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Sugarcane, the world's most harvested crop by tonnage, has shaped global history, trade and geopolitics, and is currently responsible for 80% of sugar production worldwide1. While traditional sugarcane breeding methods have effectively generated cultivars adapted to new environments and pathogens, sugar yield improvements have recently plateaued2. The cessation of yield gains may be due to limited genetic diversity within breeding populations, long breeding cycles and the complexity of its genome, the latter preventing breeders from taking advantage of the recent explosion of whole-genome sequencing that has benefited many other crops. Thus, modern sugarcane hybrids are the last remaining major crop without a reference-quality genome. Here we take a major step towards advancing sugarcane biotechnology by generating a polyploid reference genome for R570, a typical modern cultivar derived from interspecific hybridization between the domesticated species (Saccharum officinarum) and the wild species (Saccharum spontaneum). In contrast to the existing single haplotype ('monoploid') representation of R570, our 8.7 billion base assembly contains a complete representation of unique DNA sequences across the approximately 12 chromosome copies in this polyploid genome. Using this highly contiguous genome assembly, we filled a previously unsized gap within an R570 physical genetic map to describe the likely causal genes underlying the single-copy Bru1 brown rust resistance locus. This polyploid genome assembly with fine-grain descriptions of genome architecture and molecular targets for biotechnology will help accelerate molecular and transgenic breeding and adaptation of sugarcane to future environmental conditions.

Sugarcane white leaf disease associated with sugarcane white leaf (SCWL) phytoplasma is an important disease in sugarcane resulting in significant losses in production in Asian countries including the major regional producing countries of India and Thailand. In this study the morphological and biochemical traits in SCWL phytoplasma infected sugarcane plants, both asymptomatic (AS) and symptomatic (S1-S3) and their corresponding to phytoplasma loads, were investigated. This study found that as symptom development progressed, cane statues including plant height, leaf length, and leaf width, were reduced and corresponded with declines in both chlorophyll and dietary fiber content. Total soluble solids (TSS) were less in AS cane plants, being 16.83 ± 1.0 °brix compared to 20.58 ± 1.6 °brix in healthy plants, declining further with the progression of symptoms. This feature could be potentially used in the identification of AS sugarcanes. Phytoplasma titres increased from 2.36E + 05 copies/µg plant DNA in AS infected leaves, peaking at 1.20E + 08 copies/µg plant DNA in S3 infected leaves, before declining in severely (S4) infected leaves. AS infected plants also exhibited a peak in total phenolic compounds. By tracking the development of symptoms in sugarcane white leaf disease and the corresponding increases in titres of SCWL phytoplasma, decline in chlorophyll and dietary fiber, decrease in TSS, and a peak in total phenolic compounds at the asymptomatic stage, this study confirmed that SCWL phytoplasma significantly impacts the sugarcane host plants as early as the AS stage, this stage is potentially the focus point for early detection and interventions for controlling proliferation SCWL disease. [ABSTRACT FROM AUTHOR]

The dwindling availability of agricultural land, caused by factors such as rapid population growth, urban expansion, and soil contamination, has significantly increased the pressure on food production. To address this challenge, cultivating non-food crops on contaminated land has emerged as a promising solution. This approach not only frees up fertile soil for food production but also mitigates human exposure to contaminants. This work aimed to examine the impact of soil contamination with Cd, Pb, Ni, and Zn on the growth, productivity, metal accumulation, and the tolerance of five lignocellulosic non-food crops: switchgrass (Panicum virgatum L.), biomass sorghum (Sorghum bicolor L. Moench), giant reed (Arundo donax L.), African fodder cane (Saccharum spontaneum L. spp. aegyptiacum Willd. Hackel), and miscanthus (Miscanthus × giganteus Greef et Deu.). A two-year pot experiment was conducted in Greece, Italy, and Portugal, following the same protocols and applying various levels of metals: Cd (0, 4, 8 mg kg−1), Pb and Zn (0, 450, 900 mg kg−1), and Ni (0, 110, 220 mg kg−1). The experimental design was completely randomized, with three replicates for each treatment. The results showed that switchgrass and sorghum generally maintained their height and productivity under Cd and Pb stress but were adversely affected by high Zn and Ni concentrations. Giant reed and African fodder cane showed reduced height and productivity at higher Ni and Zn levels. Miscanthus exhibited resilience in height but experienced productivity reductions only at the highest Zn concentration. Heavy metal uptake varied among crops, with switchgrass and sorghum showing high Cd and Pb uptake, while giant reed accumulated the most Cd and Zn. Miscanthus had the highest Ni accumulation. The tolerance indices indicated that switchgrass and sorghum were more tolerant to Cd and Zn at lower concentrations, whereas miscanthus had lower tolerance to Cd but a higher tolerance to Zn at higher concentrations. Giant reed and African fodder cane demonstrated stable tolerance across most heavy metals. Accumulation indices highlighted the effectiveness of switchgrass and sorghum in Cd and Pb uptake, while miscanthus excelled in Ni and Zn accumulation. The cluster analysis revealed similar responses to heavy metal stress between African fodder cane and giant reed, as well as between sorghum and miscanthus, with switchgrass displaying distinct behavior. Overall, the study highlights the differential tolerance and accumulation capacities of these crops, indicating the potential for phytoremediation applications and biomass production in heavy metal-contaminated soils. [ABSTRACT FROM AUTHOR]

