Systems biology for crop improvement

Abstract

In recent years, generation of large-scale data from genome, transcriptome, proteome, metabolome, epigenome, and others, has become routine in several plant species.Most of these datasets in different crop species, however, were studied independently and as a result, full insight could not be gained on the molecular basis of complex traits and biological networks. A systems biology approach involving integration of multiple omics data, modeling, and prediction of the cellular functions is required to understand the flow of biological information that underlies complex traits. In this context, systems biology with multiomics data integration is crucial and allows a holistic understanding of the dynamic system with the different levels of biological organization interacting with external environment for a phenotypic expression. Here, we present recent progress made in the area of various omics studies-integrative and systems biology approaches with a special focus on application to crop improvement. We have also discussed the challenges and opportunities in multiomics data integration, modeling, and understanding of the biology of complex traits underpinning yield and stress tolerance in major cereals and legumes.

Designing Future Crops: Genomics-Assisted Breeding Comes of Age

“…A variety of omics platforms are available that enable accurate and high-throughput measurements of such intermediate phenotypes, including transcripts (RNA-Seq), metabolites (GC-MS, LC-MS, FTICR-MS, NMR) and proteins (MALDI-TOF-MS, iTRAQ). Integration of the multi-omics data with the genetic mapping strategies could greatly accelerate discovery of functional allelic variation [165,166]. In human genetics, intermediate phenotypes have played a pivotal role for genetic mapping of psychiatric disease.…”

Analyzing Modern Biomolecules: The Revolution of Nucleic-Acid Sequencing – Review

“…Besides, multiple stress combinations can be studied [51]. Systems biology strategies are particularly interesting, implementing holistic approaches in these scenarios, integrating different -omics and bioinformatics tools [52]. This is especially relevant in the current trend of global warming and climate change [53][54][55][56][57].…”

Data Management and Modeling in Plant Biology

“…Based on these numbers, it seems unfeasible to resolve quantity of hundreds or thousands of compounds within a GC-MS or LC-MS run. While combination of different analytical platforms promises to cover a large panel of compounds (Pazhamala et al, 2021;Zancarini et al, 2021), semi-quantitative analysis might represent a suitable approach to increase reproducibility and comparability of high-throughput analysis among quantification platforms. Here, structural elucidation of metabolic compounds based on mass spectrometry data might indicate a compound's class (De Vijlder et al, 2018).…”