inhibition of protein transport across the thylakoid through the twin arginine transporter (Tat)-dependent and Sec-dependent import pathways, resulting in the selective loss of specific protein complexes. By contrast, in mutants with a redox-insensitive ATP synthase, pmf is maintained by ATP hydrolysis, thus allowing protein transport to maintain photosynthetic activities for extended periods in the dark. Hence, a basal level of Tat-dependent, as well as, Sec-dependent import activity, in the dark helps replenishes certain components of the photosynthetic complexes and thereby aids in maintaining overall complex activity. However, the influence of a dark pmf on thylakoid protein import, by itself, could not explain all the effects we observed in this study. For example, we also observed in wild type plants a large transient buildup of thylakoid pmf and nonphotochemical exciton quenching upon sudden illumination of dark adapted plants. Therefore, we conclude that down-regulation of the ATP synthase is probably not related to preventing loss of ATP . Instead, ATP synthase redox regulation may be impacting a number of cellular processes such as (1) the accumulation of chloroplast proteins and/or ions or (2) the responses of photosynthesis to rapid changes in light intensity. A model highlighting the complex interplay between ATP synthase regulation and pmf in maintaining various chloroplast functions in the dark is presented. We uncover an unexpected role for thioredoxin modulation of the chloroplast ATP synthase in regulating the dark-stability of the photosynthetic apparatus, most likely by controlling thylakoid membrane transport of proteins and ions.
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http://dx.doi.org/10.3389/fpls.2017.01248DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5522872PMC
July 2017

Comparative ultrastructure of fruit plastids in three genetically diverse genotypes of apple (Malus × domestica Borkh.) during development.

Plant Cell Rep 2017 Oct 11;36(10):1627-1640. Epub 2017 Jul 11.

Department of Horticulture, Washington State University, Pullman, WA, USA.

Key Message: Comparative ultrastructural developmental time-course analysis has identified discrete stages at which the fruit plastids undergo structural and consequently functional transitions to facilitate subsequent development-guided understanding of the complex plastid biology. Plastids are the defining organelle for a plant cell and are critical for myriad metabolic functions. The role of leaf plastid, chloroplast, is extensively documented; however, fruit plastids-chromoplasts-are poorly understood, especially in the context of the diverse metabolic processes operating in these diverse plant organs. Recently, in a comparative study of the predicted plastid-targeted proteomes across seven plant species, we reported that each plant species is predicted to harbor a unique set of plastid-targeted proteins. However, the temporal and developmental context of these processes remains unknown. In this study, an ultrastructural analysis approach was used to characterize fruit plastids in the epidermal and collenchymal cell layers at 11 developmental timepoints in three genotypes of apple (Malus × domestica Borkh.): chlorophyll-predominant 'Granny Smith', carotenoid-predominant 'Golden Delicious', and anthocyanin-predominant 'Top Red Delicious'. Plastids transitioned from a proplastid-like plastid to a chromoplast-like plastid in epidermis cells, while in the collenchyma cells, they transitioned from a chloroplast-like plastid to a chloro-chromo-amyloplast plastid. Plastids in the collenchyma cells of the three genotypes demonstrated a diverse array of structures and features. This study enabled the identification of discrete developmental stages during which specific functions are most likely being performed by the plastids as indicated by accumulation of plastoglobuli, starch granules, and other sub-organeller structures. Information regarding the metabolically active developmental stages is expected to facilitate biologically relevant omics studies to unravel the complex biochemistry of plastids in perennial non-model systems.
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http://dx.doi.org/10.1007/s00299-017-2179-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5693628PMC
October 2017

Evaluation of multiple approaches to identify genome-wide polymorphisms in closely related genotypes of sweet cherry ( L.).

Comput Struct Biotechnol J 2017 18;15:290-298. Epub 2017 Mar 18.

Molecular Plant Sciences Graduate Program, Washington State University, Pullman, WA 99164, United States; Department of Horticulture, Washington State University, Pullman, WA 99164-6414, United States.

