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BACKGROUND: Water resource development projects are essential for increasing agricultural productivity and ensuring food security. However, these activities require the modification of pre-existing environmental settings, which may alter mosquito larval habitat availability and seasonality. The intensive utilization of current adult vector control tools results in insecticide resistance among the main vectors. When coupled with behavioural resistances, a shift in malaria vector feeding and resting behaviours could compromise the effectiveness of the current adult vector control strategies. Thus, it is important to look for new or alternative vector control interventions for immatures to complement adult control by focusing on different larval habitats and their seasonal availability. Thus, this study investigated larval habitat seasonality and seasonal larval abundance and distribution in irrigated sugar cane plantation settings in Ethiopia. METHODS: Anopheles mosquito larval habitats were surveyed and visited twice a month for a period of 14 months. Anopheline larvae and pupae were collected, reared, and fed finely ground fish food. Adults were provided with sucrose solution and kept under standard conditions. Female Anopheles mosquitoes were identified morphologically and using a species-specific PCR assay. Environmental parameters, which include habitats physico-chemical characteristics, were assessed. Larval habitat diversity and larval abundance and distribution were determined across different seasons. RESULTS: The study revealed that Anopheles gambiae sensu lato (s.l.) was the most predominant 4197(57%) vector species, followed by Anopheles coustani complex 2388 (32.8%). Molecular analysis of sub-samples of An. gambiae s.l. resulted in Anopheles arabiensis (77.9%) and Anopheles amharicus (21.5%), and the remaining 1.1% (n = 7) sub-samples were not amplified. Physico-chemical parameters such as temperature (t = 2.22, p = 0.028), conductivity (t = 3.21, p = 0.002), dissolved oxygen (t = 7.96, p = 0.001), nitrate ion (t = 2.51, p = 0.013), and ammonium ion (t = 2.26, p = 0.025) showed a significant and direct association with mosquito larval abundance. Furthermore, mosquito larval abundance was correlated with distance to the nearest houses (r = - 0.42, p = 0.001), exposure to sunlight (r = 0.34, p = 0.001), during long and short rainy season animal hoof prints, truck tires/road puddles and rain pools were negatively correlated (r = - 0.22, p = 0.01) and types of habitat (r = - 0.20, p = 0.01). Significant habitat type productivity were observed in man-made pools (t = 3.881, P = 0.01163), rain pools, animal hoof prints, (t = - 4.332, P = 0.00749 in both short and long rainy season, whereas, during dry seasons habitat type productivity almost similar and have no significance difference. CONCLUSION: The study found that different larval habitats had variable productivity in different seasons, and that physical and physicochemical features like ammonium and nitrate, as well as the distance between larval habitats and households, are related to larval production. As a result, vector control should take into account the seasonality of Anopheles larval habitat as well as the impact of pesticide application on larval source management.

BACKGROUND: Water resource development projects, such as dams and irrigation schemes, have a positive impact on food security and poverty reduction. However, such projects could increase prevalence of vector borne disease, such as malaria. This study investigate the impact of different agroecosystems and prevalence of malaria infection in Southwest Ethiopia. METHODS: Two cross-sectional surveys were conducted in the dry and wet seasons in irrigated and non-irrigated clusters of Arjo sugarcane and Gambella rice development areas of Ethiopia in 2019. A total of 4464 and 2176 study participants from 1449 households in Arjo and 546 households in Gambella enrolled in the study and blood samples were collected, respectively. All blood samples were microscopically examined and a subset of microscopy negative blood samples (n = 2244) were analysed by qPCR. Mixed effect logistic regression and generalized estimating equation were used to determine microscopic and submicroscopic malaria infection and the associated risk factors, respectively. RESULTS: Prevalence by microscopy was 2.0% (88/4464) in Arjo and 6.1% (133/2176) in Gambella. In Gambella, prevalence was significantly higher in irrigated clusters (10.4% vs 3.6%) than in non-irrigated clusters (p

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]

[Objective]To clarify the codon usage characteristics and improve expression efficiency of exogenous genes in sugarcane.[Method]Codon usage bias were analyzed by Python and CodonW1.4.2 tools based on their genomes data of three species including Saccharum officinarum (LA-purple), S. sponaneum (NP-X and AP85-441), and Erianthus fulvus (Yunnan2009-3). Neutrality-plot, ENC-plot, and Parity Rule 2(PR2)-plot analysis were also used to explore the possible factors that affect the formation of codon usage bias. Simultaneously, correlation analysis between gene expressions and codon usage bias parameters was carryd out based on transcriptome data. Finally, a comparison analysis of codon usage patterns were performed between sugarcane and the other seven main model organisms, namely, Zea mays, Sorghum bicolor, Oryza sativa, Arabidopsis thaliana, Nicotiana tabacum, Escherichia coli, and Saccharomyces cerevisiae based on the average RSCU value of three species.[Result]S. officinarum, S. sponaneum, and E. fulvus were rich in GC base pairs, the average GC content was 56.3%, and GC3 was the highest, followed by GC1 and GC2, indicating that sugarcane preferred to use synonymous codons ending with a C/G base. The average ENC value was 48.45, suggesting that sugarcane had a lower codon usage bias. According to the results of neutral-plot, ENC-plot, and PR2-plot analysis, the codon usage bias of four genomes was affected by natural selection, mutation pressure, and so on, and the natural selection dominated in them. Correlation analysis showed that codon preference parameters were significantly correlated with the actual transcription expressions of genes, but the correlation was not strong. Based on the RSCU and ∆RSCU values, thirteen identical optimal codons were confirmed, and all of them were ended with C/G base pairs. The codon usage characteristics were not different at genome-wide and chromosome level. In addition, the codon usage bias of sugarcane was similar to that of Z. mays, S. bicolor, and O. sativa, while it had a significant difference with A. thaliana, N. tabacum, E. coli, and S. cerevisiae.[Conclusion]The codon usage bias among S. officinarum, S.sponaneum and E. fulvus was highly similar, and its formation was affected by natural selection and mutation pressure factors. Meanwhile, Z. mays, O. sativa and S. bicolor could be used for elite gene function research on sugarcane as a exogenous expression system on account of their codon usage bias patterns. [ABSTRACT FROM AUTHOR]

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]

Acidovorax avenae subsp. avenae (Aaa) is the causal agent of red stripe in sugarcane, a disease characterized by two forms: leaf stripe and top rot. Despite the importance of this disease, little is known about Aaa infection mechanisms, and studies of virulence factors (VFs) have not been reported. Previous analysis of Aaa isolates obtained from sugarcane fields in Tucumán, Argentina, suggested that pathogenicity was not related to genetic groups determined by rep‐PCR analysis. Therefore, the aims of this work were to analyse VFs produced by Aaa strains from different genetic groups and to evaluate the association among VFs, between VFs and Aaa pathogenicity and between VFs and Aaa genetic diversity. Bacterial motility (sliding, swimming and twitching), extracellular enzyme activities (proteases, amylases and endoglucanases), H2O2‐mediated oxidative stress, cell adhesion and exopolysaccharide (EPS) production were assayed in 14 Aaa isolates from different genetic groups. Pearson's correlation analysis and principal component analysis (PCA) were performed. For each VF analysed, values were variable presenting quantitative traits among the strains. Significant correlations were observed among the VFs, though no clear trend was identified between them and the pathogenicity or genetic group. Results reinforce the idea that a single VF does not account for the infection outcome, but a more complex process occurs where the interplay among VFs must be considered. The results of this study are crucial because they provide insight into the infection mechanism of this bacterium. [ABSTRACT FROM AUTHOR]