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ABSTRACT Sugarcane (Saccharum spp. hybrids) are complex polyploid and aneuploid interspecific hybrids with 110–130 chromosomes. A traditional sugarcane breeding cycle takes 13–15 years and involves multiple years and locations testing of yield. To identify molecular markers associated with yield‐related traits, the LCP 85‐384 cultivar and its mapping population of 263 self‐progenies were planted in two randomly replicated field plots. The mapping population was genotyped with amplified fragment length polymorphism (AFLP), simple sequence repeats (SSR) and target region amplification polymorphism (TRAP) markers. Data on plant height, stalk number, stalk diameter and stalk weight were collected. A large variation was observed for each trait. A genome‐wide association study (GWAS) was conducted using mixed linear model (MLM), generalized linear model (GLM) and single marker regression (SMR) programmes of TASSEL 5 and FarmCPU of GAPIT 3. A total of 64 yield trait‐associated alleles were identified, including 11 for stalk number, 36 for stalk weight, 21 for stalk diameter and 5 for plant height. Of the 64 alleles, seven were linked to two traits and one to three traits. Genomic prediction (GP) was also performed by cross‐prediction with five models, namely, ridge regression best linear unbiased prediction (rrBLUP), Bayesian ridge regression (BRR), Bayesian A (BA), Bayesian B (BB), and Bayesian least absolute shrinkage and selection operator (BL). Prediction accuracy (r value) reached 0.40 for plant height, 0.36 for stalk number, 0.44 for stalk diameter and 0.54 for stalk weight with the standard errors from 0.009 to 0.012. Once verified, these markers will be a valuable tool to aid in the selection of yield‐related traits in sugarcane improvement programmes. [ABSTRACT FROM AUTHOR]

SUMMARY: Sugarcane is the main source of sugar worldwide, and 80% of the sucrose production comes from sugarcane. However, the genetic differentiation and basis of agronomic traits remain obscure. Here, we sequenced the whole‐genome of 219 elite worldwide sugarcane cultivar accessions. A total of approximately 6 million high‐quality genome‐wide single nucleotide polymorphisms (SNPs) were detected. A genome‐wide association study identified a total of 2198 SNPs that were significantly associated with sucrose content, stalk number, plant height, stalk diameter, cane yield, and sugar yield. We observed homozygous tendency of favor alleles of these loci, and over 80% of cultivar accessions carried the favor alleles of the SNPs or haplotypes associated with sucrose content. Gene introgression analysis showed that the number of chromosome segments from Saccharum spontaneum decreased with the breeding time of cultivars, while those from S. officinarum increased in recent cultivars. A series of selection signatures were identified in sugarcane improvement procession, of which 104 were simultaneously associated with agronomic traits and 45 of them were mainly associated with sucrose content. We further proposed that as per sugarcane transgenic experiments, ShN/AINV3.1 plays a positive role in increasing stalk number, plant height, and stalk diameter. These findings provide comprehensive resources for understanding the genetic basis of agronomic traits and will be beneficial to germplasm innovation, screening molecular markers, and future sugarcane cultivar improvement. Significance Statement: By whole‐genome sequencing of 219 worldwide sugarcane cultivars, our study furthers previous understanding of genetic basis of six important agronomic traits and selection signatures between cultivars and wild species, and during sugarcane cultivar improvement. Furthermore, sucrose content‐related loci were relatively fully selected and utilized in modern sugarcane cultivars, then cloning and validation of ShN/AINV3.1 would favor more increase in cane yield. [ABSTRACT FROM AUTHOR]

This study evaluated an interspecific hybrid (Saccharum spp. × S. spontaneum) population with the aim of developing germplasm for use in both sugar and bioenergy (biomass) production. Specific objectives were to determine the genetic variability and heritability among the interspecific hybrid progenies for traits of economic importance and to use the Best Linear Unbiased Predictions (BLUPs) to determine their genotypic values. The 46 interspecific hybrids used in this study originated from crossing commercial sugarcane cultivars (UT5, F152, and KK07–559) as female and S. spontaneum clones (THS98–41, THS98–91, THS98–95, THS98–94, and THS97–51) as male parents. There were significant residual variances, attributed to the small plot size, but the juice quality traits were measured with relatively higher precision than other traits. Selection recommendations varied for different traits, suggesting selection pressure could be moderate to high for juice quality traits and moderate for yield-related traits. No hybrid genotypes were found to outperform cultivar parents for traits such as commercial cane sugar and low fiber, necessitating further germplasm enhancement for improvement of varieties destined for sugar production. On the contrary, transgressive segregation was observed for cane yield and other traits influencing biomass yield. The production potential of these hybrids could be tested in larger plots across multiple locations. [ABSTRACT FROM AUTHOR]

