Sugarcane Genomics and Transcriptomics

Kaur, Lovejot; Dharshini, S. Akila Parvathy; Ram, Bakshi; Appunu, C.

doi:10.1007/978-3-319-58946-6_2

Cited by 7 publications

(10 citation statements)

References 117 publications

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“…Recent molecular biology studies of sugarcane has been conducted, including cytogenetic analysis and multi‐omic approaches (e.g. genomics, transcriptomics, proteomics and metabolomics), to identify strategies that can increase yield, sucrose content, and biotic and abiotic stress tolerance as well as to understand the mechanisms of genetic regulation networks in sugarcane cultivars that are poly‐aneuploid interspecific hybrids (Kaur et al 2017, Ali et al 2019a, b).…”

Section: Introductionmentioning

confidence: 99%

Genome‐wide analysis of mitogen‐activated protein (MAP) kinase gene family expression in response to biotic and abiotic stresses in sugarcane

Ali

Chu

et al. 2020

Physiologia Plantarum

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To systematically analyze mitogen-activated protein (MAP) kinase gene families and their expression profiles in sugarcane (Saccharum spp. hybrids; Sh) under diverse biotic and abiotic stresses, we identified 15 ShMAPKs, 6 ShMAPKKs and 16 ShMAPKKKs genes in the sugarcane cultivar R570 genome. These were also confirmed in one S. spontaneum genome and two transcriptome datasets of sugarcane trigged by Acidovorax avenae subsp. avenae (Aaa) and Xanthomonas albilineans (Xa) infections. Phylogenetic analysis revealed that four subgroups were present in each ShMAPK and ShMAPKK family and three sub-families (RAF, MEKK and ZIK) presented in the ShMAPKKK family. Conserved protein motif and gene structure analyses supported the evolutionary relationships of the three families inferred from the phylogenetic analysis. All of the ShMAPK, ShMAPKK and ShMAPKKK genes identified in Saccharum spp. R570 were distributed on chromosomes 1-7 and 9-10. RNA-seq and qRT-PCR analyses indicated that ShMAPK07 and ShMAPKKK02 were defense-responsive genes in sugarcane challenged by both Aaa and Xa stimuli, while some genes were upregulated specifically by Aaa and Xa infection. Additionally, ShMAPK05 acted as a negative regulator under drought and salinity stress, but served as a positive regulator under salicylic acid (SA) treatment. ShMAPK07 plays a positive role under drought stress, but a negative role under SA treatment. ShMAPKKK01 was negatively modulated by both salinity stress and SA treatment, whereas ShMAPKKK06 was positively regulated by both of the two stress stimuli. Our results suggest that members of MAPK cascade gene families regulate adverse stress responses through multiple signal transduction pathways in sugarcane.

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Section: Introductionmentioning

confidence: 99%

Genome‐wide analysis of mitogen‐activated protein (MAP) kinase gene family expression in response to biotic and abiotic stresses in sugarcane

Ali

Chu

et al. 2020

Physiologia Plantarum

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“…Understanding complex connections among genetics, genes, proteome, and metabolome requires integrated research on omics, bioinformatics, and computational biology. A great many sugarcane genes involved in molecular mechanisms of stress (cold, drought, and salinity stress), plant growth, and development have been explored [62]. During the recent decade, transcriptomic research has led to the identification of more than 33000 genes, involved in critical biological functions in this energy crop [63].…”

Section: Role Of Omics In the Development Of Future Energy Canementioning

confidence: 99%

Sugarcane as Future Bioenergy Crop: Potential Genetic and Genomic Approaches

Khan¹,

Mustafa²,

Joyia³

et al. 2021

Sugarcane - Biotechnology for Biofuels

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Biofuels are gaining increased scientific as well as public attention to fulfill future energy demands and can be the only potential candidates to safeguard and strengthen energy security by reducing the world’s reliance on exhausting fossil energy sources. Sugarcane is an important C4 crop with great potential to contribute to global biofuel production as sugarcane juice can be easily fermented to produce ethanol. The success of bioethanol production from sugarcane in Brazil has widened the scope of the technology and has led to increased demand of purpose-grown sugarcane for biofuel production. Scientific interventions have not only helped to improve the cane crop but industrial procedures have also been upgraded resulting in improved production of bioethanol. Likewise, advancements in omics have led to high hopes for the development of energy cane. This chapter highlights the advancements as well as potential and challenges in the production of sugarcane biofuel, focusing on genetic and genomic interventions improving the crop as energy-cane. Further, controversies in the production and usage of biofuel derived from sugarcane have also been discussed.

