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Abstract Background Saccharum spontaneum L. is a closely related species of sugarcane and has become an important genetic component of modern sugarcane cultivars. Stem development is one of the important factors for affecting the yield, while the molecular mechanism of stem development remains poorly understanding in S. spontaneum. Phenylalanine ammonia-lyase (PAL) is a vital component of both primary and secondary metabolism, contributing significantly to plant growth, development and stress defense. However, the current knowledge about PAL genes in S. spontaneum is still limited. Thus, identification and characterization of the PAL genes by transcriptome analysis will provide a theoretical basis for further investigation of the function of PAL gene in sugarcane. Results In this study, 42 of PAL genes were identified, including 26 SsPAL genes from S. spontaneum, 8 ShPAL genes from sugarcane cultivar R570, and 8 SbPAL genes from sorghum. Phylogenetic analysis showed that SsPAL genes were divided into three groups, potentially influenced by long-term natural selection. Notably, 20 SsPAL genes were existed on chromosomes 4 and 5, indicating that they are highly conserved in S. spontaneum. This conservation is likely a result of the prevalence of whole-genome replications within this gene family. The upstream sequence of PAL genes were found to contain conserved cis-acting elements such as G-box and SP1, GT1-motif and CAT-box, which collectively regulate the growth and development of S. spontaneum. Furthermore, quantitative reverse transcription polymerase chain reaction (qRT-PCR) analysis showed that SsPAL genes of stem had a significantly upregulated than that of leaves, suggesting that they may promote the stem growth and development, particularly in the + 6 stem (The sixth cane stalk from the top to down) during the growth stage. Conclusions The results of this study revealed the molecular characteristics of SsPAL genes and indicated that they may play a vital role in stem growth and development of S. spontaneum. Altogether, our findings will promote the understanding of the molecular mechanism of S. spontaneum stem development, and also contribute to the sugarcane genetic improving.

Sugarcane (Saccharum spp.), a leading sugar and energy crop, is seriously impacted by drought stress. However, the molecular mechanisms underlying sugarcane drought resistance, especially the functions of epigenetic regulators, remain elusive. Here, we show that a S. spontaneum KDM4/JHDM3 group JmjC protein, SsJMJ4, negatively regulates drought-stress responses through its H3K27me3 demethylase activity. Ectopic overexpression of SsJMJ4 in Arabidopsis reduced drought resistance possibly by promoting expression of AtWRKY54 and AtWRKY70 , encoding two negative regulators of drought stress. SsJMJ4 directly bound to AtWRKY54 and AtWRKY70 , and reduced H3K27me3 levels at these loci to ensure their proper transcription under normal conditions. Drought stress down-regulated both transcription and protein abundance of SsJMJ4, which was correlated with the reduced occupancy of SsJMJ4 at AtWRKY54 and AtWRKY70 chromatin, increased H3K27me3 levels at these loci, as well as reduced transcription levels of these genes. In S. spontaneum , drought stress-repressed transcription of SsWRKY122 , an ortholog of AtWRKY54 and AtWRKY70 , was associated with increased H3K27me3 levels at these loci. Transient overexpression of SsJMJ4 in S. spontaneum protoplasts raised transcription of SsWRKY122 , paralleled with reduced H3K27me3 levels at its loci. These results suggest that the SsJMJ4-mediated dynamic deposition of H3K27me3 is required for an appropriate response to drought stress. [ABSTRACT FROM AUTHOR]

Background: Saccharum spontaneumL. is a closely related species of sugarcane and has become an important genetic component of modern sugarcane cultivars. Stem development is one of the important factors for affecting the yield, while the molecular mechanism of stem development remains poorly understanding in S. spontaneum. Phenylalanine ammonia-lyase (PAL) is a vital component of both primary and secondary metabolism, contributing significantly to plant growth, development and stress defense. However, the current knowledge about PAL genes in S. spontaneum is still limited. Thus, identification and characterization of the PAL genes by transcriptome analysis will provide a theoretical basis for further investigation of the function of PAL gene in sugarcane. Results: In this study, 42 of PAL genes were identified, including 26 SsPAL genes from S. spontaneum, 8 ShPAL genes from sugarcane cultivar R570, and 8 SbPAL genes from sorghum. Phylogenetic analysis showed that SsPAL genes were divided into three groups, potentially influenced by long-term natural selection. Notably, 20 SsPAL genes were existed on chromosomes 4 and 5, indicating that they are highly conserved in S. spontaneum. This conservation is likely a result of the prevalence of whole-genome replications within this gene family. The upstream sequence of PAL genes were found to contain conserved cis-acting elements such as G-box and SP1, GT1-motif and CAT-box, which collectively regulate the growth and development of S. spontaneum. Furthermore, quantitative reverse transcription polymerase chain reaction (qRT-PCR) analysis showed that SsPAL genes of stem had a significantly upregulated than that of leaves, suggesting that they may promote the stem growth and development, particularly in the + 6 stem (The sixth cane stalk from the top to down) during the growth stage. Conclusions: The results of this study revealed the molecular characteristics of SsPAL genes and indicated that they may play a vital role in stem growth and development of S. spontaneum. Altogether, our findings will promote the understanding of the molecular mechanism of S. spontaneum stem development, and also contribute to the sugarcane genetic improving. [ABSTRACT FROM AUTHOR]

Saccharum spontaneum, popularly known as Kashful (KF) is a seasonal perennial grass with thin culms, mostly an abundantly growing shrub during the autumn season in southern Asia. It is used as no-cost scavenger to convincingly arrest methylene blue, a recalcitrant dye from colored effluent. FTIR, FESEM-EDX, and BET surface area characterize the material well whereas the surface activity was evaluated from zero-point charge (pHZPC = 6.720). FTIR highlights the presence of polyphenolic and carboxylate moieties. The surface texture is rod-like with intermittent non-homogeneous pores with occasional fractures. The equilibrium reaches within 60 min with the maximum adsorption capacity of 20.917 mg/g. The fibrous powder of kashful stalk (KFS) follows pseudo-second-order (R2 = 0.999 for linear and R2 = 0.985 for non-linear) kinetics and both Langmuir and Freundlich isotherm model (for linear, Langmuir R2=0.995; for non-linear, R2 = 0.994 for both Langmuir and Freundlich model). The uptake process was spontaneous (ΔG= −3.077 kJ/mol) and endothermic (ΔH = 17.815 kJ/mol). 1:1 methanol could regenerate the dye-loaded material in up to 55% and onward efficiency was conducive for three consecutive cycles. Industrial effluent analysis suggests a real-time removal of ∼55% in the first cycle. Saccharum spontaneum could be exercised to solve environmental problems related to colored water. Saccharum spontaneum, also known as wild sugarcane is an abundantly available long grass with relatively slender culms; usually 100–150 cm tall, grows in the autumn season (August-October) in the south-east part of Asia, and displays steady tillering. Being a non-preferred meal for local herbivores, the material lies abandoned as bio-waste. At the same time, the search for a newer and cleaner alternative for wastewater treatment is on the rise. In line with the waste-to-wealth protocol for a sustainable environment, we have demonstrated the facile uptake of a recalcitrant dye methylene blue (20.917 mg/g) using its stalks powder. The present method is free from any hazardous chemical activation, acid-base treatment, or pyrolysis. With the ability to treat industrial effluent, the material highlights an impactful application in a lab-to-land fashion. [ABSTRACT FROM AUTHOR]

