Comparative de novo transcriptome analysis identifies salinity stress responsive genes and metabolic pathways in sugarcane and its wild relative Erianthus arundinaceus [Retzius] Jeswiet

Sugarcane is an industry-oriented crop grown in the tropics and sub-tropics in the world. Sugarcane is a potential source of basic material for the manufacturing of sugar, ethanol, bioenergy, and biodegradable products. Traditional sweeteners such as jaggery, khandsari, and brown sugars having immense medicinal value are also produced from sugarcane^1,2. Globally, sugarcane was cultivated in 28.19 million hectares which produced 2059.74 million tonnes of canes with a productivity of 72.80 t/ha during 2019³. In India, sugarcane was cultivated in 5.06 million hectares and 405.42 million tonnes was produced with a productivity of 80.10 tonnes/hectare during 2019³. The growth, productivity, and juice quality of sugarcane are affected by abiotic stresses viz., cold, salinity, and drought. Nearly 10% of arable land or 25–30% of irrigated lands were affected by salinity in the world⁴. After the advent of modern agriculture, soil salinity has become a major environmental issue and underground water used for irrigation also contributes to the soil salinity⁵. Sugarcane is highly sensitive to salinity⁶ and affects both biomass accumulation and juice quality parameters⁷. Therefore, the development of saline tolerant varieties, gene pools, and genomic resources are helpful in sugarcane crop improvement through conventional and biotechnological approaches.

The sessile plants are sensing the salinity stress-induced osmotic and ionic stresses through the activation of calcium signalling and salt-overly sensitive pathways for exclusion of sodium^8,9. Glycosyl inositol phosphoryl ceramide sphingolipids are also involved in the sensing of salinity stress¹⁰. The salinity stress firstly reduces the water uptake causing the salinity-induced osmotic stress and secondly, increases the concentration of cytotoxic ions which causes ionic stress^5,10. The plant possesses several mechanisms to tolerate the salinity stress such as (i) accumulation of low molecular weight, water-soluble free state compounds (proline, betaine, water-soluble sugars) which help in the maintenance of osmotic adjustment and plant metabolic activities (ii) selective ion-uptake such as the exclusion of sodium and maintaining higher cytosolic K⁺/Na⁺ (iii) nullifying the effect of ROS by enzymes such as catalase, SOD and APX (iv) salinity-tolerant genes associated with sodium-hydrogen antiporter activities of vacuolar membrane, plasma membrane and, genes related to ROS scavenging enzymes¹¹. Besides, many gene networks related to signal transduction, hormone signalling, biosynthesis of secondary metabolites, amino acids and transporters significantly contribute to the salinity tolerance mechanisms in plants¹². The comparative global gene expression studies are certainly helping to dissect the various genes and metabolic pathways associated with salinity or abiotic stress tolerances in plants¹³.

Sugarcane wild relative E. arundinaceus is a potential donor for many genes related to biomass and tolerance to biotic and abiotic stresses^14,15,16. Introgression of many genes from E. arundinaceus into sugarcane through conventional and biotechnological approaches has improved the agronomic performance of sugarcane varieties^17,18. We have isolated, characterized, and overexpressed many genes from E. arundinaceus such as heat shock protein 70^14,19, DREB2²⁰, glyoxalase gene¹⁵, α-expansin 1²¹ and chilling tolerant divergence 1 (COLD1) gene²², which shows the genetic importance of E. arundinaceus in improving the tolerances to biotic and abiotic stresses in sugarcane. There were several RNASeq studies in sugarcane for many traits such as agronomic traits, cold stress, sucrose, lignin, red stripe and smut disease except for salinity tolerance^{23,24,25,26,27,28}. Hence, we performed the comparative salt transcriptome studies to identify the salinity stress-responsive genes and metabolic pathways in salt-tolerant E. arundinaceus accession IND99-907 collected from saline soils Ernakulum district, Kerala, India²⁹ and salt-sensitive genotype Co 97010^30,31. From this study, we have identified many differentially expressed genes, enriched metabolic pathways and GO terms associated with salt tolerance in salt-tolerant E. arundinaceus accession IND99-907. Our studies showed the enrichment of 27 pathways, 24 biological processes, three molecular functions and one cellular component in IND99-907 as compared to 20 pathways, two biological processes without any significant molecular function and cellular components in Co 97010 (FDR ≤ 0.05), which specifies the unique and distinct expression pattern of genes and metabolic pathways regulating the salinity stress in IND99-907 and Co 97010. The genomic resources developed from this study are useful in sugarcane crop improvement through development of genic markers and advanced biotechnological approaches.