Large-Scale Transcriptome Analysis of Two Sugarcane Genotypes Contrasting for Lignin Content

Vicentini, Renato; Bottcher, Alexandra; Brito, Mónica; Santos, A. B. dos; Creste, Silvana; Landell, Marcos Guimarães de Andrade; Cesarino, Igor; Mazzafera, Paulo

doi:10.1371/journal.pone.0134909

Cited by 70 publications

(81 citation statements)

References 76 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…The largest collection of sugarcane ESTs was generated by the SUCEST project from cDNA libraries of different tissues from several sugarcane varieties (Vettore et al., ) and was important for sugarcane gene discovery, transcript profiling, genome exploration and transcriptome and proteome analysis. Recently, the transcriptome analysis by next‐generation sequencing technology RNA‐seq has furnished important data to identify molecular key intermediaries of cell wall biosynthetic mechanism and of biomass yield and recalcitrance (Mattiello et al., ; Singh et al., ; Vicentini et al., ; Xu et al., ). On the other hand, the genome of sugarcane due to its high polyploidy is extremely complex and has not been completely sequenced or a detailed physical map produced.…”

Section: Sugarcane Genomic and Transcriptomic Resourcesmentioning

confidence: 99%

Suberin and hemicellulose in sugarcane cell wall architecture and crop digestibility: A biotechnological perspective

Figueiredo

Araújo

Llerena

et al. 2019

Food and Energy Security

Self Cite

View full text Add to dashboard Cite

Sugarcane is a highly efficient biomass producer used in the last decades for bioethanol and bioelectricity production, as well as for animal feeding. Together with lignin, suberin is a major factor for the low sugarcane biomass digestibility by ruminants. The lipid–phenolic biomolecular composition and the ultrastructure of suberin and associated waxes confer them extraordinary properties of hydrophobicity, flexibility, and anti‐microbial resistance, responsible for the low digestibility of suberized tissues. Additionally, hemicelluloses cross‐linked with suberin and lignin also contribute appreciably to cell wall recalcitrance. In this review, a main focus was given to suberin and secondly to hemicellulose and how they may interfere with ruminant digestibility. Suberin and hemicellulose deposition and biomolecular composition are genetically regulated, showing a close regulatory interplay with phenylpropanoid and fatty acid biosynthesis pathways, cutin disruption, and stress and defense responses. Understanding the bulk of transcription factors network and hormonal regulatory mechanisms will allow accurate biotechnological approaches to the production of more feasible forage sugarcane.

show abstract

Section: Sugarcane Genomic and Transcriptomic Resourcesmentioning

confidence: 99%

Suberin and hemicellulose in sugarcane cell wall architecture and crop digestibility: A biotechnological perspective

Figueiredo

Araújo

Llerena

et al. 2019

Food and Energy Security

Self Cite

View full text Add to dashboard Cite

show abstract

“…Deep sequencing of transcriptome (RNA-seq) has the potential to uncover the causal variations of a desirable trait both at the genic as well as at allelic level. At the genic level, there have been a few reports in sugarcane on differentially expressed genes (DEGs) associated with to sucrose accumulation (De Setta et al 2014;Cardoso-Silva et al, 2014;Thirugnanasambandam et al 2017Thirugnanasambandam et al , 2019, lignin accumulation (Vicentini et al 2015;Kasirajan et al 2018), photosynthesis (Mattiello et al 2015), response to infections from Gluconacetobacter (Vargas et al 2014), and smut pathogen (Wu et al 2013;Que et al 2014;Su et al, 2015;Brigida et al 2016). Recently, Singh et al (2018) investigated the allele specific expressions linked to molecular mechanism behind high biomass accumulation using BSR-Seq of parents, the F1 and 20 F2 clones of sugarcane.…”

Section: Introductionmentioning

confidence: 99%

Bulked segregant RNA-Seq reveals differential genes and non-synonymous genetic variants linked to sucrose accumulation in sugarcane

Banerjee

Kumar

Annadurai

et al. 2019

Preprint

View full text Add to dashboard Cite

Sucrose is the key economic trait in sugarcane which is a highly polyploid multi-species hybrid and shows a complex pattern of trait inheritance. The excessively large genome of sugarcane is comparatively less explored through Next Generation Sequencing tools for creating superior varieties. In this study, RNAseq libraries of two extreme bulks from a segregating full-sib population and its parents were used to identify 9905 conditionspecific non-synonymous genetic variants (NSVs), out of which 43 had a very high degree of differential enrichment (∆f >0.5) for contrasting sucrose accumulating conditions. The statistical model used in this study which was able to quantify the relative effect of NSVs on the trait detected highly significant positive and negative effect NSVs located in the coding regions of genes involved in sucrose metabolism, photosynthesis, mitochondrial electron transport, glycolysis and transcription. In addition, a few differential pre-mature stop codons that could result in production of truncated proteins were also detected in genes coding for aquaporin, GAPDH, aldolase, cytochrome C-oxidase, chlorophyll synthase and plant plasma membrane intrinsic proteins. Additionally, a total of 2140 differentially expressed genes (DEGs) linked to high sucrose accumulation were identified. Among the DEGs, sucrose phosphate synthase III, genes involved in transport, auxin signal transduction, etc., were upregulated, while those involved in electron transfer, cytochrome P450, etc., were downregulated in high sucrose accumulation conditions. This study was able to give finer insights in to the role of allelic heterozygosity on sucrose accumulation and the identified NSVs and DEGs could be useful as candidate markers in marker-assisted breeding for developing high sugar varieties.