Resumo: As pastagens naturais, um dos principais ecossistemas do mundo, estão ameaçadas e as espécies nativas são desejáveis quando se trata de restauração. Os principais processos para o sucesso da restauração das pastagens são o estabelecimento das plantas e a adição de sementes no solo. Assim, isso requer a superação das barreiras que impedem a germinação e estratégias de dispersão de sementes. Este trabalho teve como objetivo avaliar o potencial germinativo, tratamentos para superar a dormência de sementes e a dispersão por endozoocoria de espécies nativas forrageiras por bovinos. Sementes de 21 espécies nativas das quatro famílias botânicas mais comuns (Poaceae, Asteraceae, Fabaceae e Cyperaceae) foram coletadas em uma área de pastagem natural (Bioma Pampa) e utilizadas nos experimentos. Experimento I: foi realizada a germinação em condições controladas de todas as espécies e comparada com a da forragem comercial (Paspalum notatum cv. "Pensacola"). Experimento II: foram testados três tratamentos para superação da dormência das sementes (escarificação mecânica e química e priming) em seis espécies. Experimento III: foi avaliada a recuperação, viabilidade e germinação das sementes das espécies nativas Paspalum notatum Flüggé e Desmodium incanum DC em fezes de gado. Os resultados mostram que Paspalum umbrosum Trin. e Saccharum angustifolium Nees apresentam alto potencial germinativo quando comparadas à forragem comercial. Os tratamentos para superar a dormência das sementes aumentaram a germinação de D. incanum, Paspalum plicatulum Michx. e Paspalum dilatatum Poir. A recuperação total de sementes de 15% (P. notatum) e 26% (D. incanum), sem afetar a viabilidade das sementes, mostra que os bovinos são capazes de suprir o banco de sementes do solo com espécies nativas. O potencial germinativo, tratamentos para superar a dormência de sementes e dispersão endozoocórica de espécies nativas forrageiras podem ser explorados na restauração de pastagens naturais. [ABSTRACT FROM AUTHOR]

Sugarcane mosaic virus (SCMV) is the main etiological agent of sugarcane mosaic disease, which affects sugarcane and other grass crops. Despite the extensive characterization of quantitative trait loci controlling resistance to SCMV in maize, the genetic basis of this trait in sugarcane is largely unexplored. Here, a genome-wide association study was performed and machine learning coupled with feature selection was used for genomic prediction of resistance to SCMV in a diverse sugarcane panel. Nine single-nucleotide polymorphisms (SNPs) explained up to 29.9% of the observed phenotypic variance and a 73-SNP set predicted resistance with high accuracy, precision, recall, and F1 scores (the harmonic mean of precision and recall). Both marker sets were validated in additional sugarcane genotypes, in which the SNPs explained up to 23.6% of the phenotypic variation and predicted resistance with a maximum accuracy of 69.1%. Synteny analyses suggested that the gene responsible for the majority of SCMV resistance in maize is absent in sugarcane, explaining why this major resistance source has not been identified in this crop. Finally, using sugarcane RNA-Seq data, markers associated with resistance to SCMV were annotated, and a gene coexpression network was constructed to identify the predicted biological processes involved in resistance. This network allowed the identification of candidate resistance genes and confirmed the involvement of stress responses, photosynthesis, and the regulation of transcription and translation in resistance to SCMV. These results provide a practical marker-assisted breeding approach for sugarcane and identify target genes for future studies of SCMV resistance. [ABSTRACT FROM AUTHOR]

[Display omitted] • There is no high-quality reference genome for sugarcane cultivars at the current stage. • A full-length transcriptome dataset constructed at the allelic level could serve as a good reference. • Differential analysis uncovered the potential contribution of subgenome Saccharum spontaneum to sugar accumulation. • The different or even opposite expression patterns of alleles reflected the complexity of gene regulation in sugarcane. Modern sugarcane cultivars (Saccharum spp. hybrids) derived from crosses between S. officinarum and S. spontaneum , with high-sugar traits and excellent stress tolerance inherited respectively. However, the contribution of the S. spontaneum subgenome to sucrose accumulation is still unclear. To compensate for the absence of a high-quality reference genome, a transcriptome analysis method is needed to analyze the molecular basis of differential sucrose accumulation in sugarcane hybrids and to find clues to the contribution of the S. spontaneum subgenome to sucrose accumulation. PacBio full-length sequencing was used to complement genome annotation, followed by the identification of differential genes between the high and low sugar groups using differential alternative splicing analysis and differential expression analysis. At the subgenomic level, the factors responsible for differential sucrose accumulation were investigated from the perspective of transcriptional and post-transcriptional regulation. A full-length transcriptome annotated at the subgenomic level was provided, complemented by 263,378 allele-defined transcript isoforms and 139,405 alternative splicing (AS) events. Differential alternative splicing (DA) analysis and differential expression (DE) analysis identified differential genes between high and low sugar groups and explained differential sucrose accumulation factors by the KEGG pathways. In some gene models, different or even opposite expression patterns of alleles from the same gene were observed , reflecting the potential evolution of these alleles toward novel functions in polyploid sugarcane. Among DA and DE genes in the sucrose source-sink complex pathway, we found some alleles encoding sucrose accumulation-related enzymes derived from the S. spontaneum subgenome were differentially expressed or had DA events between the two contrasting sugarcane hybrids. Full-length transcriptomes annotated at the subgenomic level could better characterize sugarcane hybrids, and the S. spontaneum subgenome was found to contribute to sucrose accumulation. [ABSTRACT FROM AUTHOR]

Sugarcane is an economically important crop plant across the globe as it is the primary source of sugar and biofuel. Its growth and development are greatly influenced by water availability; therefore, in periods of water scarcity, yields are severely compromised. Small Ubiquitin‐Like Modifier (SUMO) proteases play an important role in stress responses by regulating the SUMO‐related post‐translational modification of proteins.In an attempt to enhance drought tolerance in sugarcane, this crop was genetically transformed with a cysteine protease (OVERLY TOLERANT TO SALT‐1; OTS1) from Arabidopsis thaliana using particle bombardment. Transgenic plants were analysed in terms of photosynthetic capacity, oxidative damage, antioxidant accumulation and the SUMO‐enrich protein profile was assessed.Sugarcane transformed with the AtOTS1 gene displayed enhanced drought tolerance and delayed leaf senescence under water deficit compared to the untransformed wild type (WT). The AtOTS1 transgenic plants maintained a high relative moisture content and higher photosynthesis rate when compared to the WT. In addition, when the transgene was expressed at high levels, the transformed plants were able to maintain higher stomatal conductance and chlorophyl content under moderate stress compared to the WT. Under severe water deficit stress, the transgenic plants accumulated less malondialdehyde and maintained membrane integrity. SUMOylation of total protein and protease activity was lower in the AtOTS1 transformed plants compared to the WT, with several SUMO‐enriched proteins exclusively expressed in the transgenics when exposed to water deficit stress.SUMOylation of proteins likely influenced various mechanisms contributing to enhanced drought tolerance in sugarcane. [ABSTRACT FROM AUTHOR]

Introduction: Remorins (REMs) are plant-specific membrane-associated proteins that play important roles in plant-pathogen interactions and environmental adaptations. Group I REMs are extensively involved in virus infection. However, little is known about the REM gene family in sugarcane (Saccharum spp. hyrid), the most important sugar and energy crop around world. Methods: Comparative genomics were employed to analyze the REM gene family in Saccharum spontaneum. Transcriptomics or RT-qPCR were used to analyze their expression files in different development stages or tissues under different treatments. Yeast two hybrid, bimolecular fluorescence complementation and co-immunoprecipitation assays were applied to investigate the protein interaction. Results: In this study, 65 REMs were identified from Saccharum spontaneum genome and classified into six groups based on phylogenetic tree analysis. These REMs contain multiple cis-elements associated with growth, development, hormone and stress response. Expression profiling revealed that among different SsREMs with variable expression levels in different developmental stages or different tissues. A pair of alleles, ScREM1.5e-1/-2, were isolated from the sugarcane cultivar ROC22. ScREM1.5e-1/-2 were highly expressed in leaves, with the former expressed at significantly higher levels than the latter. Their expression was induced by treatment with H2O2, ABA, ethylene, brassinosteroid, SA or MeJA, and varied upon Sugarcane mosaic virus (SCMV) infection. ScREM1.5e-1 was localized to the plasma membrane (PM), while ScREM1.5e-2 was localized to the cytoplasm or nucleus. ScREM1.5e-1/-2 can self-interact and interact with each other, and interact with VPgs from SCMV, Sorghum mosaic virus, or Sugarcane streak mosaic virus. The interactions with VPgs relocated ScREM1.5e-1 from the PM to the cytoplasm. Discussion: These results reveal the origin, distribution and evolution of the REM gene family in sugarcane and may shed light on engineering sugarcane resistance against sugarcane mosaic pathogens. [ABSTRACT FROM AUTHOR]