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

Key message: We reported the graph-based mitochondrial genomes of three foundation species (Saccharum spontaneum, S. robustum and S. officinarum) for the first time. The results revealed pan-structural variation and evolutionary processes in the mitochondrial genomes within Saccharum. Saccharum belongs to the Andropogoneae, and cultivars species in Saccharum contribute nearly 80% of sugar production in the world. To explore the genomic studies in Saccharum, we assembled 15 complete mitochondrial genomes (mitogenome) of three foundation species (Saccharum spontaneum, S. robustum and S. officinarum) using Illumina and Oxford Nanopore Technologies sequencing data. The mitogenomes of the three species were divided into a total of eight types based on contig numbers and linkages. All mitogenomes in the three species encoded 51 unique genes, including 32 protein-coding, 3 ribosomal RNA (rRNA) and 16 transfer RNA (tRNA) genes. The existence of long and short-repeat-mediated recombinations in the mitogenome of S. officinarum and S. robustum was revealed and confirmed through PCR validation. Furthermore, employing comparative genomics and phylogenetic analyses of the organelle genomes, we unveiled the evolutionary relationships and history of the major interspecific lineages in Saccharum genus. Phylogenetic analyses of homologous fragments between S. officinarum and S. robustum showed that S. officinarum and S. robustum are phylogenetically distinct and that they were likely parallel rather than domesticated. The variations between ancient (S. sinense and S. barberi) and modern cultivated species (S. hybrid) possibly resulted from hybridization involving different S. officinarum accessions. Lastly, this project reported the first graph-based mitogenomes of three Saccharum species, and a systematic comparison of the structural organization, evolutionary processes, and pan-structural variation of the Saccharum mitogenomes revealed the differential features of the Saccharum mitogenomes. [ABSTRACT FROM AUTHOR]

Saccharum complex includes genera Saccharum, Miscanthus, Erianthus, Narenga, and Tripidium. Since the Saccharum complex/Saccharinae constitutes the gene pool used by sugarcane breeders to introduce useful traits into sugarcane, studying the genomic characterization of the Saccharum complex has become particularly important. Here, we assembled graph-based mitochondrial genomes (mitogenomes) of four Saccharinae species (T. arundinaceum, E. rockii, M. sinensis, and N. porphyrocoma) using Illumina and PacBio sequencing data. The total lengths of the mitogenomes of T. arundinaceum, M. sinensis, E. rockii and N. porphyrocoma were 549,593 bp, 514,248 bp, 481,576 bp and 513,095 bp, respectively. Then, we performed a comparative mitogenomes analysis of Saccharinae species, including characterization, organelles transfer sequence, collinear sequence, phylogenetics analysis, and gene duplicated/loss. Our results provided the mitogenomes of four species closely related to sugarcane breeding, enriching the mitochondrial genomic resources of the Saccharinae. Additionally, our study offered new insights into the evolution of mitogenomes at the family and genus levels and enhanced our understanding of organelle evolution in the highly polyploid Saccharum genus. [ABSTRACT FROM AUTHOR]

Saccharum is relatively new to 33° N latitude. S. spontaneum readily hybridizes with commercial sugarcane (Saccharum spp.) and lends cold tolerance and greater yield to the hybrid progeny, called energycane. Since 2007, there have been numerous new hybrid and backcross energycane genotypes developed but there is a paucity of information about them. Twenty energycane genotypes were tested in the first season of growth from cane propagules (plant cane; PC) against Ho 02-113 (a control) for two site-years in northcentral Mississippi. Grand (exponential) growth continued into October. The prevailing paradigm is that tonnage is what matters. Except for percentage cellulose, all factors tested (dry matter yield, extractable juice volume, °Brix, theoretical ethanol from fermentation, theoretical ethanol from cellulose, and total theoretical ethanol) were greater from the second site-location compared to the first. Dry matter yield (DMY) and total theoretical ethanol yield (TTEY) were moderately correlated. Over the two years of this test only Ho 14-9213 exceeded in mean DMY of Ho 02-113. Sixteen of the 19 test genotypes in this test equaled or exceeded the mean TTEY of Ho 02-113. [ABSTRACT FROM AUTHOR]

True sugarcane seed (TSS) families offer economic, environmental, and practical advantages over clonal varieties. Identification of well-germinating and high-yielding TSS families to replace sett/settling planting is a prerequisite for direct commercial cultivation. Promising TSS families are identified through family selection, an efficient, proven, and cost-effective approach. A total of 139 crosses, with varying sets of 22, 51, and 66 crosses were produced in 2018-19, 2019-20, and 2020-21, respectively. Among the 66 TSS families evaluated, 18F02, 18F27, 19F25, 19F46, 20F10, and 20F11 outperformed the popular clonal check Co 86032, with moderate to low variability, within an acceptable range for cane (number of millable canes per clump ≥ 5.0; single cane weight ≥ 1.0 kg) and sugar (Brix% ≥ 18.0%; Sucrose% ≥ 15.0%) yield traits, accompanied by good fluff germination and seedling establishment parameters. These results implied the possibility of exploiting promising true seed-based families for commercial sugarcane cultivation. [ABSTRACT FROM AUTHOR]

