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Multi-Omics Approaches and Computational Biology in Fruit Trees
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Multi-Omics Approaches and Computational Biology in Fruit Trees

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Plant Genetics and Genomics".

Deadline for manuscript submissions: closed (15 February 2022) | Viewed by 13938

Special Issue Editors

Prof. Dr. Francesco Paolo Marra

E-Mail Website
Guest Editor
Dipartimento di Architettura (Darch), Università degli Studi di Palermo, Viale delle Scienze - Edificio 8, 90128 Palermo, Italy
Interests: plant genetic diversity; fruit quality; self-incompatibility; abiotic stress; transcriptomics; functional genomics; ecophysiology
Dr. Annalisa Marchese

E-Mail Website
Guest Editor
Department of Agricultural, Food and Forest Sciences, University of Palermo, Viale delle Scienze 13, Building 4, 90128 Palermo, Italy
Interests: plant biotechnology; plant genetics; DNA sequencing; genomics; molecular markers; microsatellites; genotyping; primer sequencing; plant breeding; genetic diversity; SSR; quantitative trait loci mapping; microsatellite genotyping; cell biology; DNA fingerprints; embryogenesis; in vitro tissue culture; plant molecular genetics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Recent advances in the “omics sciences” and the increase in the availability of genomic information and high-throughput data of fruit species make it possible to understand gene functions and speed up genetic improvement programs, assisted by new molecular tools. Next-generation sequencing methods have made it possible to understand the gene expression data in both quantitative and qualitative manner, and can be used for obtaining sequences on a large scale with high sequencing depth. Today’s geneticists and breeders live an exciting and innovative era in which the processes of molecular characterization, mapping, discovery of gene function, and identification of complex traits are simplified by these new discoveries. Agriculture is currently under the pressure of climate change, and is struggling with the needs to ensure stable productivity and safeguard environmental quality.

Agriculture is facing new challenges—water scarcity, soil salinization, pest emergence and exacerbation, and unstable production. Thus, the development/selection of resilient varieties is urgently needed for more sustainable production. This Special Issue will focus on the development and application of omics advancements in gene discovery, understanding molecular mechanisms, the identification of key genes, and the efficient utilization of available resources in fruit tree crops that, in future, might act as potential targets of molecular breeding activities to develop cultivars.

We welcome the submission of reviews, original research articles, and short communications that focus on genetic, multi-omics studies, and computational biology in fruit trees in the field of genetic improvement.

Prof. Dr. Francesco Paolo Marra
Dr. Annalisa Marchese
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • plant genetic diversity
  • fruit quality
  • abiotic stress
  • physiology
  • breeding
  • genomics

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Published Papers (4 papers)