Identification of genetic polymorphisms and subsequent development of molecular markers is important for marker assisted breeding of superior cultivars of economically important species. Sweet cherry ( L.) is an economically important non-climacteric tree fruit crop in the Rosaceae family and has undergone a genetic bottleneck due to breeding, resulting in limited genetic diversity in the germplasm that is utilized for breeding new cultivars. Therefore, it is critical to recognize the best platforms for identifying genome-wide polymorphisms that can help identify, and consequently preserve, the diversity in a genetically constrained species. For the identification of polymorphisms in five closely related genotypes of sweet cherry, a gel-based approach (TRAP), reduced representation sequencing (TRAPseq), a 6k cherry SNParray, and whole genome sequencing (WGS) approaches were evaluated in the identification of genome-wide polymorphisms in sweet cherry cultivars. All platforms facilitated detection of polymorphisms among the genotypes with variable efficiency. In assessing multiple SNP detection platforms, this study has demonstrated that a combination of appropriate approaches is necessary for efficient polymorphism identification, especially between closely related cultivars of a species. The information generated in this study provides a valuable resource for future genetic and genomic studies in sweet cherry, and the insights gained from the evaluation of multiple approaches can be utilized for other closely related species with limited genetic diversity in the breeding germplasm.
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http://dx.doi.org/10.1016/j.csbj.2017.03.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5376269PMC
March 2017

Defects in the Expression of Chloroplast Proteins Leads to HO Accumulation and Activation of Cyclic Electron Flow around Photosystem I.

Front Plant Sci 2016 13;7:2073. Epub 2017 Jan 13.

Department of Plant Biology, Michigan State UniversityEast Lansing, MI, USA; DOE-Plant Research Laboratory, Michigan State UniversityEast Lansing, MI, USA; Department of Biochemistry and Molecular Biology, Michigan State UniversityEast Lansing, MI, USA.

We describe a new member of the class of mutants in Arabidopsis exhibiting high rates of cyclic electron flow around photosystem I (CEF), a light-driven process that produces ATP but not NADPH. High cyclic electron flow 2 () shows strongly increased CEF activity through the NADPH dehydrogenase complex (NDH), accompanied by increases in thylakoid proton motive force (), activation of the photoprotective q response, and the accumulation of HO. Surprisingly, was mapped to a non-sense mutation in the TADA1 (tRNA adenosine deaminase arginine) locus, coding for a plastid targeted tRNA editing enzyme required for efficient codon recognition. Comparison of protein content from representative thylakoid complexes, the cytochrome complex, and the ATP synthase, suggests that inefficient translation of leads to compromised complex assembly or stability leading to alterations in stoichiometries of major thylakoid complexes as well as their constituent subunits. Altered subunit stoichiometries for photosystem I, ratios and properties of cytochrome hemes, and the decay kinetics of the flash-induced thylakoid electric field suggest that these defect lead to accumulation of HO in , which we have previously shown leads to activation of NDH-related CEF. We observed similar increases in CEF, as well as increases in HO accumulation, in other translation defective mutants. This suggests that loss of coordination in plastid protein levels lead to imbalances in photosynthetic energy balance that leads to an increase in CEF. These results taken together with a large body of previous observations, support a general model in which processes that lead to imbalances in chloroplast energetics result in the production of HO, which in turn activates CEF. This activation could be from either HO acting as a redox signal, or by a secondary effect from HO inducing a deficit in ATP.
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http://dx.doi.org/10.3389/fpls.2016.02073DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5233679PMC
January 2017

Limitations to photosynthesis by proton motive force-induced photosystem II photodamage.

Elife 2016 10 4;5. Epub 2016 Oct 4.

Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, United States.

The thylakoid proton motive force () generated during photosynthesis is the essential driving force for ATP production; it is also a central regulator of light capture and electron transfer. We investigated the effects of elevated on photosynthesis in a library of mutants with altered rates of thylakoid lumen proton efflux, leading to a range of steady-state extents. We observed the expected dependent alterations in photosynthetic regulation, but also strong effects on the rate of photosystem II (PSII) photodamage. Detailed analyses indicate this effect is related to an elevated electric field (Δ) component of the , rather than lumen acidification, which increased PSII charge recombination rates, producing singlet oxygen and subsequent photodamage. The effects are seen even in wild type plants, especially under fluctuating illumination, suggesting that Δ-induced photodamage represents a previously unrecognized limiting factor for plant productivity under dynamic environmental conditions seen in the field.
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http://dx.doi.org/10.7554/eLife.16921DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5050024PMC
October 2016

Structure and Genome Organization of Cherry Virus A (Capillovirus, Betaflexiviridae) from China Using Small RNA Sequencing.

