scholarly journals Transcriptomics of Differential Ripening in ‘d’Anjou’ Pear (Pyrus communis L.)

2021 ◽  
Vol 12 ◽  
Author(s):  
Loren Honaas ◽  
Heidi Hargarten ◽  
John Hadish ◽  
Stephen P. Ficklin ◽  
Sara Serra ◽  
...  
Keyword(s):  
Fruit Quality ◽  
Expression Patterns ◽  
Pyrus Communis ◽  
Accurate Estimation ◽  
Pear Fruit ◽  
Pome Fruit ◽  
Tissue Samples ◽  
European Pear ◽  
Fruit Maturity ◽  
Postharvest Management

Estimating maturity in pome fruits is a critical task that directs virtually all postharvest supply chain decisions. This is especially important for European pear (Pyrus communis) cultivars because losses due to spoilage and senescence must be minimized while ensuring proper ripening capacity is achieved (in part by satisfying a fruit chilling requirement). Reliable methods are lacking for accurate estimation of pear fruit maturity, and because ripening is maturity dependent it makes predicting ripening capacity a challenge. In this study of the European pear cultivar ‘d’Anjou’, we sorted fruit at harvest based upon on-tree fruit position to build contrasts of maturity. Our sorting scheme showed clear contrasts of maturity between canopy positions, yet there was substantial overlap in the distribution of values for the index of absorbance difference (IAD), a non-destructive spectroscopic measurement that has been used as a proxy for pome fruit maturity. This presented an opportunity to explore a contrast of maturity that was more subtle than IAD could differentiate, and thus guided our subsequent transcriptome analysis of tissue samples taken at harvest and during storage. Using a novel approach that tests for condition-specific differences of co-expressed genes, we discovered genes with a phased character that mirrored our sorting scheme. The expression patterns of these genes are associated with fruit quality and ripening differences across the experiment. Functional profiles of these co-expressed genes are concordant with previous findings, and also offer new clues, and thus hypotheses, about genes involved in pear fruit quality, maturity, and ripening. This work may lead to new tools for enhanced postharvest management based on activity of gene co-expression modules, rather than individual genes. Further, our results indicate that modules may have utility within specific windows of time during postharvest management of ‘d’Anjou’ pear.

Phenolic compounds profile, carbohydrates and external fruit quality of the ‘Concorde’ pear (Pyrus communisL.) after bagging

2012 ◽  
Vol 92 (1) ◽  
pp. 67-75 ◽  
Author(s):  
Metka Hudina ◽  
Franci Stampar ◽  
Primoz Orazem ◽  
Maja Mikulic Petkovsek ◽  
Robert Veberic
Keyword(s):  
Phenolic Compounds ◽  
Fruit Quality ◽  
Pyrus Communis ◽  
Soluble Solids ◽  
Soluble Solids Content ◽  
Pear Fruit ◽  
European Pear ◽  
Pyrus Communis L ◽  
Solids Content

Hudina, M., Stampar, F., Orazem, P., Mikulic Petkovsek, M. and Veberic, R. 2012. Phenolic compounds profile, carbohydrates and external fruit quality of the 'Concorde' pear ( Pyrus communis L.) after bagging. Can. J. Plant Sci. 92: 67–75. The practice of pre-harvest bagging has been extensively used in several fruit crops to improve the commercial value of the fruit. The purpose of this study was to investigate the effect of fruit bagging on internal and external quality of the European pear (Pyrus communis L.) cv. ‘Concorde’. Fruit quality was determined by chemical analyses (individual sugars, organic acids and phenolic compounds) and physical characteristics in 2005 and 2006. Bagging of pear fruit after June drop until harvest significantly reduced fruit length in both observed years. Fruit bagging resulted in increased firmness of the fruit only in 2006. Soluble solids content was significantly lower in bagged fruit in 2006. In 2005, bagging had no influence on firmness and soluble solids content. Bagging improved fruit surface lightness, since L* was higher in the bagged than in the control fruit in both years. Also the a* parameter was higher in bagged fruit. We noted significant influence of bagging on total sugars content. Bagging European pear fruit decreased the content of phenolic compounds in skin (catechin, chlorogenic acid, epicatechin, p-coumaric acid, quercetin 3-O-galactoside, quercetin 3-O-glucoside, quercetin 3-O-rhamnoside). The removal of bags 7 d before harvest significantly increased glucose, shikimic and fumaric acids.

scholarly journals Towards a catalog of pome tree architecture genes: the draft 'd'Anjou' genome (Pyrus communis L.)