show abstract

“…Once a better understanding of the genes controlling cell-wall biosynthesis is achieved, breeding programs will be able to accelerate the selection and development of varieties with optimized biomass composition, to generate better sugarcane biomass sources to meet the demand of biofuel production. For transcript profiling, in the context of the lack of a reference genome or a complete transcript transcriptome, most studies found in literature were conducted on sample-based references which were de novo constructed using samples from each study, such as in Vargas et al (2014), Cardoso-Silva et al (2014) and Vicentini et al (2015). This was shown to be the best strategy so far, since the genes expressed (transcriptome) in each experimental condition were different from the others, even though the major gene content would be similar.…”

Section: Discussionmentioning

confidence: 99%

“…Only two transcripts related to lignin, C4H and CCoAOMT, were found upregulated in a study on 11 high-lignin guineagrass genotypes (Stabile et al, 2012). As discussed in Vicentini et al (2015), after gathering the results of differential expression of several lignin genes, it was suggested that lignin deposition might be regulated at the transcriptional level, but also the post-transcriptional levels and by enzyme catalytic activities. Therefore, RNA-Seq data might not reflect all events in the lignin pathway, and therefore studies at post-transcriptional levels (i.e.…”

Section: Transcript Differential Expression Between the Low And High mentioning

confidence: 98%

Analysis of genes controlling biomass traits in the genome of sugarcane (Saccharum spp. hybrids)

Hoang¹

View full text Add to dashboard Cite

Sugarcane (Saccharum spp. hybrids) is a leading industrial crop in tropical and subtropical regions worldwide. More recently, sugarcane has been selected as a key feedstock for biofuels due to its rapid growth, high fiber content and favorable energy input/output ratio.Breeding sugarcane varieties with biomass for efficient conversion to biofuels can be optimized by understanding the genetic control of biomass composition. However, the genetic analysis of these traits is hindered by the genomic complexity, and the limited availability of a reference genome. The aims of this project were: the development of a high-throughput profiling method for rapid screening of the key biomass traits in a sugarcane population; the construction of a new full-length transcriptome reference database; and the identification of transcripts associated with sugar and fiber accumulation in sugarcane.For the screening of genotypes, newly developed predictive models employing nearinfrared (NIR) spectral analysis, coupled with the high performance liquid chromatography (HPLC), were shown to allow high-throughput profiling of major components in the fiber and sugar fractions in sugarcane biomass. Contrasting genotypes of low fiber and high fiber (minimum of ~29% and maximum of 61% total dry biomass) were identified amongst 331 samples from 186 sugarcane genotypes. The population studied exhibited a wide range of fiber/sugar ratio, from 0.4 (as low as that of the typical commercial sugarcane variety) to 2.2 (similar to that of energy-cane). In addition, the lignin content (the central factor in the biomass recalcitrance) ranged from 6 to 14% of the total dry biomass. To aid genotyping, a new sugarcane transcriptome (termed as SUGIT database) was constructed using PacBio full-length isoform sequencing (Iso-Seq), and a cDNA library derived from 22 diverse sugarcane genotypes, of the key tissues (leaf, internode and root), at different developmental stages (from immature to mature). Comparative analysis showed that this new SUGIT database included more full-length transcripts, longer predicted transcripts, and higher average length of the largest 1,000 proteins, compared to a de novo assembly from Illumina RNA-Seq short-read data from the same sample set. The annotation suggested that the majority (~94%) of the SUGIT database was from coding RNAs, while a very small proportion (~2%) could be long non-coding RNAs. About 70-82% of the RNASeq reads from different tissues mapped back to the SUGIT database, suggesting that it represented well the targeted tissues, while about 69% of this database was aligned with the sorghum genome, confirming the high conservation of orthologs in the genic regions of ii the two genomes. Applying the SUGIT database to differential expression analysis (FDR, false discovery rate corrected p-value <0.05), 1,649 transcript isoforms were identified as being differentially expressed between the young and mature tissues in the sugarcane plant, while 555 transcript isoforms were differentially expressed between th...

show abstract

Large-Scale Transcriptome Analysis of Two Sugarcane Genotypes Contrasting for Lignin Content

Cited by 70 publications

References 76 publications

Suberin and hemicellulose in sugarcane cell wall architecture and crop digestibility: A biotechnological perspective

Suberin and hemicellulose in sugarcane cell wall architecture and crop digestibility: A biotechnological perspective

Bulked segregant RNA-Seq reveals differential genes and non-synonymous genetic variants linked to sucrose accumulation in sugarcane

Analysis of genes controlling biomass traits in the genome of sugarcane (Saccharum spp. hybrids)

Contact Info

Product

Resources

About