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Winter survival develops efficient tolerance mechanisms in plants by regulating cold-responsive and cold-regulated genes at the transcriptional level. Hence, an insight into the expression would provide the molecular function of these cold responsive genes. In this study, an uncharacterized gene encoding a cold-regulated (Cor413) protein identified from Saccharum spontaneum (wild relative species of sugarcane) low-temperature transcriptome with environmental adaptability is isolated and characterized. The full-length coding region possesses an open reading frame of 642 bp, which encodes a putative polypeptide of 213 amino acids of molecular weight 25.6 kDa and an isoelectric point (Pi) of 9.69. The SsCor413 sequence showed a high similarity to monocot Cor413 proteins comprising a WCOR413 domain. Bioinformatics analysis revealed that Cor413 protein has multispanning transmembrane helices along with highly conserved phosphorylation sites. String analysis suggested that SsCor413 is grouped with LEA and Rab proteins that are involved in freezing tolerance. Gene ontology analysis assigned the protein to terms such as “plasma membrane,” “cold acclimation,” and “response to cold.” Sub-cellular localization experiments of sugarcane callus and onion epidermal cells indicated the nuclear localized expression. Quantitative gene expression analysis indicated that the SsCor413 gene is up-regulated in leaf and root tissues of S. spontaneum under low temperature, salinity, and water deficit stress conditions. These results highlight the potential role of SsCor413 in abiotic stress tolerance, and this gene could be a new candidate for combating multiple stresses in sugarcane.

Sugarcane is a C4 and agro-industry-based crop with a high potential for biomass production. It serves as raw material for the production of sugar, ethanol, and electricity. Modern sugarcane varieties are derived from the interspecific and intergeneric hybridization between Saccharum officinarum, Saccharum spontaneum, and other wild relatives. Sugarcane breeding programmes are broadly categorized into germplasm collection and characterization, pre-breeding and genetic base-broadening, and varietal development programmes. The varietal identification through the classic breeding programme requires a minimum of 12–14 years. The precise phenotyping in sugarcane is extremely tedious due to the high propensity of lodging and suckering owing to the influence of environmental factors and crop management practices. This kind of phenotyping requires data from both plant crop and ratoon experiments conducted over locations and seasons. In this review, we explored the feasibility of genomic selection schemes for various breeding programmes in sugarcane. The genetic diversity analysis using genome-wide markers helps in the formation of core set germplasm representing the total genomic diversity present in the Saccharum gene bank. The genome-wide association studies and genomic prediction in the Saccharum gene bank are helpful to identify the complete genomic resources for cane yield, commercial cane sugar, tolerances to biotic and abiotic stresses, and other agronomic traits. The implementation of genomic selection in pre-breeding, genetic base-broadening programmes assist in precise introgression of specific genes and recurrent selection schemes enhance the higher frequency of favorable alleles in the population with a considerable reduction in breeding cycles and population size. The integration of environmental covariates and genomic prediction in multi-environment trials assists in the prediction of varietal performance for different agro-climatic zones. This review also directed its focus on enhancing the genetic gain over time, cost, and resource allocation at various stages of breeding programmes.

Sugarcane (Saccharum spp.) is an important food, fodder and energy crop in India. Its production and productivity are mainly constrained due to water deficit stress during different growth stages. Of the root system architecture traits, deep rooting helps plants to avoid drought-induced stress by foraging moisture from deeper layers of soil. Hence, in this study, a novel drought-responsive DEEPER ROOTING 1 (DRO1) gene cloned from drought-tolerant Erianthus arundinaceus was characterized. The open reading frame of this gene is 765 bp that encodes for a single polypeptide of 254 amino acids. In silico analysis of DRO1 protein using bioinformatics tools revealed its size of 28.91 kDa with theoretical pI 5.39, instability index 67.57, aliphatic index 69.92 and GRAVY of -0.86. Subcellular localization by LocTree3 tool suggested that DRO1 protein expression is localized in the nucleus. The phylogenetic tree exhibited that DRO1 from Erianthus arundinaceus is closely associated with that of Sorghum bicolor and Triticum aestivum. Protein interaction network analysis showed DRO1 association with WOX11, which promotes the development of crown roots and ARL1 (Adventitious rootless1) required for adventitious root formation. Quantitative gene expression analysis indicated that the DRO1 gene is differentially upregulated in root tissue of E. arundinaceus and Saccharum spp. commercial hybrid under water deficit stress conditions. EaDRO1 gene can be a novel source for developing drought stress tolerant genotypes through genetic engineering approach.

In this study, full-length (1282–1330 bp) α-expansin 1 (EXPA1) gene from three different accessions belonging to Saccharum complex (Saccharum officinarum—SoEXPA1, Erianthus arundinaceus—EaEXPA1, and Saccharum spp. hybrid—ShEXPA1) was isolated using RAGE technique and characterized. The intronic and coding regions of isolated expansin genes ranged between 526–568 and 756–762 bp, respectively. An open reading frame encoding a polypeptide of 252 amino acids was obtained from S. officinarum and commercial sugarcane hybrid, whereas 254 amino acids were obtained in E. arundinaceus, a wild relative of Saccharum. Bioinformatics analysis of deduced protein revealed the presence of specific signature sequences and conserved amino acid residues crucial for the functioning of the protein. The predicted physicochemical characterization showed that the protein is stable in nature with instability index (II) value less than 40 and also clearly shown the dominance of random coil in the protein structure. Phylogenetic analysis revealed high conservation of EXPA1 among Saccharum complex and related crop species, Sorghum bicolor and Zea mays. The docking study of EXPA1 protein showed the interaction with xylose, which is present in xyloglucan of plant cell wall, elucidated the role of the expansin proteins in plant cell wall modification. This was further supported by the subcellular localization experiment in which it is clearly seen that the expansin protein localizes in the cell wall. Relative expression analysis of EXPA1 gene in Saccharum complex during drought stress showed high expression of the EaEXPA1 in comparison with SoEXPA1 and ShEXPA1 indicating possible role of EaEXPA1 in increased water-deficit stress tolerance in E. arundinaceus. These results suggest the potential use of EXPA1 for increasing the water-deficient stress tolerance levels in crop plants.