Genome Announc 2016 May 12;4(3). Epub 2016 May 12.

Key Laboratory for Fruit Biotechnology Breeding of Shandong Province, Shandong Institute of Pomology, Taian, Shandong, China

Cherry virus A (CVA) (Capillovirus, Betaflexiviridae) is widely present in cherry-growing areas. We obtained the complete genome of a CVA isolate (CVA-TA) using small RNA deep sequencing, followed by overlapping reverse transcription-PCR (RT-PCR) and rapid amplification of cDNA ends (RACE). The newly identified 5'-untranslated region (5'-UTR) from CVA-TA may form additional hairpin and loop structures to stabilize the CVA genome.
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http://dx.doi.org/10.1128/genomeA.00364-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4866854PMC
May 2016

CisSERS: Customizable In Silico Sequence Evaluation for Restriction Sites.

PLoS One 2016 12;11(4):e0152404. Epub 2016 Apr 12.

Molecular Plant Sciences Graduate Program, Washington State University, Pullman, Washington, United States of America.

High-throughput sequencing continues to produce an immense volume of information that is processed and assembled into mature sequence data. Data analysis tools are urgently needed that leverage the embedded DNA sequence polymorphisms and consequent changes to restriction sites or sequence motifs in a high-throughput manner to enable biological experimentation. CisSERS was developed as a standalone open source tool to analyze sequence datasets and provide biologists with individual or comparative genome organization information in terms of presence and frequency of patterns or motifs such as restriction enzymes. Predicted agarose gel visualization of the custom analyses results was also integrated to enhance the usefulness of the software. CisSERS offers several novel functionalities, such as handling of large and multiple datasets in parallel, multiple restriction enzyme site detection and custom motif detection features, which are seamlessly integrated with real time agarose gel visualization. Using a simple fasta-formatted file as input, CisSERS utilizes the REBASE enzyme database. Results from CisSERS enable the user to make decisions for designing genotyping by sequencing experiments, reduced representation sequencing, 3'UTR sequencing, and cleaved amplified polymorphic sequence (CAPS) molecular markers for large sample sets. CisSERS is a java based graphical user interface built around a perl backbone. Several of the applications of CisSERS including CAPS molecular marker development were successfully validated using wet-lab experimentation. Here, we present the tool CisSERS and results from in-silico and corresponding wet-lab analyses demonstrating that CisSERS is a technology platform solution that facilitates efficient data utilization in genomics and genetics studies.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0152404PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4829253PMC
August 2016

Genome sequences of Photorhabdus luminescens strains isolated from entomopathogenic nematodes from southern India.

Genom Data 2015 Dec 29;6:46-7. Epub 2015 Jul 29.

Department of Horticulture, PO Box 646414, Washington State University, Pullman, WA 99164, USA.

We report here draft whole genome sequences of three novel strains of Photorhabdus luminescens of 5.2-5.3 Mbps in size, and with a G + C content of 42.5% (each). Symbiotic γ-proteobacteria belonging to the genera, Photorhabdus (Family: Enterobacteriaceae) with their natural vectors, the entomopathogenic nematodes (EPN) (Phylum: Nematoda; Order: Rhabditida; Family: Heterorhabditidae), have emerged as important biological control agents of insect pests, and are capable of production and delivery of diverse compounds to influence host biology [1], [2], [3]. Analysis of these genomes is expected to provide enhanced insight into mechanisms of virulence, insecticidal toxin genetic diversity, antibiotic resistance and monoxenicity. The nucleotide sequence information for the three strains NBAII PLHb105, NBAII HiPL101 and NBAII H75HRPL105 has been deposited in NCBI Nucleotide database and is accessible via AZAB00000000, JTHJ00000000 and JXUR00000000 accession numbers respectively.
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http://dx.doi.org/10.1016/j.gdata.2015.07.023DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4664677PMC
December 2015

Comparative analysis of predicted plastid-targeted proteomes of sequenced higher plant genomes.

