Abstract
Key message
A transcriptome analysis reveals the transcripts and alleles differentially expressed in sugarcane genotypes with contrasting lignin composition.
Abstract
Sugarcane bagasse is a highly abundant resource that may be used as a feedstock for the production of biofuels and bioproducts in order to meet increasing demands for renewable replacements for fossil carbon. However, lignin imparts rigidity to the cell wall that impedes the efficient breakdown of the biomass into fermentable sugars. Altering the ratio of the lignin units, syringyl (S) and guaiacyl (G), which comprise the native lignin polymer in sugarcane, may facilitate the processing of bagasse. This study aimed to identify genes and markers associated with S/G ratio in order to accelerate the development of sugarcane bioenergy varieties with modified lignin composition. The transcriptome sequences of 12 sugarcane genotypes that contrasted for S/G ratio were compared and there were 2019 transcripts identified as differentially expressed (DE) between the high and low S/G ratio groups. These included transcripts encoding possible monolignol biosynthetic pathway enzymes, transporters, dirigent proteins and transcriptional and post-translational regulators. Furthermore, the frequencies of single nucleotide polymorphisms (SNPs) were compared between the low and high S/G ratio groups to identify specific alleles expressed with the phenotype. There were 2063 SNP loci across 787 unique transcripts that showed group-specific expression. Overall, the DE transcripts and SNP alleles identified in this study may be valuable for breeding sugarcane varieties with altered S/G ratio that may provide desirable bioenergy traits.
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Data Availability
All raw RNA-seq read data is available from the NCBI SRA database under the BioProject PRJNA628577, https://www.ncbi.nlm.nih.gov/bioproject/628577.
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Acknowledgements
We gratefully acknowledge the support of Angela O’Keefe for planning the field trips, helping with harvest and keeping the lab running smoothly. We are also grateful to Jane Brownlee and Patrick Mason for their assistance with the field work. Special thanks to Fernando Correr for his advice on the differential expression analysis. We also thank the University of Queensland Research Computing Centre for their support in computing and data management.
Funding
This research was supported by The Australian Research Council via the ARC-Linkage funding scheme (Project Number LP160100939). Linkage partners include Sugar Research Australia and the Joint BioEnergy Institute (http://www.jbei.org) which is supported by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research, through contract DE-AC02-05CH11231 between Lawrence Berkeley National Laboratory and the U.S. Department of Energy. The funders had no role in experimental design, sample collection, data analysis or manuscript writing/editing.
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RH, FB, AF, and KHK conceived and designed the experiments. KHK and VP conducted the majority of the experiments with assistance from HC. KHK performed the data analysis and wrote the manuscript. RH, FB, BAS, JMG, AF, VP, HC and KHK critically revised the manuscript. All authors have read and approved the manuscript.
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11103_2021_1136_MOESM1_ESM.docx
Supplementary file1 Additional file 1. Supplementary methods Statistical analyses. Table S1 Syringyl to guaiacyl (S/G) ratio of 22 sugarcane (Saccharum spp. hybrids) genotypes and their classification into high and low S/G ratio groups for the differential expression analysis. Letter groups were determined from a Tukey’s honestly significant difference test. Letter groups that differ indicate significant differences between genotypes for S/G ratio at a p-value <0.05. Table S2 RNA-Seq mapping statistics for high and low syringyl to guaiacyl (S/G) ratio sugarcane (Saccharum spp. hybrids) genotypes mapped against the SUGarcane Isoform-sequencing Transcriptome reference. Fig. S1 Mean expression of lignin biosynthesis transcripts differentially expressed between sugarcane (Saccharum spp. hybrids) genotypes with contrasting syringyl/guaiacyl (S/G) ratios (FDR p-value<0.01). Table S3 F-box protein transcripts tentatively involved in post-translational modification differentially expressed between sugarcane (Saccharum spp. hybrids) genotypes with contrasting syringyl/guaiacyl (S/G) ratios mapped against the SUGarcane Isoform-sequencing Transcriptome (SUGIT) reference (DOCX 39 kb)
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Supplementary file2 Additional file 2. Complete list of significantly differentially expressed transcripts (FDR p-value ≤ 0.01) between sugarcane (Saccharum spp. hybrids) genotypes with contrasting syringyl to guaiacyl (S/G) ratios mapped against the SUGarcane Isoform-sequencing Transcriptome reference (XLSX 136 kb)
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Supplementary file3 Additional file 3. FASTA-formatted sequences of significantly differentially expressed transcripts (FDR p-value ≤ 0.01) between sugarcane (Saccharum spp. hybrids) genotypes with contrasting syringyl to guaiacyl (S/G) ratios mapped against the SUGarcane Isoform-sequencing Transcriptome reference (DOCX 2039 kb)
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Supplementary file4 Additional file 4. Complete list of single nucleotide polymorphisms associated with syringyl to guaiacyl (S/G) ratio in sugarcane (Saccharum spp. hybrids) with Gene Ontology functional annotations and NCBI BLAST descriptions for the SNP-containing transcripts (XLSX 238 kb)
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Hodgson-Kratky, K., Perlo, V., Furtado, A. et al. Association of gene expression with syringyl to guaiacyl ratio in sugarcane lignin. Plant Mol Biol 106, 173–192 (2021). https://doi.org/10.1007/s11103-021-01136-w
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DOI: https://doi.org/10.1007/s11103-021-01136-w