Taxonomic identification, phenol biodegradation and soil remediation of the strain Rhodococcus sacchari sp. nov. Z13T.

Phenols are highly toxic chemicals that are extensively used in industry and produce large amounts of emissions. Notably, phenols released into the soil are highly persistent, causing long-term harm to human health and the environment. In this study, a gram-positive, aerobic, and rod-shaped bacterial strain, Z13T, with efficient phenol degradation ability, was isolated from the soil of sugarcane fields. Based on the physiological properties and genomic features, strain Z13T is considered as a novel species of the genus Rhodococcus, for which the name Rhodococcus sacchari sp. nov. is proposed. The type strain is Z13T (= CCTCC AB 2022327T = JCM 35797T). This strain can use phenol as its sole carbon source. Z13T was able to completely degrade 1200 mg/L phenol within 20 h; the maximum specific growth rate was µmax = 0.93174 h-1, and the maximum specific degradation rate was qmax = 0.47405 h-1. Based on whole-genome sequencing and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, strain Z13T contains a series of phenol degradation genes, including dmpP, CatA, dmpB, pcaG, and pcaH, and can metabolize aromatic compounds. Moreover, the potential of strain Z13T for soil remediation was investigated by introducing Z13T into simulated phenol-contaminated soil, and the soil microbial diversity was analyzed. The results showed that 100% of the phenol in the soil was removed within 7.5 d. Furthermore, microbial diversity analysis revealed an increase in the relative species richness of Oceanobacillus, Chungangia, and Bacillus.

Silicon induces ROS scavengers, hormone signalling, antifungal metabolites, and silicon deposition against brown stripe disease in sugarcane.

Bipolaris setariae is known to cause brown stripe disease in sugarcane, resulting in significant yield losses. Silicon (Si) has the potential to enhance plant growth and biotic resistance. In this study, the impact of Si on brown stripe disease was investigated across susceptible and resistant sugarcane varieties, utilizing four Si concentrations (0, 15, 30, and 45 g per barrel of Na2SiO3·5H2O). Si significantly reduced the incidence of brown stripe disease (7.41-59.23%) and alleviated damage to sugarcane growth parameters, photosynthetic parameters, and photosynthetic pigments. Submicroscopic observations revealed that Si induced the accumulation of silicified cells in leaves, reduced spore accumulation, decreased stomatal size, and protected organelles from B. setariae damage. In addition, Si increased the activity of antioxidant enzymes (superoxide dismutase, peroxidase, and catalase), reduced reactive oxygen species production (malondialdehyde and hydrogen peroxide) and modulated the expression of genes associated with hormone signalling (PR1, TGA, AOS, AOC, LOX, PYL8, and SnRK2), leading to the accumulation of abscisic acid and jasmonic acid and inhibiting SA synthesis. Si also activated the activity of metabolism-related enzymes (polyphenol oxidase and phenylalanine ammonia lyase) and the gene expression of PAL-dependent genes (PAL, C4H, and 4CL), regulating the accumulation of metabolites, such as chlorogenic acid and lignin. The antifungal test showed that chlorogenic acid (15ug µL-1) had a significant inhibitory effect on the growth of B. setariae. This study is the first to demonstrate the inhibitory effect of Si on B. setariae in sugarcane, highlighting Si as a promising and environmentally friendly strategy for managing brown stripe disease.

A study on waterlogging tolerance in sugarcane: a comprehensive review.

Sugarcane (Saccharum officinarum) is an important crop, native to tropical and subtropical regions and it is a major source of sugar and Bioenergy in the world. Abiotic stress is defined as environmental conditions that reduce growth and yield below the optimum level. To tolerate these abiotic stresses, plants initiate several molecular, cellular, and physiological changes. These responses to abiotic stresses are dynamic and complex; they may be reversible or irreversible. Waterlogging is an abiotic stress phenomenon that drastically reduces the growth and survival of sugarcane, which leads to a 15-45% reduction in cane's yield. The extent of damage due to waterlogging depends on genotypes, environmental conditions, stage of development and duration of stress. An improved understanding of the physiological, biochemical, and molecular responses of sugarcane to waterlogging stress could help to develop new breeding strategies to sustain high yields against this situation. The present review offers a summary of recent findings on the adaptation of sugarcane to waterlogging stress in terms of growth and development, yield and quality, as well as biochemical and adaptive-molecular processes that may contribute to flooding tolerance.

