scholarly journals Could Causal Discovery in Proteogenomics Assist in Understanding Gene–Protein Relations? A Perennial Fruit Tree Case Study Using Sweet Cherry as a Model

Cells ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 92
Author(s):  
Maria Ganopoulou ◽  
Michail Michailidis ◽  
Lefteris Angelis ◽  
Ioannis Ganopoulos ◽  
Athanassios Molassiotis ◽  
...  
Keyword(s):  
Protein Level ◽  
Sweet Cherry ◽  
Prunus Avium ◽  
Fruit Trees ◽  
Causal Modeling ◽  
Causal Discovery ◽  
Complex Nature ◽  
Targeted Analysis ◽  
Genome Wide ◽  
Biological Interpretation

Genome-wide transcriptome analysis is a method that produces important data on plant biology at a systemic level. The lack of understanding of the relationships between proteins and genes in plants necessitates a further thorough analysis at the proteogenomic level. Recently, our group generated a quantitative proteogenomic atlas of 15 sweet cherry (Prunus avium L.) cv. ‘Tragana Edessis’ tissues represented by 29,247 genes and 7584 proteins. The aim of the current study was to perform a targeted analysis at the gene/protein level to assess the structure of their relation, and the biological implications. Weighted correlation network analysis and causal modeling were employed to, respectively, cluster the gene/protein pairs, and reveal their cause–effect relations, aiming to assess the associated biological functions. To the best of our knowledge, this is the first time that causal modeling has been employed within the proteogenomics concept in plants. The analysis revealed the complex nature of causal relations among genes/proteins that are important for traits of interest in perennial fruit trees, particularly regarding the fruit softening and ripening process in sweet cherry. Causal discovery could be used to highlight persistent relations at the gene/protein level, stimulating biological interpretation and facilitating further study of the proteogenomic atlas in plants.

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

2017 ◽  
Vol 15 ◽  
pp. 290-298 ◽  
Author(s):  
Seanna Hewitt ◽  
Benjamin Kilian ◽  
Ramyya Hari ◽  
Tyson Koepke ◽  
Richard Sharpe ◽  
...  
Keyword(s):  
Sweet Cherry ◽  
Prunus Avium ◽  
Genome Wide ◽  
Prunus Avium L

scholarly journals A draft genome of sweet cherry ( Prunus avium L.) reveals genome‐wide and local effects of domestication

2020 ◽  
Vol 103 (4) ◽  
pp. 1420-1432 ◽  
Author(s):  
Sara Pinosio ◽  
Fabio Marroni ◽  
Andrea Zuccolo ◽  
Nicola Vitulo ◽  
Stephanie Mariette ◽  
...  
Keyword(s):  
Sweet Cherry ◽  
Prunus Avium ◽  
Draft Genome ◽  
Local Effects ◽  
Genome Wide ◽  
Prunus Avium L

Susceptibility of sweet and sour cherry cultivars/genotypes to feeding damage caused by Bryobia rubrioculus (Acari: Tetranychidae)

2018 ◽  
Vol 23 (1) ◽  
pp. 78
Author(s):  
Nazila Honarparvar ◽  
Mohammad Khanjani ◽  
Rostislav Zemek ◽  
Naser Bouzari
Keyword(s):  
Sweet Cherry ◽  
Prunus Avium ◽  
Sour Cherry ◽  
Fruit Trees ◽  
Mean Value ◽  
White Background ◽  
Analysis Technique ◽  
The Mean ◽  
Color Scanner ◽  
Area Percentage

The sweet cherry Prunus avium L. and sour cherry Prunus cerasus L. are considered important fruit trees, providing valuable and delicious fruit worldwide. We compared the susceptibility of 10 cultivars of sweet cherry and 5 genotypes of sour cherry to Bryobia rubrioculus Scheuten feeding by manually counting brown spots and by measuring damaged leaf area using a computerized image analysis technique. Damaged leaves were individually scanned on a common flatbed color scanner on a white background. The cultivars and genotypes of sweet and sour cherries, based on the mean area percentage having feeding symptoms on the leaves, were classified into three groups: (1) "susceptible", i.e., Hamedan, BN 5150, BT 5148, Zard-90, KB 9 and KB 10; (2) "semi-resistant", i.e., KB 21, Sabima, BT 5124, KB 25 and Lambert; and (3) "resistant", i.e., Haj Yousefi, BO 5187, BT 5154 and Siah Mashhad. A corresponding increase in the mean value of the symptom area was observed as the number of adult brown mites increased per disc. The results of both methods were compared, and the advantages of each method were discussed.