2021 ◽  
Author(s):  
Huiting Zhang ◽  
Eric K Wafula ◽  
Jon Eilers ◽  
Alex Harkess ◽  
Paula E Ralph ◽  
...  
Keyword(s):  
Agronomic Traits ◽  
Rapid Development ◽  
Draft Genome ◽  
Gene Families ◽  
Pyrus Communis ◽  
Tree Architecture ◽  
Model Organisms ◽  
Pome Fruit ◽  
European Pear ◽  
Plant Genomes

The rapid development of sequencing technologies has led to a deeper understanding of horticultural plant genomes. However, experimental evidence connecting genes to important agronomic traits is still lacking in most non-model organisms. For instance, the genetic mechanisms underlying plant architecture are poorly understood in pome fruit trees, creating a major hurdle in developing new cultivars with desirable architecture, such as dwarfing rootstocks in European pear (Pyrus communis). Further, the quality and content of genomes vary widely. Therefore, it can be challenging to curate a list of genes with high-confidence gene models across reference genomes. This is often an important first step towards identifying key genetic factors for important traits. Here we present a draft genome of P. communis 'd'Anjou' and an improved assembly of the latest P. communis 'Bartlett' genome. To study gene families involved in tree architecture in European pear and other rosaceous species, we developed a workflow using a collection of bioinformatic tools towards curation of gene families of interest across genomes. This lays the groundwork for future functional studies in pear tree architecture. Importantly, our workflow can be easily adopted for other plant genomes and gene families of interest.

scholarly journals Integrative Analysis of the Core Fruit Lignification Toolbox in Pear Reveals Targets for Fruit Quality Bioengineering

Biomolecules ◽  
2019 ◽  
Vol 9 (9) ◽  
pp. 504 ◽  
Author(s):  
Yunpeng Cao ◽  
Xiaoxu Li ◽  
Lan Jiang
Keyword(s):  
Fruit Quality ◽  
Expression Patterns ◽  
Lignin Biosynthesis ◽  
Integrative Analysis ◽  
Bimolecular Fluorescence Complementation ◽  
Pear Fruit ◽  
Cell Content ◽  
Tandem Gene Duplication ◽  
Stone Cell ◽  
Chinese White

Stone cell content is an important factor affecting pear fruit flavor. Lignin, a major component of pear stone cells, hinders the quality and value of commercial fruit. The completion of the Chinese white pear (Pyrus bretschneideri) genome sequence provides an opportunity to perform integrative analysis of the genes encoding the eleven protein families (i.e., PAL, C4H, 4CL, HCT, C3H, CSE, CCoAOMT, CCR, F5H, COMT, and CAD) in the phenylpropanoid pathway. Here, a systematic study based on expression patterns and phylogenetic analyses was performed to identify the members of each gene family potentially involved in the lignification in the Chinese white pear. The phylogenetic analysis suggested that 35 P. bretschneideri genes belong to bona fide lignification clade members. Compared to other plants, some multigene families are expanded by tandem gene duplication, such as HCT, C3H, COMT, and CCR. RNA sequencing was used to study the expression patterns of the genes in different tissues, including leaf, petal, bud, sepal, ovary, stem, and fruit. Eighteen genes presented a high expression in fruit, indicating that these genes may be involved in the biosynthesis of lignin in pear fruit. Similarly to what has been observed for Populus trichocarpa, a bimolecular fluorescence complementation (BiFC) experiment indicated that P. bretschneideri C3H and C4H might also interact with each other to regulate monolignol biosynthesis in P. bretschneideri, ultimately affecting the stone cell content in pear fruits. The identification of the major genes involved in lignin biosynthesis in pear fruits provides the basis for the development of strategies to improve fruit quality.