Abstract Background Sugarcane (Saccharum spp.) holds exceptional global significance as a vital crop, serving as a primary source of sucrose, bioenergy, and various by-products. The optimization of sugarcane breeding by fine-tuning essential traits has become crucial for enhancing crop productivity and stress resilience. Leucine-rich repeat receptor-like kinases (LRR-RLK) genes present promising targets for this purpose, as they are involved in various aspects of plant development and defense processes. Results Here, we present a detailed overview of phylogeny and expression of 288 (495 alleles) and 312 (1365 alleles) LRR-RLK genes from two founding Saccharum species, respectively. Phylogenetic analysis categorized these genes into 15 subfamilies, revealing considerable expansion or reduction in certain LRR-type subfamilies. Compared to other plant species, both Saccharum species had more significant LRR-RLK genes. Examination of cis-acting elements demonstrated that SsLRR-RLK and SoLRR-RLK genes exhibited no significant difference in the types of elements included, primarily involved in four physiological processes. This suggests a broad conservation of LRR-RLK gene function during Saccharum evolution. Synteny analysis indicated that all LRR-RLK genes in both Saccharum species underwent gene duplication, primarily through whole-genome duplication (WGD) or segmental duplication. We identified 28 LRR-RLK genes exhibiting novel expression patterns in response to different tissues, gradient development leaves, and circadian rhythm in the two Saccharum species. Additionally, SoLRR-RLK104, SoLRR-RLK7, SoLRR-RLK113, and SsLRR-RLK134 were identified as candidate genes for sugarcane disease defense response regulators through transcriptome data analysis of two disease stresses. This suggests LRR-RLK genes of sugarcane involvement in regulating various biological processes, including leaf development, plant morphology, photosynthesis, maintenance of circadian rhythm stability, and defense against sugarcane diseases. Conclusions This investigation into gene duplication, functional conservation, and divergence of LRR-RLK genes in two founding Saccharum species lays the groundwork for a comprehensive genomic analysis of the entire LRR-RLK gene family in Saccharum. The results reveal LRR-RLK gene played a critical role in Saccharum adaptation to diverse conditions, offering valuable insights for targeted breeding and precise phenotypic adjustments.

Background: Sugarcane (Saccharum spp.) holds exceptional global significance as a vital crop, serving as a primary source of sucrose, bioenergy, and various by-products. The optimization of sugarcane breeding by fine-tuning essential traits has become crucial for enhancing crop productivity and stress resilience. Leucine-rich repeat receptor-like kinases (LRR-RLK) genes present promising targets for this purpose, as they are involved in various aspects of plant development and defense processes. Results: Here, we present a detailed overview of phylogeny and expression of 288 (495 alleles) and 312 (1365 alleles) LRR-RLK genes from two founding Saccharum species, respectively. Phylogenetic analysis categorized these genes into 15 subfamilies, revealing considerable expansion or reduction in certain LRR-type subfamilies. Compared to other plant species, both Saccharum species had more significant LRR-RLK genes. Examination of cis-acting elements demonstrated that SsLRR-RLK and SoLRR-RLK genes exhibited no significant difference in the types of elements included, primarily involved in four physiological processes. This suggests a broad conservation of LRR-RLK gene function during Saccharum evolution. Synteny analysis indicated that all LRR-RLK genes in both Saccharum species underwent gene duplication, primarily through whole-genome duplication (WGD) or segmental duplication. We identified 28 LRR-RLK genes exhibiting novel expression patterns in response to different tissues, gradient development leaves, and circadian rhythm in the two Saccharum species. Additionally, SoLRR-RLK104, SoLRR-RLK7, SoLRR-RLK113, and SsLRR-RLK134 were identified as candidate genes for sugarcane disease defense response regulators through transcriptome data analysis of two disease stresses. This suggests LRR-RLK genes of sugarcane involvement in regulating various biological processes, including leaf development, plant morphology, photosynthesis, maintenance of circadian rhythm stability, and defense against sugarcane diseases. Conclusions: This investigation into gene duplication, functional conservation, and divergence of LRR-RLK genes in two founding Saccharum species lays the groundwork for a comprehensive genomic analysis of the entire LRR-RLK gene family in Saccharum. The results reveal LRR-RLK gene played a critical role in Saccharum adaptation to diverse conditions, offering valuable insights for targeted breeding and precise phenotypic adjustments. [ABSTRACT FROM AUTHOR]

Societal Impact Statement Summary Sugarcane (Saccharum cvs.) is one of the most important cash crops globally. Related varieties and species of cane grasses of the genus Saccharum are also important subsistence crops in the Indo‐Pacific region. Despite the significance of these crops globally and recent advances in genetic characterisation, the histories and geographies of domestication are poorly understood. A scenario for the geodomestication of sugarcane is proposed to highlight the diversity of Saccharum species and their significance for future proofing sugarcane. The historical agrobiodiversity of cane grasses, together with practices of cultivation, uses and associated forms of practical and symbolic knowledge, provide culturally appropriate bases for crop improvement.An historical scenario for the domestication of sugarcane (Saccharum cvs.) is proposed based on a literary review of a range of agronomic, archaeobotanical, archaeological, genetic, historical, linguistic and phytogeographic sources. The proposed scenario outlines a protracted, multistage domestication process for the extended period before the directed breeding programmes that led to the development of modern commercial cultivars over the last 100 years or so. First, the initial management, cultivation and translocation of Saccharum robustum within the circum‐New Guinea region produced cultiwilds (viz., morphogenetically wild plants cultivated and translocated by people) and, arguably, some S. robustum cultivars. Second, the spontaneous generation of sugar‐rich pith in some S. robustum plants and subsequent anthropic selection led to the development of ‘domesticated’ Saccharum officinarum within the circum‐New Guinea region. Third, the dispersal under cultivation of S. officinarum cultivars brought them into contact with wild‐type Saccharum spontaneum populations around the Indo‐Pacific, which led to the development of sugarcane (S. officinarum × spontaneum) hybrids that were subsequently cultivated and selected vegetatively. These ancient hybrids Saccharum barberi and Saccharum sinense became regionally important in India and China, respectively.Although much research has focussed on clarifying the Saccharum lineages directly contributing to the major commercial sugarcane cultivar lineages, such a teleological interpretation misses a vast range of agrobiodiversity in terms of the plants (S. robustum, S. officinarum, S. barberi, S. sinense and S. cvs.); domestication status (wild, cultiwild and domestic); and, practices (associated with cultivation, use and traditional knowledge) in the past. The diversity of plants and practices in the past provides the historical backdrop against which any linear interpretation of sugarcane domestication should be understood. This historical reconstruction of domestication processes draws attention to this agrobiodiversity, which can inform breeding programmes seeking to diversify and improve sugarcane cultivars for commercial and subsistence agriculture into the future. [ABSTRACT FROM AUTHOR]

