Systems Biology for Smart Crops and Agricultural Innovation: Filling the Gaps between Genotype and Phenotype for Complex Traits Linked with Robust Agricultural Productivity and Sustainability

Abstract

In recent years, rapid developments in several omics platforms and next generation sequencing technology have generated a huge amount of biological data about plants. Systems biology aims to develop and use wellorganized and efficient algorithms, data structure, visualization, and communication tools for the integration of these biological data with the goal of computational modeling and simulation. It studies crop plant systems by systematically perturbing them, checking the gene, protein, and informational pathway responses; integrating these data; and finally, formulating mathematical models that describe the structure of system and its response to individual perturbations. Consequently, systems biology approaches, such as integrative and predictive ones, hold immense potential in understanding of molecular mechanism of agriculturally important complex traits linked to agricultural productivity. This has led to identification of some key genes and proteins involved in networks of pathways involved in input use efficiency, biotic and abiotic stress resistance, photosynthesis efficiency, root, stem and leaf architecture, and nutrient mobilization. The developments in the above fields have made it possible to design smart crops with superior agronomic traits through genetic manipulation of key candidate genes.

Calcium Biofortification: Three Pronged Molecular Approaches for Dissecting Complex Trait of Calcium Nutrition in Finger Millet (Eleusine coracana) for Devising Strategies of Enrichment of Food Crops

“…One of the greatest challenges of biology in the post genomic era understands the functional connections between genes, transcripts, proteins, metabolites and nutrients (Kumar et al, 2015a). This understanding will highly beneficial for the plant biofortification processes.…”

“…A detailed transcriptome wide study of calcium (Ca 2+ ) sensors and transporters was carried out to identify the differentially expressed genes during developing spikes of finger millet and can serve as potential candidate genes having role in seed calcium accumulation (Singh et al, 2014, 2016). Transgenics for Ca 2+ Exchanger ( CAX ), an important Ca 2+ transporter that pump Ca 2+ inside vacuoles were developed, which resulted in significant Ca 2+ increase but deleterious effects like mineral imbalance, stunted plant growth and other structural changes were also seen (Kumar et al, 2015a). GPHCPB45 was found to be more efficient calcium (Ca 2+ ) accumulator at low external calcium (Ca 2+ ) concentrations, whereas GPHCPB1 was found to be more responsive to increased external calcium (Ca 2+ ) concentration (Singh et al, 2014).…”

Gene Discovery and Advances in Finger Millet [Eleusine coracana (L.) Gaertn.] Genomics—An Important Nutri-Cereal of Future

“…Out of 82 genes, 12 were found to be different from the rice orthologs (Singh et al, 2014; Kumar et al, 2015b). Nineteen Ca 2+ transporter genes identified from developing seed transcriptome data of finger millet showed 33–90% variation in amino acid sequence compared to rice Ca 2+ transporter (Kumar et al, 2015c). High level of correlation between the expression of “EcCAX3” a calcium exchanger gene and the amount of calcium accumulated in spikes could be utilized in a future biofortification program (Singh et al, 2014; Singh U. M. et al, 2015).…”

In Silico Identification of Mimicking Molecules as Defense Inducers Triggering Jasmonic Acid Mediated Immunity against Alternaria Blight Disease in Brassica Species

“…Many efforts have been made by scientists to develop disease resistant transgenic plants with limited success to develop complete de novo resistance against Alternaria blight due to lack of knowledge about the resistance gene homologs (Mondal et al, 2003; Taj et al, 2004; Marmath et al, 2011; Kumar et al, 2014). It has been realized that mere use of transgenic technology is no longer useful for development of resistance toward diseases like Alternaria blight (Kumar et al, 2015). So, there is required use of innovative approaches in agricultural sciences to tackle such type of problems.…”