BACKGROUND: Herbivory risk is mediated by plant traits related to nutrition and defense that can vary within a species by genotype and age. Prior herbivore damage accrued by a plant can also interact with these traits to alter future herbivory potential by changing plant quantity or quality. Sugarcane (Saccharum spp.) is a perennial crop where aboveground biomass is harvested annually and with varieties differing in nutrition and defenses, making it conducive to evaluating varietal resistance mechanisms. Using data from 16 sugarcane varieties and 28 years, we assessed damage from the primary pest in Louisiana, the sugarcane borer (Diatraea saccharalis, SCB), relative to variety, crop year (ratoon), plant traits, and incidence of prior herbivory. RESULTS: SCB damage differed among varieties but not crop year, mostly following previously established classifications of SCB resistance, and correlated with select nutritional and defense traits. Within a crop year, the probability of SCB damage increased with prior conspecific damage on the same stalk. However, the strength of this prior damage effect did not match known resistance patterns but still differed with variety. CONCLUSIONS: Interactions of plant variety, traits, and prior pest damage but not age impacted sugarcane borer risk. Borer damage was associated with nutritional traits of fiber and sugar content, but not consistently with defensive traits like high stalk wax or hair density, indicating there may be additional resistance traits or indirect impacts of these traits on predators. Published 2023. This article is a U.S. Government work and is in the public domain in the USA. [ABSTRACT FROM AUTHOR]

Saccharum species are of great importance as fruit crops due to their economic and food value. S. fulvum is a wild relative of sugarcane that has a wide geographic distribution and is well-adapted to various environmental conditions. It exhibits high resistance to pests, diseases, drought, cold, and degraded soils, making it a valuable resource for sugarcane research. Here, we report the chloroplast genome of S. fulvum. This chloroplast genome was 141,151 bp in length with a GC content of 38.41%. The large single-copy, small single-copy, and inverted repeat regions were 83,030 bp, 12,533 bp, and 22,794 bp in length, respectively. The chloroplast genome contained 111 different genes, including 77 protein-coding genes, 4 rRNA genes, and 30 tRNA genes. Phylogenetic analysis indicated that S. fulvum was closely related to S. narenga. This study not only enriches the genome information of Saccharum, but also will be useful for the evolutionary study of the family Poaceae. [ABSTRACT FROM AUTHOR]

The World Collection of Sugarcane and Related Grasses, maintained at the USDA-ARS in Miami, FL, is one of the largest sugarcane germplasm repositories in the world. However, the genetic integrity of the Saccharum spp. germplasm in this collection has not been fully analyzed. In this study, we employed a single-dose SNP panel to genotype 901 sugarcane accessions, representing six Saccharum species and various hybrids. Our analysis uncovered a high rate of clone mislabeling in the collection. Specifically, we identified 86 groups of duplicates, characterized by identical SNP genotypes, which encompassed 211 accessions (23% of the total clones), while 135 groups, constituting 471 clones (52% of the total), exhibited near-identical genotypes. In addition, twenty-seven homonymous groups were detected, which shared the same clone name but differed in SNP genotypes. Hierarchical analysis of population structure partitioned the Saccharum germplasm into five clusters, corresponding to S. barberi, S. sinense, S. officinarum, S. spontaneum and S. robustum/S. edule. An assignment test, based on the five Saccharum species, enabled correcting 141 instances of mislabeled species memberships and inaccuracies. Moreover, we clarified the species membership and parentage of 298 clones that had ambiguous passport records (e.g., ‘Saccharum spp’, ‘unknown’, and ‘hybrid’). Population structure and genetic diversity in these five species were further supported by Principal Coordinate Analysis and neighbor-joining clustering analysis. Analysis of Molecular Variance revealed that within-species genetic variations accounted for 85% of the total molecular variance, with the remaining 15% attributed to among-species genetic variations. The single-dose SNP markers developed in this study offer a robust tool for characterizing sugarcane germplasm worldwide. These findings have important implications for sugarcane genebank management, germplasm exchange, and crop genetic improvement.

Due to complex polyploid, sugarcane whole genome sequencing and characterization lag far behind other crops. PCR-based DNA markers are a viable low-cost option to evaluate genetic diversity and verify genotypes. In this study, the 5S ribosomal RNA-intergenic spacer (ITS) of 171 accessions of Saccharum spp. and Tripidium spp. was dissected, including 30 accessions of S. officinarum, 71 of S. spontaneum, 17 of S. robustum, 25 of S. barberi, 13 of S. sinense, 2 of S. edule, 5 sugarcane cultivars (Saccharum spp. hybrids), 6 of Tripidium spp. (formally Erianthus spp.), and 2 of unknown species. The ITS spacers were amplified from 10 ng of the leaf DNA of each accession with the universal PCR primers PI and PII. The PCR-amplified spacers (amplicons) were analyzed by both agarose gel and capillary electrophoresis (CE). While agarose gel electrophoresis revealed five banding patterns, a total of 42 polymorphic amplicons, ranging from 60 to 506 bp, were detected by CE. Three amplicons, 234-, 235-, and 236-bp in size, were amplified from all accessions of six Saccharum species, except for three S. robustum accessions (Molokai 5573, NG 57-054, and NG 77-235) that lacked the 236-bp amplicon. The 234-, 235-, 236-bp banding pattern found in S. spontaneum was less consistent than other Saccharum species, sometimes missing a few but not all the bands in this region. An amplicon of 61-bp was amplified only from the sugarcane hybrid varieties. The PI/PII patterns indicated diversity and subpopulations within Saccharum, which could potentially be used in Breeding. Moreover, all Saccharum-specific amplicons were mostly absent in Tripidium spp. accessions, which produced 405-bp and 406-bp amplicons, and any pattern of the exceptions indicated misidentification. The T. bengalense accession Kalimpong had a unique CE-banding pattern that was different from all other accessions. Although the clustering pattern of the 42 amplicons only discriminated at the genus level, these amplicons helped identify nine misclassified accessions. This study further demonstrates that these PI/PII amplicons could be particularly useful markers for breeders at sugarcane field stations to quickly confirm and discriminate among the accessions of germplasm collections. [ABSTRACT FROM AUTHOR]

• Sodium silicate can be used as a bio-stimulant agent during the commercial micropropagation of sugarcane hybrids. • Silicon helps to increase morphological and photosynthetic pigments responses in sugar cane in vitro. • The stomatal index and stomatal occlusion are not altered with the application of silicon. • Acclimatization survival rate increases with the presence of silicon. Sugarcane (Saccharum spp. hybrids) is used as raw material in the agri-food and bioenergy industries. Plant tissue culture (PTC) allows production of many propagules in a relatively short time and limited space. Silicon (Si) is considered a non-essential element, and studies have demonstrated a positive impact on the development of plants obtained through PTC. This study aimed to evaluate the bio-stimulant effect of sodium silicate (Na 2 SiO 3) on the in vitro propagation of sugarcane (CP 72-2086 and Mex 69-290). Plant tips were established for each variety. The shoots obtained were then cultivated in an MS medium supplemented with different concentrations of Na 2 SiO 3 (0, 2.5, 5.0, and 10.0 mg L−1). After 30 d, morphometric analysis, quantification of photosynthetic pigments, and stomatal index measurements were performed. The results showed that 10.0 mg L−1 of Na 2 SiO 3 had a positive effect on the morphology of both varieties. The CP 72-2086 variety had a 0.5 number of shoots, 6.36 leaves and 5.8 roots more compared to the control. In contrast, the Mex 69-290 variety had more sizable proportion of shoot length (1.42 times), root length (2.20 times), and dry weight (1.33 times) compared to the control. However, 2.5 and 5.0 mg L−1 of Na 2 SiO 3 decreased the responses of variables evaluated in both varieties compared to the highest concentration. While the addition of Na 2 SiO 3 in both varieties had a bio-stimulant effect on the content of photosynthetic pigments. Results obtained suggest that Na 2 SiO 3 can be used as a bio-stimulant agent during the commercial micropropagation of sugarcane hybrids. [ABSTRACT FROM AUTHOR]