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Research

14 pages, 1605 KiB  
Article
Transcriptomic Analysis of the Pistacia vera (L.) Fruits Enable the Identification of Genes and Hormone-Related Gene Linked to Inflorescence Bud Abscission
by Jubina Benny, Antonio Giovino, Francesco Paolo Marra, Bipin Balan, Federico Martinelli, Tiziano Caruso and Annalisa Marchese
Genes 2022, 13(1), 60; https://doi.org/10.3390/genes13010060 - 27 Dec 2021
Cited by 7 | Viewed by 3021
Abstract
Pistacia vera (L.) is an alternate bearing species. The tree produces axillary inflorescence buds every year. Still, they abscise in “ON” overloaded shoots, causing a limited production in the following “OFF” year, causing a significant and unfavorable production fluctuation. In this work, we [...] Read more.
Pistacia vera (L.) is an alternate bearing species. The tree produces axillary inflorescence buds every year. Still, they abscise in “ON” overloaded shoots, causing a limited production in the following “OFF” year, causing a significant and unfavorable production fluctuation. In this work, we carried out de novo discovery and transcriptomic analysis in fruits of “ON” and “OFF” shoots of the cultivar Bianca. We also investigated whether the fruit signaling pathway and hormone biosynthesis directly or indirectly linked to the premature fall of the inflorescence buds causing alternate bearing. We identified 1536 differentially expressed genes (DEGs) in fruits of “ON” vs. “OFF” shoots, which are involved primarily in sugar metabolism, plant hormone pathways and transcription factors. The premature bud abscission linked to the phenomenon is attributable to a lack of nutrients (primarily sugar) and the possible competition between the same branches’ sinks (fruits vs. inflorescence buds). Hormone pathways are involved as a response to signals degradation and remobilization of carbon and nutrients due to the strengthening of the developing embryos. Genes of the secondary metabolism and transcription factors are also involved in tailoring the individual branches response to the nutritional stress and sink competition. Crosstalk among sugar and various hormone-related genes, e.g., ethylene, auxin, ABA and cytokinin, were determined. The discovery of putative biomarkers like callose synthase 5, trehalose-6-phosphate synthase, NAD(P)-linked oxidoreductase and MIOX2, Jasmonate, and salicylic acid-related genes can help to design precision farming practices to mitigate the alternate bearing phenomenon to increase farming profitability. The aim of the analysis is to provide insight into the gene expression profiling of the fate of “ON” and “OFF” fruits associated with the alternate bearing in the pistachio. Full article
(This article belongs to the Special Issue Multi-Omics Approaches and Computational Biology in Fruit Trees)
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19 pages, 2334 KiB  
Article
Autochthonous Austrian Varieties of Prunus avium L. Represent a Regional Gene Pool, Assessed Using SSR and AFLP Markers
by Elisabeth Schüller, Felicidad Fernández Fernández, Laima Antanaviciute, Ulrike Anhalt-Brüderl, Andreas Spornberger and Astrid Forneck
Genes 2021, 12(3), 322; https://doi.org/10.3390/genes12030322 - 24 Feb 2021
Cited by 8 | Viewed by 2609
Abstract
Sweet cherry production faces new challenges that necessitate the exploitation of genetic resources such as varietal collections and landraces in breeding programs. A harmonized approach to characterization is key for an optimal utilization of germplasm in breeding. This study reports the genotyping of [...] Read more.
Sweet cherry production faces new challenges that necessitate the exploitation of genetic resources such as varietal collections and landraces in breeding programs. A harmonized approach to characterization is key for an optimal utilization of germplasm in breeding. This study reports the genotyping of 63 sweet cherry accessions using a harmonized set of 11 simple sequence repeat (SSR) markers optimized in two multiplexed PCR reactions. Thirty-eight distinct allelic profiles were identified. The set of SSR markers chosen proved highly informative in these germplasm; an average of 6.3 alleles per locus, a PIC value of 0.59 and above-average expected and observed heterozygosity levels were detected. Additionally, 223 amplified fragment length polymorphism (AFLP) markers derived from eight selective primer combinations were employed to further differentiate 17 closely related accessions, confirming the SSR analysis. Genetic relationships between internationally known old cultivars were revealed: SSR fingerprints of “Schneiders Späte Knorpelkirsche” and “Germersdorfer” were found to be identical to those of the standard cultivar “Noire de Meched”, among others, whereas four accessions known as “Hedelfinger Riesenkirsche” and four known as “Große Schwarze Knorpelkirsche” showed allelic differences at various loci. The genetic diversity of locally-grown cultivars worldwide might be currently underestimated. Several autochthonous Austrian sweet cherry germplasm accessions were genotyped for the first time and their genetic relationships analyzed and discussed. Interestingly, seven Austrian sweet cherry landraces were shown to be clearly genetically separated from international and modern varieties, indicating that Austrian germplasm could include valuable genetic resources for future breeding efforts. Full article
