Research Topic

Functional Genomics in Fruit Trees: from ‘Omics to Sustainable Biotechnologies

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Over the last decade, the sequencing of several genomes, coupled with rapid advances in bioinformatics, provided powerful tools for detailed molecular studies on crop plants other than traditional model species. The availability of sequencing data is only a starting point since bioinformatics approaches are ...

Over the last decade, the sequencing of several genomes, coupled with rapid advances in bioinformatics, provided powerful tools for detailed molecular studies on crop plants other than traditional model species. The availability of sequencing data is only a starting point since bioinformatics approaches are not sufficient to define gene roles. To deepen this knowledge, it is necessary to understand how thousands of genes can interact each other to determine the structure of a plant and how the metabolic pathways in which they are involved contribute to plant development and adaptation to the environment.

Fruit trees are economically important species and, as long-living plants, represent an important challenge to understand adaptation to environmental stresses. Detailed functional analyses are often difficult in woody species, because of their biological features and because of the recalcitrance of some species to plant transformation and/or regeneration, limiting efforts to use standard genetic and biotechnological approaches for functional genomics studies or plant breeding.

Specifically, fruit tree species are difficult to study at genetic and molecular levels (1) because of their perennial nature, (2) for the limited information on gene identity and function, genetic markers directly associated to the control of a character, (3) due to the unavailability of well-defined molecular genetic linkage maps and (4) because development of mapping population and map-based studies are not easy. However, the recent increase in fruit crop genomic resource availability can be used for developing an improved understanding of gene function and developing improved genotypes. In particular, sequence and omics information has been used for analyzing and understanding genome structures and complexities, comparative and functional genomics and to mine useful genes and molecular markers.

This Research Topic aims to summarize recent findings on functional genomics related to economically important fruit tree species worldwide. Research articles focusing on “-omics” technologies – such as genomics, epigenetics, transcriptomics, proteomics, metabolomics and phenomics - and covering a broad range of questions relative to discovery and characterization of novel genes, crop traits, MAS and comparative genomics are welcome, as well as contributions related to transgenic approaches and studies concerning the improvement of transgenesis and genome editing protocols in woody species.

In particular, this Research Topic will present a broad range of innovative approaches to experimentally address the following topics in fruit tree interest:
- Genotyping and phenotyping
- Comparative genomics
- Discovery and characterization of novel genes
- Fruit drops and seedlessness
- Biotic and abiotic stress responses
- Application of molecular markers to assist breeding
- Transformation technology and genetic engineering, including cisgenesis and genome editing
- Genetic characterization of somaclonal variation and mutants

The article collection will help provide a link between interesting candidate genes emerging from ‘-omics’ analyses and reverse genetic and genome editing protocols, in order to clarify relevant molecular pathways in woody plants related e.g. to plant development or adaptation to the environment.

Please note, descriptive studies using omics approaches will be considered for review only if they address further insights into the functional characterization of the molecular pathways described.


Important Note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.

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