Plant Biology and Biotechnology: Focus on Genomics and Bioinformatics

Orlov, Yuriy L.; Иванисенко, В. А.; Dobrovolskaya, O. B.; Chen, Ming

doi:10.3390/ijms23126759

Cited by 4 publications

(3 citation statements)

References 35 publications

(56 reference statements)

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“…Overall, The potential benefits of omics data integration for crop plant breeding are numerous [ 79 ]. By integrating data from different omics technologies, researchers can gain a more comprehensive understanding of the molecular processes underlying crop growth, development, and responses to environmental stresses [ 80 ]. The functional annotation of the plant gene and gene-phenotype association could be found by new text mining tools [ 81 , 82 ].…”

Section: Recent Developments In Omics Data Integration For Crop Plant...mentioning

confidence: 99%

Integrating omics databases for enhanced crop breeding

Chao

Zhang

et al. 2023

Journal of Integrative Bioinformatics

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Crop plant breeding involves selecting and developing new plant varieties with desirable traits such as increased yield, improved disease resistance, and enhanced nutritional value. With the development of high-throughput technologies, such as genomics, transcriptomics, and metabolomics, crop breeding has entered a new era. However, to effectively use these technologies, integration of multi-omics data from different databases is required. Integration of omics data provides a comprehensive understanding of the biological processes underlying plant traits and their interactions. This review highlights the importance of integrating omics databases in crop plant breeding, discusses available omics data and databases, describes integration challenges, and highlights recent developments and potential benefits. Taken together, the integration of omics databases is a critical step towards enhancing crop plant breeding and improving global food security.

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Section: Recent Developments In Omics Data Integration For Crop Plant...mentioning

confidence: 99%

Integrating omics databases for enhanced crop breeding

Chao

Zhang

et al. 2023

Journal of Integrative Bioinformatics

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“…Accordingly, miRNAs are substantial contributors to plant stress responses and provide an effective tool for manipulating plant stress tolerance, receiving significant attention from researchers (Liu & Chen, 2010; Nogoy et al, 2018; Zhang & Wang, 2015). In recent years, the emergence of systems biology tools, including robust computational analysis and advanced statistical methods, has made it possible to uncover some aspects of miRNAs‐mediated stress responses in plants (Dangi et al, 2018; Orlov et al, 2022; Pirrò et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

Evidence that miR168a contributes to salinity tolerance of Brassica rapa L. via mediating melatonin biosynthesis

Shamloo‐Dashtpagerdi

Lindlöf

Tahmasebi

2022

Physiologia Plantarum

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Melatonin is a master regulator of diverse biological processes, including plant's abiotic stress responses and tolerance. Despite the extensive information on the role of melatonin in response to abiotic stress, how plants regulate endogenous melatonin content under stressful conditions remains largely unknown. In this study, we computationally mined Expressed Sequence Tag (EST) libraries of salinity‐exposed Chinese cabbage (Brassica rapa) to identify the most reliable differentially expressed miRNA and its target gene(s). In light of these analyses, we found that miR168a potentially targets a key melatonin biosynthesis gene, namely O‐METHYLTRANSFERASE 1 (OMT1). Accordingly, molecular and physiochemical evaluations were performed in a separate salinity experiment using contrasting B. rapa genotypes. Then, the association between B. rapa salinity tolerance and changes in measured molecular and physiochemical characteristics was determined. Results indicated that the expression profiles of miR168a and OMT1 significantly differed between B. rapa genotypes. Moreover, the expression profiles of miR168a and OMT1 significantly correlated with more melatonin content, robust antioxidant activities, and better ion homeostasis during salinity stress. Our results suggest that miR168a plausibly mediates melatonin biosynthesis, mainly through the OMT1 gene, under salinity conditions and thereby contributes to the salinity tolerance of B. rapa. To our knowledge, this is the first report on the role of miR168a and OMT1 in B. rapa salinity response.

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“…The BGRS conference series has a history of initiating successful Special Issues on bioinformatics in the bioinformatics journals. The recent examples include special issues at Frontiers in genetics and MDPI International Journal of Molecular Sciences on biomedical applications – “High-Throughput Sequencing-Based Investigation of Chronic Disease Markers and Mechanisms” [ 29 ], “Medical Genetics, Genomics and Bioinformatics” [ 30 , 31 ], and on plant biology – special issue “Plant Biology and Biotechnology” [ 32 ]. We have presented special issues “Research Topics of the Bioinformatics of Gene Regulation” [ 33 ], and the series of the matical issues on genome regulation and systems biology at Frontiers in Genetics journal – Research Topic “Bioinformatics of genome regulation and systems biology” repeating the BGRS conference name and collecting the materials discussed at BGRS\SB meetings [ 34 , 35 ].…”

mentioning

confidence: 99%

BGRS: bioinformatics of genome regulation and data integration

Orlov,

Chen,

Kolchanov

et al. 2023

Journal of Integrative Bioinformatics

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Plant Biology and Biotechnology: Focus on Genomics and Bioinformatics

Abstract: The study of molecular mechanisms of plant stress response is important for agrobiotechnology applications as it was discussed at series of recent bioinformatics conferences [...]

Cited by 4 publications

References 35 publications

Integrating omics databases for enhanced crop breeding

Integrating omics databases for enhanced crop breeding

Evidence that miR168a contributes to salinity tolerance of Brassica rapa L. via mediating melatonin biosynthesis

BGRS: bioinformatics of genome regulation and data integration

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