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Sugarcane cultivation in India dates back to 5000 BC, but its genetic improvement through breeding commenced only in the nineteenth century. A major breakthrough in yield improvement happened in 1918 with the release of the first interspecific hybrid cultivar Co 205. This cultivar replaced all earlier varieties and made interspecific hybrids the basis of future sugarcane improvement. The tri-specific hybrids {(S. officinarum × S. spontaneum) × S. barberi} developed at Indian Council of Agriculture Research-Sugarcane Breeding Institute (ICAR-SBI) as Coimbatore canes (Co canes) were popular in India and in several other countries as varieties or parents. Improved sugarcane varieties have made a major contribution in increasing yield from 30.9 t/ha in 1930 to 79.6 t/ha during 2018–2019 and sugar recovery from 8.96% to 11.01% in the same period. A national network of sugarcane varietal improvement programme involving 24 sugarcane centres covering the entire country now operates. This program is based on seedlings derived from an annual crossing program at the National Hybridization Garden at ICAR-SBI, Coimbatore. Varietal testing is conducted by 36 centres and has identified 124 varieties through All India Coordinated Research Programme (Sugarcane) for five agroclimatic zones in the country since 1982. During 2000 to 2019, 67 varieties were released for commercial cultivation. Among the present varieties, Co 0238, cultivated on 2.77 Mha, and Co 86032, on 0.89 Mha are the two predominant varieties in India. The pace of varietal improvement has remained high through studies on breeding and selection methodologies, expanding the genetic base and genetic diversity of parental pools for nuclear and cytoplasmic genes and targeted genetic improvement of important traits. This has improved precision and efficiency of breeding. Micropropagation has been a success for rapid multiplication and accelerated adoption of new varieties. Genetic improvement of sugarcane through conventional breeding is increasingly complemented by molecular research to improve biotic and abiotic stress tolerance, specifically for red rot and drought, and biomass, to make sugarcane a major source of both a sugar and renewable energy.

Red rot caused by the fungus Colletotrichum falcatum is the main disease limiting sugarcane productivity in several countries including the major producer India. The genetic basis for red rot resistance is unclear. We studied a panel of 305 sugarcane clones from the Australian breeding program for disease response phenotype and genotype using an Affymetrix® Axiom® array, to better understand the genetic basis of red rot resistance. SNP markers highly significantly associated with red rot response (≤ 10-8) were identified. Markers with largest effect were located in a single 14.6 Mb genomic region of sorghum (the closest diploid relative of sugarcane with a sequenced genome) suggesting the presence of a major-effect QTL. By genomic selection, the estimated selection accuracy was ~0.42 for red rot resistance. This was increased to ~0.5 with the addition of 29 highly significant SNPs as fixed effects. Analysis of genes nearby the markers linked to the QTL revealed many biotic stress responsive genes within this QTL, with the most significant SNP co-locating with a cluster of four chitinase A genes. The SNP markers identified here could be used to predict red rot resistance with high accuracy at any stage in the sugarcane breeding program.

The glyoxalase pathway is a check point to monitor the elevation of methylglyoxal (MG) level in plants and is mediated by glyoxalase I (Gly I) and glyoxalase II (Gly II) enzymes in the presence of glutathione. Recent studies established the presence of unique DJ-1/PfpI domain containing protein named glyoxalase III (Gly III) in prokaryotes, involved in the detoxification of MG into D-lactic acid through a single step process. In the present study, eleven transgenic sugarcane events overexpressing EaGly III were assessed for salinity stress (100 mM and 200 mM NaCl) tolerance. Lipid peroxidation as well as cell membrane injury remained very minimal in all the transgenic events indicating reduced oxidative damage. Transgenic events exhibited significantly higher plant water status, gas exchange parameters, chlorophyll, carotenoid, and proline content, total soluble sugars, SOD and POD activity compared to wild type (WT) under salinity stress. Histological studies by taking the cross section showed a highly stable root system in transgenic events upon exposure to salinity stress. Results of the present study indicate that transgenic sugarcane events overexpressing EaGly III performed well and exhibited improved salinity stress tolerance.