The modern cultivars of sugarcane (Saccharum spp.) are highly polyploid and accumulate aneuploidies due to their history of domestication, genetic improvement and interspecific hybrid origin involving the domesticated sweet species Saccharum officinarum ('noble cane') and the wild Saccharum spontaneum, both with an evolutionary history of polyploidy. The first hybrids were backcrossed with S. officinarum, and selection from progenies in subsequent generations established the genetic basis of modern cultivars. Saccharum genome complexity has inspired several molecular studies that have elucidated aspects of sugarcane genome constitution, architecture and cytogenetics. Herein, we conducted a comparative analysis of the meiotic behaviour of representatives of the parentals S. officinarum and S. spontaneum, and the commercial variety, SP80‐3280. S. officinarum, an octoploid species, exhibited regular meiotic behaviour. In contrast, S. spontaneum and SP80‐3280 exhibited several abnormalities from metaphase I to the end of division. We reported and typified, for the first time, the occurrence of peri‐ and paracentric inversions. Using in‐situ hybridisation techniques, we were able to determine how pairing association occurred at diakinesis, the origin of lagging chromosomes and, in particular, the mitotic chromosome composition of SP80‐3280. Interestingly, S. spontaneum and recombinant chromosomes showed the most marked tendency to produce laggards in both divisions. Future attempts to advance knowledge on sugarcane genetics and genomics should take meiotic chromosome behaviour information into account. [ABSTRACT FROM AUTHOR]

Sugarcane crop is irrigated using surface, overhead, and drip irrigation methods. Increased water use in sugarcane is a major concern around the world, implying the need for water accounting, developing water-efficient hybrids and water-saving agro-techniques for long-term conservation and use of water. "Water Footprint (WF)" is a measure of both direct and indirect water usage accountable for any product and/or process. In praxis, 'Green Water Footprint' (GWF) and 'Blue Water Footprint' (BWF) are extremely crucial for the restoration of essential ecosystem services (ES), such as sugarcane production. The WF metric was used as a priority tool in our study to evaluate water-efficient sugarcane hybrids, germplasm clones, deficit irrigation scheduling, crop geometry, and water conservation measures. Precise and accurate WF quantification would supplement the decision-making processes for managing available water resources in sugarcane agriculture. In split plot experimental design two research investigations on water management in sugarcane were undertaken at the ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu, India. The major objective of the research trails was to find out suitable sugarcane hybrids and agronomic management practices to minimise water usage in sugarcane cultivation in water stressed and drought prone areas of tropical India. Our investigation comprised two phases; the first one being assessment of the impact of deficit irrigation scheduling, planting techniques and water conservation measures in sugarcane production, while the second phase dealt with genotypic evaluation under variable irrigation scheduling. Results showed that BWF reduced significantly in the first ratoon crop due to deficit irrigation scheduling coupled with planting of two budded setts and application of sugarcane trash at the rate of 5 t ha−1. Sugarcane hybrids viz., Co 85019, Co 10026, Co 12009, Co 13014, Co 14002, Co 14025, Co 15015, and Co 15018 were more water efficient, with a lower total WF. Among the germplasm clones, Fiji 55, ISH 111, ISH 107, Pathri, and Gungera exhibited lower GWF, BWF and total WF. [ABSTRACT FROM AUTHOR]

Manganese toxicity has limited sugarcane (Saccharum spp. hybrid.) growth and production in acidic soils in south China. The rhizosphere plays an irreplaceable role in plant adaptation to soil abiotic stress, but the responses of the sugarcane rhizosphere to manganese toxicity are still unknown. We designed pot experiments in Mn-rich acidic soil, collected the sugarcane rhizosphere and bulk soil samples, and then investigated the changes in Mn-related soil parameters and microbiome. The results indicated that the water-soluble and exchangeable manganese concentrations in the sugarcane rhizosphere were significantly lower than that in the bulk soil, which was not associated with soil pH changes. In contrast, the number of bacteria and the activity of peroxidase, sucrase, urease, and laccase in the rhizosphere were significantly higher. The 16S rDNA sequencing results showed that the bacterial diversity and quantity along with the abundance of Proteobacteria in the rhizosphere were significantly higher than in the bulk soil, while the abundance of Acidobacteria was lower than in the bulk soil. The soil laccase activity and the number of bacteria decreased significantly with the increase in the manganese toxicity stress. Finally, the relative abundance of proteins associated with manganese transportation and oxidation was significantly higher in the rhizosphere soil. In summary, the Mn-induced response of the rhizosphere is an important mechanism in sugarcane adaptation to manganese toxicity in acidic soil. [ABSTRACT FROM AUTHOR]

Interspecific hybridization between commercial and wild canes followed by backcrossing may transfer favorable alleles responsible for drought tolerance in sugarcane. Our study aimed to assess the distribution of BC1 individuals on leaf anatomy and to classify them regarding heterosis values. Five BC1 populations were established using a commercial Saccharum spp. hybrid as a donor female and the F1 interspecific hybrids as recurrent males. Leaf anatomy included leaf thickness (LT), cuticle thickness (CT), the vertical length of bulliform cell (VBC), stomatal crypt depth (SCD), percent CT, percent VBC, and percent SCD. The anatomical traits of BC1 showed high phenotypic variations, and all populations can be divided into three groups based on their heterosis values. Heterosis seemed to be genotype and trait dependent as the estimates varied considerably across populations and observed traits, ranging from negative on LT to positive on VBC. Group I (BC1-1) showed positive heterosis on percent CT, percent VBC, and percent SCD. Dendrogram analysis revealed that some clones in population BC1-1 were promising regarding stalk weight and leaf anatomy, making them desirable for further clone selections. Backcrossing with commercial canes resulted in higher BC1 means than their mid-parents despite low heterosis on leaf anatomy. [ABSTRACT FROM AUTHOR]

Soil salinity affects plant growth, compromising sugarcane cultivation in regions with great production potential. Saccharum complex genotypes that respond positively to growth under saline environment can be used in the diversification of sugarcane cultivars to obtain greater economic returns. The objective of this study was to evaluate growth‐related traits of Saccharum genotypes grown under the presence and absence of salinity. The experiment was carried out in a 32 × 2 factorial scheme in a randomized block design with three replicates. The first factor consisted of 32 genotypes of the Saccharum complex and the second factor consisted of the presence and absence of salinity. The salinity provided higher mean values than the environment without salinity for plant height in the genotypes G9, G11, G13, G22 and G28, leaf number for G9 and G24, leaf area index for G9 and stem diameter for G1, G11 and G24. Among the genotypes tested, G1, G9, G11, G13, G22, G24 and G28 were the most promising genotypes and could be used for breeding new sugarcane cultivars of enhanced salinity tolerance. [ABSTRACT FROM AUTHOR]

The World Collection of Sugarcane and Related Grasses, maintained at the USDA-ARS in Miami, FL, is one of the largest sugarcane germplasm repositories in the world. However, the genetic integrity of the Saccharum spp. germplasm in this collection has not been fully analyzed. In this study, we employed a single-dose SNP panel to genotype 901 sugarcane accessions, representing six Saccharum species and various hybrids. Our analysis uncovered a high rate of clone mislabeling in the collection. Specifically, we identified 86 groups of duplicates, characterized by identical SNP genotypes, which encompassed 211 accessions (23% of the total clones), while 135 groups, constituting 471 clones (52% of the total), exhibited near-identical genotypes. In addition, twenty-seven homonymous groups were detected, which shared the same clone name but differed in SNP genotypes. Hierarchical analysis of population structure partitioned the Saccharum germplasm into five clusters, corresponding to S. barberi, S. sinense, S. officinarum, S. spontaneum and S. robustum/S. edule. An assignment test, based on the five Saccharum species, enabled correcting 141 instances of mislabeled species memberships and inaccuracies. Moreover, we clarified the species membership and parentage of 298 clones that had ambiguous passport records (e.g., ‘Saccharum spp’, ‘unknown’, and ‘hybrid’). Population structure and genetic diversity in these five species were further supported by Principal Coordinate Analysis and neighbor- joining clustering analysis. Analysis of Molecular Variance revealed that within- species genetic variations accounted for 85% of the total molecular variance, with the remaining 15% attributed to among-species genetic variations. The single-dose SNP markers developed in this study offer a robust tool for characterizing sugarcane germplasm worldwide. These findings have important implications for sugarcane genebank management, germplasm exchange, and crop genetic improvement. [ABSTRACT FROM AUTHOR]