NAP (NAC-like, Activated by APETALA3/PISTILLATA) is a subfamily of the transcription factor NAC gene family, which is widely involved in regulating plant growth and development, leaf senescence, and response to hormones and abiotic stress. Firstly, the NAP subfamily members were identified from the genomic database of Saccharum spontaneum, and phylogenetic analysis, conserved domains, and cis-regulatory elements were predicted using comparative genomics and various bioinformatics methods. Secondly, the allele SsNAP2a of the SsNAP2 member was isolated from the cDNA library of a wide accession SES208. The relative expression characteristics of the SsNAP2a were detected by qRT-PCR under hormone and abiotic stresses at different growth and development stages. Finally, transient overexpression and subcellular localization performed the function of SsNAP2a gene. The results showed that five NAP subfamily members were identified in the genome of S. spontaneum. The subcellular localization predicted that the encoded proteins of all members were localized in the nucleus. The Ka/Ks ratio of five gene pairs was less than 1, indicating that purifying selection was crucial in the evolution. Phylogenetic analysis revealed that 46 NAP members, including five representative angiosperms (Arabidopsis thaliana, Ananas comosus, Oryza sativa, Zea mays, and Sorghum bicolor), 12 reported species, and the S. spontaneum, were classified into four Clades. The evolution order was Clade I > Clade II > Clade III > Clade IV. In addition, the promoter regions of SsNAP members predicted many cis-acting elements in response to abscisic acid, jasmonic acid, low temperature, and other stresses. We speculated that they were involved in various hormone and abiotic stress-related response pathways. Furthermore, the full-length cDNA sequence of the SsNAP2a gene (GenBank accession number: OQ335094) was isolated from the wild accession SES208, with an open reading frame of 1173 bp and encoding 390 amino acid residues. The amino acid sequence similarity between SsNAP2 and SsNAP2a proteins was 97.70%. There was a difference of 10 amino acid residues, indicating that the autopolyploid allelic sequences of Saccharum species were significant difference. The qRT-PCR demonstrated that the SsNAP2a gene was constitutively expressed in various tissues of S. spontaneum, especially in the senescent bark and root, and its expression level was significantly induced under the treatment of ethylene, ET, abscisic acid (ABA), low temperature at 4, and high temperature at 40 . However, the relative expression level of the SsNAP2a gene was significantly down-regulated under 8% polyethylene glycol (PEG) stress. Subcellular localization revealed that the SsNAP2a-GFP fusion protein was located in the cell nucleus of Nicotiana benthamiana leaves. After transient overexpression of the SsNAP2a gene for seven days, the leaves of N. benthamiana displayed obvious curling and shriveling phenotype. The relative expression level of ET synthesis-related genes (NtEFE26, NtAccdeaminase) was significantly up-regulated, while salicylic acid, jasmonic acid, and ABA synthesis-related genes (NtPR-1a/c, NtPR3, and NtAREB1) were significantly down-regulated, indicating that the SsNAP2a gene was involved in multiple hormone signaling pathways to induce leaf senescence. These results lay a foundation for exploring the biological functions of NAP subfamily gene members involved in sugarcane leaf senescence and provide candidate gene resources for breeding anti-senescence new cultivars. [ABSTRACT FROM AUTHOR]

Autopolyploidy and allopolyploidy may represent an evolutionary advantage and are more common in plants than assumed. However, less attention has been paid to autopolyploidy than to allopolyploidy, and its evolutionary consequences are largely unclear, especially for plants with high ploidy levels. In this study, we developed oligonucleotide (oligo)-based chromosome painting probes to identify individual chromosomes in S. spontaneum. Using fluorescence in situ hybridization (FISH), we investigated chromosome behavior during pachytene, metaphase, anaphase, and telophase of meiosis I (MI) in autotetraploid, autooctoploid, and autodecaploid S. spontaneum clones. All autopolyploid clones showed stable diploidized chromosome behavior; so that homologous chromosomes formed almost exclusively bivalents during MI. Two copies of homologous chromosome 8 with similar sizes in the autotetraploid clone showed preferential pairing with each other with respect to the other copies. However, sequence variation analysis showed no apparent differences among homologs of chromosome 8 and all other chromosomes. We suggest that either the stable diploidized pairing or the preferential pairing between homologous copies of chromosome 8 in the studied autopolyploid sugarcane are accounted for by unknown mechanisms other than DNA sequence similarity. Our results reveal evolutionary consequences of stable meiotic behavior in autopolyploid plants.

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ICAR-Sugarcane Breeding Institute, Research Centre, Kannur, maintains the world's most extensive collection (3375) of Saccharum spp, varieties and allied genera. Wild sugarcane, Saccharum spontaneum and allied genera Erianthus spp. are considered resistant sources to various biotic and abiotic stresses. Considering the importance of disease resistance in breeding programmes, we monitored and surveyed various foliar diseases of 516 wild germplasm clones at Kannur that is congenial for the severe occurrence of foliar diseases. Brown spot, ring spot, orange rust and smut were recorded in S. spontaneum clones, whereas only Pokkah boeng was recorded in Erianthus spp. All the S. spontaneum clones were found to be resistant to ring spot disease except one clone, Ponape 3, which showed an intermediate reaction. About 41.14% of the clones showed resistance to brown spot and 98% to orange rust. Only two clones, IND 85-497 and IND 85-522, showed Smut. All clones of Erianthus were free from these diseases, probably indicating resistance to them and only one clone IJ 76-172 exhibited the symptoms of Pokkah boeng. In the controlled condition testing (CCT) with a number of collections of S. spontaneum and Erianthus spp, most clones were found to be resistant or moderately resistant to red rot and only a few clones showed susceptible reaction. The present study confirmed that most of the clones of the wild species are resistant various diseases. These clones could be effectively used in resistance breeding programmes to develop high-yielding sugarcane varieties with disease resistance. [ABSTRACT FROM AUTHOR]

Invasive C4 grasses can inhibit the natural regeneration of secondary forest in tropical landscapes after the cessation of intensive use for grazing and agriculture. In Panama, invasive Saccharum spontaneum forms dense stands that require active management to re-establish forest successional processes. In this region, restoration strategies typically involve clearing grass cover manually and applying fertilizer prior to planting tree seedlings. However, if fertilizers alleviate nutrient limitation and enhance grass competition with tree seedlings, these practices may exacerbate the costs of Saccharum control and hamper restoration goals. Here, we evaluated how S. spontaneum responds to nitrogen and phosphorus addition in the field to determine whether S. spontaneum is nutrient limited in this system. S. spontaneum was limited by both nitrogen and phosphorus, as revealed through increased foliar nutrient concentrations. S. spontaneum biomass was significantly greater in both nitrogen and phosphorus addition plots after both the first growth period (early rainy season) and second growth period (late rainy season), with stronger effects of nutrient limitation during the second growth period for both N limitation and N and P co-limitation. Nutrient limitation in S. spontaneum highlights a potential risk of fertilizer applications during restoration, agriculture, and agroforestry activities in which invasion of this aggressive weed is a challenge to land management.

Abstract Background Cyclic nucleotide-gated ion channels (CNGCs) are nonselective cation channels that are ubiquitous in eukaryotic organisms. As Ca2+ channels, some CNGCs have also proven to be K+-permeable and involved in plant development and responses to environmental stimuli. Sugarcane is an important sugar and energy crop worldwide. However, reports on CNGC genes in sugarcane are limited. Results In this study, 16 CNGC genes and their alleles were identified from Saccharum spontaneum and classified into 5 groups based on phylogenetic analysis. Investigation of gene duplication and syntenic relationships between S. spontaneum and both rice and Arabidopsis demonstrated that the CNGC gene family in S. spontaneum expanded primarily by segmental duplication events. Many SsCNGCs showed variable expression during growth and development as well as in tissues, suggesting functional divergence. Light-responsive cis-acting elements were discovered in the promoters of all the identified SsCNGCs, and the expression of most of the SsCNGCs showed a diurnal rhythm. In sugarcane, the expression of some SsCNGCs was regulated by low-K+ treatment. Notably, SsCNGC13 may be involved in both sugarcane development and its response to environmental stimuli, including response to low-K+ stress. Conclusion This study identified the CNGC genes in S. spontaneum and provided insights into the transcriptional regulation of these SsCNGCs during development, circadian rhythm and under low-K+ stress. These findings lay a theoretical foundation for future investigations of the CNGC gene family in sugarcane.