The auxin/indoleacetic acid (Aux/IAA) family plays a central role in regulating gene expression during auxin signal transduction. Nonetheless, there is limited knowledge regarding this gene family in sugarcane. In this study, 92 members of the IAA family were identified in Saccharum spontaneum, distributed on 32 chromosomes, and classified into three clusters based on phylogeny and motif compositions. Segmental duplication and recombination events contributed largely to the expansion of this superfamily. Additionally, cis-acting elements in the promoters of SsIAAs involved in plant hormone regulation and stress responsiveness were predicted. Transcriptomics data revealed that most SsIAA expressions were significantly higher in stems and basal parts of leaves, and at nighttime, suggesting that these genes might be involved in sugar transport. QRT-PCR assays confirmed that cold and salt stress significantly induced four and five SsIAAs, respectively. GFP-subcellular localization showed that SsIAA23 and SsIAA12a were localized in the nucleus, consistent with the results of bioinformatics analysis. In conclusion, to a certain extent, the functional redundancy of family members caused by the expansion of the sugarcane IAA gene family is related to stress resistance and regeneration of sugarcane as a perennial crop. This study reveals the gene evolution and function of the SsIAA gene family in sugarcane, laying the foundation for further research on its mode of action. [ABSTRACT FROM AUTHOR]

Background: Sucrose accumulation in sugarcane is affected by several environmental and genetic factors, with plant moisture being of critical importance for its role in the synthesis and transport of sugars within the cane stalks, affecting the sucrose concentration. In general, rainfall and high soil humidity during the ripening stage promote plant growth, increasing the fresh weight and decreasing the sucrose yield in the humid region of Colombia. Therefore, this study aimed to identify markers associated with sucrose accumulation or production in the humid environment of Colombia through a genome-wide association study (GWAS). Results: Sucrose concentration measurements were taken in 220 genotypes from the Cenicaña's diverse panel at 10 (early maturity) and 13 (normal maturity) months after planting. For early maturity data was collected during plant cane and first ratoon, while at normal maturity it was during plant cane, first, and second ratoon. A total of 137,890 SNPs were selected after sequencing the 220 genotypes through GBS, RADSeq, and whole-genome sequencing. After GWAS analysis, a total of 77 markers were significantly associated with sucrose concentration at both ages, but only 39 were close to candidate genes previously reported for sucrose accumulation and/or production. Among the candidate genes, 18 were highlighted because they were involved in sucrose hydrolysis (SUS6, CIN3, CINV1, CINV2), sugar transport (i.e., MST1, MST2, PLT5, SUT4, ERD6 like), phosphorylation processes (TPS genes), glycolysis (PFP-ALPHA, HXK3, PHI1), and transcription factors (ERF12, ERF112). Similarly, 64 genes were associated with glycosyltransferases, glycosidases, and hormones. Conclusions: These results provide new insights into the molecular mechanisms involved in sucrose accumulation in sugarcane and contribute with important genomic resources for future research in the humid environments of Colombia. Similarly, the markers identified will be validated for their potential application within Cenicaña's breeding program to assist the development of breeding populations. [ABSTRACT FROM AUTHOR]

Plant resistance against biotic stressors is significantly influenced by pathogenesis-related 1 (PR1) proteins. This study examines the systematic identification and characterization of PR1 family genes in sugarcane (Saccharum spontaneum Np-X) and the transcript expression of selected genes in two sugarcane cultivars (ROC22 and Zhongtang3) in response to Ustilago scitaminea pathogen infection. A total of 18 SsnpPR1 genes were identified at the whole-genome level and further categorized into four groups. Notably, tandem and segmental duplication occurrences were detected in one and five SsnpPR1 gene pairs, respectively. The SsnpPR1 genes exhibited diverse physio-chemical attributes and variations in introns/exons and conserved motifs. Notably, four SsnpPR1 (SsnpPR1.02/05/09/19) proteins displayed a strong protein–protein interaction network. The transcript expression of three SsnpPR1 (SsnpPR1.04/06/09) genes was upregulated by 1.2–2.6 folds in the resistant cultivar (Zhongtang3) but downregulated in the susceptible cultivar (ROC22) across different time points as compared to the control in response to pathogen infection. Additionally, SsnpPR1.11 was specifically upregulated by 1.2–3.5 folds at 24–72 h post inoculation (hpi) in ROC22, suggesting that this gene may play an important negative regulatory role in defense responses to pathogen infection. The genetic improvement of sugarcane can be facilitated by our results, which also establish the basis for additional functional characterization of SsnpPR1 genes in response to pathogenic stress. [ABSTRACT FROM AUTHOR]