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“…The transcriptomic analysis of sugarcane has been carried by applying the efficient and up-to-date molecular techniques, such as cDNA microarrays [72], Roche/454 and Illumina/Solexa [8], RNA-seq, qPCR and microscopy [46], for exploring gene expression profiles from cells/tissues and their effects on structural and functional changes during sugarcane growth and development [73]. The functional characterization and annotation of genes responsible for important agronomic traits are very important and assistive in sugarcane variety improvement for enhancing the productivity.…”

Section: Sugarcane Transcriptomicsmentioning

confidence: 99%

“…Sugarcane improvement based on conventional breeding is highly challenging due to this crop posing narrow genetic pools and a complicated genome [6]. Recently, numerous researches about molecular biology have been investigated in sugarcane, including cytogenetic analysis and omics research (genomics, transcriptomics, proteomics, and metabolomics) in order to achieve higher yields, higher sucrose content, and biotic and abiotic stress tolerance, as well as to understand their genetic regulation and mechanisms [6,7,8,9].…”

Section: Introductionmentioning

confidence: 99%

“…The omics approaches benefit from the understanding of the complex connections among genetic makeup, genes, proteins, and metabolites, but they rely seriously on analytical methods, such as bioinformatics, computational analysis, etc., and many other disciplines of biology [6]. A great amount of new information has been obtained regarding the molecular mechanisms of sugarcane resistance and tolerance to herbicides, cold, drought, and salinity stress, as well as plant development [7,8]. In early genomic research, molecular marker approaches helped to elucidate the genome structure of modern sugarcane genotypes and derive phylogenetic relationships among the Saccharum complex; Also, much work was carried out on sugarcane genome mapping experiments to detect marker-trait associations and to validate the position of different essential genes [6,10].…”

Section: Introductionmentioning

confidence: 99%

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Sugarcane Omics: An Update on the Current Status of Research and Crop Improvement

Ali

Khan

Sharif

et al. 2019

Plants

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Sugarcane is an important crop from Poaceae family, contributing about 80% of the total world’s sucrose with an annual value of around US$150 billion. In addition, sugarcane is utilized as a raw material for the production of bioethanol, which is an alternate source of renewable energy. Moving towards sugarcane omics, a remarkable success has been achieved in gene transfer from a wide variety of plant and non-plant sources to sugarcane, with the accessibility of efficient transformation systems, selectable marker genes, and genetic engineering gears. Genetic engineering techniques make possible to clone and characterize useful genes and also to improve commercially important traits in elite sugarcane clones that subsequently lead to the development of an ideal cultivar. Sugarcane is a complex polyploidy crop, and hence no single technique has been found to be the best for the confirmation of polygenic and phenotypic characteristics. To better understand the application of basic omics in sugarcane regarding agronomic characters and industrial quality traits as well as responses to diverse biotic and abiotic stresses, it is important to explore the physiology, genome structure, functional integrity, and collinearity of sugarcane with other more or less similar crops/plants. Genetic improvements in this crop are hampered by its complex genome, low fertility ratio, longer production cycle, and susceptibility to several biotic and abiotic stresses. Biotechnology interventions are expected to pave the way for addressing these obstacles and improving sugarcane crop. Thus, this review article highlights up to date information with respect to how advanced data of omics (genomics, transcriptomic, proteomics and metabolomics) can be employed to improve sugarcane crops.

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Sugarcane Genomics and Transcriptomics

Cited by 7 publications

References 117 publications

Genome‐wide analysis of mitogen‐activated protein (MAP) kinase gene family expression in response to biotic and abiotic stresses in sugarcane

Genome‐wide analysis of mitogen‐activated protein (MAP) kinase gene family expression in response to biotic and abiotic stresses in sugarcane

Sugarcane as Future Bioenergy Crop: Potential Genetic and Genomic Approaches

Sugarcane Omics: An Update on the Current Status of Research and Crop Improvement

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