An assessment of the influence of weather parameters on flowering of 1459 world germplasm collections of Saccharum spontaneum L. collected over a century (1916-2016) and maintained in the field germplasm at Coimbatore during 2017 to 2019 flowering seasons was undertaken. The collections were from 23 states of India and exotic regions belonging to various latitudes. Accessions from Karnataka, Kerala, Andhra Pradesh, and Tamil Nadu recorded profuse flowering along with Madhya Pradesh, Maharashtra, Rajasthan, Odisha and Tripura accessions in all the three seasons even though they are latitudinally displaced. Inherent limited latitudinal tolerance was noticed in these clones. Maximum number of accessions was found to be in flowering during October month irrespective of the planting date. Statistical analysis has been carried out by calculating correlation coefficients between different pairs of weather parameters and t- test for finding out the significance. Relative humidity in the forenoon as well in the afternoon had a significant positive correlation and solar radiation had a highly negative correlation on flowering. Rainfall and rainy days had positive correlation on flowering during season I of flowering. Ideal temperature condition for S. spontaneum panicle development and pollen fertility under Coimbatore condition was found to be 30° C during day and 22° C at night. Utilization of these new flowering accessions and late flowering germplasm in the future breeding programme will enhance the commercial cultivars in sugarcane and aid in the development of improved varieties.

Commercial sugarcane hybrids are derivatives from Saccharum officinarum and Saccharum spontaneum hybrids containing the full complement of S. officinarum and a few S. spontaneum chromosomes and recombinants with favorable agronomic characters from both the species. The combination of the two sub-genomes in varying proportions in addition to the recombinants presents a challenge in the study of gene expression and regulation in the hybrid. We now report the transcriptome analysis of the two progenitor species and a modern commercial sugarcane hybrid through long read sequencing technology. Transcripts were profiled in the two progenitor species S. officinarum (Black Cheribon), and S. spontaneum (Coimbatore accession) and a recent high yielding, high sugar variety Co 11015. The composition and contribution of the progenitors to a hybrid with respect to sugar, biomass, and disease resistance were established. Sugar related transcripts originated from S. officinarum while several stress and senescence related transcripts were from S. spontaneum in the hybrid. The hybrid had a higher number of transcripts related to sugar transporters, invertases, transcription factors, trehalose, UDP sugars, and cellulose than the two progenitor species. Both S. officinarum and the hybrid had an abundance of novel genes like sugar phosphate translocator, while S. spontaneum had just one. In general, the hybrid shared a larger number of transcripts with S. officinarum than with S. spontaneum, reflecting the genomic contribution, while the progenitors shared very few transcripts between them. The common isoforms among the three genotypes and unique isoforms specific to each genotype indicate that there is a high scope for improvement of the modern hybrids by utilizing novel gene isoforms from the progenitor species. [ABSTRACT FROM AUTHOR]

It is well-known that LRRII-RLK gene family widely exists in plants. These genes are receptor like kinase (RLK), which play a significant role in plant development and biological stress. Up till now, there is no systematic identification and analysis of the LRRII-RLK gene family in sugarcane. Here, we identified 27 LRRII-RLK genes in Saccharum spontaneum, which were distributed on 17 chromosomes. Phylogenetic tree showed the classification of these genes into three different branches including NIK, SERK, and LRRII-C. Furthermore, we observed the significant amplification in the LRRII-C branch. Next, we characterized the cis-regulatory elements, which identified 32 different types of cis elements in the gene promoters, primarily involved in light response, stress response, regulation of hormone mechanism, and plant growth. Interestingly, SsLRRII-RLK genes were detected to be conserved with 35 collinear gene pairs and multiple conserved motifs. These genes were mainly amplified by segmental replication and had undergone strict purification selection during the evolution, according to their Ka/Ks ratios. Furthermore, the relative expression level of SsLRRII-RLK genes varied in different tissues of sugarcane. Additionally, some genes expressed differently during distinct periods of day and night, suggesting that they were associated with plant growth regulation and photosynthesis. Noticeably, the relative expression pattern of SsLRRII-RLK genes varied significantly under different disease conditions (sugarcane pokkah boeng disease and mosaic disease). In conclusion, these genes might play a role in pathogenesis and viral replication. The results of this study are helpful to further understand the evolutionary process of LRRII-RLK gene in sugarcane. This data provides a preliminary theoretical basis for the functional study of LRRII-RLK gene during photosynthesis, growth and development, and disease conditions in sugarcane. [ABSTRACT FROM AUTHOR]

Invasive C 4 grasses can inhibit the natural regeneration of secondary forest in tropical landscapes after the cessation of intensive use for grazing and agriculture. In Panama, invasive Saccharum spontaneum forms dense stands that require active management to re-establish forest successional processes. In this region, restoration strategies typically involve clearing grass cover manually and applying fertilizer prior to planting tree seedlings. However, if fertilizers alleviate nutrient limitation and enhance grass competition with tree seedlings, these practices may exacerbate the costs of Saccharum control and hamper restoration goals. Here, we evaluated how S. spontaneum responds to nitrogen and phosphorus addition in the field to determine whether S. spontaneum is nutrient limited in this system. S. spontaneum was limited by both nitrogen and phosphorus, as revealed through increased foliar nutrient concentrations. S. spontaneum biomass was significantly greater in both nitrogen and phosphorus addition plots after both the first growth period (early rainy season) and second growth period (late rainy season), with stronger effects of nutrient limitation during the second growth period for both N limitation and N and P co-limitation. Nutrient limitation in S. spontaneum highlights a potential risk of fertilizer applications during restoration, agriculture, and agroforestry activities in which invasion of this aggressive weed is a challenge to land management [ABSTRACT FROM AUTHOR]

Abstract Background Karyotype dynamics driven by chromosomal rearrangements has long been considered as a fundamental question in the evolutionary genetics. Saccharum spontaneum, the most primitive and complex species in the genus Saccharum, has reportedly undergone at least two major chromosomal rearrangements, however, its karyotypic evolution remains unclear. Results In this study, four representative accessions, i.e., hypothetical diploid sugarcane ancestor (sorghum, x = 10), Sa. spontaneum Np-X (x = 10, tetraploid), 2012–46 (x = 9, hexaploid) and AP85–441 (x = 8, tetraploid), were selected for karyotype evolution studies. A set of oligonucleotide (oligo)-based barcode probes was developed based on the sorghum genome, which allowed universal identification of all chromosomes from sorghum and Sa. spontaneum. By comparative FISH assays, we reconstructed the karyotype evolutionary history and discovered that although chromosomal rearrangements resulted in greater variation in relative lengths of some chromosomes, all chromosomes maintained a conserved metacentric structure. Additionally, we found that the barcode oligo probe was not applicable for chromosome identification in both Sa. robustum and Sa. officinarum species, suggesting that sorghum is more distantly related to Sa. robustum and Sa. officinarum compared with Sa. spontaneum species. Conclusions Our study demonstrated that the barcode oligo-FISH is an efficient tool for chromosome identification and karyotyping research, and expanded our understanding of the karyotypic and chromosomal evolution in the genus Saccharum.