SUMMARY: The sugarcane (Saccharum spp.) genome is one of the most complex of all. Modern varieties are highly polyploid and aneuploid as a result of hybridization between Saccharum officinarum and S. spontaneum. Little research has been done on meiotic control in polyploid species, with the exception of the wheat Ph1 locus harboring the ZIP4 gene (TaZIP4‐B2) which promotes pairing between homologous chromosomes while suppressing crossover between homeologs. In sugarcane, despite its interspecific origin, bivalent association is favored, and multivalents, if any, are resolved at the end of prophase I. Thus, our aim herein was to investigate the purported genetic control of meiosis in the parental species and in sugarcane itself. We investigated the ZIP4 gene and immunolocalized meiotic proteins, namely synaptonemal complex proteins Zyp1 and Asy1. The sugarcane ZIP4 gene is located on chromosome 2 and expressed more abundantly in flowers, a similar profile to that found for TaZIP4‐B2. ZIP4 expression is higher in S. spontaneum a neoautopolyploid, with lower expression in S. officinarum, a stable octoploid species. The sugarcane Zip4 protein contains a TPR domain, essential for scaffolding. Its 3D structure was also predicted, and it was found to be very similar to that of TaZIP4‐B2, reflecting their functional relatedness. Immunolocalization of the Asy1 and Zyp1 proteins revealed that S. officinarum completes synapsis. However, in S. spontaneum and SP80‐3280 (a modern variety), no nuclei with complete synapsis were observed. Importantly, our results have implications for sugarcane cytogenetics, genetic mapping, and genomics. Significance Statement: Our work provides insights into the genetic control of meiosis in sugarcane (Saccharum spp.), a man made polyploid and fertile plant of interspecific constitution. Inspired by the discoveries of the Ph1 locus, which harbors the ZIP4 gene in wheat, we identified this meiotic gene in both parental species and in two current sugarcane varieties. We analyzed both gene and protein sequence conservation, protein domains, and predicted the 3D‐protein structure. We also investigated the level of ZIP4 expression in different sugarcane tissues. Like its role in wheat, ZIP4 seems to promote pairing between homologous chromosomes while suppressing crossover between homeologs in Saccharum. Using immunocytology, we were able to determine synaptonemal complex polymerization during prophase I, using Asy1 and Zyp1 sugarcane specific antibodies, revealing synapsis defects in all genotypes except Saccharum officinarum, a parental species with regular meiotic behavior. [ABSTRACT FROM AUTHOR]

Sugarcane cultivation is targeted with early varieties having stable higher CCS (commercial cane sugar) yield potential. Therefore, studies were made on 18 traits over three years (2016-19) with seven genotypes at Regional Research Station, PAU, Faridkot. Different multivariate statistical techniques were used for assessing the potential of CCS contributing traits and clonal stability. The observed significant differences due to varieties, years and their interactions were self explaining the role of genotypic differences and weather factors. Cane yield t/ha (CY), CCS t/ha (CCS.T) and their contributing traits were positively loaded on different axes in principal component analyses (PCA). Single cane weight (SCW) was observed to be the primary contributing trait for CY; while brix % and sucrose % for CCS %, and CY for CCS.T were the major contributing traits. CoPb 13181 was observed the most suitable clone for the region. Further, Eberhart & Russell's model was found more appropriate for judging the genotype(s) to environment specificity while "GGE Biplot" was best to evaluate the environments for their discriminating power to genotypes. [ABSTRACT FROM AUTHOR]

Fifty-five sugarcane genotypes from around the world were collected and evaluated for potential use as parental material in the USDA ARS Canal Point (CP) sugarcane breeding program in Florida, USA. The genotypes were planted in a trial with four check cultivars on organic soils with four replications, and data were collected for two years [i.e., plant cane (PC) and first ratoon (FR) crops] to assess sucrose-yield-related traits and the cane-yield-related traits in PC. Using a multivariate analysis, variation was observed in all cane—[i.e., stalk weight, stalk population and cane yield] and sugar-yield-related traits [i.e., Brix, Pol, sucrose content and commercial recoverable sucrose (CRS)]. The mean CRS content was greater in the FR crop than the PC crop. Significant variations were attributed to genotype (G), crop cycles (C) and G × C effects. Variations between crop cycles were highly significant for all sucrose yield components, which could complicate the downstream selection of genotypes for sucrose yield. Based on CRS content, genotypes could be grouped into six distinct clusters. Based on plant cane data, cane yield traits (stalk weight, stalk population and cane yield) were used to estimate the breeding values of parents. Of the 55 genotypes, 8 had significantly greater t-BLUP values for cane yield, along with CP 00-1101. Combined sucrose yield traits, (Brix, Pol and sucrose content) from the two crops were used to estimate the breeding values of parents. Of the 55 genotypes, 10 genotypes had significantly greater t-BLUP values for CRS, along with CP 00-1101, CP 96-1252 and CP 01-2390, and can be considered as elite parents in future breeding efforts. These results provide a foundation for the efficient integration of genetic diversity in developing commercial cultivars, with improved sucrose yields, into the CP sugarcane breeding program. [ABSTRACT FROM AUTHOR]