scholarly journals C-Partitioning in Sweet Cherry (Prunus avium L) During Early Spring

HortScience ◽  
2004 ◽  
Vol 39 (4) ◽  
pp. 887C-887
Author(s):  
Marlene Ayala ◽  
Greg Lang*
Keyword(s):  
Sweet Cherry ◽  
Prunus Avium ◽  
Fruit Set ◽  
Primary Source ◽  
Fruit Trees ◽  
Reproductive Organs ◽  
Early Spring ◽  
Young Leaves ◽  
C Partitioning ◽  
Storage Reserves

In deciduous fruit trees, some storage reserves accumulate during fall and are used for early spring growth. In sweet cherry (Prunus avium L), stored reserves are critical for early growth and there is a transition phase during which current photoassimilates become the primary source for support of reproductive and vegetative sinks. As little is known about this transition, an experiment using 4-year-old `Regina' sweet cherry on the semidwarfing rootstock, Gisela 6, was established. Using whole canopy exposure chambers, five trees were pulsed with high levels of 13CO2 on three different dates during fall (Sept.-Oct). At leaf drop, leaves, buds, wood, bark and roots were sampled for GCMS analysis of pre-winter storage reserves. The major storage organs (those which had the highest change in isotopic ratios) were roots and wood in the trunk and branches. During spring, newly developing organs (flowers, fruits and young leaves) were sampled weekly from bloom to stage III of fruit development for additional GCMS analysis. The stored 13C was mobilized and partitioned to flowers, fruits and young leaves from early spring until one week after fruit set. The highest 13C levels in growing sinks were observed between bloom and fruit set. The isotopic composition of new organs did not differ initially (3 May). During the three next sampling dates (10-24 May) reproductive organs had higher 13C levels compared to vegetative growth. The role of storage reserves, as a source of assimilates for early spring growth and their implications for crop development, will be discussed.

scholarly journals Genome-Wide Identification of the Xyloglucan endotransglucosylase/Hydrolase (XTH) and Polygalacturonase (PG) Genes and Characterization of their Role in Fruit Softening of Sweet Cherry

2021 ◽  
Vol 22 (22) ◽  
pp. 12331
Author(s):  
Zefeng Zhai ◽  
Chen Feng ◽  
Yanyan Wang ◽  
Yueting Sun ◽  
Xiang Peng ◽  
...  
Keyword(s):  
Cell Wall ◽  
Sweet Cherry ◽  
Prunus Avium ◽  
Fruit Softening ◽  
Fruit Firmness ◽  
Xyloglucan Endotransglycosylase ◽  
Genome Wide ◽  
Fruit Development And Ripening ◽  
Sweet Cherry Cultivars

Fruit firmness is an important economical trait in sweet cherry (Prunus avium L.) where the change of this trait is related to cell wall degradation. Xyloglucan endotransglycosylase/hydrolase (XTH) and polygalacturonases (PGs) are critical cell-wall-modifying enzymes that occupy a crucial position in fruit ripening and softening. Herein, we identified 18 XTHs and 45 PGs designated PavXTH1-18 and PavPG1-45 based on their locations in the genome of sweet cherry. We provided a systematical overview of PavXTHs and PavPGs, including phylogenetic relationships, conserved motifs, and expression profiling of these genes. The results showed that PavXTH14, PavXTH15 and PavPG38 were most likely to participated in fruit softening owing to the substantial increment in expression during fruit development and ripening. Furthermore, the phytohormone ABA, MeJA, and ethephon significantly elevated the expression of PavPG38 and PavXTH15, and thus promoted fruit softening. Importantly, transient expression PavXTH14, PavXTH15 and PavPG38 in cherry fruits significantly reduced the fruit firmness, and the content of various cell wall components including hemicellulose and pectin significantly changed correspondingly in the transgenic fruit. Taken together, these results present an extensive analysis of XTHs and PGs in sweet cherry and provide potential targets for breeding softening-resistant sweet cherry cultivars via manipulating cell wall-associated genes.