The improved sugarcane varieties grown in and around the world are majorly evolved through interspecific hybridization of Saccharum species. Only few promising hybrids have been developed from allied genera such as Erianthus and Sclerostachya. Several other genera, including Phragmites, Vetivera, Narenga and Neyurida, deserve further research. Successful exploitation of these allied genera resources require careful characterization, evaluation and conservation using different methods including tissue culture techniques. Among them, Phragmites australis is used to remediate waste water and remove heavy metals. In this study, meristem tip culture was standardized for five clones of Phragmites to evaluate their response and growth. Among the five clones of Phragmites studied, two clones (IND 89-711 and IND04-1326) showed better regeneration and growth. The in vitro derived plants were compared with the mother plants using four SRAP markers to check their genetic fidelity. Monomorphic bands were obtained in both the in-vitro and mother plants. No polymorphism was detected, thus proving the genetic uniformity of the micropropgated plants.

Background: Cyclic nucleotide-gated ion channels (CNGCs) are nonselective cation channels that are ubiquitous in eukaryotic organisms. As Ca2+ channels, some CNGCs have also proven to be K+-permeable and involved in plant development and responses to environmental stimuli. Sugarcane is an important sugar and energy crop worldwide. However, reports on CNGC genes in sugarcane are limited. Results: In this study, 16 CNGC genes and their alleles were identified from Saccharum spontaneum and classified into 5 groups based on phylogenetic analysis. Investigation of gene duplication and syntenic relationships between S. spontaneum and both rice and Arabidopsis demonstrated that the CNGC gene family in S. spontaneum expanded primarily by segmental duplication events. Many SsCNGCs showed variable expression during growth and development as well as in tissues, suggesting functional divergence. Light-responsive cis-acting elements were discovered in the promoters of all the identified SsCNGCs, and the expression of most of the SsCNGCs showed a diurnal rhythm. In sugarcane, the expression of some SsCNGCs was regulated by low-K+ treatment. Notably, SsCNGC13 may be involved in both sugarcane development and its response to environmental stimuli, including response to low-K+ stress. Conclusion: This study identified the CNGC genes in S. spontaneum and provided insights into the transcriptional regulation of these SsCNGCs during development, circadian rhythm and under low-K+ stress. These findings lay a theoretical foundation for future investigations of the CNGC gene family in sugarcane. [ABSTRACT FROM AUTHOR]

SUMMARY: Saccharum spontaneum and Saccharum officinarum contributed to the genetic background of modern sugarcane cultivars. Saccharum spontaneum has shown a higher net photosynthetic rate and lower soluble sugar than S. officinarum. Here, we analyzed 198 RNA‐sequencing samples to investigate the molecular mechanisms for the divergences of photosynthesis and sugar accumulation between the two Saccharum species. We constructed gene co‐expression networks based on differentially expressed genes (DEGs) both for leaf developmental gradients and diurnal rhythm. Our results suggested that the divergence of sugar accumulation may be attributed to the enrichment of major carbohydrate metabolism and the oxidative pentose phosphate pathway. Compared with S. officinarum, S. spontaneum DEGs showed a high enrichment of photosynthesis and contained more complex regulation of photosynthesis‐related genes. Noticeably, S. spontaneum lacked gene interactions with sulfur assimilation stimulated by photorespiration. In S. spontaneum, core genes related to clock and photorespiration displayed a sensitive regulation by the diurnal rhythm and phase‐shift. Small subunit of Rubisco (RBCS) displayed higher expression in the source tissues of S. spontaneum. Additionally, it was more sensitive under a diurnal rhythm, and had more complex gene networks than that in S. officinarum. This indicates that the differential regulation of RBCS Rubisco contributed to photosynthesis capacity divergence in both Saccharum species. Significance Statement: We analyzed 198 RNA‐seq samples to construct gene co‐expression networks based on differentially expressed genes for both leaf developmental gradients and diurnal rhythm between the two founding Saccharum species. By analyzing the characteristics of leaf gradient transcriptome and time point transcriptome of two Saccharum species, we provided a foundation for understanding the differentiation law of photosynthesis and sugar metabolism of two founding Saccharum species. [ABSTRACT FROM AUTHOR]

In plants, the multi-gene family of dual-function hexokinases (HXKs) plays an important role in sugar metabolism and sensing, that affects growth and stress adaptation. Sugarcane is an important sucrose crop and biofuel crop. However, little is known about the HXK gene family in sugarcane. A comprehensive survey of sugarcane HXKs, including physicochemical properties, chromosomal distribution, conserved motifs, and gene structure was conducted, identifying 20 members of the SsHXK gene family that were located on seven of the 32 Saccharum spontaneum L. chromosomes. Phylogenetic analysis showed that the SsHXK family could be divided into three subfamilies (group I, II and III). Motifs and gene structure were related to the classification of SsHXKs. Most SsHXKs contained 8–11 introns which was consistent with other monocots. Duplication event analysis indicated that HXKs in S. spontaneum L. primarily originated from segmental duplication. We also identified putative cis-elements in the SsHXK promoter regions which were involved in phytohormone, light and abiotic stress responses (drought, cold et al.). During normal growth and development, 17 SsHXKs were constitutively expressed in all ten tissues. Among them, SsHXK2, SsHXK12 and SsHXK14 had similar expression patterns and were more highly expressed than other genes at all times. The RNA-seq analysis showed that 14/20 SsHXKs had the highest expression level after cold stress for 6 h, especially SsHXK15, SsHXK16 and SsHXK18. As for drought treatment, 7/20 SsHXKs had the highest expression level after drought stress for 10 days, 3/20 (SsHKX1, SsHKX10 and SsHKX11) had the highest expression level after 10 days of recovery. Overall, our results revealed the potential biological function of SsHXKs, which may provide information for in-depth functional verification. [ABSTRACT FROM AUTHOR]

Forty three Saccharum spontaneum accessions were evaluated using eighteen drought tolerance related traits. The Euclidean based dendrogram divided the accessions into three different clusters. Euclidean distances ranged from 7.65 to 140.23. The maximum distance was reported between the accessions IND 99-849 and IND03- 1247. From the PCA analysis, it is observed that 47.03% of the total variation was accounted by the first two principal components. The variables factor map visualized that stalk height at 90 days and stalk height during stress were the two important variables contributing maximum to the total variation. In the case of Euclidean distance based clustering cluster I included drought tolerant accessions while it was cluster II and III for PCA based clustering accessions viz., IND 99-847, IND 08-1500, IND 08-1491, IND 99-984, IND 02-1186 etc. were identified as promising under drought condition. These accessions can be utilized in the sugarcane improvement programmes for abiotic stress tolerance. The understanding of genetic diversity present in germplasm is important for their proper utilization, management and conservation.

Genetic engineering approach is a viable method to impart abiotic stress tolerance in crop plants. The genomic compatability between Saccharum and related genera allows for broader application in sugarcane improvement programme in terms of improved hybrid productivity and adaptability. NAC tf (NAM ATAF CUC transcription factor) was found to be one of the most stress responsive transcription factors consisting of consortium of genes acting against both abiotic and biotic stress. Several studies have proved the involvement of NAC protein in imparting stress tolerance. Based on their response to abiotic stimuli, a set of NAC genes have been designated as Stress associated NAC (SNACs). We have sequenced NAC1 gene from Erianthus sp-IK76- 91 which is a stress tolerant species closely related to sugarcane. A 1.8 kb fragment was amplified in oxidative stress tolerant Erianthus using NAC1 specific primers. Gene construct was developed with binary vector pRI and the isolated gene was sequenced. BLASTn analysis of recombinant pRI 909 showed 88.61% homology with the Sorghum bicolor NAC1 gene. The oxidative stress responsive pRI::EaNAC construct developed can be further utilised to transform high yielding susceptible sugarcane varieties to benefit them in adapting to multiple abiotic stresses.

