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A total of 85 NAC genes of sugarcane (ScNAC) were retrieved from GRASSIUS (grass regulatory information server). An overview of this gene family is presented including conserved domains, phylogenies, comparative analysis of NAC genes of sugarcane with its closest relative sorghum and with other monocot species. Among the Poaceae family, the NAC genes from sugarcane showed high sequence identity with most of the NAC genes of Sorghum bicolor . A highly conserved two proline residues, a glycine, phenyl alanine and leucine residues are present in N-terminal domain. Conserved amino acid residues and phylogeny helps us to classify the ScNAC gene family into two major groups (Group I and II) and five subgroups (A–E). The analysis of phylogenetic tree of NAC protein sequences of sugarcane with sorghum, rice, maize and Arabidopsis reveals distinct clades with several orthologs and paralogs. A total of 30 pairs of paralogous NAC genes were identified in sugarcane. Based on the orthology, putative stress associated NAC genes were predicted in sugarcane. These stress associated NAC genes of sugarcane and their orthologs from other species were clustered in the phylogenetic tree and shared common motifs, revealing the possibility of functional similarities within this subgroup.

Sugarcane (Saccharum spp. hybrid) contributes to 80% of world sugar production and is a valuable source of biomass for the production of lignocellulosic ethanol making it an important commercial crop. Drought stress is one of the major abiotic stress factors which reduces the productivity and quality of sugarcane. Increase in the intensity and duration of drought coupled with the rising demand of sugar warrants the development of drought-tolerant sugarcane. Genetic engineering offers potential strategies to develop superior sugarcane varieties that improve crop productivity in drought-prone environments. Thus, with a view to develop drought-tolerant sugarcane, in the present study, an expansin gene which confers drought tolerance, was transformed into sugarcane. An expansin gene (EaEXPA1) from Erianthus arundinaceus, a wild relative of sugarcane, was overexpressed in the commercial sugarcane variety Co 86032 through Agrobacterium-mediated transformation. Transgenic lines exhibited significantly higher level of EaEXPA1 expression over the control plants. The performance evaluation of V1 transgenics under the drought stress revealed significantly higher relative water content, cell membrane thermostability, chlorophyll content, photosynthetic efficiency (Fv/Fm) and gas-exchange parameters than untransformed control plants. Here, it is reported for the first time that the overexpression of EaEXPA1 in sugarcane enhances drought tolerance. Thus, EaEXPA1 can be a potential target gene for improving drought tolerance in sugarcane.

Low-temperature (LT) stress is known to restrain sugarcane productivity in sub-tropical regions significantly. Many researchers have prioritized their work towards developing climate-resilient sugarcane varieties incorporating genome of stress-tolerant sugarcane related wild-type species in the pre-breeding programs. However, the lack of genomic resources for wild-type sugarcane limits the identification and utilization of stress-related genes in molecular breeding. In this study, for the first time, we generated ∼182 million RNA-seq paired-end reads for Saccharum spontaneum roots grown under low temperature (10 °C) at different time intervals (0 h, 3 h, 6 h, 12 h, 24 h, and 48 h), to identify LT stress responsive genes and pathways. These data were assembled into 141,409 unigenes and subsequently used to identify 2715 upregulated and 1710 downregulated transcripts under LT stress. Combining evidences from GO enrichment, KEGG pathways, histological studies, biochemical assays, and physiological analysis, our results revealed several key genes and pathways involved in cold acclimatization in the S. spontaneum roots. Transcription profiling of roots during LT stress revealed cold stress sensors (i.e., proline, MDA, calcium-dependent kinase, G-coupled proteins, and histidine kinase) that trigger and activate signal transduction through transcription factors (i.e., MYB, ERF, ARF2, DREB, CAMTA, and C2H2) resulting in upregulation of LT stress responsive genes (i.e, annexin, LEA, germins, LT dehydrins, osmotins, and COR) thereby enhancing cold tolerance. Also, transcriptomic analysis envisaged cold responsive metabolic pathways such as phenylpropanoid and sugar metabolism stimulate the synthesis of flavonoid, sucrose, galactose, raffinose, and fructose, antioxidants, phytohormones, and secondary metabolites, and thus trigger cold-responsive transcriptional regulation. Together, this study provides insights into cold tolerance of wild sugarcane roots to LT stress, thus providing a foundation for developing climate-resilient sugarcane varieties.