A field experiment was conducted to investigate the effect of water stress on early and mid-late categories of Co-canes, i.e., [Co 98014, Co 0118, Co 0238, Co 07023, Co 15023 (early) and Co 0124, Co 05011, Co 11027, Co 15027, Co 12029 (mid-late)]. The experiment consists of stress treatments in main plot, i.e. (control and water stress) and ten Co-canes in subplot were laid out in factorial randomized block design with three replications. The water stress was imposed by withholding irrigation during formative phase. The observations recorded on morphological, physiological and yield attributes have suggested possible key characteristics of water stress tolerance. Leaf area and cane length exhibited 37.3% and 26.53% reduction under drought condition in comparison to the control. Co 05011 (78.77%) and Co 0238 (76.88%) showed/maintained better RWC under stress condition with mean reduction of 16.70% over Co-canes RWC. Water stress also caused reduction in gas exchange traits and the associated pigments by 56.57% in stomatal conductance (gS), 56.55% in photosynthetic rate (pN), 38.21% in transpiration rate (E), 28.01% in internal CO2 (Ci) and 16.86% in the chlorophyll content. Maximum water use efficiency (pN/E) under drought stress was recorded in Co 0238 (4.12) and Co 98014 (3.93). Total number of tillers, number of millable canes, single cane weight and cane yield were also reduced under water stress but Co 98014, Co 05011, Co 0238, Co 12029 and Co 15023 showed lesser reduction in these traits. Further, the cane yield data were subjected to different drought tolerance indices viz. stress susceptibility index, stress tolerance index and yield index. Results obtained from physiological and yield attributes as well as tolerance indices indicated that Co 98014, Co 05011, Co 0238 and Co 12029 had the potential to grow well under water stress conditions for sustaining sugarcane production and hence could be used as tolerant germplasm in crop improvement programs.

Drought is one of the most important environmental constraints limiting sugarcane (Saccharum spp.) production worldwide. It is estimated that nearly 60% of the total sugarcane area suffers from water stress. Using the important physiological markers, drought tolerance potential of elite sugarcane clones is evaluated every year at ICAR-Sugarcane Breeding Institute, Coimbatore to identify those suitable for cultivation in drought prone areas of India. The present study is the field evaluation of six sugarcane clones in the advanced varietal trial conducted during the year 2018–2019, wherein the relevance of physiological traits conferring adaptive tolerance to drought is reinstated. In the formative phase, drought stress resulted in an average reduction of 20.5, 36.5, 22.1, 5.9 and 4.7 per cent in shoot population, plant height, leaf area index, SPAD chlorophyll index and photochemical efficiency (Fv/Fm) respectively. However, the clones Co 12009 and Co 12012 showed relatively better growth attributes both under control and drought stress which were on par with the resistant standards Co 86032 and Co 99004. Drought induced 12.6, 15.7, 23.5 and 32.9% reduction in internodal length, cane height, single cane weight and cane yield, however the clones Co 12009 and Co 12012 recorded comparatively higher cane yield of 86.6 and 94.1 tonnes/ha under drought condition, respectively. The clones Co 12009 and Co 12012 were rated as tolerant due to their ability to sustain cane yield and juice quality potential under drought stress, which might be attributed to retaining superior morphological and physiological traits.

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.

This investigation aimed to optimize the time, pH, pressure, and temperature of sugarcane juice pasteurization and to develop a “ready to serve” bottled sugarcane juice with a high preservation efficiency. Fresh sugarcane juice was extracted from sugarcane genotype Co 89003, and beverage samples were collected using three different treatments: sulphitation of juice with the addition of potassium metabisulphite (KMS-25, 50, 100, and 150 ppm), acidification of juice (addition of citric acid, to reduce the pH of the juice to 4.8, 4.5, and 4.25), and steam treatment of the canes (5 min, 10, and 15 min at 7 psi). In all treatments, the juice was pasteurized in glass bottles @ 65 °C for 25 min and stored at low temperature (5 °C) in pre-sterilized glass bottles. Juice properties such as the ˚Brix, total sugar, pH, and total phenolic content decreased with storage, whereas the microbial count, titrable acidity, and reducing sugar content significantly increased during storage. The addition of KMS, citric acid, and the steam treatment reduced the browning of juice and maintained the color of juice during storage, by inhibiting the polyphenol oxidase enzyme activity, from 0.571 unit/mL to 0.1 unit/mL. Among the selected treatments, sugarcane juice with KMS (100 and 150 ppm) and steam treatment of the canes for 5 and 10 min at 7 psi showed the minimum changes in physico-chemical properties, sensory qualities, and restricted microbial growth. Thesulphitation treatment with pasteurization proved best for increasing the shelf life of sugarcane juice upto 90 days with refrigeration. Similarly, the steam-subjected cane juice (10 and 15 min at 7 psi) could be effectively preserved for upto 30 days with refrigeration, without any preservative.