Sugarcane production benefitted from useful genes imparted from Saccharum spontaneum L. Interspecific hybrids were evaluated for sugar and biomass traits in three environments, including two plants and one ratoon crop. The objective was to estimate genetic parameters for traits in this population and to develop appropriate breeding strategies and germplasm for use in variety development in both the sugar and bioenergy industries. Heritability was highest with all three environments considered; however, the increase was minimal compared with estimates from the first ratoon crop, suggesting resources will be better spent selecting in the first ratoon crop. Significant differences (p < 0.05) found among families for sucrose content‐related traits warrant selecting first among families before selecting among genotypes within families for these traits. The same was not true for cane yield and its components. Heritability was low to moderate (> 0.3 < 0.47) for cane yield and its components and high (> 0.7) for all other traits, suggesting early selection in small plots could emphasize sucrose content‐related traits. Selecting intensely for a highly heritable trait in one stage can influence genetic variation of another trait in subsequent stages. Therefore, multivariate selection methods were employed that identified groups of genotypes with characteristics distinct to both industries. The S. spontaneum parents dominated trait variation in the hybrid population. Consequently, although genotypes with potential for the sugar industry would have to undergo rounds of backcrossing to recover good sugar characteristics, genotypes with immediate potential in the bioenergy industry were easily identified in this population. Core Ideas: Sugarcane production for the sugar industry has benefitted from useful genes imparted from Saccharum spontaneum L.There is interest in exploiting S. spontaneum L. to improve production in the sugar and energy (biomass) industries.The resourcefulness of an interspecific hybrid population to produce germplasm for both industries was evaluated.Genotypes with immediate potential in the bioenergy industry were easily identified in this population.Genotypes with potential for the sugar industry would have to undergo backcrossing to recover good sugar attributes. [ABSTRACT FROM AUTHOR]

Sugarcane (Saccharum spp.) is an important crop for sugar and bioethanol production worldwide. To maintain and increase sugarcane yields in marginal areas, the use of nitrogen (N) fertilizers is essential, but N overuse may result in the leaching of reactive N to the natural environment. Despite the importance of N in sugarcane production, little is known about the molecular mechanisms involved in N homeostasis in this crop, particularly regarding ammonium (NH4+), the sugarcane's preferred source of N. Here, using a sugarcane bacterial artificial chromosome (BAC) library and a series of in silico analyses, we identified an AMMONIUM TRANSPORTER (AMT) from the AMT2 subfamily, sugarcane AMMONIUM TRANSPORTER 3;3 (ScAMT3;3), which is constitutively and highly expressed in young and mature leaves. To characterize its biochemical function, we ectopically expressed ScAMT3;3 in heterologous systems (Saccharomyces cerevisiae and Arabidopsis thaliana). The complementation of triple mep mutant yeast demonstrated that ScAMT3;3 is functional for NH3/H+ cotransport at high availability of NH4+ and under physiological pH conditions. The ectopic expression of ScAMT3;3 in the Arabidopsis quadruple AMT knockout mutant restored the transport capacity of 15N-NH4+ in roots and plant growth under specific N availability conditions, confirming the role of ScAMT3;3 in NH4+ transport in planta. Our results indicate that ScAMT3;3 belongs to the low-affinity transport system (Km 270.9 µM; Vmax 209.3 µmol g-1 root DW h-1). We were able to infer that ScAMT3;3 plays a presumed role in NH4+ source-sink remobilization in the shoots via phloem loading. These findings help to shed light on the functionality of a novel AMT2-type protein and provide bases for future research focusing on the improvement of sugarcane yield and N use efficiency. [ABSTRACT FROM AUTHOR]

Plant parts such as seeds, berries, roots, leaves, bark, or flowers can be used medicinally. This practise is known as herbal medicine, botanical medicine, or phytomedicine. Outside of mainstream treatment, herbalists have long used herbalism for conventional medicine. Grewia subinaequalisDC in the family Tiliaceae, only one genus, Grewia, yields edible fruit. Saccharum officinarum is a species of grass belonging to the genus Saccharum that is characterised by its robust growth and size. Neisosperma oppositifolium is a tree that typically exhibits a height range of 6 to 25 metres, although it has been observed to vary from as low as 2.5 metres to extraordinarily high heights of 45 metres, and in rare cases, even up to 60 metres. The presence of moisture in crude pharmaceuticals is an unavoidable factor that should be minimised to the greatest extent possible. The process of drying significantly influences both the quality and purity of the material. [ABSTRACT FROM AUTHOR]

BackgroundTo ensure food security, sub-Saharan Africa has initiated massive water resource development projects, such as irrigated agriculture, in recent years. However, such environmental modifications affect the survivorship and development of mosquitoes, which are vectors of different diseases. This study aimed at determining the effects of irrigation practices on development and survivorship of Anopheles gambiae s.l. in Ethiopia.MethodsA life table experiment was conducted to examine the effect of environmental modification on survivorship of both immature and adult An. gambiae s.l. in irrigated and non-irrigated areas. The pupation rate and development time of the immatures and adult longevity and fecundity were compared between the two settings.ResultsThe estimated mean survival time of female An. gambiae s.l. in the irrigated and non-irrigated areas was 37.9 and 31.3 days, respectively. A survival analysis showed that adult females of An. gambiae s.l. placed in an irrigated area lived significantly longer than those in a non-irrigated area (χ2 = 18.3, df = 1, P

Humicola grisea var. thermoidea is a thermophilic ascomycete and important enzyme producer that has an efficient enzymatic system with a broad spectrum of thermostable carbohydrate-active (CAZy) enzymes. These enzymes can be employed in lignocellulose biomass deconstruction and other industrial applications. In this work, the genome of H. grisea var. thermoidea was sequenced. The acquired sequence reads were assembled into a total length of 28.75 Mbp. Genome features correlate with what was expected for thermophilic Sordariomycetes. The transcriptomic data showed that sugarcane bagasse significantly upregulated genes related to primary metabolism and polysaccharide deconstruction, especially hydrolases, at both pH 5 and pH 8. However, a number of exclusive and shared genes between the pH values were found, especially at pH 8. H. grisea expresses an average of 211 CAZy enzymes (CAZymes), which are capable of acting in different substrates. The top upregulated genes at both pH values represent CAZyme-encoding genes from different classes, including acetylxylan esterase, endo-1,4-β-mannosidase, exoglucanase, and endoglucanase genes. For the first time, the arsenal that the thermophilic fungus H. grisea var. thermoidea possesses to degrade the lignocellulosic biomass is shown. Carbon source and pH are of pivotal importance in regulating gene expression in this organism, and alkaline pH is a key regulatory factor for sugarcane bagasse hydrolysis. This work paves the way for the genetic manipulation and robust biotechnological applications of this fungus. IMPORTANCE Most studies regarding the use of fungi as enzyme producers for biomass deconstruction have focused on mesophile species, whereas the potential of thermophiles has been evaluated less. This study revealed, through genome and transcriptome analyses, the genetic repertoire of the biotechnological relevant thermophile fungus Humicola grisea. Comparative genomics helped us to further understand the biology and biotechnological potential of H. grisea. The results demonstrate that this fungus possesses an arsenal of carbohydrate-active (CAZy) enzymes to degrade the lignocellulosic biomass. Indeed, it expresses more than 200 genes encoding CAZy enzymes when cultivated in sugarcane bagasse. Carbon source and pH are key factors for regulating the gene expression in this organism. This work shows, for the first time, the great potential of H. grisea as an enzyme producer and a gene donor for biotechnological applications and provides the base for the genetic manipulation and robust biotechnological applications of this fungus.