PLoS One 2014 13;9(11):e112870. Epub 2014 Nov 13.

Department of Horticulture, Washington State University, Pullman, WA, United States of America; Molecular Plant Science Graduate Program, Washington State University, Pullman, WA, United States of America.

Plastids are actively involved in numerous plant processes critical to growth, development and adaptation. They play a primary role in photosynthesis, pigment and monoterpene synthesis, gravity sensing, starch and fatty acid synthesis, as well as oil, and protein storage. We applied two complementary methods to analyze the recently published apple genome (Malus × domestica) to identify putative plastid-targeted proteins, the first using TargetP and the second using a custom workflow utilizing a set of predictive programs. Apple shares roughly 40% of its 10,492 putative plastid-targeted proteins with that of the Arabidopsis (Arabidopsis thaliana) plastid-targeted proteome as identified by the Chloroplast 2010 project and ∼57% of its entire proteome with Arabidopsis. This suggests that the plastid-targeted proteomes between apple and Arabidopsis are different, and interestingly alludes to the presence of differential targeting of homologs between the two species. Co-expression analysis of 2,224 genes encoding putative plastid-targeted apple proteins suggests that they play a role in plant developmental and intermediary metabolism. Further, an inter-specific comparison of Arabidopsis, Prunus persica (Peach), Malus × domestica (Apple), Populus trichocarpa (Black cottonwood), Fragaria vesca (Woodland Strawberry), Solanum lycopersicum (Tomato) and Vitis vinifera (Grapevine) also identified a large number of novel species-specific plastid-targeted proteins. This analysis also revealed the presence of alternatively targeted homologs across species. Two separate analyses revealed that a small subset of proteins, one representing 289 protein clusters and the other 737 unique protein sequences, are conserved between seven plastid-targeted angiosperm proteomes. Majority of the novel proteins were annotated to play roles in stress response, transport, catabolic processes, and cellular component organization. Our results suggest that the current state of knowledge regarding plastid biology, preferentially based on model systems is deficient. New plant genomes are expected to enable the identification of potentially new plastid-targeted proteins that will aid in studying novel roles of plastids.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0112870PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4231079PMC
December 2015

Comparative analysis of virus-specific small RNA profiles of three biologically distinct strains of Potato virus Y in infected potato (Solanum tuberosum) cv. Russet Burbank.

Virus Res 2014 Oct 15;191:153-60. Epub 2014 Jul 15.

Department of Plant Pathology, Washington State University, Pullman, WA, USA. Electronic address:

Deep sequencing technology has enabled the analysis of small RNA profiles of virus-infected plants and could provide insights into virus-host interactions. Potato virus Y is an economically important viral pathogen of potato worldwide. In this study, we investigated the nature and relative levels of virus-derived small interfering RNAs (vsiRNAs) in potato cv. Russet Burbank infected with three biologically distinct and economically important strains of PVY, the ordinary strain (PVY-O), tobacco veinal-necrotic strain (PVY-N) and tuber necrotic strain (PVY-NTN). The analysis showed an overall abundance of vsiRNAs of 20-24nt in PVY-infected plants. Considerable differences were present in the distribution of vsiRNAs as well as total small RNAs. The 21nt class was the most prevalent in PVY-infected plants irrespective of the virus strain, whereas in healthy potato plants, the 24nt class was the most dominant. vsiRNAs were derived from every position in the PVY genome, though certain hotspots were identified for each of the PVY strains. Among the three strains used, the population of vsiRNAs of different size classes was relatively different with PVY-NTN accumulating the highest level of vsiRNAs, while PVY-N infected plants had the least population of vsiRNAs. Unique vsiRNAs mapping to PVY genome in PVY-infected plants amounted to 3.13, 1.93 and 1.70% for NTN, N and O, respectively. There was a bias in the generation of vsiRNAs from the plus strand of the genome in comparison to the negative strand. The highest number of total vsiRNAs was from the cytoplasmic inclusion protein gene (CI) in PVY-O and PVY-NTN strains, whereas from PVY-N, the NIb gene produced maximum total vsiRNAs. These findings indicate that the three PVY strains interact differently in the same host genetic background and provided insights into virus-host interactions in an important food crop.
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http://dx.doi.org/10.1016/j.virusres.2014.07.005DOI Listing
October 2014

