Differential expression in leaves of Saccharum genotypes contrasting in biomass production provides evidence of genes involved in carbon partitioning

Abstract

Background The development of biomass crops aims to meet industrial yield demands, in order to optimize profitability and sustainability. Achieving these goals in an energy crop like sugarcane relies on breeding for sucrose accumulation, fiber content and stalk number. To expand the understanding of the biological pathways related to these traits, we evaluated gene expression of two groups of genotypes contrasting in biomass composition. Results First visible dewlap leaves were collected from 12 genotypes, six per group, to perform RNA-Seq. We found a high number of differentially expressed genes, showing how hybridization in a complex polyploid system caused extensive modifications in genome functioning. We found evidence that differences in transposition and defense related genes may arise due to the complex nature of the polyploid Saccharum genomes. Genotypes within both biomass groups showed substantial variability in genes involved in photosynthesis. However, most genes coding for photosystem components or those coding for phosphoenolpyruvate carboxylases (PEPCs) were upregulated in the high biomass group. Sucrose synthase (SuSy) coding genes were upregulated in the low biomass group, showing that this enzyme class can be involved with sucrose synthesis in leaves, similarly to sucrose phosphate synthase (SPS) and sucrose phosphate phosphatase (SPP). Genes in pathways related to biosynthesis of cell wall components and expansins coding genes showed low average expression levels and were mostly upregulated in the high biomass group. Conclusions Together, these results show differences in carbohydrate synthesis and carbon partitioning in the source tissue of distinct phenotypic groups. Our data from sugarcane leaves revealed how hybridization in a complex polyploid system resulted in noticeably different transcriptomic profiles between contrasting genotypes.

The Wild Sugarcane and Sorghum Kinomes: Insights Into Expansion, Diversification, and Expression Patterns

“…In Experiment 2, described by Correr et al (2020) , we used samples from the SP80-3280, RB72454, and RB855156 hybrid cultivars; TUC71-7 and US85-1008 hybrids; White Transparent and Criolla Rayada S. officinarum genotypes; IN84-58, IN84-88, Krakatau, and SES205A Ssp genotypes; and IJ76-318 Saccharum robustum genotypes. For six genotypes – SP80-3280, RB72454, US85-1008, White Transparent, IN84-58, and SES205A – we collected and sequenced three biological replicates, while the others were represented by one biological replicate; all samples were represented by three technical replicates.…”

“…In Experiment 2, described by Correr et al (2020) After collection, samples were immediately frozen in liquid nitrogen and stored at −80°C until processed. Total RNA was extracted from 200 mg of ground roots and 50 mg of ground leaves or culms using an RNeasy Plant Mini Kit (Qiagen, Valencia, CA, United States).…”

Temporal Gene Expression in Apical Culms Shows Early Changes in Cell Wall Biosynthesis Genes in Sugarcane

“…We use the same steps for quality control as Correr et al (2020a) . The resulting high quality reads were used for de novo assembly using TRINITY v.2.5.1 ( Grabherr et al, 2011 ) considering the parameters as previously described by Correr et al (2020b) .…”

Temporal Gene Expression in Apical Culms Shows Early Changes in Cell Wall Biosynthesis Genes in Sugarcane

“…We use the same steps for quality control as Correr et al (2020a). The resulting high quality reads were used for de novo assembly using TRINITY v.2.5.1 (Grabherr et al, 2011) considering the parameters as previously described by Correr et al (2020).…”