The low temperature (LT) conditions that prevail during winter in subtropical regions of India drastically affect the growth and yield of sugarcane. To identify low-temperature-tolerant agronomical acceptable genotypes for immediate deployment as donor parents in the subtropical sugarcane breeding program, 34 sugarcane clones belonging to 7 genetically diverse groups were evaluated under three crop environments, viz., spring planting, winter ratoon and spring ratoon, during 2015–2016 and 2016–2017. In the winter ratoon crop, commercial cane sugar and cane yield were reduced, whereas sucrose % was increased over the spring planted crop and the spring ratoon crop. The wild species and introgressed hybrid groups showed improvement for yield and quality traits in the winter ratoon crop, whereas commercial and near commercial groups showed reduction for these traits over the plant and spring ratoon crops. The tropical cultivars group was the poorest performer irrespective of the traits and crops. Yield per se under a stress environment was adjudged as the best selection criteria. For classification of sugarcane clones according to their low temperature tolerance, an index named winter tolerance index (WTI) is proposed which takes into account the winter sprouting index (WSI), winter growth and yield per se of the winter ratoon crop. The WTI had significant positive association with WSI, cane yield, millable cane population and cane length. As per the WTI ratings, the wild species of Saccharum complex and introgressed hybrid groups were rated as excellent WT clones. Subtropical commercial or advanced generation groups were poor WT clones, and tropical commercial cultivars group were winter sensitive clones. Clones such as AS04-635, AS04-1687, IK76-48, GU07-2276, IND00-1040, IND00-1038 and IND00-1039 had excellent tolerance, and GU07-3849, AS04-245, Co 0238, AS04-2097 and GU07-3774 had good WTI scores. The variety, Co 0238, may be continued for cultivation under LT regions with prophylactic measurers for red rot, while other clones listed above may be utilized in subtropical breeding programs.

Sugarcane transgenic overexpressing EaGly III from Erianthus arundinaceus showed enhanced water deficit stress tolerance. Methylglyoxal (MG), an α-ketoaldehyde formed from either glycolysis or TCA cycle, is capable of causing total cellular damage via the generation of reactive oxygen species (ROS), advanced glycation end products (AGEs) and nucleic acid degradation. Glyoxalase pathway is a ubiquitous pathway known for detoxification of MG, involving key enzymes glyoxalase I (Gly I) and glyoxalase II (Gly II). Recently, a novel and an additional enzyme in glyoxalase pathway, viz., glyoxalase III (Gly III), has been discovered which possesses DJ-1/PfpI domain recognized for detoxifying MG in a single step process without requirement of any coenzyme. In the present study, a Gly III gene isolated from Erianthus arundinaceus, a wild relative of sugarcane, overexpressed in commercially cultivated sugarcane hybrid Co 86032 was assessed for drought tolerance. Morphometric observations revealed that transgenic sugarcane overexpressing EaGly III acquired drought tolerance trait. Oxidative damage caused by triggering generation of ROS has been determined to be low in transgenic plants as compared to wild type (WT). Transgenics resulted in higher relative water content, chlorophyll content, gas exchange parameters, photosynthetic efficiency, proline content and soluble sugars upon water deficit stress. In addition, higher and stable level of superoxide dismutase and peroxidase activities were observed along with minimal lipid peroxidation during drought stress signifying the tolerance mechanism exhibited by transgenic events. There was no significant structural change observed in the root anatomy of transgenic plants. Altogether, EaGly III gene could be considered as a potential candidate for conferring water deficit stress tolerance for sugarcane and other agricultural crops.

Plant nuclear factor (NF-Y) is a transcription activating factor, consisting of three subunits, and plays a key regulatory role in many stress-responsive mechanisms including drought and salinity stresses. NF-Ys function both as complex and individual subunits. Considering the importance of sugarcane as a commercial crop with high socio-economic importance and the crop being affected mostly by water deficit stress and salinity stress causing significant yield loss, nuclear transcriptional factor NF-YB2 was focused in this study. Plant nuclear factor subunit B2 from Erianthus arundinaceus (EaNF-YB2), a wild relative of sugarcane which is known for its drought and salinity stress tolerance, and commercial Saccharum hybrid Co 86032 (ShNF-YB2) was isolated and characterized. Both EaNF-YB2 and ShNF-YB2 genes are 543 bp long that encodes for a polypeptide of 180 amino acid residues. Comparison of EaNF-YB2 and ShNF-YB2 gene sequences revealed nucleotide substitutions at nine positions corresponding to three synonymous and six nonsynonymous amino acid substitutions that resulted in variations in physiochemical properties. However, multiple sequence alignment (MSA) of NF-YB2 proteins showed conservation of functionally important amino acid residues. In silico analysis revealed NF-YB2 to be a hydrophilic and intracellular protein, and EaNF-YB2 is thermally more stable than that of ShNF-YB2. Phylogenetic analysis suggested the lower rate of evolution of NF-YB2. Subcellular localization in sugarcane callus revealed NF-YB2 localization at nucleus that further evidenced it to be a transcription activation factor. Comparative RT-qPCR experiments showed a significantly higher level of NF-YB2 expression in E. arundinaceus when compared to that in the commercial Saccharum hybrid Co 86032 under drought and salinity stresses. Hence, EaNF-YB2 could be an ideal candidate gene, and its overexpression in sugarcane through genetic engineering approach might enhance tolerance to drought and salinity stresses.