An attempt was made to identify the chromosomes from different species genomes in BC₂ progenies of Erianthus procerus x Saccharum officinarum through multi-color GISH (MCGISH). The BC₂ population was derived from the cross between a BC1 hybrid (GU 12-14) and a commercial variety, Co 16018. The BC2 progenies were studied for their somatic chromosome number and two cytotypes were observed, i.e., 2n=92 (2) and 2n=96 (5). GISH revealed that the majority of progenies were having nine Erianthus chromosomes, except 2 clones (25-5 and 25-10) were having nine Erianthus chromosomes with one chromosome fragment. The methodology for multi-color GISH was standardized and it distinguished the chromosomes from different genomes. Interspecific recombination was also detected in somatic cells of one BC₂ clone, 25-10. The hybridity of the introgressed lines has been confirmed with amplification of Erianthus specific tandem repeat sequences.

Sugarcane breeding programs incorporate foreign material to broaden the genetic base, expanding the gene pool. In South America, the Inter-university Network for the Development of the Sugarcane Industry (RIDESA) and Estación Experimental Agroindustrial Obispo Colombres (EEAOC) sugarcane breeding programs from Brazil and Argentina, respectively, have never exchanged materials. In that sense, the knowledge of the genetic diversity and population structure among sugarcane genotypes of both germplasm banks, determined in a reliable way through their molecular profiles, will provide valuable information to select the best parental accessions for crossing aimed at the efficient introgression of desirable alleles. For that, the aim was to determine the genetic diversity and population structure of 96 Saccharum commercial hybrids from RIDESA and EEAOC sugarcane breeding programs by using TRAP, SSR and markers related to disease resistance (e.g. Bru1 and G1). Genetic structure was determined through genetic similarity analysis, analysis of molecular variance (AMOVA), Multidimensional scaling (MDS), and a Bayesian method. Average PIC values were 0.25 and 0.26, Ho values were 0.24 and 0.28, and He values were 0.25 and 0.28, for TRAP and SSR primers, respectively. Genetic similarity, MDS, and analysis of structure revealed that Brazilian and Argentinean genotypes clustered in two groups clearly differentiated, whereas AMOVA suggested that there is more variability within programs than between them. Regarding Bru1 markers, Brazilian genotypes showed high frequency of haplotype 1 (71.4%) whereas Argentinean genotypes showed high frequency of haplotype 4 (80.8%); haplotypes 1 and 4 are indicated for the presence and absence of the brown rust resistance gene (Bru1), respectively. Respecting the G1 marker, most of the evaluated genotypes (60.4%) showed the presence of the fragment, in a similar proportion for genotypes of both programs. In conclusion, the exchange of materials, at least the most diverse genotypes, between RIDESA and EEAOC breeding programs will allow extending the genetic base of their germplasm banks, and the knowledge of genetic diversity will help breeders to better manage crosses, increasing the probability of obtaining more productive varieties. [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]

Plant nuclear factor (NF-Y) is a transcriptional activating factor composed of three subfamilies: NF-YA, NF-YB, and NF-YC. These transcriptional factors are reported to function as activators, suppressors, and regulators under different developmental and stress conditions in plants. However, there is a lack of systematic research on the NF-Y gene subfamily in sugarcane. In this study, 51 NF-Y genes (ShNF-Y), composed of 9 NF-YA, 18 NF-YB, and 24 NF-YC genes, were identified in sugarcane (Saccharum spp.). Chromosomal distribution analysis of ShNF-Ys in a Saccharum hybrid located the NF-Y genes on all 10 chromosomes. Multiple sequence alignment (MSA) of ShNF-Y proteins revealed conservation of core functional domains. Sixteen orthologous gene pairs were identified between sugarcane and sorghum. Phylogenetic analysis of NF-Y subunits of sugarcane, sorghum, and Arabidopsis showed that ShNF-YA subunits were equidistant while ShNF-YB and ShNF-YC subunits clustered distinctly, forming closely related and divergent groups. Expression profiling under drought treatment showed that NF-Y gene members were involved in drought tolerance in a Saccharum hybrid and its drought-tolerant wild relative, Erianthus arundinaceus. ShNF-YA5 and ShNF-YB2 genes had significantly higher expression in the root and leaf tissues of both plant species. Similarly, ShNF-YC9 had elevated expression in the leaf and root of E. arundinaceus and in the leaf of a Saccharum hybrid. These results provide valuable genetic resources for further sugarcane crop improvement programs. [ABSTRACT FROM AUTHOR]

Background and aimsModern sugarcane cultivars (Saccharum spp.) are high polyploids, aneuploids (2n = ~12x = ~120) derived from interspecific hybridizations between the domesticated sweet species Saccharum officinarum and the wild species S. spontaneum.MethodsTo analyse the architecture and origin of such a complex genome, we analysed the sequences of all 12 hom(oe)ologous haplotypes (BAC clones) from two distinct genomic regions of a typical modern cultivar, as well as the corresponding sequence in Miscanthus sinense and Sorghum bicolor, and monitored their distribution among representatives of the Saccharum genus.Key resultsThe diversity observed among haplotypes suggested the existence of three founding genomes (A, B, C) in modern cultivars, which diverged between 0.8 and 1.3 Mya. Two genomes (A, B) were contributed by S. officinarum; these were also found in its wild presumed ancestor S. robustum, and one genome (C) was contributed by S. spontaneum. These results suggest that S. officinarum and S. robustum are derived from interspecific hybridization between two unknown ancestors (A and B genomes). The A genome contributed most haplotypes (nine or ten) while the B and C genomes contributed one or two haplotypes in the regions analysed of this typical modern cultivar. Interspecific hybridizations likely involved accessions or gametes with distinct ploidy levels and/or were followed by a series of backcrosses with the A genome. The three founding genomes were found in all S. barberi, S. sinense and modern cultivars analysed. None of the analysed accessions contained only the A genome or the B genome, suggesting that representatives of these founding genomes remain to be discovered.ConclusionsThis evolutionary model, which combines interspecificity and high polyploidy, can explain the variable chromosome pairing affinity observed in Saccharum. It represents a major revision of the understanding of Saccharum diversity.

Sugarcane (Saccharum spp.) is a widely cultivated crop that fulfils approximately 75% of the sucrose demand worldwide. Owing to its polyploidy and complex genetic nature, it is difficult to identify and map genes related to complex traits, such as sucrose content. However, association mapping is one of the alternatives for identifying genes or markers for marker-assisted selection. In the present study, EST-SSR primers were obtained from in silico studies. The functionality of each primer was tested using Blast2Go software, and 30 EST-SSR primers related to sugar content were selected. These markers were validated using association analysis. A total of 70 F1 diverse genotypes for sugar content were phenotypes with two check lines. All parameters related to sugar content were recorded. The results showed a significant variation between the genotypes for sugar yield traits such as Brix value, purity, and sucrose content, etc. Correlation studies revealed that the Brix%, sucrose content, and sucrose recovery were significantly correlated. An association analysis was performed using mixed linear model to avoid false positive associations. The association analysis revealed that the SEM 407 marker was significantly associated with Brix% and sucrose content. The SEM 407 primers are putatively related to diphosphate-fructose-6-phosphate 1-phosphotransferase which is associated with Brix% and sucrose content. This functional marker can be used for marker-assisted selection for sugar yield traits in sugarcane that could accelerate the sugarcane breeding program. [ABSTRACT FROM AUTHOR]

Sugarcane (Saccharum spp.) is an important cash crop, and drought is an important factors limiting its yield. To study the drought resistance mechanism of sugarcane, the transcriptomes of two sugarcane varieties with different levels of drought resistance were compared under different water shortage levels. The results showed that the transcriptomes of the two varieties were significantly different. The differentially expressed genes were enriched in starch and sucrose metabolism, linoleic acid metabolism, glycolysis/gluconeogenesis, and glyoxylate and dicarboxylate metabolic pathways. Unique trend genes of the variety with strong drought resistance (F172) were significantly enriched in photosynthesis, mitogen-activated protein kinases signaling pathway, biosynthesis of various plant secondary metabolites, and cyanoamino acid metabolism pathways. Weighted correlation network analysis indicated that the blue4 and plum1 modules correlated with drought conditions, whereas the tan and salmon4 modules correlated with variety. The unique trend genes expressed in F172 and mapped to the blue4 module were enriched in photosynthesis, purine metabolism, starch and sucrose metabolism, betaalanine metabolism, photosynthesis-antenna proteins, and plant hormone signal transduction pathways. The expression of genes involved in the photosynthesis-antenna protein and photosynthesis pathways decreased in response to water deficit, indicating that reducing photosynthesis might be a means for sugarcane to respond to drought stress. The results of this study provide insights into drought resistance mechanisms in plants, and the related genes and metabolic pathways identified may be helpful for sugarcane breeding in the future. [ABSTRACT FROM AUTHOR]

O objetivo do experimento consistiu no reconhecimento de cultivares mais produtivas para a região Colonial do Oeste Catarinense, tendo em vista, entre outros, o aspecto da resistência à geada.

