Cytogenomics and Mutagenomics in Plant Functional Biology and Breeding

Talukdar, Dibyendu; Sinjushin, Andrey

doi:10.1007/978-81-322-2172-2_5

Cited by 19 publications

(12 citation statements)

References 166 publications

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“…Virus induced gene silencing (VIGS) is a reverse genetic technique to analyze the functions of genes that manifest in tomato crop in response to biotic and abiotic stress (Saand et al, 2015). Through comparative genomics, various mutants have been identified that are related to crop growth, development, and stress tolerance in rice, maize, wheat, and barley (Talukdar and Sinjushin, 2015). A soybean mutation has been found to alter the transcriptomic profiling of GmNARK (Glycine max leucine-rich repeat receptor kinase) rhizobia independent nodulation through the jasmonate pathway (Pathan and Sleper, 2008).…”

Section: Functional Genomics and Mutagenomicsmentioning

confidence: 99%

“…The specific reverse genetic techniques utilized to screen/induce mutations for crops that include, RNA Interference (RNAi) and (VIGS). When mutant alleles are not available, the reverse genetic techniques can be used to knockdown or silence the phenotype of gene, allowing analysis of gene function (Talukdar and Sinjushin, 2015). Furthermore, those reverse genetic approaches have been utilized to screen for mutations in wheat, rice, maize, barley, tomato, sunflower, cotton, chickpea (Cicer arietinum L.), pea (Pisum sativum L.), and soybean crops including RNAi and gene silencing technologies (Dwivedi et al, 2008;Gupta et al, 2008;Tomlekova, 2010).…”

Section: Functional Genomics and Mutagenomicsmentioning

confidence: 99%

“…These omics-based approaches have proved themselves to be valuable for exploring the genetic and molecular basis of crop development through modifications in DNA, transcript levels, proteins, metabolites, and mineral nutrient against a backdrop of environmental and physiological stress responses (Muthamilarasan et al, 2019). Several omics approaches, such as genomics, mutagenomics, transcriptomics, proteomics, metabolomics, phenomics, and ionomics, have revealed each corresponding molecular biological facet integrated with plant systems (Salt et al, 2008;Houle et al, 2010;Talukdar and Sinjushin, 2015;Wu et al, 2017;Muthamilarasan et al, 2019). The advent of next-generation sequencing (NGS) technologies has led to high throughput and rapid data generation for genomes, epigenomes, transcriptomes, proteomes, metabolomes, and phenomes (Großkinsky et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

“…The integration of multiple omics approaches could elucidate gene functions and networks under conditions of physiological and environmental stress (Singh et al, 2013). Comprehensive multiomics approaches with robust techniques have been used to identify and decipher essential components of stress responses, senescence, and yields in various economically important crops including wheat, soybean, and millet (Deshmukh et al, 2014;Talukdar and Sinjushin, 2015;Muthamilarasan and Prasad, 2017;Shah et al, 2018;Yadav et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

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Applications of Multi-Omics Technologies for Crop Improvement

et al. 2021

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Multiple “omics” approaches have emerged as successful technologies for plant systems over the last few decades. Advances in next-generation sequencing (NGS) have paved a way for a new generation of different omics, such as genomics, transcriptomics, and proteomics. However, metabolomics, ionomics, and phenomics have also been well-documented in crop science. Multi-omics approaches with high throughput techniques have played an important role in elucidating growth, senescence, yield, and the responses to biotic and abiotic stress in numerous crops. These omics approaches have been implemented in some important crops including wheat (Triticum aestivum L.), soybean (Glycine max), tomato (Solanum lycopersicum), barley (Hordeum vulgare L.), maize (Zea mays L.), millet (Setaria italica L.), cotton (Gossypium hirsutum L.), Medicago truncatula, and rice (Oryza sativa L.). The integration of functional genomics with other omics highlights the relationships between crop genomes and phenotypes under specific physiological and environmental conditions. The purpose of this review is to dissect the role and integration of multi-omics technologies for crop breeding science. We highlight the applications of various omics approaches, such as genomics, transcriptomics, proteomics, metabolomics, phenomics, and ionomics, and the implementation of robust methods to improve crop genetics and breeding science. Potential challenges that confront the integration of multi-omics with regard to the functional analysis of genes and their networks as well as the development of potential traits for crop improvement are discussed. The panomics platform allows for the integration of complex omics to construct models that can be used to predict complex traits. Systems biology integration with multi-omics datasets can enhance our understanding of molecular regulator networks for crop improvement. In this context, we suggest the integration of entire omics by employing the “phenotype to genotype” and “genotype to phenotype” concept. Hence, top-down (phenotype to genotype) and bottom-up (genotype to phenotype) model through integration of multi-omics with systems biology may be beneficial for crop breeding improvement under conditions of environmental stresses.

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Section: Functional Genomics and Mutagenomicsmentioning

confidence: 99%

Section: Functional Genomics and Mutagenomicsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Applications of Multi-Omics Technologies for Crop Improvement

et al. 2021

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“…The commonly practiced cytological techniques (reviewed in Talukdar & Sinjushin, 2015) for studying plant somatic chromosome structure differ in their achievable resolution, and thus appropriateness for a given line of inquiry. Fiber FISH (e.g., Wang, Zhang, Jiang, & Zhang, 2013), involves isolation of interphase chromosomes from mitotic nuclei (e.g., leaf cells) that are used to prepare extended DNA fibers, which can then be probed with DNA or epigenetic marker probes (e.g., Blower, Sullivan, & Karpen, 2002).…”

Section: Background Informationmentioning

confidence: 99%

Metaphase Chromosome Preparation from Soybean (Glycine max) Root Tips

2017

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This unit presents a highly reliable protocol to produce and screen metaphase chromosome spreads from root tip cell suspensions of soybean (Glycine max), or other legumes. The procedures represent soybean‐optimized versions of protocols developed for maize. The use of pressurized nitrous oxide to reliably generate metaphase‐arrested chromosomes is crucial to overcoming one of the challenges of working with tiny and numerous soybean chromosomes. © 2017 by John Wiley & Sons, Inc.

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