Plant nuclear factor (NF-Y) is a transcription activating factor, consisting of three subunits, and plays a key regulatory role in many stress-responsive mechanisms including drought and salinity stresses. NF-Ys function both as complex and individual subunits. Considering the importance of sugarcane as a commercial crop with high socio-economic importance and the crop being affected mostly by water deficit stress and salinity stress causing significant yield loss, nuclear transcriptional factor NF-YB2 was focused in this study. Plant nuclear factor subunit B2 from Erianthus arundinaceus (EaNF-YB2), a wild relative of sugarcane which is known for its drought and salinity stress tolerance, and commercial Saccharum hybrid Co 86032 (ShNF-YB2) was isolated and characterized. Both EaNF-YB2 and ShNF-YB2 genes are 543 bp long that encodes for a polypeptide of 180 amino acid residues. Comparison of EaNF-YB2 and ShNF-YB2 gene sequences revealed nucleotide substitutions at nine positions corresponding to three synonymous and six nonsynonymous amino acid substitutions that resulted in variations in physiochemical properties. However, multiple sequence alignment (MSA) of NF-YB2 proteins showed conservation of functionally important amino acid residues. In silico analysis revealed NF-YB2 to be a hydrophilic and intracellular protein, and EaNF-YB2 is thermally more stable than that of ShNF-YB2. Phylogenetic analysis suggested the lower rate of evolution of NF-YB2. Subcellular localization in sugarcane callus revealed NF-YB2 localization at nucleus that further evidenced it to be a transcription activation factor. Comparative RT-qPCR experiments showed a significantly higher level of NF-YB2 expression in E. arundinaceus when compared to that in the commercial Saccharum hybrid Co 86032 under drought and salinity stresses. Hence, EaNF-YB2 could be an ideal candidate gene, and its overexpression in sugarcane through genetic engineering approach might enhance tolerance to drought and salinity stresses. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s13205-020-02295-1) contains supplementary material, which is available to authorized users.

Sugarcane (Saccharum spp.) crop is vulnerable to many abiotic stresses such as drought, salinity, waterlogging, cold and high temperature due to climate change. Over the past few decades new breeding and genomic approaches have been used to enhance the genotypic performance under abiotic stress conditions. In sugarcane, introgression of genes from wild species and allied genera for abiotic stress tolerance traits plays a significant role in the development of several stress-tolerant varieties. Moreover, the genomics and transcriptomics approaches have helped to elucidate the key genes/TFs and pathways involved in abiotic stress tolerance in sugarcane. Several novel miRNAs families /proteins or regulatory elements that are responsible for drought, salinity, and cold tolerance have been identified through high-throughput sequencing. The existing sugarcane monoploid genome sequence information opens new gateways and opportunities for researchers to improve the desired traits through efficient genome editing tools, such as the clustered regularly interspaced short palindromic repeat-Cas (CRISPR/Cas) system. TALEN mediated mutations in a highly conserved region of the caffeic acid O-methyltransferase (COMT) of sugarcane significantly reduces the lignin content in the cell wall which is amenable for biofuel production from lignocellulosic biomass. In this review, we focus on current breeding with genomic approaches and their substantial role in enhancing cane production under the abiotic stress conditions, which is expected to provide new insights to plant breeders and biotechnologists to modify their strategy in developing stress-tolerant sugarcane varieties, which can highlight the future demand of cane, bio-energy, and viability of sugar industries.

