Augmentation of crop productivity through interventions of omics technologies in India: challenges and opportunities

Pathak, Rajesh Kumar; Baunthiyal, Mamta; Pandey, Dinesh; Kumar, Anil

doi:10.1007/s13205-018-1473-y

Cited by 24 publications

(8 citation statements)

References 224 publications

(387 reference statements)

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“…The results of present study also revealed that these genes might be not expressed during developing spikes stage. Transcriptome of an organism varies over time and depends upon several factors, including stage of development and environmental conditions (Pathak et al 2018).…”

Section: Genome-wide Identification Of Ros-scavenging Genes In Finger Milletmentioning

confidence: 99%

Comparative analysis of ROS-scavenging gene families in finger millet, rice, sorghum, and foxtail millet revealed potential targets for antioxidant activity and drought tolerance improvement

Avashthi

Pathak

Gaur

et al. 2020

Netw Model Anal Health Inform Bioinforma

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Antioxidants play a key role in maintaining cell activity in plants and animals by scavenging reactive oxygen species. Hence, it is very important to understand genes associated with antioxidant activity for improving the varieties. In this study, we compared structural and functional aspects of antioxidant genes viz., APX, DHAR, MDHAR, GR, and SOD of two contrasting genotypes viz. GP-1 (low Ca 2+ ) and GP-45 (high Ca 2+ ) of finger millet with other cereal crops such as rice, sorghum, and foxtail millet. The structural analysis shows that all genes are conserved and shares almost the same domains such as ascorbate peroxidase, glutathione dehydrogenase, glutathione reductase, Fe, and Cu-Zn superoxide dismutase domains which play a significant role in antioxidant activity and drought tolerance. These genes were mainly localized in chloroplast and cytoplasm which prove that both are the major ROS-scavenging sites. Furthermore, several putative cis-acting regulatory elements such as AuxRE, DRE, GARE, G-box, GATA-box, MBS, MYBR, and W-box are also studied and found that these genes are involved in defense mechanisms which allow responses against drought stress. Antioxidant activity of these genes was compared using expression analysis in terms of FPKM values and found that the genes of low Ca 2+ genotype are highly expressed compared to the genes of high Ca 2+ genotype and the genes of rice, sorghum, and foxtail millet. These results revealed that a low Ca 2+ genotype of finger millet has higher antioxidant activity in comparison to high Ca 2+ genotype and other cereal crops. Based on the results, we hypothesize that these candidate genes could be a target to develop highly antioxidative potential and drought tolerant genotypes of other cereal crops through appropriate breeding approaches.

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Section: Genome-wide Identification Of Ros-scavenging Genes In Finger Milletmentioning

confidence: 99%

Comparative analysis of ROS-scavenging gene families in finger millet, rice, sorghum, and foxtail millet revealed potential targets for antioxidant activity and drought tolerance improvement

Avashthi

Pathak

Gaur

et al. 2020

Netw Model Anal Health Inform Bioinforma

Self Cite

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“…The omics era has taught us to follow a holistic approach while interpreting the complex biological systems starting from molecular to cellular level ( Pathak et al, 2018 ). As the cost of the omics analyses continues to decrease, different high-throughput omics data are made available.…”

Section: Challenges and Future Perspectivesmentioning

confidence: 99%

Advances in Multi-Omics Approaches for Molecular Breeding of Black Rot Resistance in Brassica oleracea L.