Microbes living inside or around sugarcane (Saccharum spp.) are crucial for their resistance to abiotic and biotic stress, growth, and development. Sequences of microbial genomes and genes are helpful to understand the function of these microbes. However, there is currently a lack of such knowledge in sugarcane. Here, we combined Nanopore and Illumina sequencing technologies to successfully construct the first high-quality metagenome-assembled genomes (MAGs) and gene catalogues of sugarcane culturable microbes (GCSCMs), which contained 175 species-level genome bins (SGBs), and 7,771,501 non-redundant genes. The SGBs included 79 novel culturable bacteria genomes, and 3 bacterial genomes with nitrogen-fixing gene clusters. Four single scaffold near-complete circular MAGs (cMAGs) with 0% contamination were obtained from Nanopore sequencing data. In conclusion, we have filled a research gap in the genomes and gene catalogues of culturable microbes of sugarcane, providing a vital data resource for further understanding the genetic basis and functions of these microbes. In addition, our methodology and results can provide guidance and reference for other plant microbial genome and gene catalogue studies. [ABSTRACT FROM AUTHOR]

A homeobox transcription factor is a conserved transcription factor, ubiquitous in eukaryotes, that regulates the tissue formation of structure, cell differentiation, proliferation, and cancer. This study identified the homeobox transcription factor family and its distribution in Phoma sorghina var. saccharum at the whole genome level. It elucidated the gene structures and evolutionary characteristics of this family. Additionally, knockout experiments were carried out and the preliminary function of these transcription factors was studied. Through bioinformatics approaches, nine homeobox transcription factors (PsHOX1–PsHOX9) were identified in P. sorghina var. saccharum, and these contained HOX-conserved domains and helix–turn–helix secondary structures. Nine homeobox gene deletion mutants were obtained using the homologous recombinant gene knockout technique. Protoplast transformation was mediated by polyethylene glycol (PEG) and the transformants were identified using PCR. The knockouts of PsHOX1, PsHOX2, PsHOX3, PsHOX4, PsHOX6, PsHOX8, and PsHOX9 genes resulted in a smaller growth diameter in P. sorghina var. saccharum. In contrast, the knockouts of the PsHOX3, PsHOX6, and PsHOX9 genes inhibited the formation of conidia and led to a significant decrease in the pathogenicity. This study's results will provide insights for understanding the growth and development of P. sorghina var. saccharum. The pathogenic mechanism of the affected sugarcane will provide an essential theoretical basis for preventing and controlling sugarcane twisted leaf disease. [ABSTRACT FROM AUTHOR]

'CP 10‐1620' (Reg. no. CV‐216, PI 693837) sugarcane (a complex hybrid of Saccharum spp.) was developed through cooperative research conducted by the USDA–ARS, the University of Florida, and the Florida Sugar Cane League, Inc. At the June 7, 2018, Florida Sugarcane Variety Committee Meeting, CP 10‐1620 was released to growers for mineral (sand) soils in Florida, and seed was available in September 2018. CP 10‐1620 was selected from a polycross of 'CP 00‐1100' × 'CP 05‐1740' (Cross no. X07‐1225) made at Canal Point, FL, in December 2007. Neither the female parent, CP 00‐1100, nor the male parent, CP 05‐1740, is a commercial cultivar. Cane yield of CP 10‐1620 on sand soils, averaged across 12 harvests through three crop cycles (plant cane, first ratoon, and second ratoon), was 11.0% higher (P < 0.05) than the combined mean of three checks, 'CL 88‐4730', 'CP 96‐1252', and 'CPCL 97‐2730', which are commercial checks for sand soils. The commercial recoverable sucrose for CP 10‐1620 was not significantly lower than the combined mean of the checks but the higher cane yield resulted in 8.4% higher (P < 0.05) sucrose yield than the combined mean of the checks. CP 10‐1620 was released because of its high cane yields on sand soils, and its acceptable levels of resistance to brown rust (caused by Puccinia melanocephala H. & P. Sydow), leaf scald (caused by Xanthomonas albilineans Ashby, Dowson), Sugarcane mosaic virus strain E (mosaic), smut (caused by Sporisorium scitamineum), Sugarcane yellow leaf virus, and ratoon stunt [caused by Leifsonia xyli subsp. xyli (Davis et al.) Evtushenko]. CP 10‐1620 was moderately susceptible to orange rust (caused by Puccinia kuehnii E. J. Butler), and it has high freeze tolerance. CP 10‐1620 tested positive for the Bru1 locus, which is an indicator of brown rust resistance. Core Ideas: CP 10‐1620 is a new sugarcane cultivar in Florida.CP 10‐1620 has high yields of cane and sucrose in Florida.CP 10‐1620 is resistant or moderately resistant to the typical diseases found in Florida.CP 10‐1620 is the result of a cooperative effort between the USDA, UF IFAS, and the Florida Sugar Cane League.CP 10‐1620 has high cold tolerance. [ABSTRACT FROM AUTHOR]

