Leaf transcriptome profiling of contrasting sugarcane genotypes for drought tolerance under field conditions

Abstract

Drought is the most detrimental abiotic stress to sugarcane production. Nevertheless, transcriptomic analyses remain scarce for field-grown plants. Here we performed comparative transcriptional profiling of two contrasting sugarcane genotypes, 'IACSP97-7065' (drought-sensitive) and 'IACSP94-2094' (drought-tolerant) grown in a drought-prone environment. Physiological parameters and expression profiles were analyzed at 42 (May) and 117 (August) days after the last rainfall. The first sampling was done under mild drought (soil water potential of -60 kPa), while the second one was under severe drought (soil water potential of -75 kPa). Microarray analysis revealed a total of 622 differentially expressed genes in both sugarcane genotypes under mild and severe drought stress, uncovering about 250 exclusive transcripts to 'IACSP94-2094' involved in oxidoreductase activity, transcriptional regulation, metabolism of amino acids, and translation. Interestingly, the enhanced antioxidant system of 'IACSP94-2094' may protect photosystem II from oxidative damage, which partially ensures stable photochemical activity even after 117 days of water shortage. Moreover, the tolerant genotype shows a more extensive set of responsive transcription factors, promoting the fine-tuning of drought-related molecular pathways. These results help elucidate the intrinsic molecular mechanisms of a drought-tolerant sugarcane genotype to cope with ever-changing environments, including prolonged water deficit, and may be useful for plant breeding programs.

Figure 1

Physiological parameters of sugarcane leaves under drought conditions. Drought-sensitive (IACSP97-7065) and -tolerant (IACSP94-2094) sugarcane genotypes were evaluated at 42 (mild drought) and 117 (severe drought) days after the last rainfall and compared with the corresponding controls (irrigated). From the 42nd day after the last rainfall, the soil water potential has progressively reduced from −60 to −75 kPa. (a) Chlorophyll a (Chl a), (b) Chlorophyll b (Chl b), (c) Leaf CO₂ assimilation (P_N), (d) Non-photochemical quenching (NPQ) processes, (e) Potential quantum efficiency of PSII (F_v/F_m), (f) Effective quantum efficiency of PSII (Φ_PSII). Only statistical differences between irrigated vs. drought within the same genotype are shown.

Figure 2

Differentially expressed genes in leaves of contrasting sugarcane genotypes. (a) MA-plot of the microarray experiment. The spots located outside the green line (confidence level set to p = 0.9) indicate differentially expressed genes (DEGs). Venn diagrams represent the DEGs identified as down- and up-regulated in leaves of sugarcane sensitive (IACSP97-7065) and tolerant (IACSP94-2094) genotypes under (b) mild and (c) severe drought stress.

Figure 3

Functional enrichment of differentially expressed genes. Statistically significant enriched GO (Gene Ontology) terms encompassing ‘biological process’ and ‘molecular function’ are represented for the sensitive (IACSP97-7065—red) and tolerant (IACSP94-2094—blue) sugarcane genotypes under (a) mild and (b) severe drought stress (p ≤ 0.05).

Figure 4

Gene expression validation by quantitative real-time PCR (RT-qPCR) analysis. Leaf transcriptional changes are represented as log₂Fold-change (bars) for both sensitive (IACSP97-7065—red) and tolerant (IACSP94-2094—blue) sugarcane genotypes under (a) mild and (b) severe drought stress, compared to the respective irrigated controls. Gene symbol was based on orthology to rice (Oryza sativa). Error bar represents the standard deviation and the asterisk (*) indicates statistical significance (p ≤ 0.05).