Research Topic

Applications of Next Generation Sequencing to Unravel Horticultural Crop Responses and Adaptation to Environmental Stresses

About this Research Topic

In the last few decades, Plant Biology has experienced a dramatic renovation by the advent of Next Generation Sequencing (NGS) technologies. Since the first efforts in decoding the Arabidopsis genome, sequencing technologies, especially NGS, have moved forward rapidly. This technology has opened a vast range of new scenarios and offering an inestimable repertoire of possibilities to plant scientist, paving the way to genome/transcriptome sequencing in several non-model species of agricultural and economical interest. The open architecture of RNA-seq technologies has improved the way we can profile gene expression, enabling investigations at the whole-transcriptome level. High throughput DNA sequencing has made also genome re-sequencing efforts possible, for instance, the identification of important source of variants, valuable to design novel molecular markers. Ultimately, this technology has been recently employed in a direct Genotype by Sequencing (GBS) approach, a strategy that is rapidly adopted as routine technique in different genetic mapping study, especially oriented at marker-trait association analysis
Although the wealth of knowledge derived by the implementation of NGS technologies in genomes and transcriptomics, their application in horticultural species still remains limited. Horticultural crops represent an important fraction of the overall agricultural production, especially for their well-known benefit on human diet and health. Despite this, the resolution of important problems is compelling. The complete picture of fruit ripening mechanism is far from being elucidated and most of the cultivated varieties are susceptible to major diseases. Moreover, horticultural crops would also have to maintain their agronomical performance in environment with changing conditions for severe climate change effect, such as increased CO2 concentration, increased temperature, and water deficiency. Thus, a better knowledge of the fundamental mechanisms governing plant physiology and tolerance to biotic and abiotic stresses would certainly improve the sustainable intensification of plant production and their use.

To this end, Frontiers in Plant Science is dedicating a Research Topic to studies addressing all these issues through the application of NGS technologies. Data obtained by the employment of NGS technologies to investigate the genome, transcriptome, and epigenetic variations, as well as the application of network analysis to these data, will play a fundamental role in improving our understanding of gene regulatory networks governing crop responses to biological and environmental stresses. This gain of knowledge would be essential to empower a systematic improvement of crop breeding with the aim to develop new enhanced genotypes characterized by high performances in adverse conditions.
Articles that describe original research, methods, opinions, and reviews are welcome. We encourage submission of studies addressing genomic, epigenomic, transcriptomic, as well as bioinformatics-oriented studies aimed to understand how environmental factors influence fruit crop performances and adaptation through molecular modifications.


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.

In the last few decades, Plant Biology has experienced a dramatic renovation by the advent of Next Generation Sequencing (NGS) technologies. Since the first efforts in decoding the Arabidopsis genome, sequencing technologies, especially NGS, have moved forward rapidly. This technology has opened a vast range of new scenarios and offering an inestimable repertoire of possibilities to plant scientist, paving the way to genome/transcriptome sequencing in several non-model species of agricultural and economical interest. The open architecture of RNA-seq technologies has improved the way we can profile gene expression, enabling investigations at the whole-transcriptome level. High throughput DNA sequencing has made also genome re-sequencing efforts possible, for instance, the identification of important source of variants, valuable to design novel molecular markers. Ultimately, this technology has been recently employed in a direct Genotype by Sequencing (GBS) approach, a strategy that is rapidly adopted as routine technique in different genetic mapping study, especially oriented at marker-trait association analysis
Although the wealth of knowledge derived by the implementation of NGS technologies in genomes and transcriptomics, their application in horticultural species still remains limited. Horticultural crops represent an important fraction of the overall agricultural production, especially for their well-known benefit on human diet and health. Despite this, the resolution of important problems is compelling. The complete picture of fruit ripening mechanism is far from being elucidated and most of the cultivated varieties are susceptible to major diseases. Moreover, horticultural crops would also have to maintain their agronomical performance in environment with changing conditions for severe climate change effect, such as increased CO2 concentration, increased temperature, and water deficiency. Thus, a better knowledge of the fundamental mechanisms governing plant physiology and tolerance to biotic and abiotic stresses would certainly improve the sustainable intensification of plant production and their use.

To this end, Frontiers in Plant Science is dedicating a Research Topic to studies addressing all these issues through the application of NGS technologies. Data obtained by the employment of NGS technologies to investigate the genome, transcriptome, and epigenetic variations, as well as the application of network analysis to these data, will play a fundamental role in improving our understanding of gene regulatory networks governing crop responses to biological and environmental stresses. This gain of knowledge would be essential to empower a systematic improvement of crop breeding with the aim to develop new enhanced genotypes characterized by high performances in adverse conditions.
Articles that describe original research, methods, opinions, and reviews are welcome. We encourage submission of studies addressing genomic, epigenomic, transcriptomic, as well as bioinformatics-oriented studies aimed to understand how environmental factors influence fruit crop performances and adaptation through molecular modifications.


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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Submission Deadlines

09 April 2018 Manuscript

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Manuscripts can be submitted to this Research Topic via the following journals:

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Topic Editors

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Submission Deadlines

09 April 2018 Manuscript

Participating Journals

Manuscripts can be submitted to this Research Topic via the following journals:

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