scholarly journals Preliminary Insights in Sensory Profile of Sweet Cherries

Foods ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 612
Author(s):  
Vânia Silva ◽  
Sandra Pereira ◽  
Alice Vilela ◽  
Eunice Bacelar ◽  
Francisco Guedes ◽  
...  
Keyword(s):  
Sweet Cherry ◽  
Prunus Avium ◽  
Sugar Content ◽  
Principal Component ◽  
Titratable Acidity ◽  
Physicochemical Characteristics ◽  
Quality Parameters ◽  
Sensory Profile ◽  
Soluble Solids ◽  
Sensory Data

Sweet cherry (Prunus avium L.) is a fruit appreciated by consumers for its well-known physical and sensory characteristics and its health benefits. Being an extremely perishable fruit, it is important to know the unique attributes of the cultivars to develop cultivation or postharvest strategies that can enhance their quality. This study aimed to understand the influence of physicochemical characteristics of two sweet cherry cultivars, Burlat and Van, on the food quality perception. Several parameters (weight, dimensions, soluble solids content (SSC), pH, titratable acidity (TA), colour, and texture) were measured and correlated with sensory data. Results showed that cv. Van presented heavier and firmer fruits with high sugar content. In turn, cv. Burlat showed higher pH, lower TA, and presented redder and brightest fruits. The principal component analysis revealed an evident separation between cultivars. Van cherries stood out for their sensory parameters and were classified as more acidic, bitter, and astringent, and presented a firmer texture. Contrarily, Burlat cherries were distinguished as being more flavourful, succulent, sweeter, and more uniform in terms of visual and colour parameters. The results of the sensory analysis suggested that perceived quality does not always depend on and/or recognize the quality parameters inherent to the physicochemical characteristics of each cultivar.

Biochemical and phenotypic characterization of sweet cherry (Prunus avium L.) cultivars with induced surface pitting

2021 ◽  
Vol 175 ◽  
pp. 111494
Author(s):  
Excequel Ponce ◽  
Blanca Alzola ◽  
Natalia Cáceres ◽  
Madeline Gas ◽  
Catalina Ferreira ◽  
...  
Keyword(s):  
Sweet Cherry ◽  
Prunus Avium ◽  
Phenotypic Characterization ◽  
Prunus Avium L

scholarly journals Multi-year analyses on three populations reveal the first stable QTLs for tolerance to rain-induced fruit cracking in sweet cherry (Prunus avium L.)

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
José Quero-García ◽  
Philippe Letourmy ◽  
José Antonio Campoy ◽  
Camille Branchereau ◽  
Svetoslav Malchev ◽  
...  
Keyword(s):  
Confidence Intervals ◽  
Sweet Cherry ◽  
Prunus Avium ◽  
Linear Models ◽  
Basic Research ◽  
Fruit Weight ◽  
Phenotypic Variance ◽  
Fruit Cracking ◽  
The Stability ◽  
Sweet Cherry Cultivars

AbstractRain-induced fruit cracking is a major problem in sweet cherry cultivation. Basic research has been conducted to disentangle the physiological and mechanistic bases of this complex phenomenon, whereas genetic studies have lagged behind. The objective of this work was to disentangle the genetic determinism of rain-induced fruit cracking. We hypothesized that a large genetic variation would be revealed, by visual field observations conducted on mapping populations derived from well-contrasted cultivars for cracking tolerance. Three populations were evaluated over 7–8 years by estimating the proportion of cracked fruits for each genotype at maturity, at three different areas of the sweet cherry fruit: pistillar end, stem end, and fruit side. An original approach was adopted to integrate, within simple linear models, covariates potentially related to cracking, such as rainfall accumulation before harvest, fruit weight, and firmness. We found the first stable quantitative trait loci (QTLs) for cherry fruit cracking, explaining percentages of phenotypic variance above 20%, for each of these three types of cracking tolerance, in different linkage groups, confirming the high complexity of this trait. For these and other QTLs, further analyses suggested the existence of at least two-linked QTLs in each linkage group, some of which showed confidence intervals close to 5 cM. These promising results open the possibility of developing marker-assisted selection strategies to select cracking-tolerant sweet cherry cultivars. Further studies are needed to confirm the stability of the reported QTLs over different genetic backgrounds and environments and to narrow down the QTL confidence intervals, allowing the exploration of underlying candidate genes.

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