The whole world adores sugars and sweeteners, yet many people wonder whether eating of sugars affects the human health. The science of sugar has elaborately studied and lot of research was done to know about myth and reality of sugar consumption. Misperception prevails on glucose and fructose-containing sweeteners and therefore, doubts related to metabolic properties of simple sugars and confusion related to various definitions for mentioning added sugar need to be clarified. General belief on sugar and components weakens the nutrient availability of diet is inconclusive. The sugar uptake up to 25% of the total caloric need is accepted by the US dietic association. A food safety guideline of Europe says that vouched patterns of food intake are more important than fixing maximum limit for consumption. The relation between sugar intake and obesity is debatable. The research findings argue that magnitude of the glycaemic index does not correlate with body weight and basically, added sugars alone are not responsible for increase in body mass index. Generally, well-being groups, health experts and dieticians divided in their views on intake of sweeteners and beverages as integral portion of their stable food for a longevity and healthy lifestyle. Therefore, the conflicting views and findings regarding sugar and health profile need to be further explored. It is expected that new researches shall further explore the effects of sugar on human health and answer the important queries held around health value of sugars.

The study analyses the extent, pattern and degree of spatial integration of sugar markets in India, as well as relationship of white sugar export prices of India and global market. The pattern and degree of integration were assessed by testing for the existence of the law of one price (LOOP) and ascertaining the speed of adjustment towards long-run equilibrium, using various tests by using cointegrated methods. Results indicated that only 4 of 11 sugar markets are cointegrated. The supply of sugar appears to be the most important factor shaping the long-run behaviour of its price levels in India. No single market is found to be the price leader. The prices of sugar exported by India to the global market were not cointegrated and did not conform to LOOP. Decontrolling of sugar sector from the clutches of monthly release mechanism plays an insignificant role in determining the relationship of sugar prices in the global market. The study suggests sugar policy reforms, consistent export and import strategies and abolition of export quota are absolutely essential for market integration and convergence of prices in the domestic and global market.

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 important commercial crop of India. Both saline and sodic soils also contribute significantly in affecting cane yield and sugar recovery. In view of this, Effort was made to screen 32 genotypes of sugarcane of diverse genetic background against soil salinity at Nain farm, Panipat. (CSSRI, Karnal) during 2015-16. The soil salinity of the experimental area varies greatly from 2.25 dSm-1 to 29.04 dSm-1 at different crop intervals. Under this experiment, 9 entries were planted under various levels of electrical conductivity. Based on the performance of these entries, an experiment was planted for further evaluation at ICAR-SBI-RC, Karnal under four salinity level of irrigation waters viz., Normal, 4 EC.iw: 4 dSm-1, EC.iw: 8 dSm-1 and EC.iw: 12 dSm-1 Five clones were identified as tolerant and six clones were moderately tolerant whereas Six genotypes were found highly sensitive clones. These tolerant and moderately tolerant clones may be utilized in breeding programme towards development of salinity tolerant 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.

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.

Table S2. RT-PCR primers for the amplification of different isoforms of Glyoxalase I and II from E. arundinaceus and commercial sugarcane hybrid. (DOCX 13 kb)

Table S1. Verify3D showing the percentage of residues that had an average score of >â 0.2 and evaluation of the predicted modelled structures of glyoxalase proteins. A score over 0.2 residues is considered as reliable and those displaying lower scores are of loops. ERRAT analysis of glyoxalase I (A), glyoxalase II (B) and glyoxalase III (C) had also shown good scores on overall quality factor for both E. arundinaceus and commercial sugarcane hybrid. (DOCX 12 kb)

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.

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.

Twenty elite sugarcane Co canes were tested in mutlilocation trials at 10 locations of Tamil Nadu under Institute-Industry collaborative programme. These genotypes were evaluated under randomized block design with three replications; yield and quality contributing parameters were recorded at 240, 300 and 360 days after planting. Analysis revealed the superiority of Co 13001 for early sucrose accumulation potential at 240 days and Co 14016 for good ratoonability potential with high cane yield through increased millable cane population.

