ArticleBMC genomics2016
De novo analysis of transcriptome reveals genes associated with leaf abscission in sugarcane (Saccharum officinarum L.).
Article in BMC genomics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
- Article
- Exploring the genetic basis of heterosis in eucalypt growth based on transcriptome analysis.BMC genomics · 2025Article
- Genomic loci associated with leaf abscission contribute to machine picking and environmental adaptability in upland cotton (Gossypium hirsutum L.).Journal of advanced research · 2024Article
- Article
- Transcriptomic and Proteomic Landscape of Sugarcane Response to Biotic and Abiotic Stressors.International journal of molecular sciences · 2023Review
- Developing new sugarcane varieties suitable for mechanized production in China: principles, strategies and prospects.Frontiers in plant science · 2023Article
- Review
- Single-Molecule Long-Read Sequencing of Purslane (Plants (Basel, Switzerland) · 2021Article
- Functional characterization of PETIOLULE-LIKE PULVINUS (PLP) gene in abscission zone development in Medicago truncatula and its application to genetic improvement of alfalfa.Plant biotechnology journal · 2021Article
- The Wild Sugarcane and Sorghum Kinomes: Insights Into Expansion, Diversification, and Expression Patterns.Frontiers in plant science · 2021Article
- Evaluation of Cotton (Plants (Basel, Switzerland) · 2020Article
- Amino Acid and Carbohydrate Metabolism Are Coordinated to Maintain Energetic Balance during Drought in Sugarcane.International journal of molecular sciences · 2020Article
- Molecular Mechanisms Underlying Sugarcane Response to Aluminum Stress by RNA-Seq.International journal of molecular sciences · 2020Article
- Petal abscission in fragrant roses is associated with large scale differential regulation of the abscission zone transcriptome.Scientific reports · 2020Article
- Transcriptome Profiling Provides Molecular Insights into Auxin-Induced Adventitious Root Formation in Sugarcane (Plants (Basel, Switzerland) · 2020Article
- Comparative transcriptomics of an arctic foundation species, tussock cottongrass (Eriophorum vaginatum), during an extreme heat event.Scientific reports · 2020Article
- High-throughput sequencing reveals genes associated with high-temperature stress tolerance in sugarcane.3 Biotech · 2020Article
- Transcriptome analysis of the effect of GA3 Biotech · 2019Article
- Sugarcane Omics: An Update on the Current Status of Research and Crop Improvement.Plants (Basel, Switzerland) · 2019Review
- Leaf Transcriptome Assembly ofGenes · 2019Article
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Authors and funding
12 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundSugarcane (Saccharum officinarum L.) is an important sugar crop which belongs to the grass family and can be used for fuel ethanol production. The growing demands for sugar and biofuel is asking for breeding a sugarcane variety that can shed their leaves during the maturity time due to the increasing cost on sugarcane harvest.
resultsTo determine leaf abscission related genes in sugarcane, we generated 524,328,950 paired reads with RNA-Seq and profiled the transcriptome of new born leaves of leaf abscission sugarcane varieties (Q1 and T) and leaf packaging sugarcane varieties (Q2 and B). Initially, 275,018 transcripts were assembled with N50 of 1,177 bp. Next, the transcriptome was annotated by mapping them to NR, UniProtKB/Swiss-Prot, Gene Ontology and KEGG pathway databases. Further, we used TransDecoder and Trinotate to obtain the likely proteins and annotate them in terms of known proteins, protein domains, signal peptides, transmembrane regions and rRNA transcripts. Different expression analysis showed 1,202 transcripts were up regulated in leaf abscission sugarcane varieties, relatively to the leaf packaging sugarcane varieties. Functional analysis told us 62, 38 and 10 upregulated transcripts were involved in plant-pathogen interaction, response to stress and abscisic acid associated pathways, respectively. The upregulation of transcripts encoding 4 disease resistance proteins (RPM1, RPP13, RGA2, and RGA4), 6 ABC transporter G family members and 16 transcription factors including WRK33 and heat stress transcription factors indicate they may be used as candidate genes for sugarcane breeding. The expression levels of transcripts were validated by qRT-PCR. In addition, we characterized 3,722 SNPs between leaf abscission and leaf packaging sugarcane plants.
conclusionOur results showed leaf abscission associated genes in sugarcane during the maturity period. The output of this study provides a valuable resource for future genetic and genomic studies in sugarcane.
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