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Applied Sciences
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Applications of Advanced Genomic and Phenomic Technologies for Plant Improvement
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Applications of Advanced Genomic and Phenomic Technologies for Plant Improvement

A special issue of Applied Sciences (ISSN 2076-3417). This special issue belongs to the section "Applied Biosciences and Bioengineering".

Deadline for manuscript submissions: closed (31 December 2020) | Viewed by 5035

Special Issue Editor

Prof. Dr. Alexios Polidoros

E-Mail Website
Guest Editor
Laboratory of Genetics and Plant Breeding, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece
Interests: plant’s ability to cope with stress, including genetic and epigenetic responses, establishment of principles and criteria for breeding stress-tolerant crop plants; integration of genomic, transcriptomic, and phenomic analysis in modern breeding
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Global agriculture is facing three colossal challenges: an increasing world population, the adverse effects of climate change, and the diminishing genetic resources for cultivated species. Thus, there is an urgent need to find innovative solutions to rise agricultural production and maintain food security.

Plant breeding has always been the only resource of suitable plant types for cultivation. Conventional breeding has been an art and science performed over the last century by specialists and trained scientists reliant on plant phenotype to select the best individuals for cultivar improvement. However, because of the intervention of unstable environmental conditions, plant phenotype is not always a good representation of a superior genotype.  Modern plant breeding is minimizing its “art” component, taking advantage of the scientific progress and novel analytical methods to enable the prediction of plant performance from biological entities. In other words, it seeks to increase the accuracy of prediction of plant performance by accurately associating an individual genotype to a specific phenotype.

Genomic tools based on next-generation sequencing (NGS) technologies, such as whole-genome sequencing, de novo sequencing and re-sequencing, transcriptome sequencing (mRNA-seq and/or miRNA-seq), target re-sequencing, exome and reduced-representation sequencing, gene panel and amplicon sequencing, generate a wealth of genomic information for virtually any crop. Combined with precise high-throughput phenotyping systems referred to as phenomics, these innovative technologies provide analytical tools for predicting plant performance from genetic data.

Genomics and phenomics, with the support of powerful bioinformatic and image analysis software, can revolutionize crop improvement by identifying the genetic basis of agriculturally important traits and increase the genetic gain by direct genotypic selection of high-breeding-value individuals in a plant breeding population.

This Special Issue will provide a platform to present research results in all applications of advanced genomics and phenomics tools related to crop improvement and to discuss current trends and future prospects of progress in these fields for modern plant breeding.

Prof. Dr. Alexios Polidoros
Guest Editor

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. Applied Sciences is an international peer-reviewed open access semimonthly 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 2400 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 Breeding
  • High-throughput technologies
  • Next-generation sequencing
  • Genomics
  • Transcriptomics
  • Genomic selection
  • Genotyping
  • Phenomics
  • Image analysis
  • Phenotyping
  • Molecular markers
  • Marker-assisted selection
  • SNPs
  • Bioinformatics

Published Papers (2 papers)

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Research

15 pages, 2832 KiB  
Article
Genotype May Influence Bacterial Diversity in Bark and Bud of Vitis vinifera Cultivars Grown under the Same Environment
by Murad Awad, Georgios Giannopoulos, Photini V. Mylona and Alexios N. Polidoros
Appl. Sci. 2020, 10(23), 8405; https://doi.org/10.3390/app10238405 - 26 Nov 2020
Cited by 4 | Viewed by 2126
Abstract
Viticulture is globally an important economic activity, and grapevine microbiomes hold a significant role in influencing yield and quality. Earlier studies showed that cultivar and agronomic management affect grapevine microbiome structure and, potentially, the quality of the end product. While microbial dynamics and [...] Read more.
Viticulture is globally an important economic activity, and grapevine microbiomes hold a significant role in influencing yield and quality. Earlier studies showed that cultivar and agronomic management affect grapevine microbiome structure and, potentially, the quality of the end product. While microbial dynamics and ecology were established on some grapevine tissues, i.e., leaves and grapes, there is less knowledge deciphering microbiomes on other tissues, i.e., barks and buds. Moreover, although the impact on the microbiome of the so-called “vitivinicultural terroir” is well established, there are limited data considering microbiomes of genetically diverse cultivars within the same environment. Our study aims to explore microbiome diversity on bud and bark tissues of 37 different grapevine cultivars under the same environment and agronomic management. We targeted the V2-9 regions of the 16S rRNA gene of the microbiomes in bark and buds at the onset of new vegetation and bud expansion using Ion Torrent sequencing technology. Our results show that these tissues display high bacterial diversity regardless of cultivars’ use. Proteobacteria, Bacteroidetes, and Actinobacteria were the most prevalent among 11 detected phyla. The genotype of the cultivar seems to affect bacterial diversity and structure (p < 0.001) within the same environment. Our approach highlights the efficiency of high-throughput sequencing to unfold microbiomes of several grapevine parts that could be an important source of microbial inoculation and an important molecular fingerprint of the wine and grape end products. Full article
(This article belongs to the Special Issue Applications of Advanced Genomic and Phenomic Technologies for Plant Improvement)
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15 pages, 1864 KiB  
Article
Recurrent Water Deficit and Epigenetic Memory in Medicago sativa L. Varieties
by Yannis E. Ventouris, Eleni Tani, Evangelia V. Avramidou, Eleni M. Abraham, Styliani N. Chorianopoulou, Dimitrios N. Vlachostergios, Georgios Papadopoulos and Aliki Kapazoglou
Appl. Sci. 2020, 10(9), 3110; https://doi.org/10.3390/app10093110 - 29 Apr 2020
Cited by 13 | Viewed by 2496
Abstract
Global DNA methylation changes in response to recurrent drought stress were investigated in two common Greek Medicago sativa L. varieties (Lamia and Chaironia-Institute of Ιndustrial and Forage Crops). The water deficit was implemented in two phases. At the end of the first phase, [...] Read more.
Global DNA methylation changes in response to recurrent drought stress were investigated in two common Greek Medicago sativa L. varieties (Lamia and Chaironia-Institute of Ιndustrial and Forage Crops). The water deficit was implemented in two phases. At the end of the first phase, which lasted for 60 days, the plants were cut at the height of 5 cm and were watered regularly for two months before being subjected to the second drought stress, which lasted for two weeks. Finally, the following groups of plants were formed: CC (controls both in phase I and phase II), CD2 (Controls in phase I, experiencing drought in phase II), and D1D2 (were subjected to drought in both phase I and phase II). At the end of phase II, samples were taken for global DNA methylation analysis with the Methylation Sensitive Amplification Polymorphism (MSAP) method, and all plants were harvested in order to measure the fresh and dry weight of roots and shoots. The variety Lamia responded better, especially the D1D2 group, compared to Chaironia in terms of root and shoot dry weight. Additionally, the shoots of Lamia had a constant water status for CD2 and D1D2 group of plants. According to DNA methylation analysis by the MSAP method, Lamia had lower total DNA methylation percentage after the second drought episode (D1D2) as compared to the plants CD2 that had experienced only one drought episode. On the other hand, the total DNA methylation percentage of Chaironia was almost the same in plants grown under recurrent drought stress conditions compared to control plants. In conclusion, the decrease of DNA methylation of Lamia stressed plants probably indicates the existence of an epigenetic mechanism that may render drought tolerance. Full article
(This article belongs to the Special Issue Applications of Advanced Genomic and Phenomic Technologies for Plant Improvement)
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