'CP 13‐1954' (Reg. no. CV‐218, PI 704104) sugarcane (Saccharum spp. hybrid) was developed through cooperative research conducted by the USDA–ARS, the University of Florida, and the Florida Sugar Cane League, Inc., and released to growers for organic (muck) soils in Florida in June 2020. The parentage of CP 13‐1954 is 'CP 85‐1491' × Poly 09‐24. Based on the results of three crops (plant cane, first ratoon, and second ratoon) in field trials conducted at five locations, CP 13‐1954 had higher cane yield (16.2%), sucrose yield (15.6%), and economic index (29.7%) at P <.05 compared with the reference cultivar, 'CP 96‐1252'. CP 13‐1954 stalks are usually taller than the reference cultivar, 'CP 00‐1101', with small‐to‐medium diameter, and exhibits resistance to ratoon stunting disease, Sugarcane mosaic virus strain E, brown rust, orange rust, and smut and moderate resistance to leaf scald on muck soils in Florida. CP 13‐1954 has Bru1 locus that provides resistance against brown rust. CP 13‐1954 showed moderate cold tolerance among all the tested cultivars. Core Ideas: CP 13‐1954 is a new sugarcane cultivar released for organic soils in Florida.CP 13‐1954 yields higher than commercial checks in organic soils in Florida.CP 13‐1954 is resistant to most of the common sugarcane diseases in Florida.CP 13‐1954 has moderate level of freeze tolerance. [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]

Motivation Constructing a phylogenetic tree requires calculating the evolutionary distance between samples or species via large-scale resequencing data, a process that is both time-consuming and computationally demanding. Striking the right balance between accuracy and efficiency is a significant challenge. Results To address this, we introduce a new algorithm, MIKE (MinHash-based k -mer algorithm). This algorithm is designed for the swift calculation of the Jaccard coefficient directly from raw sequencing reads and enables the construction of phylogenetic trees based on the resultant Jaccard coefficient. Simulation results highlight the superior speed of MIKE compared to existing state-of-the-art methods. We used MIKE to reconstruct a phylogenetic tree, incorporating 238 yeast, 303 Zea , 141 Ficus , 67 Oryza , and 43 Saccharum spontaneum samples. MIKE demonstrated accurate performance across varying evolutionary scales, reproductive modes, and ploidy levels, proving itself as a powerful tool for phylogenetic tree construction. Availability and implementation MIKE is publicly available on Github at https://github.com/Argonum-Clever2/mike.git. [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]

Variety development of sugarcane (Saccharum spp. hybrids) is necessary to continue improving sugar yields and selecting photosynthetic traits can improve sugar production through increased carbon inputs. In this study, gas exchange and whole-plant measurements were made on 55 sugarcane genotypes in Louisiana. Variation in the relationship between photosynthetic rate and stomatal conductance suggests that sugarcane exhibits variation in both photosynthetic capacity and CO2 substrate availability. Genotypes that reached maximum photosynthetic rate (TRMPR) in the gas-exchange cuvette more quickly had greater CO2 assimilation during transitory periods. Temporary shading and fluctuating light are common transitory conditions in the field, so increasing TRMPR can improve photosynthesis in water-abundant regions. Canopy leaf area was positively correlated with stalk mass, but gas-exchange traits were not correlated with whole-plant traits. A better understanding of the relationship between leaf and whole-plant traits is necessary to identify physiological traits that lead to increased genetic gain. [ABSTRACT FROM AUTHOR]

Drought stress is one of the main environmental factors that cause negative impacts on sugarcane (Saccharum spp.) crops. The identification of drought-tolerant varieties is essential to boost the sugar-energy sector in agricultural years with an incidence of drought stress. Two experiments were conducted under greenhouse conditions to evaluate the degree of drought tolerance of 13 sugarcane varieties (CTC2, CTC4, IACSP95-5000, RB825336, RB835054, RB855035, RB855156, RB855453, RB855536, RB867515, RB965902, RB966928 and SP80-1842) when exposed to restrictions of 50% (moderate water deficiency) and 25% (severe water deficiency) of the soil's water retention capacity. Twelve drought tolerance indices were calculated from the production of shoot dry matter without water restriction (YP) and under moderate or severe water deficit (YS). The RB855035, RB855453 and RB 965902 varieties have greater drought tolerance, and are the most suitable to be cultivated in regions with moderate and severe water restriction. The RB855536 and IACSP95-5000 varieties have greater susceptibility to moderate and severe water deficit. Tolerance indices MP, DI, STI, GMP, YI, k1STI, k2STI and HM were the most suitable for identifying the sugarcane varieties with greater drought tolerance and high potential for shoot dry matter production. under conditions of moderate and severe water stress. [ABSTRACT FROM AUTHOR]