A DETAILED DESCRIPTION OF Co 12029 (KARAN 13): A NEW MIDLATE SUGARCANE VARIETY RELEASED FOR COMMERCIAL CULTIVATION IN NORTH WEST ZONE OF INDIA

The information and communication support for sugarcane crop has been mainly conventional with limited personalized extension services to reach all the cane growers spread across the country. The diversity of agro ecological situations, varied technologies recommended and needs of sugarcane farmers further mount to this challenge. Information and Communication Technology and in particular mobile technologies are seen as a game changer in agriculture. It is commanding therefore for the sugarcane technology dissemination system operating across the states, to shift from being predominantly traditional, to harness the potentialities of information technology bridging the barriers of time and space. Keeping this in view, the ICAR-Sugarcane Breeding Institute of the Indian Council of Agricultural Research, has developed an interactive androidbased mobile app, Cane Adviser to serve to the needs of the stakeholders in sugarcane cultivation. The paper explains how Cane Adviser was developed methodically taking into account the information needs of the target audience, deciding the various modules to be embedded in the app and how it was evaluated before hosting in google play store. Explaining the various particulars of the mobile app, the paper details the role of Cane Adviser in disseminating sugarcane technologies and timely delivery of information tailor-made to the cane growers and cane development personnel so as to get enhanced cane productivity

Morphological Characterization for four candidate varieties i.e. Co 0238, Co 0118, Co 0237 and Co 05011 was done using National Test Guideline for DUS testing on sugarcane. Observations on 27 DUS descriptors were recorded as per the guideline developed by task force constituted by PPV and FR Authority. During the year 2012-13 and 2013-14 candidate variety Co 0238 and Co 0118 were tested along with the nine reference varieties. It was found that both the varieties were distinct, uniform and stable with respect to the reference collection. Similarly, candidate varieties Co 05011 and Co 0237 were also tested along with eight reference varieties and found distinct, uniform and the population of these varieties were also stable. Therefore, DUS testing of these varieties qualify the criteria for registration into new varieties under PPV and FR Act.

Sugarcane (Saccharum sp.) is predominantly grown in both tropics and subtropics in India, and the subtropics alone contribute more than half of sugarcane production. Sugarcane active growth period in subtropics is restricted to 8–9 months mainly due to winter’s low temperature stress prevailing during November to February every year. Being a commercial crop, tolerance to low temperature is important in sugarcane improvement programs. Development of cold tolerant sugarcane varieties require a deep knowledge on molecular mechanism naturally adapted by cold tolerant genotypes during low temperature stress. To understand gene regulation under low temperature stress, control and stressed (10 °C, 24 h) leaf samples of cold tolerant S. spontaneum IND 00-1037 collected from high altitude region in Arunachal Pradesh were used for transcriptome analysis using the Illumina NextSeq 500 platform with paired-end sequencing method. Raw reads of 5.1 GB (control) and 5.3 GB (stressed) obtained were assembled using trinity and annotated with UNIPROT, KEGG, GO, COG and SUCEST databases, and transcriptome was validated using qRT-PCR. The differential gene expression (DGE) analysis showed that 2583 genes were upregulated and 3302 genes were down-regulated upon low temperature stress. A total of 170 cold responsive transcriptional factors belonging to 30 families were differentially regulated. CBF6 (C-binding factor), a DNA binding transcriptional activation protein associated with cold acclimation and freezing tolerance was differentially upregulated. Many low temperature responsive genes involved in various metabolic pathways, viz. cold sensing through membrane fluidity, calcium and lipid signaling genes, MAP kinases, phytohormone signaling and biosynthetic genes, antioxidative enzymes, membrane and cellular stabilizing genes, genes involved in biosynthesis of polyunsaturated fatty acids, chaperones, LEA proteins, soluble sugars, osmoprotectants, lignin and pectin biosynthetic genes were also differentially upregulated. Potential cold responsive genes and transcriptional factors involved in cold tolerance mechanism in cold tolerant S. spontaneum IND 00-1037 were identified. Together, this study provides insights into the cold tolerance to low temperature stress in S. spontaneum, thus opening applications in the genetic improvement of cold stress tolerance in sugarcane. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s13205-018-1194-2) contains supplementary material, which is available to authorized users.

Production of recombinant proteins in plants is referred to as molecular farming. Plant-based production of pharmaceutical and nonpharmaceutical products is gaining momentum around the world. Many plant species have become a promising alternative over the traditional expression systems to produce a variety of valuable or high-value bioltableogical molecules of pharmaceutical and nonpharmaceutical products. Plants are preferred as a platform for production of recombinant proteins because of the low costs and greater scalability of plant production systems without incurring the high costs associated with downstream processing and purification. Of the plant systems, sugarcane represents an ideal candidate for biofactory applications due to its large biomass, rapid growth rate, efficient carbon fixation pathway, a well-developed storage tissue system, minimal transgene dispersal due to vegetative method of propagation, high quantity of extractable juice with very low protein content (0.01–0.02%), and a well-established downstream processing technology. The unique aspect of sugarcane is the extraction of large juice volume (700 mL) by crushing 1 kg of cane. Therefore, sugarcane is possibly an efficient platform for molecular farming.

