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 the variation between these groups may be partly due to the expansion of the Saccharum genomes by differential transposition and defense related genes. 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.

Allele expression biases in mixed-ploid sugarcane accessions

“…Genotypic and transcriptomic information of Saccharum genotypes was used to investigate the expression of different alleles. To characterize expression profiles, we used a set of six genotypes with three replicas each from a previous gene expression study (Correr et al ., 2020) - IN84-58, RB72454, SES205A, SP80-3280, US85-1008 and White Transparent. These genotypes represent two groups of accessions contrasting in key biomass traits - fiber content and tillering capacity.…”

“…Information regarding those genotypes can be found in the supplementary material (Table 1 in Additional File 1). Herein we used as a reference the longest isoforms of a transcriptome assembled de novo using the RNA-Seq reads of the full set of genotypes (Correr et al ., 2020).…”

“…Instead of relying only on genomic information, approaches using transcriptomes have proven useful in investigation of likely cellular functions of putative genes, aiming to obtain molecular markers from functional genomic regions. Thus, analyses of transcriptomic data have made it possible to assess gene expression to compare different organs and developmental stages (Casu et al ., 2007; Mattiello et al ., 2015) and to contrast specific genotypes (Vicentini et al ., 2015) or groups of accessions (Correr et al ., 2020; Kasirajan et al ., 2018).…”