Microarray analysis of gene expression patterns during fruit development in European pear (Pyrus communis)

2013 ◽  
Vol 164 ◽  
pp. 466-473 ◽  
Author(s):  
Kenji Nashima ◽  
Tokurou Shimizu ◽  
Chikako Nishitani ◽  
Toshiya Yamamoto ◽  
Hirokazu Takahashi ◽  
...  
Keyword(s):  
Gene Expression ◽  
Microarray Analysis ◽  
Fruit Development ◽  
Expression Patterns ◽  
Pyrus Communis ◽  
Gene Expression Patterns ◽  
European Pear

scholarly journals Assessing Preharvest Field Temperature and At-harvest Fruit Quality for Prediction of Soft Scald Risk of ‘Honeycrisp’ Apple Fruit during Cold Storage

HortScience ◽  
2019 ◽  
Vol 54 (5) ◽  
pp. 910-915 ◽  
Author(s):  
Rachel Leisso ◽  
Ines Hanrahan ◽  
Jim Mattheis
Keyword(s):  
Fruit Quality ◽  
Cold Storage ◽  
Titratable Acidity ◽  
Apple Fruit ◽  
Soluble Solids ◽  
Ethylene Concentration ◽  
Quality Control Laboratory ◽  
Fruit Maturity ◽  
Postharvest Management ◽  
Soft Scald

‘Honeycrisp’ apple is susceptible to the postharvest chilling disorder soft scald that renders fruit unmarketable. Reducing or preventing this disorder is an important component of ‘Honeycrisp’ postharvest management. In commercial settings, advanced fruit maturity and orchard history contribute to an estimation of soft scald susceptibility, but additional at-harvest information indicative of soft scald risk would enable better management decisions. In this study, we obtained fruit from commercial orchards for 3 successive years, and assessed field growing degree days (GDD), field chilling hours (CH), and fruit quality metrics at harvest, followed by soft scald incidence assessment at 12 weeks of cold storage. The analyses indicated starch index, soluble solids content (SSC), internal ethylene concentration, titratable acidity (TA), peel background color, firmness, GDD, or CH do not reliably indicate fruit susceptibility to soft scald. However, SSC and TA were elevated in fruit that later developed soft scald, and a higher number of GDD also sometimes preceded soft scald, which is consistent with advanced fruit maturity that can enhance soft scald risk. Overall, results suggest that other tools may be required to accurately predict postharvest soft scald on a quality control laboratory scale. The statistical analyses applied to the present study would have utility for assessing other soft scald prediction tools or markers.

scholarly journals Multiple season-long sprays of ethephon or NAA combined with calcium chloride on ‘Honeycrisp’ apples: I. Effect on bloom and fruit quality attributes

2019 ◽  
Vol 99 (4) ◽  
pp. 444-459
Author(s):  
John A. Cline
Keyword(s):  
Calcium Chloride ◽  
Fruit Quality ◽  
Quality Attributes ◽  
Naphthaleneacetic Acid ◽  
Fruit Firmness ◽  
Biennial Bearing ◽  
Fruit Drop ◽  
Fruit Maturity ◽  
Return Bloom ◽  
Honeycrisp Apples

‘Honeycrisp’ apple trees are highly prone to biennial bearing and predisposed to bitter pit. The hypothesis that tank mix sprays of ethephon (ETH), naphthaleneacetic acid (NAA), and 1-aminocyclopropane carboxylic acid (ACC) combined with calcium chloride (CaCl2) can mitigate these production problems was tested in a 3-yr study. Mature ‘Honeycrisp’ trees were treated with either three or six summer applications of 150 mg L−1 ETH or 5 mg L−1 NAA, all tank-mixed with and without CaCl2, or two or five applications of 150 mg L−1 ACC (without CaCl2). Treatments were applied at 10-d intervals and initiated between 21 and 26 June. All treatments had little effect on enhancing return bloom of ‘Honeycrisp’. NAA, ETH, and CaCl2 all influenced fruit maturity and quality at harvest to varying degrees and across years. Fruit treated with NAA were firmer compared with untreated fruit in 2 out of 3 yr, whereas overall, fruit treated with six sprays of ETH had lower fruit firmness and were more mature. NAA had less influence on fruit quality attributes at harvest than did ETH, and decreased pre-harvest fruit drop (PFD). PFD increased with ETH in 1 out of 2 yr, whereas ACC and NAA both decreased PFD in 1 out of 2 yr. Overall, ETH and NAA, with or without CaCl2, had significant but inconsistent effects on fruit quality and maturity, all dependent on the year and number of applications. Adding CaCl2 decreased fruit firmness in 2 out of 3 yr.