Commercial sugarcane hybrids are derivatives from Saccharum officinarum and Saccharum spontaneum hybrids containing the full complement of S. officinarum and a few S. spontaneum chromosomes and recombinants with favorable agronomic characters from both the species. The combination of the two sub-genomes in varying proportions in addition to the recombinants presents a challenge in the study of gene expression and regulation in the hybrid. We now report the transcriptome analysis of the two progenitor species and a modern commercial sugarcane hybrid through long read sequencing technology. Transcripts were profiled in the two progenitor species S. officinarum (Black Cheribon), and S. spontaneum (Coimbatore accession) and a recent high yielding, high sugar variety Co 11015. The composition and contribution of the progenitors to a hybrid with respect to sugar, biomass, and disease resistance were established. Sugar related transcripts originated from S. officinarum while several stress and senescence related transcripts were from S. spontaneum in the hybrid. The hybrid had a higher number of transcripts related to sugar transporters, invertases, transcription factors, trehalose, UDP sugars, and cellulose than the two progenitor species. Both S. officinarum and the hybrid had an abundance of novel genes like sugar phosphate translocator, while S. spontaneum had just one. In general, the hybrid shared a larger number of transcripts with S. officinarum than with S. spontaneum, reflecting the genomic contribution, while the progenitors shared very few transcripts between them. The common isoforms among the three genotypes and unique isoforms specific to each genotype indicate that there is a high scope for improvement of the modern hybrids by utilizing novel gene isoforms from the progenitor species.

Abstract Background Sugarcane is an important crop for sugar production worldwide. The Sugars Will Eventually be Exported Transporters (SWEETs) are a group of sugar transporters recently identified in sugarcane. In Saccharum spontaneum, SsSWEET13c played a role in the sucrose transportation from the source to the sink tissues, which was found to be mainly active in the mature leaf. However, the function and regulation of SWEETs in sugarcane remain elusive despite extensive studies performed on sugar metabolism. Results In this study, we showed that SsSWEET13c is a member of SWEET gene family in S. spontaneum, constituting highest circadian rhythm-dependent expression. It is a functional gene that facilitates plant root elongation and increase fresh weight of Arabidopsis thaliana, when overexpressed. Furthermore, yeast one-hybrid assays indicate that 20 potential transcription factors (TFs) could bind to the SsSWEET13c promoter in S. spontaneum. We combined transcriptome data from developmental gradient leaf with distinct times during circadian cycles and stems/leaves at different growth stages. We have uncovered that 14 out of 20 TFs exhibited positive/negative gene expression patterns relative to SsSWEET13c. In the source tissues, SsSWEET13c was mainly positively regulated by SsbHLH34, SsTFIIIA-a, SsMYR2, SsRAP2.4 and SsbHLH035, while negatively regulated by SsABS5, SsTFIIIA-b and SsERF4. During the circadian rhythm, it was noticed that SsSWEET13c was more active in the morning than in the afternoon. It was likely due to the high level of sugar accumulation at night, which was negatively regulated by SsbZIP44, and positively regulated by SsbHLH34. Furthermore, in the sink tissues, SsSWEET13c was also active for sugar accumulation, which was positively regulated by SsbZIP44, SsTFIIIA-b, SsbHLH34 and SsTFIIIA-a, and negatively regulated by SsERF4, SsHB36, SsDEL1 and SsABS5. Our results were further supported by one-to-one yeast hybridization assay which verified that 12 potential TFs could bind to the promoter of SsSWEET13c. Conclusions A module of the regulatory network was proposed for the SsSWEET13c in the developmental gradient of leaf and circadian rhythm in S. spontaneum. These results provide a novel understanding of the function and regulation of SWEET13c during the sugar transport and biomass production in S. spontaneum.

Insufficient water is a leading environmental problem that affects overall crop development, productivity, and sometimes total crop failure. It brings a number of morpho-physiological and cellular disturbances. The purpose of this study was carried out to assess the effects of photosynthetic pigments and antioxidative enzyme activities of Saccharum spontaneum cv. GX83-10 plants during mild to severe water stress conditions. After 90 days of bud setts germination, S. spontaneum plants were sustained up to 15 days of withdrawing water. Our results indicated that the stressed plants were negatively affected, such as growth, biomass, photosynthetic loss, and significant reduction in photosynthetic CO2 assimilation rate. Severe water stress enhanced the level of osmolytes, i.e., proline, soluble protein, soluble sugar, and malondialdehyde, as well as catalase, peroxidase, and superoxide dismutase enzyme activities. Antioxidative enzyme activities in S. spontaneum plant leaves were improved and enhanced the metabolism of superoxide, leading to enhanced water stress tolerance efficiency. The present findings may help in better understanding of S. spontaneum antioxidative defense systems in drought-stressed conditions. [ABSTRACT FROM AUTHOR]

Excessive use of nitrogen (N) fertilizer for sugarcane cultivation is a significant cause of greenhouse gas emission. N use-efficiency (NUE) of sugarcane is relatively low, and considerable effort is now directed to exploit biological nitrogen fixation (BNF) in sugarcane. We hypothesize that genetic basebroadening of sugarcane using high-BNF Saccharum spontaneum, a wild progenitor of sugarcane, will help develop N-efficient varieties. We found remarkable genetic variation for BNF and growth in S. spontaneum accessions, and BNF in some accessions remained highly resilient to inorganic N application. Physiological and molecular analyses of two S. spontaneum accessions with high-BNF capacity and growth, namely G152 and G3, grown under N replete and low N conditions showed considerable similarity for total N, NH4-N, soluble sugar, indoleacetic acid, gibberellic acid, zeatin and abscisic acid content; yet, they were strikingly different at molecular level. Global gene expression analysis of G152 and G3 grown under contrasting N supply showed genotype effect explaining much of the gene expression variation observed. Differential gene expression analysis found an overrepresentation of carbohydrate and amino acid metabolism and transmembrane transport genes in G152 and an enrichment of lipid metabolism and single-organism processes genes in G3, suggesting that distinctly divergent metabolic strategies are driving N-related processes in these accessions. This was attested by the remarkable variation in carbon, N, amino acid and hormone metabolism-related gene expression in G152 and G3 under high- and low-N supply. We conclude that both accessions may be achieving similar BNF and growth phenotypes through overlapping but distinctly different biochemical and molecular mechanisms. [ABSTRACT FROM AUTHOR]

Wild sugarcane (Saccharum spontaneum L.) is an invasive plant species in the Central American region. Due to its low nutrient and water requirements, it can grow fast and displace native species. Therefore, its biomass is considered a waste to prevent the further distribution of the specie. This study investigates the production and characterization of wild sugarcane biochar to provide a use for its waste. The produced biochar was used for atrazine adsorption in aqueous solutions to provide a possible application of this biochar near the water bodies that were often detected to be contaminated with atrazine. The biochar was produced via top-lit updraft gasification with airflow rates between 8 to 20 L/min, achieving yields ranging from 22.9 to 27.5%. Batch experiments revealed that biochar made at 12 L/min presented the best removal efficiency (37.71–100%) and the maximum adsorption capacity (qm = 0.42 mg/g). Langmuir (R2 = 0.94–0.96) and Freundlich (R2 = 0.89–0.97) described the experimental data appropriately. Fourier transform infrared spectroscopy suggested that atrazine removal in wild sugarcane biochar could be mainly due to carboxylic functional groups. In addition, the biochar organic carbon composition contributed to a higher removal capacity in biochar produced at different airflow rates. [ABSTRACT FROM AUTHOR]