Sugarcane is an important commercial crop belonging to Poaceae family and is a major source of sucrose and ethanol production worldwide. Sugarcane’s large genome size, aneuploidy of commercial cultivars, and polyploidy of interspecific hybrids have always imposed a challenge for generation of genomic and transcriptomics resources for crop improvement. Despite of these hurdles, linkage maps based on different segregating populations has been constructed. Efforts to map QTLs controlling various traits are being carried out and map-based cloning has also been tried. Available EST data can now be used for SNP mining, expression profiling, discovering new genes, etc. The comparative analysis of sugarcane and sorghum genome revealed high similarity between the two genomes. This information will further expedite sugarcane improvement initiatives. The advent of high-throughput sequencing technologies such as Roche/454 and Illumina/Solexa is being used to gain knowledge on transcriptome of the cell under different stress conditions. RNA-seq can provide the sequences of all RNA molecules, including mRNA, rRNA, tRNA, and noncoding RNAs, produced in one or a population of cells. The data generated can be used to measure transcript levels, to find novel genes, fusion transcript, and splice junctions. Knowledge of the sugarcane transcriptome can provide information about synthesis of various biomolecules and their interactions with other metabolic pathways in the complex sugarcane genome. Both genomic and transcriptome resources of sugarcane are immensely important for improving yield as well as quality of sugarcane; this will help sugarcane farming community to a great extent.

Genomic constitution of commercially cultivated sugarcane varieties over the world is derived from few basic species clones of Saccharum complex. In order to impart new cytoplasmic and nuclear genome in sugarcane hybrids, untapped wild species of Saccharum spontaneum (S), Erianthus arundinaceus (E) and E. bengalense (Eb) were utilized to produce different combinations i.e., E. arundinaceus x S. spontaneum (ES), S. spontaneum x E. arundinaceus (SE) and S. spontaneum x E. bengalense (SEb) intergeneric hybrids (H). Subsequently, these resulting hybrids were repeatedly used as pistil parent and crossed with commercial sugarcane varieties as pollen parent for three (G3) to four (G4) generations to produce an array of advanced generation hybrids. Twenty six such advanced generation hybrids (G3 and G4) derived were evaluated for quality and yield contributing traits at 300 and 360 days after planting during 2010–2011 and 11–12 in augmented block design along with standard sugarcane varieties. The presence of E. arundinaceus cytoplasmic DNA was validated in intergeneric hybrids by PCR–RFLP of the amplified chloroplast DNA for psbC-trnS. Performance of ESH G3 and SEH G4 hybrids were comparable and some E. arundinaceus cytoplasm introgressed hybrids performed on par with standard varieties for yield and quality traits. Few intergeneric hybrids exhibited wider acclimatization in diverse agro-climatic conditions. Some of these intergeneric hybrids have potential for commercial cultivation and their utilization in breeding programme could help in broadening the genetic base and also for wider adaptability of future sugarcane varieties.

Sunburn injury on sugarcane leaves is an abiotic disorder caused by high temperature combined with hot waves during summer. The natural incidence of sunburn injury at Karnal (Haryana, India) was recorded in subtropical sugarcane varieties from 2010 to 2013. The sunburn severity index was higher during the year 2010 and 2012. In sunburn affected plants, the injury appeared initially near the apex of newly unfurled leaf and then progressed towards the middle of leaf lamina. The affected leaf lamina remained pale green for 2–3 days and then parched. The relative water content and chlorophyll content were reduced substantially in the sunburn affected leaves. In subtropical States of India, sunburn injury is expected to occur during 3rd or 4th week of May provided if the maximum air temperature is above 39 °C and if there is no precipitation during two preceding and succeeding weeks. Among the weather parameters, the maximum temperature and wind speed exerted greater influence on sunburn. An index called sunburn severity index is proposed to assess the severity of sunburn injury. Two hundred sugarcane varieties and clones were screened at Karnal (2010–2013) for the natural incidence of sunburn. One hundred twenty clones were tolerant, 103 clones were moderately tolerant and 4 clones (Co 87268, CoPant 84211, Co 0238, and Co 98014) were susceptible. Nonetheless, there was no significant reduction in stalk length, stalk diameter, internode number, cane weight and HR brix of sunburn affected plants.