scholarly journals miRNA Expression Characterizes Histological Subtypes and Metastasis in Penile Squamous Cell Carcinoma

Cancers ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 1480
Author(s):  
Hiresh Ayoubian ◽  
Joana Heinzelmann ◽  
Sebastian Hölters ◽  
Oybek Khalmurzaev ◽  
Alexey Pryalukhin ◽  
...  
Keyword(s):  
Microarray Data ◽  
Expression Patterns ◽  
Hpv Infection ◽  
Differentially Expressed ◽  
Histological Subtypes ◽  
Specific Expression ◽  
Tissue Samples ◽  
Qrt Pcr ◽  
Differentially Expressed Mirnas ◽  
The Impact

Although microRNAs are described as promising biomarkers in many tumor types, little is known about their role in PSCC. Thus, we attempted to identify miRNAs involved in tumor development and metastasis in distinct histological subtypes considering the impact of HPV infection. In a first step, microarray analyses were performed on RNA from formalin-fixed, paraffin-embedded tumor (22), and normal (8) tissue samples. Microarray data were validated for selected miRNAs by qRT-PCR on an enlarged cohort, including 27 tumor and 18 normal tissues. We found 876 significantly differentially expressed miRNAs (p ≤ 0.01) between HPV-positive and HPV-negative tumor samples by microarray analysis. Although no significant differences were detected between normal and tumor tissue in the whole cohort, specific expression patterns occurred in distinct histological subtypes, such as HPV-negative usual PSCC (95 differentially expressed miRNAs, p ≤ 0.05) and HPV-positive basaloid/warty subtypes (247 differentially expressed miRNAs, p ≤ 0.05). Selected miRNAs were confirmed by qRT-PCR. Furthermore, microarray data revealed 118 miRNAs (p ≤ 0.01) that were significantly differentially expressed in metastatic versus non-metastatic usual PSCC. The lower expression levels for miR-137 and miR-328-3p in metastatic usual PSCC were validated by qRT-PCR. The results of this study confirmed that specific miRNAs could serve as potential diagnostic and prognostic markers in single PSCC subtypes and are associated with HPV-dependent pathways.

scholarly journals iNOS Expression by Tumor-Infiltrating Lymphocytes, PD-L1 and Prognosis in Non-Small-Cell Lung Cancer

Cancers ◽  
2020 ◽  
Vol 12 (11) ◽  
pp. 3276
Author(s):  
Alexandra Giatromanolaki ◽  
Avgi Tsolou ◽  
Eleftheria Daridou ◽  
Maria Kouroupi ◽  
Katerina Chlichlia ◽  
...  
Keyword(s):  
Immune Response ◽  
Overall Survival ◽  
Small Cell Lung Carcinoma ◽  
Expression Patterns ◽  
Tumor Infiltrating Lymphocytes ◽  
Small Cell ◽  
Small Cell Lung ◽  
Tissue Samples ◽  
Cell Lung Carcinoma ◽  
Infiltrating Lymphocytes

Background: Inducible Nitric Oxygen Synthase (iNOS) promotes the generation of NO in tissues. Its role in tumor progression and immune response is unclear. Methods: The immunohistochemical expression patterns of iNOS were studied in a series of 98 tissue samples of non-small-cell lung carcinoma (NSCLC), in parallel with the expression of hypoxia and anaerobic metabolism markers, PD-L1 and tumor-infiltrating lymphocytes (TILs). Results: iNOS is expressed by cancer cells in 19/98 (19.4%), while extensive expression by cancer-associated fibroblasts occurs in 8/98 (8.2%) cases. None of these patterns relate to stage or prognosis. Extensive infiltration of the tumor stroma by iNOS-expressing TILs (iNOS+TILs) occurs in 47/98 (48%) cases. This is related to low Hypoxia-Inducible Factor 1α (HIF1α), high PD-L1 expression and a better overall survival (p = 0.002). Expression of PD-L1, however, mitigates the beneficial effect of the presence of iNOS+TIL. Conclusions: Extensive expression of iNOS by TILs occurs in approximately 50% of NSCLCs, and this is significantly related to an improved overall survival. This brings forward the role of iNOS in anti-neoplastic lymphocyte biology, supporting iNOS+TILs as a putative marker of immune response. The value of this biomarker as a predictive and treatment-guiding tool for tumor immunotherapy demands further investigation.