The use of plants for the production of plant-made pharmaceuticals (PMPs), plant-made vaccines (PMVs) and plant-made substances of industrial interests through transgenic approach is the sole objective of plant molecular (PM) farming, and it holds great promises in the plant industry. PM farming is advantageous in terms of saving production costs, large-scale production of drugs, animal and human virus-free products, easier storage and transportation of drugs and oral applicability (e.g. edible vaccines). Plant system also offers different platforms, viz. seed-, leaf-, stem-, root- and whole plant-based production in transgenic lines. The other systems such as bacterial, microbial eukaryotes, mammalian cells, insect cells and transgenic animals are expensive. Therefore, transgenic plants have been the subject of considerable attention as new generation bioreactors with respect to their advantages, such as the safety of recombinant proteins (antibodies, enzymes, vaccines, growth factors, etc.) and their potential for the large-scale and low-cost production. However, some of the key challenges that PM farming is facing include technical, economic, safety and regulatory as well as public acceptance. This chapter discusses in detail the challenges in obtaining products from transgenic plants such as expression of the recombinant proteins, downstream processing and purification, glycosylation, regulatory challenges and environmental risks.

Prospecting for potential novel Bacillus thuringiensis with new holotype crystal toxins was carried out in the Western ghats hill range of Karnataka state, India. From the soil samples collected three Bt isolates SBIKWG 12, SBIKWG 24 and SBIKWG 70 were isolated. Of these while the two isolates, namely SBIKWG 12 and SBIKWG 24 produced bipyramidal crystal toxins, the third isolate produced spherical crystal. PCR screening of the isolates revealed the presence of lepidopteran and coleopteran active cry genes. Partial sequences obtained from these isolates revealed the presence of multiple crystal toxin genes. BlastX analysis of the partial gene sequences indicated the potential for the occurrence of new holotype crystal toxin genes in SBIKWG 24 and SBIKWG 70.

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.

In this study, full-length (1282–1330 bp) α-expansin 1 (EXPA1) gene from three different accessions belonging to Saccharum complex (Saccharum officinarum—SoEXPA1, Erianthus arundinaceus—EaEXPA1, and Saccharum spp. hybrid—ShEXPA1) was isolated using RAGE technique and characterized. The intronic and coding regions of isolated expansin genes ranged between 526–568 and 756–762 bp, respectively. An open reading frame encoding a polypeptide of 252 amino acids was obtained from S. officinarum and commercial sugarcane hybrid, whereas 254 amino acids were obtained in E. arundinaceus, a wild relative of Saccharum. Bioinformatics analysis of deduced protein revealed the presence of specific signature sequences and conserved amino acid residues crucial for the functioning of the protein. The predicted physicochemical characterization showed that the protein is stable in nature with instability index (II) value less than 40 and also clearly shown the dominance of random coil in the protein structure. Phylogenetic analysis revealed high conservation of EXPA1 among Saccharum complex and related crop species, Sorghum bicolor and Zea mays. The docking study of EXPA1 protein showed the interaction with xylose, which is present in xyloglucan of plant cell wall, elucidated the role of the expansin proteins in plant cell wall modification. This was further supported by the subcellular localization experiment in which it is clearly seen that the expansin protein localizes in the cell wall. Relative expression analysis of EXPA1 gene in Saccharum complex during drought stress showed high expression of the EaEXPA1 in comparison with SoEXPA1 and ShEXPA1 indicating possible role of EaEXPA1 in increased water-deficit stress tolerance in E. arundinaceus. These results suggest the potential use of EXPA1 for increasing the water-deficient stress tolerance levels in crop plants. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s13205-019-1719-3) contains supplementary material, which is available to authorized users.

Sugarcane is a C4 grass grown in tropical and subtropical regions, cultivated in 22 million hectares in more than 100 countries (FAOSTAT 2008, http://faostatfaoorg/defaultaspx). Major sugar requirement of the world is met by sugarcane. It contributes almost 75% of total sugar produced from all the sugar crops. Sugarcane is also used for generation of biofuel and bagasse as lignocellulosic raw material for paper industries. Sucrose content and cane weight are the key traits determining the income of sugarcane farmers and industries. In general, sugarcane varieties in cultivation are capable to accumulate higher sucrose in the stems to levels more than 50% of the stem dry weight. Ability of sugarcane to produce and store higher concentration of sucrose in the mature internodes has made the crop more suitable for commercial sucrose extraction. In this chapter, we reviewed the work carried out by various sugarcane researchers around the world on sugarcane biotechnology in relation to sucrose enhancement using various molecular approaches and technologies.