Potentials, Challenges, and Genetic and Genomic Resources for Sugarcane Biomass Improvement

Kandel, Ramkrishna; Yang, Xiping; Jiang, Song; Wang, Jianping

doi:10.3389/fpls.2018.00151

Cited by 29 publications

(20 citation statements)

References 122 publications

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“…Finally, sugarcane is an important industrial crop with a great potential for biofuel and biomaterial production to reduce our dependence on fossil fuel energy. Modification of sugarcane biomass can be tailored by genetic approaches for a better composition for converting to biofuels and other high value molecules (Waclawovsky et al, 2010; de Souza et al, 2014; Furtado et al, 2014; Hoang et al, 2015; Kandel et al, 2018). The sugarcane genome is complex, and this hinders the sequencing progress and understanding of the genome structure and functions, compared to progress made for other grass species including sorghum and maize in recent years (Souza et al, 2011; Thirugnanasambandam et al, 2018).…”

Section: Discussionmentioning

confidence: 99%

The Impact of cDNA Normalization on Long-Read Sequencing of a Complex Transcriptome

et al. 2019

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Normalization of cDNA is widely used to improve the coverage of rare transcripts in analysis of transcriptomes employing next-generation sequencing. Recently, long-read technology has been emerging as a powerful tool for sequencing and construction of transcriptomes, especially for complex genomes containing highly similar transcripts and transcript-spliced isoforms. Here, we analyzed the transcriptome of sugarcane, a highly polyploidy plant genome, by PacBio isoform sequencing (Iso-Seq) of two different cDNA library preparations, with and without a normalization step. The results demonstrated that, while the two libraries included many of the same transcripts, many longer transcripts were removed, and many new generally shorter transcripts were detected by normalization. For the same input cDNA and data yield, the normalized library recovered more total transcript isoforms and number of predicted gene families and orthologous groups, resulting in a higher representation for the sugarcane transcriptome, compared to the non-normalized library. The non-normalized library, on the other hand, included a wider transcript length range with more longer transcripts above ∼1.25 kb and more transcript isoforms per gene family and gene ontology terms per transcript. A large proportion of the unique transcripts comprising ∼52% of the normalized library were expressed at a lower level than the unique transcripts from the non-normalized library, across three tissue types tested including leaf, stalk, and root. About 83% of the total 5,348 predicted long noncoding transcripts was derived from the normalized library, of which ∼80% was derived from the lowly expressed fraction. Functional annotation of the unique transcripts suggested that each library enriched different functional transcript fractions. This demonstrated the complementation of the two approaches in obtaining a complete transcriptome of a complex genome at the sequencing depth used in this study.

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Section: Discussionmentioning

confidence: 99%

The Impact of cDNA Normalization on Long-Read Sequencing of a Complex Transcriptome

et al. 2019

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“…hybrids), a type of sugarcane that has been bred for use as a bioenergy feedstock, has great potential as a source of lignocellulose and/or sugar for sustainably producing biofuels (Kandel et al 2018). Nevertheless, the cultivation and productivity of energycane has been hampered by its narrow genetic base and disease susceptibility because most modern energycane varieties were derived from few interspecific hybrids between S. officinarum L. and S. spontaneum L. (Wang et al 2013). To improve disease resistance in energycane, two other genera (Miscanthus and Erianthus) that share a close phylogenetic relationship with energycane have received appreciable attention (Tew and Cobill 2008).…”

Section: Introductionmentioning

confidence: 99%

“…To improve disease resistance in energycane, two other genera (Miscanthus and Erianthus) that share a close phylogenetic relationship with energycane have received appreciable attention (Tew and Cobill 2008). For instance, intergeneric crosses between S. officinarum 'Ludashi' and Erianthus rockii have been used to introgress brown rust resistance into energycane (Wang et al 2013). Miscane, a hybrid of Saccharum × Miscanthus, has been noted to exhibit increased cold tolerance and disease resistance compared with ordinary Saccharum and therefore can potentially facilitate disease resistance introgression back into energycane through backcrossing (Chen and Lo 1989).…”

Section: Introductionmentioning

confidence: 99%

“…Markers tagging quantitative trait loci (QTL) and other genomic signals exhibiting statistically significant associations with traits have been identified in energycane (Yang et al 2018), which can potentially facilitate marker-assisted selection (MAS) in energycane breeding programs. Given the success of MAS breeding programs in other crops (Okogbenin et al 2007;Xu and Crouch 2008;Jiang 2013;Yohannes et al 2015), the potential of MAS to develop disease-resistant energycane crops is promising. Nevertheless, MAS-based breeding approaches are undermined by several factors.…”

Section: Introductionmentioning

confidence: 99%

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Evaluation of genomic selection and marker-assisted selection in Miscanthus and energycane

et al. 2019

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Although energycane (Saccharum spp. hybrids) is widely used as a source of lignocellulosic biomass for bioethanol, breeding this crop for disease resistance is challenging due to its narrow genetic base. Therefore, efforts are underway to introgress novel sources of genetic resistance from Miscanthus into energycane. Given that disease resistance in energycane could be either qualitative or quantitative in nature, careful examination of a wide variety of genomicenabled breeding approaches will be crucial to the success of such an undertaking. Here we examined the efficiency of both genomic selection (GS) and markerassisted selection (MAS) for traits simulated under different genetic architectures in F 1 and BC 1 populations of Miscanthus × Miscanthus and sugarcane × sugarcane crosses. We observed that the performance of MAS was comparable and sometimes superior to GS for traits simulated with four quantitative trait nucleotides (QTNs). In contrast, as the number of simulated QTN increased, all four GS models that were evaluated tended to outperform MAS, select more phenotypically optimal F 1 individuals, and accurately predict simulated trait values in subsequent BC 1 generations. We therefore conclude that GS is preferable to MAS for introgressing genetic sources of horizontal disease resistance from Miscanthus to energycane, while MAS remains a suitable option for introgressing vertical disease resistance.

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“…Sugarcane bagasse contains 22% lignin, 24% hemicellulose, and 43% cellulose whereas sweet sorghum has 21% lignin, 27% hemicellulose, and 45% cellulose with theoretical ethanol production of 12,938 and 5,804 kg per ha respectively. Though sugarcane has higher productivity as compared with its counterparts (sweet sorghum, sugar beet) yet further improvement in its fiber and sugar contents is desired to transform it into energy cane [32].…”

Section: Sugarcane a Bioenergy Source: An Overviewmentioning

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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Potentials, Challenges, and Genetic and Genomic Resources for Sugarcane Biomass Improvement

Cited by 29 publications

References 122 publications

The Impact of cDNA Normalization on Long-Read Sequencing of a Complex Transcriptome

The Impact of cDNA Normalization on Long-Read Sequencing of a Complex Transcriptome

Evaluation of genomic selection and marker-assisted selection in Miscanthus and energycane

Sugarcane as Future Bioenergy Crop: Potential Genetic and Genomic Approaches

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