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

Abstract

Multiple genes in sugarcane control sucrose accumulation and the biosynthesis of cell wall components; however, it is unclear how these genes are expressed in its apical culms. To better understand this process, we sequenced mRNA from +1 stem internodes collected from four genotypes with different concentrations of soluble solids. Culms were collected at four different time points, ranging from six to 12-month-old plants. Here we show differentially expressed genes related to sucrose metabolism and cell wall biosynthesis, including genes encoding invertases, sucrose synthase and cellulose synthase. Our results showed increased expression of invertases in IN84-58, the genotype with lower sugar and higher fiber content, as well as delayed expression of secondary cell wall-related cellulose synthase for the other genotypes. Interestingly, genes involved with hormone metabolism were differentially expressed across time points in the three genotypes with higher soluble solids content. A similar result was observed for genes controlling maturation and transition to reproductive stages, possibly a result of selection against flowering in sugarcane breeding programs. These results indicate that carbon partitioning in apical culms of contrasting genotypes is mainly associated with differential cell wall biosynthesis, and may include early modifications for subsequent sucrose accumulation. Co-expression network analysis identified transcription factors related to growth and development, showing a probable time shift for carbon partitioning occurred in 10-month-old plants.

Multiomic insights into sucrose accumulation in sugarcane

“…We employed three biological replicates and three technical replicates. RNA-Seq libraries were prepared and sequencing was performed on the HiSeq 2500 Illumina platform following the protocol described by Hosaka et al (2021).…”

Gene coexpression networks provide deeper insights into sucrose accumulation in sugarcane cultivars

“…Differential expression analyses between contrasting sugarcane genotypes have already provided important inferences for specific sugarcane traits (Correr et al, 2020;Hosaka et al, 2021). Using such an approach, we performed several comparisons among genotypes and tissues with contrasting sugar accumulation, forming a set of DEGs with high potential to be involved in sucrose metabolism, which were then evaluated considering the network structure and the functional modules established.…”

“…All sucrose enzymes described on (b) interact to form UTP-glucose-1-phosphate uridylyltransferase, which catalyzes the interconversion of glucose and fructose, acting as a signal for the production of other nucleotide-sugars and being a primordial glycosyl contributor for polysaccharides biosynthesis (Hosaka et al, 2021;Wang et al, 2019). This enzyme was found in other groups of the network (10,35,115), indicating a putative functional connection of these modules that should be a target for further investigations.…”

“…Plants were grown for 95 days and root samples were collected avoiding tiller roots, as described by Aono et al (2021). For Exp2, in addition to hybrids (SP80-3280, RB72454, RB855156, TUC71-7 and US85-1008), S. officinarum old plants in the field with three replicates (Hosaka et al, 2021). In Exp4, we used hybrid cultivars (SP80-3280 and IACSP93-3046), a S. spontaneum (Krakatau) and a S. officinarum genotype (Badilla De Java).…”

“…In such a network, there is a tendency of transcripts with similar expression patterns to be grouped in a coexpressed network module (Langfelder et al, 2008;Mall et al, 2017b), comprising groups of genes that are functionally cohesive, coregulated or correspond to similar biological pathways (Mitra et al, 2013b). Such network categorization into groups of highly connected network nodes can enable the identification of novel gene associations (Langfelder et al, 2008;Poehlman et al, 2019) which, in sugarcane, has shown promising results Hosaka et al, 2021).…”