This study aimed to determine the photosynthetic performance and differences in chlorophyll fluorescence (ChlF) parameters between Eulophia dentata and its companion species Bletilla formosana and Saccharum spontaneum when subjected to different photosynthetic photon flux density (PPFDs). Leaf surfaces were then illuminated with 50, 100 (low PPFDs), 300, 500, 800 (moderate PPFDs); 1,000; 1,500; and 2,000 (high PPFDs) μmol m-2.s-1, and the ChlF parameters were measured during the whole process. Increasing nonphotochemical quenching of ChlF and decreasing potential quantum efficiency of PSII, actual quantum efficiency of PSII, and quantum efficiency ratio of PSII in dark recovery from 0-60 min were observed in all leaves. A significant and negative relationship was detected between energy-dependent quenching (qE) and photoinhibition percent in three species under specific PPFD conditions, whereas a significant and positive relationship was detected between photoinhibitory quenching (qI) and photoinhibition percent. The qE and qI can be easily measured in the field and provide useful ecological indexes for E. dentata species restoration, habitat creation, and monitoring.

BackgroundLignin deposited in plant cell walls negatively affects biomass conversion into advanced bioproducts. There is therefore a strong interest in developing bioenergy crops with reduced lignin content or altered lignin structures. Another desired trait for bioenergy crops is the ability to accumulate novel bioproducts, which would enhance the development of economically sustainable biorefineries. As previously demonstrated in the model plant Arabidopsis, expression of a 3-dehydroshikimate dehydratase in plants offers the potential for decreasing lignin content and overproducing a value-added metabolic coproduct (i.e., protocatechuate) suitable for biological upgrading.ResultsThe 3-dehydroshikimate dehydratase QsuB from Corynebacterium glutamicum was expressed in the bioenergy crop switchgrass (Panicum virgatum L.) using the stem-specific promoter of an O-methyltransferase gene (pShOMT) from sugarcane. The activity of pShOMT was validated in switchgrass after observation in-situ of beta-glucuronidase (GUS) activity in stem nodes of plants carrying a pShOMT::GUS fusion construct. Under controlled growth conditions, engineered switchgrass lines containing a pShOMT::QsuB construct showed reductions of lignin content, improvements of biomass saccharification efficiency, and accumulated higher amount of protocatechuate compared to control plants. Attempts to generate transgenic switchgrass lines carrying the QsuB gene under the control of the constitutive promoter pZmUbi-1 were unsuccessful, suggesting possible toxicity issues associated with ectopic QsuB expression during the plant regeneration process.ConclusionThis study validates the transfer of the QsuB engineering approach from a model plant to switchgrass. We have demonstrated altered expression of two important traits: lignin content and accumulation of a co-product. We found that the choice of promoter to drive QsuB expression should be carefully considered when deploying this strategy to other bioenergy crops. Field-testing of engineered QsuB switchgrass are in progress to assess the performance of the introduced traits and agronomic performances of the transgenic 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]

Flowering is a crucial phase for angiosperms to continue their species propagation and is highly regulated. In the current review, flowering in sugarcane and the associated mechanisms are elaborately presented. In sugarcane, flowering has two effects, wherein it is a beneficial factor from the breeder's perspective and crucial for crop improvement, but commercially, it depletes the sucrose reserves from the stalks; hence, less value is assigned. Different species of Saccharum genus are spread across geographical latitudes, thereby proving their ability to grow in multiple inductive daylengths of different locations according in the habituated zone. In general, sugarcane is termed an intermediate daylength plant with quantitative short-day behaviour as it requires reduction in daylength from 12 h 55 min to 12 h or 12 h 30 min. The prime concern in sugarcane flowering is its erratic flowering nature. The transition to reproductive stage which reverts to vegetative stage if there is any deviation from ambient temperature and light is also an issue. Spatial and temporal gene expression patterns during vegetative to reproductive stage transition and after reverting to vegetative state could possibly reveal how the genetic circuits are being governed. This review will also shed a light on potential roles of genes and/or miRNAs in flowering in sugarcane. Knowledge of transcriptomic background of circadian, photoperiod, and gibberellin pathways in sugarcane will enable us to better understand of variable response in floral development. [ABSTRACT FROM AUTHOR]

In sugarcane (Saccharum spp. hybrids) cultivation, viral diseases pose a great challenge across the globe. Yellow leaf (YL) disease is one of the important viral diseases caused by Sugarcane yellow leaf virus (ScYLV), a positive-sense ssRNA virus, genus Polerovirus, family Solemoviridae. The disease symptoms appear in later stages of crop growth during grand growth to maturity phase with intense midrib yellowing in the abaxial leaf surface. At present, this disease is managed through tissue (meristem) culture and healthy seed nurseries in India. However, the virus-free plants are infected quickly by secondary inoculum from aphid vectors in the field, which necessitates the importance of developing YL-resistant varieties. We screened about 600–625 sugarcane parental clones to identify true YL resistance based on 0–5 disease rating scale since 2015 and categorised them as resistant, moderately resistant, moderately susceptible, susceptible and highly susceptible. Leaf samples were collected from all these categories of plants during 2018–20 for the viral titre estimation through absolute quantification method (qRT-PCR assay). The viral load was invariably high in all categories of susceptible samples that ranged from 4.40 × 102 to 8.429 × 106, whereas in YL-free asymptomatic clones, the viral load ranged from 82.35 ± 5.90 to 5.121 × 104. The results clearly indicated that highest viral titre of 105–107 copies was present in all the susceptible clones irrespective of their disease severity grades. Our results clearly established that about 22.85% of apparently resistant sugarcane clones remained free from YL symptoms with significantly low ScYLV titre although we could not find a significant correlation between virus titre and symptom expression. The identified resistant parents will serve as sources of YL resistance to develop virus resistant sugarcane varieties. [ABSTRACT FROM AUTHOR]

Drought is a worldwide problem seriously influencing sugarcane (Saccharum L. spp. hybrids) production. The long-term domestication and selective breeding in artificial environments may have reduced the drought resistance of sugarcane. The objective of this study was to determine drought tolerance in a 138-genotype of elite sugarcane hybrids using the membership function value of drought tolerance (MFVD). Based on the drought-tolerant coefficient (DC) of four yield traits (biomass, stalk weight, stalk diameter and stalk height) and bud survival rate (SR) at different growth stage under well-watered (WW) and water-stressed (WS) conditions. As expected, genotype means decreased for all five traits with WS, and the decrease of biomass, stalk weight, stalk diameter, stalk height and bud survival rate (SR) was ≥ 24%. The broad sense heritability of five morphological traits (B, SW, SH, SD and SR) was relatively high. Correlation coefficients analysis revealed that the MFVD was significantly positively correlated with the DCB, DCSW, DCSH and DCSD at the growth stage and SR at the seedling stage. Results indicated that these characters were closely related to the drought resistance of sugarcane. Regression models built based on MFVD indicated that the variation of drought tolerant coefficient of 4 traits at the growth stage and SR at the seeding stage could explain the total variation. Thus, these five traits could be used as drought resistance indicators for screening drought resistance cultivars in sugarcane. The MFVD based on the DC of each yield traits and SR indicated that ten out of the138 sugarcane hybrids had high drought resistance, while 14 genotypes were highly susceptible to the drought, which can be used as ideal experimental materials to study the mechanism of sugarcane genotypes with contrasting drought sensitivities in response to drought stress. Our results help to fill the knowledge gap regarding to the sugarcane production under stress, shed light on sugarcane drought tolerance and provided useful information to the sugarcane breeders and producers which could be used in variety selecting and developing for dry prone regions. [ABSTRACT FROM AUTHOR]

Abstract The objective of this work was to evaluate the efficiency of early screening in the selection of sugarcane (Saccharum spp.) families for cold tolerance in a controlled environment. Fourteen sugarcane families were evaluated for leaf damage and chlorophyll content, in a controlled environment and in the field, after cold stress. The variance components and genotypic values of the families were estimated via REML/BLUP, as well as the genetic correlations between variables and environments. The heritabilities in the narrow sense and for family averages showed values above 0.23 and 0.76, respectively, and a genetic coefficient of variation above 13%, which confirmis the existence of variability and enables selection in both environments. The genetic correlations ranged from 0.59 to 0.88 and were significant for all combinations of variables and environments. The average coincidence index for the families between environments was 60% for the selected group and 85% for the unselected group. The early screening in the first stages of selection is efficient in breeding for cold tolerance in sugarcane families.