Saccharum spontaneum L., a wild relative of sugarcane, is known for its adaptability to environmental stresses, particularly cold stress. In the present study, an attempt was made for transcriptome profiling of the low temperature (10°C) tolerant S. spontaneum clone IND 00-1037 collected from high altitude regions of Arunachal Pradesh, North Eastern India. The Illumina Nextseq500 platform yielded a total of 47.63 and 48.18 million reads corresponding to 4.7 and 4.8 gigabase pairs (Gb) of processed reads for control and cold stressed (10°C for 24h) samples, respectively. These reads were de novo assembled into 214,611 unigenes with an average length of 801bp. Further, all unigenes were aligned to GO, KEGG and COG databases in order to identify novel genes and pathways responsive upon low temperature conditions. The differential gene expression analysis revealed that about 2583 genes were upregulated and 3302 genes were down regulated during the stress. This is perhaps the comprehensive transcriptome data of a low temperature tolerant clone of S. spontaneum. This study would aid in identifying novel genes and also in future genomic studies pertaining to sugarcane and its wild relatives.

Fifteen elite sugarcane clones along with five zonal standard varieties were evaluated under four production environments in the sub-tropical climate. AMMI model was employed to assess the magnitude of Genotype x environment (GE) interaction and the stability of sugarcane clones across environments. AMMI analysis revealed the significant difference among tested clones and environments. It has shown 43.17% of the variation in cane yield which could be attributed to environmental effects. The genotypic effects accounted for 45.76% variation with 11.06% of GEI effects. The early maturing high sugar varieties, Co 0238 and Co 0118 gave 89.27 t/ha and 80.11 t/ha cane yield, respectively and thus considered as widely adapted genotypes across the environments and can be recommended for commercial cultivation in sub-tropical region. Co 98014 and Co 05011 exhibited better adaptability in ratoon trials and appeared to be suitable for multiple ratoon. Considering IPCA score, CoS 767 was most stable standard (check) across the environments. With regards to the environments, E2 (spring season plant crop) and E1 (autumn season plant crop) placed on the upper right half of perpendicular axis of AMMI biplot due to the positive interactions and hence both E2 and E1 are the favourable environments for obtaining higher cane yield.

Eighteen clones involving Erianthus, as one of the parents, were evaluated in a randomised block design under sub-tropical conditions of Karnal (Haryana, India). Fifteen characters, which contribute towards stalk yield and juice-quality, were studied. The growth of these clones was monitored during peak winter months of December and January. Significant variability existed among the clones for all the traits studied, except for pol % in juice at 10-month crop age, indicating potentiality of the clones to select desirable types. Nine clones showed significant increase in stalk length during winter months over the better standard Co 1148. Whereas 6 clones developed more number of leaves than Co 1148. Both these characters showed high genetic variability, high heritability and hence, high expected genetic gain. Path analysis revealed that these traits contributed about 16%, 5% and 4% to the total genetic variability in juice quality traits (pol % and CCS %), stalk yield and CCS yield, respectively. Growth in winter months has resulted in an increase in stalk yield and CCS yield. This may help in reducing the yield gap between tropical and sub-tropical regions. Majority of clones showed resistance to red rot disease (major disease of sugarcane in sub-tropical region). Hence, hybridization of Erianthus with sugarcane has resulted in introgression of genes for cold tolerance and red rot resistance. As Erianthus is known for its hardiness, resistance, of these clones, to other abiotic and biotic stresses is to be ascertained.

General (GSI) and specific (SSI) selection indices were constructed for three open-mating populations of sugarcane (Saccharum spp.) seedlings and their ratoon stages. Though specific indices were found to be the most effective in improving mean brix yield in their own source populations, but the GSI was better to SSI in other populations as indicated by higher mean values and more number of superior clones at selection and evaluation stages. This indicated the wider applicability of the GSI over SSI. Inspite of better expected genetic advance through GSI in ratoon crop, the actual gain in brix yield attained, through GSI, was better in seedlings.

Two hundred ninety eight sugarcane genetic resources including 129 varieties, 109 exotic clones, 21 inter-specific hybrids (ISH) and 39 inter-generic hybrids (IGH) were screened against stalk borer under field condition at Sugarcane Breeding Institute, Regional Centre, Karnal during year 2011–13. The percent incidence of stalk borer varied from 2.38 to 70.00% while the infestation index varied from 0.18 to 12.95. None of the studied germplasm was free from stalk borer infestation, however 10.85% varieties, 37.61% exotic (foreign hybrids) clones, 28.57% inter-specific hybrids and 69.23% inter-generic hybrids were least susceptible to stalk borer (infestation index was