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

Ali, Ahmad; Khan, Mehran; Sharif, Rahat; Mujtaba, Muhammad; Gao, San‐Ji

doi:10.3390/plants8090344

Cited by 54 publications

(33 citation statements)

References 138 publications

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“…plays a crucial role in sugar and biofuel production, accounting for 80% of sugar production in the world. Genetic improvement of modern sugarcane cultivars hits a bottleneck through conventional hybrid breeding as a result of sugarcane complex genome, heterogenous and polyploid-aneuploid nature [3].…”

Section: Introductionmentioning

confidence: 99%

Transcription Factors in Plant Stress Responses: Challenges and Potential for Sugarcane Improvement

Javed

Shabbir

Ali

et al. 2020

Plants

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172

107

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Increasing vulnerability of crops to a wide range of abiotic and biotic stresses can have a marked influence on the growth and yield of major crops, especially sugarcane (Saccharum spp.). In response to various stresses, plants have evolved a variety of complex defense systems of signal perception and transduction networks. Transcription factors (TFs) that are activated by different pathways of signal transduction and can directly or indirectly combine with cis-acting elements to modulate the transcription efficiency of target genes, which play key regulators for crop genetic improvement. Over the past decade, significant progresses have been made in deciphering the role of plant TFs as key regulators of environmental responses in particular important cereal crops; however, a limited amount of studies have focused on sugarcane. This review summarizes the potential functions of major TF families, such as WRKY, NAC, MYB and AP2/ERF, in regulating gene expression in the response of plants to abiotic and biotic stresses, which provides important clues for the engineering of stress-tolerant cultivars in sugarcane.

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Section: Introductionmentioning

confidence: 99%

Transcription Factors in Plant Stress Responses: Challenges and Potential for Sugarcane Improvement

Javed

Shabbir

Ali

et al. 2020

Plants

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172

107

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“…Sugarcane (Saccharum spp. interspecific hybrids), a major industrial crop, contributes approximately 80% of global sugar production with an annual value of USD150 billion [1]. Sugarcane has a large, complex genome due to its high and variable chromosome number and polyploidy [2].…”

Section: Introductionmentioning

confidence: 99%

Transcriptome Profiling Provides Molecular Insights into Auxin-Induced Adventitious Root Formation in Sugarcane (Saccharum spp. Interspecific Hybrids) Microshoots

Lakshmanan

et al. 2020

Plants

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Adventitious root (AR) formation was enhanced following the treatment of sugarcane microshoots with indole-3-butyric acid (IBA) and 1-naphthalene acetic acid (NAA) combined, suggesting that auxin is a positive regulator of sugarcane microshoot AR formation. The transcriptome profile identified 1737 and 1268 differentially expressed genes (DEGs) in the basal tissues (5 mm) of sugarcane microshoots treated with IBA+NAA compared to nontreated control on the 3rd and 7th days post-auxin or water treatment (days post-treatment—dpt), respectively. To understand the molecular changes, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed. This analysis showed that DEGs associated with the pathways were associated with plant hormone signaling, flavonoid and phenylpropanoid biosyntheses, cell cycle, and cell wall modification, and transcription factors could be involved in sugarcane microshoot AR formation. Furthermore, qRT–PCR analysis was used to validate the expression patterns of nine genes associated with root formation and growth, and the results were consistent with the RNA-seq results. Finally, a hypothetical hormonal regulatory working model of sugarcane microshoot AR formation is proposed. Our results provide valuable insights into the molecular processes associated with auxin-induced AR formation in sugarcane.

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“…Sugarcane accounts for 80% of sugar production worldwide, and also provides cellulosic biomass for grazing livestock and biofuel production [1]. Modern sugarcane cultivars (2n = 100-130) originate from the nobilization process, which involves interspecific hybridization between Saccharum officinarum (also known as noble cane, 2n = 80) and S. spontaneum (2n = 40-128) and further backcrossing to S. officinarum [2].…”

Section: Introductionmentioning

confidence: 99%

Global Gene Responses of Resistant and Susceptible Sugarcane Cultivars to Acidovorax avenae subsp. avenae Identified Using Comparative Transcriptome Analysis

Chu

Zhou

et al. 2019

Microorganisms

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Red stripe disease in sugarcane caused by Acidovorax avenae subsp. avenae (Aaa) is related to serious global losses in yield. However, the underlying molecular mechanisms associated with responses of sugarcane plants to infection by this pathogen remain largely unknown. Here, we used Illumina RNA-sequencing (RNA-seq) to perform large-scale transcriptome sequencing of two sugarcane cultivars to contrast gene expression patterns of plants between Aaa and mock inoculations, and identify key genes and pathways involved in sugarcane defense responses to Aaa infection. At 0–72 hours post-inoculation (hpi) of the red stripe disease-resistant cultivar ROC22, a total of 18,689 genes were differentially expressed between Aaa-inoculated and mock-inoculated samples. Of these, 8498 and 10,196 genes were up- and downregulated, respectively. In MT11-610, which is susceptible to red stripe disease, 15,782 genes were differentially expressed between Aaa-inoculated and mock-inoculated samples and 8807 and 6984 genes were up- and downregulated, respectively. The genes that were differentially expressed following Aaa inoculation were mainly involved in photosynthesis and carbon metabolism, phenylpropanoid biosynthesis, plant hormone signal transduction, and plant–pathogen interaction pathways. Further, qRT-PCR and RNA-seq used for additional validation of 12 differentially expressed genes (DEGs) showed that eight genes in particular were highly expressed in ROC22. These eight genes participated in the biosynthesis of lignin and coumarin, as well as signal transduction by salicylic acid, jasmonic acid, ethylene, and mitogen-activated protein kinase (MAPK), suggesting that they play essential roles in sugarcane resistance to Aaa. Collectively, our results characterized the sugarcane transcriptome during early infection with Aaa, thereby providing insights into the molecular mechanisms responsible for bacterial tolerance.

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

Cited by 54 publications

References 138 publications

Transcription Factors in Plant Stress Responses: Challenges and Potential for Sugarcane Improvement

Transcription Factors in Plant Stress Responses: Challenges and Potential for Sugarcane Improvement

Transcriptome Profiling Provides Molecular Insights into Auxin-Induced Adventitious Root Formation in Sugarcane (Saccharum spp. Interspecific Hybrids) Microshoots

Global Gene Responses of Resistant and Susceptible Sugarcane Cultivars to Acidovorax avenae subsp. avenae Identified Using Comparative Transcriptome Analysis

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