scholarly journals Altered Expression of ESR1, ESR2, PELP1 and c-SRC Genes Is Associated with Ovarian Cancer Manifestation

2021 ◽  
Vol 22 (12) ◽  
pp. 6216
Author(s):  
Monika Englert-Golon ◽  
Mirosław Andrusiewicz ◽  
Aleksandra Żbikowska ◽  
Małgorzata Chmielewska ◽  
Stefan Sajdak ◽  
...  
Keyword(s):  
Ovarian Cancer ◽  
Cancer Biology ◽  
Expression Patterns ◽  
Control Group ◽  
Tissue Samples ◽  
Altered Expression ◽  
Depth Study ◽  
Tyrosine Protein Kinase ◽  
Ovarian Tumorigenesis ◽  
Protein Immunoreactivity

Ovarian cancer remains the leading cause of death due to gynecologic malignancy. Estrogen-related pathways genes, such as estrogen receptors (ESR1 and ESR2) and their coregulators, proline-, glutamic acid-, and leucine-rich protein 1 (PELP1), and proto-oncogene tyrosine-protein kinase c-Src (SRC) are involved in ovarian cancer induction and development, still they require in-depth study. In our study, tissue samples were obtained from 52 females of Caucasian descent (control group without cancerous evidence (n = 27), including noncancerous benign changes (n = 15), and the ovarian carcinoma (n = 25)). Using quantitative analyses, we investigated ESRs, PELP1, and SRC mRNA expression association with ovarian tumorigenesis. Proteins’ presence and their location were determined by Western blot and immunohistochemistry. Results showed that PELP1 and SRC expression levels were found to differ in tissues of different sample types. The expression patterns were complex and differed in the case of ovarian cancer patients compared to controls. The most robust protein immunoreactivity was observed for PELP1 and the weakest for ESR1. The expression patterns of analyzed genes represent a potentially interesting target in ovarian cancer biology, especially PELP1. This study suggests that specific estrogen-mediated functions in the ovary and ovary-derived cancer might result from different local interactions of estrogen with their receptors and coregulators.

scholarly journals Identification of cell-type-specific marker genes from co-expression patterns in tissue samples

2021 ◽  
Author(s):  
Yixuan Qiu ◽  
Jiebiao Wang ◽  
Jing Lei ◽  
Kathryn Roeder
Keyword(s):  
Single Cell ◽  
Expression Patterns ◽  
R Package ◽  
Supplementary Information ◽  
Marker Genes ◽  
Specific Marker ◽  
Cell Type ◽  
Correlation Pattern ◽  
Tissue Samples ◽  
Bulk Data

Abstract Motivation Marker genes, defined as genes that are expressed primarily in a single cell type, can be identified from the single cell transcriptome; however, such data are not always available for the many uses of marker genes, such as deconvolution of bulk tissue. Marker genes for a cell type, however, are highly correlated in bulk data, because their expression levels depend primarily on the proportion of that cell type in the samples. Therefore, when many tissue samples are analyzed, it is possible to identify these marker genes from the correlation pattern. Results To capitalize on this pattern, we develop a new algorithm to detect marker genes by combining published information about likely marker genes with bulk transcriptome data in the form of a semi-supervised algorithm. The algorithm then exploits the correlation structure of the bulk data to refine the published marker genes by adding or removing genes from the list. Availability and implementation We implement this method as an R package markerpen, hosted on CRAN (https://CRAN.R-project.org/package=markerpen). Supplementary information Supplementary data are available at Bioinformatics online.

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