Sugarcane is a species of tall grass with high biomass and sucrose production, and the world's largest crop by production quantity. Its evolutionary environment adaptation and anthropogenic breeding response have resulted in a complex autopolyploid genome. Few efforts have been reported in the literature to document this organism's gene co-expression and annotation, and, when available, use different gene identifiers that cannot be easily associated across studies. This data descriptor paper presents a dataset that consolidates expression matrices of two Saccharum spontaneum AP85-441 genome versions and an algorithm implemented in Python to mechanically obtain this dataset. The data are processed from the allele-level information of the two sources, with BLASTn used bidirectionally to suggest feasible mappings between the two sets of alleles, and a graph-matching optimization algorithm to maximize global identity and uniqueness of genes. Association tables are used to consolidate the expression values from alleles to genes. The contributed expression matrices comprise 96 experiments and 109,050 and 35,516 from the two genome versions. They can represent significant computational cost reduction for further research on, e.g., sugarcane co-expression network generation, functional annotation prediction, and stress-specific gene identification. Dataset: https://github.com/mauriciogeteg/sugarcane-gene-expression. Dataset License: CC-BY-NC. [ABSTRACT FROM AUTHOR]

Background: Karyotype dynamics driven by chromosomal rearrangements has long been considered as a fundamental question in the evolutionary genetics. Saccharum spontaneum, the most primitive and complex species in the genus Saccharum, has reportedly undergone at least two major chromosomal rearrangements, however, its karyotypic evolution remains unclear. Results: In this study, four representative accessions, i.e., hypothetical diploid sugarcane ancestor (sorghum, x = 10), Sa. spontaneum Np-X (x = 10, tetraploid), 2012–46 (x = 9, hexaploid) and AP85–441 (x = 8, tetraploid), were selected for karyotype evolution studies. A set of oligonucleotide (oligo)-based barcode probes was developed based on the sorghum genome, which allowed universal identification of all chromosomes from sorghum and Sa. spontaneum. By comparative FISH assays, we reconstructed the karyotype evolutionary history and discovered that although chromosomal rearrangements resulted in greater variation in relative lengths of some chromosomes, all chromosomes maintained a conserved metacentric structure. Additionally, we found that the barcode oligo probe was not applicable for chromosome identification in both Sa. robustum and Sa. officinarum species, suggesting that sorghum is more distantly related to Sa. robustum and Sa. officinarum compared with Sa. spontaneum species. Conclusions: Our study demonstrated that the barcode oligo-FISH is an efficient tool for chromosome identification and karyotyping research, and expanded our understanding of the karyotypic and chromosomal evolution in the genus Saccharum. [ABSTRACT FROM AUTHOR]

Sugarcane is a major crop for sugar production around the world. The complexity of the sugarcane genome creates challenges for the use of both conventional and molecular breeding methods to improve sugarcane at a genetic level. DNA sequencing is an important tool to assess how the genus Saccharum and the genera of the Saccharum complex are interrelated. Here, we identify the kinship of Nepal2013-6 (Saccharum spontaneum, x = 10) using a tetra-primer amplification refractory mutation system (ARMS) PCR. Based on rDNA-ITS sequence analysis, the accession Nepal2013-6 falls within a single cluster with S. spontaneum (Yunnan82-114 and SES208), which is consistent with the previous results. Moreover, fluorescence in situ hybridization (FISH) results indicate that the 5S rDNA spots are consistent with the chromosomal ploidy in the analytical Saccharum materials, whereas 35S rDNA has similar or fewer sites than the ploidy. Therefore, 5S rDNA FISH patterns would be more suitable than 35S rDNA for chromosomal ploidy analysis in S. spontaneum with varied basic chromosome number x = 8, 9, 10. Altogether, these results indicate that the rDNA sequences will be a useful marker for further rapidly identifying the relationship and ploidy of S. spontaneum in sugarcane breeding. [ABSTRACT FROM AUTHOR]

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Saccharum spontaneum is the major donor of important traits like vigour, hardiness and ratooning potential to modern sugarcane cultivars. Identifying S. spontaneum clones with high early vigour and tillering ability is essential to include them in hybridization program. Forty three Saccharum spontaneum accessions were evaluated for number of tillers per clump, stalk length, stalk diameter, number of leaves on the main stem, leaf length and leaf lamina width at 90 days after planting. Variance components for these traits indicated high heritability coupled with genetic advance for leaf width and stalk length indicating the preponderance of additive gene action for these traits. The comprehensive index Ci value, Smith-Hazel’s selection index (SHI) and rank sums of all the traits indicated six clones viz., IND 99-848, IND 99-881, IND 99-849, IND 99-850, IND 99-984 and IND 99-847 were superior clones and can be utilised in pre breeding programmes as potential donors in identification of bioenergy canes. Among the methods studied, DTOPSIS was comparatively effective in selecting the genotypes.

Flowering in sugarcane (Saccharum spp.), a vital industrial crop for the production of sugar and energy, have always imposed a challenge for its agricultural productivity and breeding. Despite this, the molecular mechanisms controlling sugarcane flowering, particularly the roles of epigenetic regulators, remain largely unknown. Here, we demonstrate that SsJMJ11, a S. spontaneum KDM5/JHDM1 subfamily JmjC protein, promotes flowering by acting as a H3K4me3 demethylase. Ectopic overexpression of SsJMJ11 in Arabidopsis accelerated flowering possibly by downregulating the expression of AtFLC and AtCDF1, which are well-known flowering repressors. SsJMJ11 directly bound to AtFLC and AtCDF1, and decreased their H3K4me3 levels. In S. spontaneum, long day photoperiod enhanced the transcription of SsJMJ11, associated with the elevated SsCO , SsFT3 and reduced SsCDF1&2 transcript levels. Transient overexpression of SsJMJ11 in S. spontaneum protoplasts inhibited the expression of SsCDF1&2 , in parallel with decreased H3K4me3 levels at its loci. The findings suggest that the dynamic deposition of H3K4me3 mediated by SsJMJ11 is required for proper flowering time in sugarcane. • SsJMJ11 and SsJMJ26 are specific H3K4 demethylases. • Overexpression of SsJMJ11 promotes flowering in Arabidopsis. • SsJMJ11 represses the expression of AtFLC and AtCDF1 by reducing its H3K4me3 levels. • SsJMJ11 inhibits the expression of SsCDF1&2 by reducing its H3K4me3 levels. [ABSTRACT FROM AUTHOR]

Abstract Background In plants, a critical balance between differentiation and proliferation of stem cells at the shoot apical meristem zone is essential for proper growth. The spatiotemporal regulation of some crucial genes dictates the formation of a boundary within and around budding organs. The boundary plays a pivotal role in distinguishing one tissue type from another and provides a defined shape to the organs at their developed stage. NAM/CUC subfamily of the NAC transcription factors control the boundary formation during meristematic development. Results Here, we have identified the CUP-SHAPED COTYLEDON (CUC) genes in sugarcane and named SsCUC2 (for the orthologous gene of CUC1 and CUC2) and SsCUC3. The phylogenetic reconstruction showed that SsCUCs occupy the CUC2 and CUC3 clade together with monocots, whereas eudicot CUC2 and CUC3 settled separately in the different clade. The structural analysis of CUC genes showed that most of the CUC3 genes were accompanied by an intron gain during eudicot divergence. Besides, the study of SsCUCs expression in the RNA-seq obtained during different stages of ovule development revealed that SsCUCs express in developing young tissues, and the expression of SsCUC2 is regulated by miR164. We also demonstrate that SsCUC2 (a monocot) could complement the cuc2cuc3 mutant phenotype of Arabidopsis (eudicot). Conclusions This study further supports that CUC2 has diverged in CUC1 and CUC2 during the evolution of monocots and eudicots from ancestral plants. The functional analysis of CUC expression patterns during sugarcane ovule development and ectopic expression of SsCUC2 in Arabidopsis showed that SsCUC2 has a conserved role in boundary formation. Overall, these findings improve our understanding of the functions of sugarcane CUC genes. Our results reveal the crucial functional role of CUC genes in sugarcane.