et al. 2021

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Brassica oleracea is one of the most important species of the Brassicaceae family encompassing several economically important vegetables produced and consumed worldwide. But its sustainability is challenged by a range of pathogens, among which black rot, caused by Xanthomonas campestris pv. campestris (Xcc), is the most serious and destructive seed borne bacterial disease, causing huge yield losses. Host-plant resistance could act as the most effective and efficient solution to curb black rot disease for sustainable production of B. oleracea. Recently, ‘omics’ technologies have emerged as promising tools to understand the host-pathogen interactions, thereby gaining a deeper insight into the resistance mechanisms. In this review, we have summarized the recent achievements made in the emerging omics technologies to tackle the black rot challenge in B. oleracea. With an integrated approach of the omics technologies such as genomics, proteomics, transcriptomics, and metabolomics, it would allow better understanding of the complex molecular mechanisms underlying black rot resistance. Due to the availability of sequencing data, genomics and transcriptomics have progressed as expected for black rot resistance, however, other omics approaches like proteomics and metabolomics are lagging behind, necessitating a holistic and targeted approach to address the complex questions of Xcc-Brassica interactions. Genomic studies revealed that the black rot resistance is a complex trait and is mostly controlled by quantitative trait locus (QTL) with minor effects. Transcriptomic analysis divulged the genes related to photosynthesis, glucosinolate biosynthesis and catabolism, phenylpropanoid biosynthesis pathway, ROS scavenging, calcium signalling, hormonal synthesis and signalling pathway are being differentially expressed upon Xcc infection. Comparative proteomic analysis in relation to susceptible and/or resistance interactions with Xcc identified the involvement of proteins related to photosynthesis, protein biosynthesis, processing and degradation, energy metabolism, innate immunity, redox homeostasis, and defence response and signalling pathways in Xcc–Brassica interaction. Specifically, most of the studies focused on the regulation of the photosynthesis-related proteins as a resistance response in both early and later stages of infection. Metabolomic studies suggested that glucosinolates (GSLs), especially aliphatic and indolic GSLs, its subsequent hydrolysis products, and defensive metabolites synthesized by jasmonic acid (JA)-mediated phenylpropanoid biosynthesis pathway are involved in disease resistance mechanisms against Xcc in Brassica species. Multi-omics analysis showed that JA signalling pathway is regulating resistance against hemibiotrophic pathogen like Xcc. So, the bonhomie between omics technologies and plant breeding is going to trigger major breakthroughs in the field of crop improvement by developing superior cultivars with broad-spectrum resistance. If multi-omics tools are implemented at the right scale, we may be able to achieve the maximum benefits from the minimum. In this review, we have also discussed the challenges, future prospects, and the way forward in the application of omics technologies to accelerate the breeding of B. oleracea for disease resistance. A deeper insight about the current knowledge on omics can offer promising results in the breeding of high-quality disease-resistant crops.

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“…By contrast, Asia had the one of the highest malnourishment rates in the world (11.4%) but with high pesticide use rates (3.64 kg/ha). Despite the possibilities of manipulating bacterial communities for more sustainable bioremediation processes, the very concept of omics introduces several problems: they are more expensive and complex approaches than the traditional analyses and require more powerful bioinformatics systems to analyze the large amounts of data generated ( Pathak et al., 2018 ). Without help to implement and fund omic technologies, developing agricultural countries will have greater problems in achieving self-sufficiency to solve problems of environment.…”

Section: Bacterial Xenobiotic Responses By Omics-based Approaches Andmentioning

confidence: 99%

Herbicide bioremediation: from strains to bacterial communities

Pileggi

Sadowsky

2020

Heliyon

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There is high demand for herbicides based on the necessity to increase crop production to satisfy world-wide demands. Nevertheless, there are negative impacts of herbicide use, manifesting as selection for resistant weeds, production of toxic metabolites from partial degradation of herbicides, changes in soil microbial communities and biogeochemical cycles, alterations in plant nutrition and soil fertility, and persistent environmental contamination. Some herbicides damage non-target microorganisms via directed interference with host metabolism and via oxidative stress mechanisms. For these reasons, it is necessary to identify sustainable, efficient methods to mitigate these environmental liabilities. Before the degradation process can be initiated by microbial enzymes and metabolic pathways, microorganisms need to tolerate the oxidative stresses caused by the herbicides themselves. This can be achieved via a complex system of enzymatic and non-enzymatic antioxidative stress systems. Many of these response systems are not herbicide specific, but rather triggered by a variety of substances. Collectively, these nonspecific response systems enhance the survival and fitness potential of microorganisms. Biodegradation studies and remediation approaches have relied on individually selected strains to effectively remediate herbicides in the environment. Nevertheless, it has been shown that microbial communication systems that modulate social relationships and metabolic pathways inside biofilm structures among microorganisms are complex; therefore, use of isolated strains for xenobiotic degradation needs to be enhanced using a community-based approach with biodegradation pathway integration. Bioremediation efforts can use omics-based technologies to gain a deeper understanding of the molecular complexes of bacterial communities to achieve to more efficient elimination of xenobiotics. With this knowledge, the possibility of altering microbial communities is increased to improve the potential for bioremediation without causing other environmental impacts not anticipated by simpler approaches. The understanding of microbial community dynamics in free-living microbiota and those present in complex communities and in biofilms is paramount to achieving these objectives. It is also essential that non-developed countries, which are major food producers and consumers of pesticides, have access to these techniques to achieve sustainable production, without causing impacts through unknown side effects.

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Augmentation of crop productivity through interventions of omics technologies in India: challenges and opportunities

Cited by 24 publications

References 224 publications

Comparative analysis of ROS-scavenging gene families in finger millet, rice, sorghum, and foxtail millet revealed potential targets for antioxidant activity and drought tolerance improvement

Comparative analysis of ROS-scavenging gene families in finger millet, rice, sorghum, and foxtail millet revealed potential targets for antioxidant activity and drought tolerance improvement

Advances in Multi-Omics Approaches for Molecular Breeding of Black Rot Resistance in Brassica oleracea L.

Herbicide bioremediation: from strains to bacterial communities

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