Role of bacterial communities in the natural suppression of Rhizoctonia solani bare patch disease of wheat (Triticum aestivum L.).

Appl Environ Microbiol 2013 Dec 20;79(23):7428-38. Epub 2013 Sep 20.

Department of Plant Pathology, Washington State University, Pullman, Washington, USA.

Rhizoctonia bare patch and root rot disease of wheat, caused by Rhizoctonia solani AG-8, develops as distinct patches of stunted plants and limits the yield of direct-seeded (no-till) wheat in the Pacific Northwest of the United States. At the site of a long-term cropping systems study near Ritzville, WA, a decline in Rhizoctonia patch disease was observed over an 11-year period. Bacterial communities from bulk and rhizosphere soil of plants from inside the patches, outside the patches, and recovered patches were analyzed by using pyrosequencing with primers designed for 16S rRNA. Taxa in the class Acidobacteria and the genus Gemmatimonas were found at higher frequencies in the rhizosphere of healthy plants outside the patches than in that of diseased plants from inside the patches. Dyella and Acidobacteria subgroup Gp7 were found at higher frequencies in recovered patches. Chitinophaga, Pedobacter, Oxalobacteriaceae (Duganella and Massilia), and Chyseobacterium were found at higher frequencies in the rhizosphere of diseased plants from inside the patches. For selected taxa, trends were validated by quantitative PCR (qPCR), and observed shifts of frequencies in the rhizosphere over time were duplicated in cycling experiments in the greenhouse that involved successive plantings of wheat in Rhizoctonia-inoculated soil. Chryseobacterium soldanellicola was isolated from the rhizosphere inside the patches and exhibited significant antagonism against R. solani AG-8 in vitro and in greenhouse tests. In conclusion, we identified novel bacterial taxa that respond to conditions affecting bare patch disease symptoms and that may be involved in suppression of Rhizoctonia root rot and bare batch disease.
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http://dx.doi.org/10.1128/AEM.01610-13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3837727PMC
December 2013

Application of Cydia pomonella expressed sequence tags: Identification and expression of three general odorant binding proteins in codling moth.

Insect Sci 2013 Oct 6;20(5):559-74. Epub 2012 Dec 6.

USDA-ARS, Yakima Agricultural Research Laboratory, Wapato, WA, 98951.

The codling moth, Cydia pomonella, is one of the most important pests of pome fruits in the world, yet the molecular genetics and the physiology of this insect remain poorly understood. A combined assembly of 8 341 expressed sequence tags was generated from Roche 454 GS-FLX sequencing of eight tissue-specific cDNA libraries. Putative chemosensory proteins (12) and odorant binding proteins (OBPs) (18) were annotated, which included three putative general OBP (GOBP), one more than typically reported for other Lepidoptera. To further characterize CpomGOBPs, we cloned cDNA copies of their transcripts and determined their expression patterns in various tissues. Cloning and sequencing of the 698 nt transcript for CpomGOBP1 resulted in the prediction of a 163 amino acid coding region, and subsequent RT-PCR indicated that the transcripts were mainly expressed in antennae and mouthparts. The 1 289 nt (160 amino acid) CpomGOBP2 and the novel 702 nt (169 amino acid) CpomGOBP3 transcripts are mainly expressed in antennae, mouthparts, and female abdomen tips. These results indicate that next generation sequencing is useful for the identification of novel transcripts of interest, and that codling moth expresses a transcript encoding for a new member of the GOBP subfamily.
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http://dx.doi.org/10.1111/j.1744-7917.2012.01560.xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4255946PMC
October 2013