ArticlePloS one2017
Association of gene expression with biomass content and composition in sugarcane.
Article in PloS one, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 35 citations in OpenAlex.
- Sampling strategies for sugarcane using either clonal replicates or diverse genotypes can bias the conclusions of RNA-Seq studies.Genetics and molecular biology · 2023Article
- The Long Read Transcriptome of Rice (Oryza sativa ssp. japonica var. Nipponbare) Reveals Novel Transcripts.Rice (New York, N.Y.) · 2022Article
- Identification of potential MTAs and candidate genes for juice quality- and yield-related traits in Saccharum clones: a genome-wide association and comparative genomic study.Molecular genetics and genomics : MGG · 2022Article
- Association of gene expression with syringyl to guaiacyl ratio in sugarcane lignin.Plant molecular biology · 2021Article
- Applying Molecular Phenotyping Tools to Explore Sugarcane Carbon Potential.Frontiers in plant science · 2021Review
- The Wild Sugarcane and Sorghum Kinomes: Insights Into Expansion, Diversification, and Expression Patterns.Frontiers in plant science · 2021Article
- Unraveling the Genome of a High Yielding Colombian Sugarcane Hybrid.Frontiers in plant science · 2021Article
- Variation in sugarcane biomass composition and enzymatic saccharification of leaves, internodes and roots.Biotechnology for biofuels · 2020Article
- Overexpression of an evolutionarily conserved drought-responsive sugarcane gene enhances salinity and drought resilience.Annals of botany · 2019Article
- Genomic resources for energy cane breeding in the post genomics era.Computational and structural biotechnology journal · 2019Review
- The Impact of cDNA Normalization on Long-Read Sequencing of a Complex Transcriptome.Frontiers in genetics · 2019Article
- Transcriptome analysis highlights key differentially expressed genes involved in cellulose and lignin biosynthesis of sugarcane genotypes varying in fiber content.Scientific reports · 2018Article
- Article
- Potentials, Challenges, and Genetic and Genomic Resources for Sugarcane Biomass Improvement.Frontiers in plant science · 2018Review
- Long Non-coding RNAs in Endothelial Biology.Frontiers in physiology · 2018Review
- Association of variation in the sugarcane transcriptome with sugar content.BMC genomics · 2017Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
About 64% of the total aboveground biomass in sugarcane production is from the culm, of which ~90% is present in fiber and sugars. Understanding the transcriptome in the sugarcane culm, and the transcripts that are associated with the accumulation of the sugar and fiber components would facilitate the modification of biomass composition for enhanced biofuel and biomaterial production. The Sugarcane Iso-Seq Transcriptome (SUGIT) database was used as a reference for RNA-Seq analysis of variation in gene expression between young and mature tissues, and between 10 genotypes with varying fiber content. Global expression analysis suggests that each genotype displayed a unique expression pattern, possibly due to different chromosome combinations and maturation amongst these genotypes. Apart from direct sugar- and fiber-related transcripts, the differentially expressed (DE) transcripts in this study belonged to various supporting pathways that are not obviously involved in the accumulation of these major biomass components. The analysis revealed 1,649 DE transcripts between the young and mature tissues, while 555 DE transcripts were found between the low and high fiber genotypes. Of these, 151 and 23 transcripts respectively, were directly involved in sugar and fiber accumulation. Most of the transcripts identified were up-regulated in the young tissues (2 to 22-fold, FDR adjusted p-value <0.05), which could be explained by the more active metabolism in the young tissues compared to the mature tissues in the sugarcane culm. The results of analysis of the contrasting genotypes suggests that due to the large number of genes contributing to these traits, some of the critical DE transcripts could display less than 2-fold differences in expression and might not be easily identified. However, this transcript profiling analysis identified full-length candidate transcripts and pathways that were likely to determine the differences in sugar and fiber accumulation between tissue types and contrasting genotypes.
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