Miscanthus is a perennial wild grass that is of global importance for paper production, roofing, horticultural plantings, and an emerging highly productive temperate biomass crop. We report a chromosome-scale assembly of the paleotetraploid M. sinensis genome, providing a resource for Miscanthus that links its chromosomes to the related diploid Sorghum and complex polyploid sugarcanes. The asymmetric distribution of transposons across the two homoeologous subgenomes proves Miscanthus paleo-allotetraploidy and identifies several balanced reciprocal homoeologous exchanges. Analysis of M. sinensis and M. sacchariflorus populations demonstrates extensive interspecific admixture and hybridization, and documents the origin of the highly productive triploid bioenergy crop M. × giganteus. Transcriptional profiling of leaves, stem, and rhizomes over growing seasons provides insight into rhizome development and nutrient recycling, processes critical for sustainable biomass accumulation in a perennial temperate grass. The Miscanthus genome expands the power of comparative genomics to understand traits of importance to Andropogoneae grasses.

BackgroundDespite extensive irrigation development in Ethiopia, limited studies assessed the impact of irrigation on malaria vector mosquito composition, abundance and seasonality. This study aimed to evaluate the impact of sugarcane irrigation on species composition, abundance and seasonality of malaria vectors.MethodsAdult Anopheles mosquitoes were collected using CDC light traps from three irrigated and three non-irrigated clusters in and around Arjo-Didessa sugarcane irrigation scheme in southwestern Ethiopia. Mosquitoes were surveyed in four seasons: two wet and two dry, in 2018 and 2019. Mosquito species composition, abundance and seasonality were compared between irrigated and non-irrigated clusters. Anopheles mosquitoes were sorted out to species using morphological keys and molecular techniques. Chi square was used to test the relationships between Anopheles species occurrence, and environmental and seasonal parameters.ResultsOverall, 2108 female Anopheles mosquitoes comprising of six species were collected. Of these, 92.7% (n = 1954) were from irrigated clusters and 7.3% (n = 154) from the non-irrigated. The Anopheles gambiae complex was the most abundant (67.3%) followed by Anopheles coustani complex (25.3%) and Anopheles pharoensis (5.7%). PCR-based identification revealed that 74.7% (n = 168) of the An. gambiae complex were Anopheles arabiensis and 22.7% (n = 51) Anopheles amharicus. The density of An. gambiae complex (both indoor and outdoor) was higher in irrigated than non-irrigated clusters. The overall anopheline mosquito abundance during the wet seasons (87.2%; n = 1837) was higher than the dry seasons (12.8%; n = 271).ConclusionThe ongoing sugarcane irrigation activities in Arjo-Didessa created conditions suitable for malaria transmitting Anopheles species diversity and abundance. This could drive malaria transmission in Arjo-Didessa and its environs in both dry and wet seasons. Currently practiced malaria vector interventions need to be strengthened by including larval source management to reduce vector abundance in the irrigated areas.

BackgroundThe trend analysis of malaria data from health facilities is useful for understanding dynamics of malaria epidemiology and inform for future malaria control planning. Changes in clinical malaria characteristics, like gender and age distribution are good indicators of declining malaria transmission. This study was conducted to determine the malaria trend at Arjo-Didessa sugar development site and its vicinity, southwest Ethiopia, from 2008 to 2017.MethodsMonthly malaria confirmed case data from 2008 to 2017 was extracted from 11 health facilities based on clinical registers at Arjo sugar development site and its vicinity, southwest Ethiopia. Both positivity rate and malaria incidence rate were calculated. Changes in malaria parasite species and seasonality were analysed; age structure and gender distribution were compared between different study periods. Trend in malaria incidence and climatic impact were analysed and past LLIN and IRS campaigns were used as dynamics modifier.ResultsOver a period of 10 years, 54,020 blood film were collected for malaria diagnosis in the health facilities at the area, of which 18,049 (33.4%) were confirmed malaria cases by both microscopically and RDT. Plasmodium falciparum, Plasmodium vivax, and mixed infection (P. falciparum and P. vivax) accounted for 8660 (48%), 7649 (42.4%), and 1740 (9.6%) of the malaria cases, respectively. The study also revealed that P. vivax was the predominant over P. falciparum for 4 years (2010, 2014, 2015 and 2016). There was a remarkable reduction of overall malaria infection during the 10 years. Malaria has been reported in all age groups, but age distribution showed that vast majority of cases were adults age 15 years and above 13,305 (73.7%). In all age groups, males were more significantly affected than females (χ2 = 133.0, df = 2, P

Saccharum yield decline results from long-term monoculture practices. Changes in cropping management can improve soil health and productivity. Below-ground bacterial community diversity and composition across soybean (Glycine max (L.) Merr) cover crop, Saccharum monoculture (30+ year) and fallowed soil were determined. Near full length (~1,400 base pairs) of 16S rRNA gene sequences were extracted from the rhizospheres of sugarcane and soybean and fallowed soil were compared. Higher soil bacterial diversity was observed in the soybean cover crop than sugarcane monoculture across all measured indices (observed operationational taxonomic units, Chao1, Shannon, reciprocal Simpson and Jackknife). Acidocateria, Proteobacteria, Bacteroidetes and Planctomycetes were the most abundant bacterial phyla across the treatments. Indicator species analysis identified nine indicator phyla. Planctomycetes, Armatimonadetes and candidate phylum FBP were associated with soybean; Proteobacteria and Firmicutes were linked with sugarcane and Gemmatimonadetes, Nitrospirae, Rokubacteria and unclassified bacteria were associated with fallowed soil. Non-metric multidimensional scaling analysis showed distinct groupings of bacterial operational taxonomic units (97% identity) according to management system (soybean, sugarcane or fallow) indicating compositional differences among treatments. This is confirmed by the results of the multi-response permutation procedures (A = 0.541, p = 0.00045716). No correlation between soil parameters and bacterial community structure was observed according to Mantel test (r = 211865, p = 0.14). Use of soybean cover-crop fostered bacterial diversity and altered community structure. This indicates cover crops could have a restorative effect and potentially promote sustainability in long-term Saccharum production systems. [ABSTRACT FROM AUTHOR]

The production of fertile inflorescences is essential to make crosses for the development of new varieties of sugarcane. Within the Saccharum species and commercial hybrids of sugarcane, there is a wide range in flowering times and some varieties rarely flower; this can make it impossible to achieve some desired crosses. While photoperiod houses can assist with inducing some varieties to flower or synchronise flowering, understanding the expression of genes within the flowering pathway could provide an explanation for such variation. To this end experiments were designed to assess the photoperiod conditions within a controlled environment facility and measure changes in expression of 18 genes associated with flowering during the initial four weeks of the floral induction period at three time points across the day-light cycle. Two sugarcane varieties were selected for their differences in flowering propensity, Q208 and Q183, flowering and non-flowering, respectively. The 18 genes examined were associated with photoperiod perception, the circadian clock, the floral pathway, and floral meristem identity. Of these, 16 were detected and showed differences in expression during the light cycle and over the 4 weeks under photoperiod induction in Q208. The assessment of a subset of those genes in Q183 showed higher expression levels of ShLHY, ShCO and ShTFL1 in Q183 than Q208. One of the genes, TFL1 is a known flowering inhibitor of the penultimate step prior to floral induction. These gene profiles build on the proposed sugarcane flowering pathway and highlight key genes for manipulation to promote and synchronise flowering to assist sugarcane breeding programmes. [ABSTRACT FROM AUTHOR]