Copyright of Diversitas Journal is the property of Diversitas Journal and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Sugarcane (Saccharum spp.) is a perennial crop belongs to the genus Saccharum. It is the richest source of sucrose, which accumulates in the stalk internodes which is used for sugar. Fusarium spp. is an airborne fungus to cause pokkah boeing disease (PBD) in cane. The infection first appears on leaves, so that leaves show whitish and curling or twisting symptom, which are seen on top portion of the plants. A field experiment was conducted during cropping sessions of 2021-22 and 2022-23. Surveys were conducted to study the incidence and severity of the disease. During the survey, observations recorded ranged between 5 to 50 per cent incidence of the disease in major cane growing areas of North-East Uttar Pradesh in India. To determine the level of resistance of sugarcane varieties against PBD, 30 sugarcane varieties were evaluated. Out of 30 evaluated sugarcane varieties, 15 varieties showed resistant reaction, 6 varieties showed moderately susceptible reaction, 4 varieties showed susceptible reaction and remaining five varieties CoPant-18221, Co-15025, Co-18021, S-374/17 and S-171/17 showed highly susceptible reaction against pokkah boeing disease. [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]

[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]

Copyright of Acta Agronomica Sinica is the property of Crop Science Society of China and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

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]

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]

RESUMO O presente estudo teve por objetivo analisar a exposição aos agrotóxicos e os danos à saúde dos trabalhadores das plantações de cana-de-açúcar em Pernambuco. Trata-se de pesquisa participante desenvolvida em territórios rurais de cinco municípios com forte expressão em área plantada de cana-de-açúcar. Os dados primários foram produzidos em oficinas com trabalhadores rurais para construção de diagnóstico rural participativo, analisados mediante condensação de significados e interpretados à luz do referencial teórico da epidemiologia crítico latino-americana. Os resultados estão apresentados em três seções: i) Fluxograma do trabalho nas plantações de cana-de-açúcar; ii) Exposição aos agrotóxicos utilizados nas lavouras; iii) Danos à saúde do trabalhador. Conclui-se que a exposição permanente aos agrotóxicos envolve o trabalho nas plantações de cana-de-açúcar e emerge de um construto histórico e socioambiental, em que se encontram subsumidos os modos de vida dos territórios sob o domínio do agronegócio canavieiro. Recomendam-se políticas públicas de fomento à agricultura familiar com diversificação, escoamento e distribuição da produção agroecológica, além do fortalecimento da Atenção Primária à Saúde e de ações integradas de vigilância epidemiológica, sanitária, ambiental e do trabalhador.

The article introduces ScDB, a comprehensive database dedicated to Saccharum, which facilitates functional genomics and molecular biology studies in sugarcane. Sugarcane is an important sugar crop used for the production of sugar and biofuels. The complexity of the sugarcane genome has historically posed challenges for researchers, but recent advancements in genome research have led to the assembly of the genomes of various sugarcane species. ScDB provides access to genomic assembly sequences, annotations, and transcriptome data for six Saccharum species and Erianthus rufipilus. The database includes various tools and modules for search, analysis, and visualization, and it will continue to be updated with more sugarcane genome data and other omics data in the future. [Extracted from the article]

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]

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]

Locally produced soil amendments can play a vital role in sustainable agriculture, enhancing soil quality and crop plant growth. This study investigated the impact of locally sourced biochar (BC) and ash, obtained from Maerua crassifolia Forssk. (wood), and Saccharum kajkaiense, Melderis (grass) on soil properties and okra (Abelmoschus esculentus) biomass. We assessed different application rates (10% and 20%), either separately or combined with the potting soil/peat (Biomix). Biomix application reduced soil pH (7.9),and increased soil organic mater (OM) (51.9%), NO3-1 (17.5%) levels, water holding capacity (WHC) (22.9%), and dry biomass (37.7%) of okra compared no Biomix application. Among BC and ash amendments, grass ash excelled, increasing okra biomass by 132.7%, followed by wood BC and grass BC. However, wood ash had a slight negative effect on okra dry weight and also increased the soil EC (6.12 dS m-1). Wood ash had higher K levels (758 mg kg-1) but lower Na (159 mg kg-1) compared to control (51 mg kg-1 K and 235 mg kg-1 Na). Both BC amendments raised soil organic matter (OM) by 7.63-8.69%, while wood and grass ash slightly increased soil P (57.7-64.6 mg kg-1). However, wood and grass BC reduced soil P to 44 mg kg-1. Grass ash raised NO3 levels (25.5%) compared to the control. The interaction of Biomix with wood and grass amendments decreased soil EC, increased soil OM, NO3 level and plant dry weight of okra. Wood and grass BC (20%) with Biomix enhanced the soil OM by 11%. The combination of 10% grass ash and Biomix resulted in the highest NO3 levels at 170 mg kg-1. Furthermore, the combination of Biomix and 10% grass ash produced the most significant increase (204.3%) in plant dry weight compared to the control. In conclusion, locally sourced biochar and ash amendments, particularly grass ash in combination with potting soil/peat (Biomix), demonstrated significant potential to enhance soil quality and crop biomass, offering valuable insights for sustainable agricultural practices. [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 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]

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]