Sugarcane, a cash crop, is easily affected by low temperature, which results in a decrease in yield and sugar production. Breeding a new variety with cold tolerance is an essential strategy to reduce loss from cold stress. The identification of germplasms and genes/proteins with cold tolerance is a vital step in breeding sugarcane varieties with cold tolerance via a conventional program and molecular technology. In this study, the physiological and biochemical indices of 22 genotypes of S. spontaneum were measured, and the membership function analysis method was used to comprehensively evaluate the cold tolerance ability of these genotypes. The physiological and biochemical indices of these S. spontaneum genotypes showed a sophisticated response to low temperature. On the basis of the physiological and chemical indices, the genotypes were classified into different cold tolerance groups. Then, the high-tolerance genotype 1027 and the low-tolerance genotype 3217 were selected for DIA-based proteomic analysis by subjecting them to low temperature. From the four comparison groups, 1123, 1341, 751, and 1693 differentially abundant proteins (DAPs) were identified, respectively. The DAPs based on genotypes or treatments participated in distinct metabolic pathways. Through detailed analysis of the DAPs, some proteins related to protein homeostasis, carbohydrate and energy metabolism, amino acid transport and metabolism, signal transduction, and the cytoskeleton may be involved in sugarcane tolerance to cold stress. Furthermore, five important proteins related to cold tolerance were discovered for the first time in this study. This work not only provides the germplasms and candidate target proteins for breeding sugarcane varieties with cold tolerance via a conventional program and molecular breeding, but also helps to accelerate the determination of the molecular mechanism underlying cold tolerance in sugarcane. [ABSTRACT FROM AUTHOR]

In this study, we report Phenacoccus saccharifolii (green) on sugarcane in Tamil Nadu, India, though an earlier unreported isolated occurrence was observed by us in the farmers' fields at Pugalur, Tamil Nadu. This pest has now become a major threat to sugarcane cultivation across the state as it can often kill the infested canes with or without the association of the fungal disease, pokkah boeng. Field observations revealed that the ratoon crop was affected more than the plant crop in the same locality. This species was found in large colonies, primarily between the --2 and +1 leaf of the sugarcane plant and hence, named as crown mealybug. Infestation leads to severe mottling in the leaf whorl and death of the central shoot. To the best of our knowledge, there are no earlier studies on the occurrence of this mealybug on Saccharum spontaneum L. Well-developed colonies showed high activity of three encyrtid parasitoids, viz. Aenasius phenococci (Ashmead), Aenasius arizonensis (Girault) and Leptomastix dactylopii Howard in the areas surveyed. [ABSTRACT FROM AUTHOR]

NRAMP(natural resistance-associated macrophage proteins), which can transport metal ions such as Fe2+, Mn2+, Zn2+ and Cd2+, plays an essential role in response to heavy metal stress in plant. To better understand the characteristics of the ScNRAMP gene family, bioinformatics methods were employed to identify and comprehensively analyze ScNRAMP gene family which includes protein physicochemical properties, gene structure, cis-acting elements, conserved motif, domain and evolutionary relationships. The results were as follows: A total of 29 ScNRAMP genes were identified in the Saccharum spontaneum genome; These 29 genes were unevenly distributed on 19 chromosomes, and contained 6 to 10 conserved motifs; The encoded proteins were all unstable proteins with no signal peptides and the subcellular locations were all on the plasma membrane; The number of membranes ranged from 6 to 12, and the secondary structure was composed of α-helix and random coils as the main components; Moreover, cis-acting elements analysis suggested that ScNRAMP may be involved in regulation of stress and development by involving in phytohormone metabolism; The tissue-specific analysis based on RNA-seq transcriptomics expression data of Saccharum spontaneum, showed that spatiotemporal expression of 29 ScNRAMP genes in the leaves and stems of sugarcane at different development stages; Phylogenetic analysis showed that the 29 ScNRAMP genes can be divided into three subfamilies (I, Ⅱ and Ⅲ). This study can be useful to better understand the ScNRAMP gene family and provide significant candidate genes that respond to the stress of heavy metals in sugarcane for further study. [ABSTRACT FROM AUTHOR]

Drought is the abiotic factor that adversely affects plant growth, development survival, and crop productivity, posing a substantial threat to sustainable agriculture worldwide, especially in warm and dry areas. However, the extent of damage depends upon the crop growth stage, severity and frequency of the stress. In general, the reproductive growth phase is more sensitive to stresses causing a substantial loss in crop productivity. Saccharum spontaneum (L.) is the most variable wild relative of sugarcane with potential for use in sugarcane crop improvement programs. In the present study addresses the transcriptomic analysis of drought stress imposed by polyethylene glycol-6000 (PED-6000; w/v-25%) on the root tip tissues of S. spontaneum GX83-10. The analysis of microarrays of drought-stressed roots was performed at 0 (CK), 2 (T2), 4 (T4), 8 (T8) and 24 h (T24). The analyzed data were compared with the gene function annotations of four major databases, such as Nr, KOG/COG, Swiss-Prot, and KEGG, and a total of 62,988 single-gene information was obtained. The differently expressed genes of 56237 (T4), 59319 (T8), and 58583 (T24), among which CK obtained the most significant number of expressed genes (35920) as compared to T24, with a total of 53683 trend genes. Gene ontology (GO) and KEGG analysis were performed on the 6 important trends, and a total of 598 significant GO IDs and 42 significantly enriched metabolic pathways. Furthermore, these findings also aid in the selection of novel genes and promoters that can be used to potentially produce crop plants with enhanced stress resistance efficiency for sustainable agriculture. [ABSTRACT FROM AUTHOR]

Sugarcane (Saccharum spp.) is an economically vital crop that is a primary source of sugar in our food and is also used for ethanol production. Various studies have been performed to understand the molecular mechanisms underlying sugar accumulation in sugarcane, but the complex, polyploid genome has posed many challenges. Here, we analyzed the recently sequenced genomes of two sugarcane varieties: Saccharum spontaneum, a geographically widespread, stress tolerant, and low sugar-accumulating wild relative of domesticated sugarcane, and Saccharum officinarum, a high sugar-accumulating variety, to investigate the composition and roles of two sugar transporter protein families, Sucrose Transporters (SUTs) and Tonoplast Sugar Transporters (TSTs). We found an increase in the number of alleles for various SUT and TST genes in S. officinarum and S. spontaneum compared to sorghum and other grass species, and we identified new putative TST genes previously uncharacterized. We analyzed expression levels of these genes in various tissues at different stages and identified SUTs and TSTs likely involved in sugar transport and storage. We hypothesize that these sugar transporter genes in S. officinarum, particularly TSTs, contribute to the ability of modern sugarcane hybrid varieties to accumulate large amounts of sugar in the stem. [ABSTRACT FROM AUTHOR]