Physiological and transcriptional analyses of developmental stages along sugarcane leaf

Abstract

BackgroundSugarcane is one of the major crops worldwide. It is cultivated in over 100 countries on 22 million ha. The complex genetic architecture and the lack of a complete genomic sequence in sugarcane hamper the adoption of molecular approaches to study its physiology and to develop new varieties. Investments on the development of new sugarcane varieties have been made to maximize sucrose yield, a trait dependent on photosynthetic capacity. However, detailed studies on sugarcane leaves are scarce. In this work, we report the first molecular and physiological characterization of events taking place along a leaf developmental gradient in sugarcane.ResultsPhotosynthetic response to CO2 indicated divergence in photosynthetic capacity based on PEPcase activity, corroborated by activity quantification (both in vivo and in vitro) and distinct levels of carbon discrimination on different segments along leaf length. Additionally, leaf segments had contrasting amount of chlorophyll, nitrogen and sugars. RNA-Seq data indicated a plethora of biochemical pathways differentially expressed along the leaf. Some transcription factors families were enriched on each segment and their putative functions corroborate with the distinct developmental stages. Several genes with higher expression in the middle segment, the one with the highest photosynthetic rates, were identified and their role in sugarcane productivity is discussed. Interestingly, sugarcane leaf segments had a different transcriptional behavior compared to previously published data from maize.ConclusionThis is the first report of leaf developmental analysis in sugarcane. Our data on sugarcane is another source of information for further studies aiming to understand and/or improve C4 photosynthesis. The segments used in this work were distinct in their physiological status allowing deeper molecular analysis. Although limited in some aspects, the comparison to maize indicates that all data acquired on one C4 species cannot always be easily extrapolated to other species. However, our data indicates that some transcriptional factors were segment-specific and the sugarcane leaf undergoes through the process of suberizarion, photosynthesis establishment and senescence.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-015-0694-z) contains supplementary material, which is available to authorized users.

Suberin and hemicellulose in sugarcane cell wall architecture and crop digestibility: A biotechnological perspective

“…The largest collection of sugarcane ESTs was generated by the SUCEST project from cDNA libraries of different tissues from several sugarcane varieties (Vettore et al., ) and was important for sugarcane gene discovery, transcript profiling, genome exploration and transcriptome and proteome analysis. Recently, the transcriptome analysis by next‐generation sequencing technology RNA‐seq has furnished important data to identify molecular key intermediaries of cell wall biosynthetic mechanism and of biomass yield and recalcitrance (Mattiello et al., ; Singh et al., ; Vicentini et al., ; Xu et al., ). On the other hand, the genome of sugarcane due to its high polyploidy is extremely complex and has not been completely sequenced or a detailed physical map produced.…”

Peer Review #1 of "The sugarcane mitochondrial genome: assembly, phylogenetics and transcriptomics (v0.1)"

“…In contrast, the SP80-3280 chloroplast was assembled from TruSeq synthetic long reads (Table 1), using our standard assembly pipeline, except for the following changes in Mirabait parameters: -k 32 -n 150. The SP80-3280 chloroplast was also assembled from transcriptomic data (SRA: SRR1979660 and SRR1979664) (Mattiello et al, 2015). Transcriptomic assembly resulted in six contigs covering all the chloroplast apart from the ribosomal RNA region, where there were 26 overlapping contigs.…”

Bulked segregant RNA-Seq reveals differential genes and non-synonymous genetic variants linked to sucrose accumulation in sugarcane

“…Deep sequencing of transcriptome (RNA-seq) has the potential to uncover the causal variations of a desirable trait both at the genic as well as at allelic level. At the genic level, there have been a few reports in sugarcane on differentially expressed genes (DEGs) associated with to sucrose accumulation (De Setta et al 2014;Cardoso-Silva et al, 2014;Thirugnanasambandam et al 2017Thirugnanasambandam et al , 2019, lignin accumulation (Vicentini et al 2015;Kasirajan et al 2018), photosynthesis (Mattiello et al 2015), response to infections from Gluconacetobacter (Vargas et al 2014), and smut pathogen (Wu et al 2013;Que et al 2014;Su et al, 2015;Brigida et al 2016). Recently, Singh et al (2018) investigated the allele specific expressions linked to molecular mechanism behind high biomass accumulation using BSR-Seq of parents, the F1 and 20 F2 clones of sugarcane.…”