(This article belongs to the Special Issue Multi-Omics Approaches and Computational Biology in Fruit Trees)
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14 pages, 14082 KiB  
Article
Analyzing Differentially Expressed Genes and Pathways Associated with Pistil Abortion in Japanese Apricot via RNA-Seq
by Ting Shi, Shahid Iqbal, Aliya Ayaz, Yang Bai, Zhenpeng Pan, Xiaopeng Ni, Faisal Hayat, Muhammad Saqib Bilal, Muhammad Khuram Razzaq and Zhihong Gao
Genes 2020, 11(9), 1079; https://doi.org/10.3390/genes11091079 - 15 Sep 2020
Cited by 16 | Viewed by 3870
Abstract
Reproduction is a critical stage in the flower development process, and its failure causes serious problems affecting fruit quality and yield. Pistil abortion is one of the main factors in unsuccessful reproduction and occurs in many fruit plants. In Japanese apricot, the problem [...] Read more.
Reproduction is a critical stage in the flower development process, and its failure causes serious problems affecting fruit quality and yield. Pistil abortion is one of the main factors in unsuccessful reproduction and occurs in many fruit plants. In Japanese apricot, the problem of pistil abortion is very common and affects fruit quality and plant yield; however, its molecular mechanism is not clearly understood. Therefore, in the current study, we used RNA-Seq to identify the differentially expressed genes (DEGs) and pathways actively involved in pistil abortion. A total of 3882 differentially expressed genes were found after cutoff and pairwise comparison analysis. According to KEGG pathway analysis, plant hormone signaling transduction and metabolic pathways were found most significantly enriched in this study. A total of 60 transcription factor families such as MADS-box, NAC and TCP showed their role in this process. RT-qPCR assays confirmed that the expression levels were consistent with RNA-Seq results. This study provides an alternative to be considered for further studies and understanding of pistil abortion processes in Japanese apricot, and it provides a reference related to this issue for other deciduous fruit crops. Full article
(This article belongs to the Special Issue Multi-Omics Approaches and Computational Biology in Fruit Trees)
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20 pages, 2988 KiB  
Article
Transcriptome Analysis of Pistacia vera Inflorescence Buds in Bearing and Non-Bearing Shoots Reveals the Molecular Mechanism Causing Premature Flower Bud Abscission
by Jubina Benny, Francesco Paolo Marra, Antonio Giovino, Bipin Balan, Tiziano Caruso, Federico Martinelli and Annalisa Marchese
Genes 2020, 11(8), 851; https://doi.org/10.3390/genes11080851 - 25 Jul 2020
Cited by 12 | Viewed by 3740
Abstract
The alteration of heavy (“ON/bearing”) and light (“OFF/non-bearing”) yield in pistachio (Pistacia vera L.) has been reported to result from the abscission of inflorescence buds on high yielding trees during the summer, but the regulatory mechanisms involved in this bud abscission remain [...] Read more.
The alteration of heavy (“ON/bearing”) and light (“OFF/non-bearing”) yield in pistachio (Pistacia vera L.) has been reported to result from the abscission of inflorescence buds on high yielding trees during the summer, but the regulatory mechanisms involved in this bud abscission remain unclear. The analysis provides insights into the transcript changes between inflorescence buds on bearing and non-bearing shoots, that we indicated as “ON” and “OFF”, and shed light on the molecular mechanisms causing premature inflorescence bud abscission in the pistachio cultivar “Bianca” which can be related to the alternate bearing behavior. In this study, a transcriptome analysis was performed in inflorescence buds of “ON” and “OFF” shoots. A total of 14,330 differentially expressed genes (DEGs), most of which are involved in sugar metabolism, plant hormone pathways, secondary metabolism and oxidative stress pathway, were identified. Our results shed light on the molecular mechanisms underlying inflorescence bud abscission in pistachio and we proposed a hypothetical model behind the molecular mechanism causing this abscission in “ON” shoots. Results highlighted how changes in genes expressed in nutrient pathways (carbohydrates and mineral elements) in pistachio “ON” vs. “OFF” inflorescence buds triggers a cascade of events involving trehalose-6-phosphate and target of rapamycin (TOR) signaling, SnRK1 complex, hormones, polyamines and ROS which end, through programmed cell death and autophagy phenomena, with the abscission of inflorescence buds. This is the first study reporting gene expression profiling of the fate of “ON” and “OFF” inflorescence buds associated with the alternate bearing in the pistachio. Full article
(This article belongs to the Special Issue Multi-Omics Approaches and Computational Biology in Fruit Trees)
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