Effects of sugarcane cultivation on aquatic macroinvertebrate community structure: a historical comparative case study in São Paulo State.

Over two decades, the area with sugarcane has more than doubled, from 4.8 million hectares in 2000 to 10 million in 2018, in Brazil. São Paulo State is mostly responsible for the sugarcane production in the country, accounting for 51% of the national production. In 2008, a study was conducted analysing the relationship between sugarcane cultivation and the aquatic macroinvertebrate community, showing the impacts of sugarcane on the macroinvertebrate aquatic fauna. The present study aims to gather actual information on the aquatic macroinvertebrate community in the same streams studied in 2008, to make a historical comparison with studies previously carried out. Eight streams were selected; four located in areas of sugarcane cultivation and four located in preserved areas. Three samples were carried out between 2018 and 2020. The aquatic macroinvertebrates were collected using a D-frame aquatic net (250 µm) including riffle and pools areas and identified using specific identification keys. The results of the historical assessment showed better ecological conditions of the streams in 2008 when compared to 2018 in areas of sugarcane cultivation, suggesting that the environmental impact was maintained and increased after ten years.

Sugarcane bagasse biochar boosts maize growth and yield in salt-affected soil by improving soil enzymatic activities.

Salinization is a leading threat to soil degradation and sustainable crop production. The application of organic amendments could improve crop growth in saline soil. Thus, we assessed the impact of sugarcane bagasse (SB) and its biochar (SBB) on soil enzymatic activity and growth response of maize crop at three various percentages (0.5%, 1%, and 2% of soil) under three salinity levels (1.66, 4, and 8 dS m-1). Each treatment was replicated three times in a completely randomized block design with factorial settings. The results showed that SB and SBB can restore the impact of salinization, but the SBB at the 2% addition rate revealed promising results compared to SB. The 2% SBB significantly enhanced shoot length (23.4%, 26.1%, and 41.8%), root length (16.8%, 20.8%, and 39.0%), grain yield (17.6%, 25.1%, and 392.2%), relative water contents (11.2%, 13.1%, and 19.2%), protein (17.2%, 19.6%, and 34.9%), and carotenoid (16.3, 30.3, and 49.9%) under different salinity levels (1.66, 4, and 8 dS m-1, respectively). The 2% SBB substantially drop the Na+ in maize root (28.3%, 29.9%, and 22.4%) and shoot (36.1%, 37.2%, and 38.5%) at 1.66, 4, and 8 dS m-1. Moreover, 2% SBB is the best treatment to boost the urease by 110.1%, 71.7%, and 91.2%, alkaline phosphatase by 28.8%, 38.8%, and 57.6%, and acid phosphatase by 48.4%, 80.1%, and 68.2% than control treatment under 1.66, 4 and 8 dS m-1, respectively. Pearson analysis showed that all the growth and yield parameters were positively associated with the soil enzymatic activities and negatively correlated with electrolyte leakage and sodium. The structural equational model (SEM) showed that the different application percentage of amendments significantly influences the growth and physiological parameters at all salinity levels. SEM explained the 81%, 92%, and 95% changes in maize yield under 1.66, 4, and 8 dS m-1, respectively. So, it is concluded that the 2% SBB could be an efficient approach to enhance the maize yield by ameliorating the noxious effect of degraded saline soil.

An enhanced productivity of pink oyster mushroom with improved nutritional profile, characterization and attempt for commercial exploitation.

BACKGROUND: An attempt has been made to explore the nutritional profile of pink oyster mushrooms that have been grown in various agricultural residues, including sugarcane bagasse, rice straw, coconut coir and sawdust, along with other nutrient supplements such as defatted mustard and chickpea powder, for appropriate growth and fruiting body formation in a short span of time. The spawn production was experimented with five different grain varieties. The study became interesting when the observations differed slightly from the traditional practices, with the addition of defatted mustard supplements resulting in a positive correlation with respect to reducing the fruiting time, as well as improving yield and the nutritional profile of Pleurotus djamor. RESULTS: An elevated yield of 651.93 g kg-1 was recorded in the medium where the RS and DM were used in the ratio of 1:0.01 (rice straw +1% w/w defatted mustard) bag, whereas, in terms of protein content, a maximum yield of 32.57 ± 0.79 mg g-1 was observed when SB:DM was in the same ratio (sugarcane bagasse +1% w/w defatted mustard) bag. CONCLUSION: To confer the best outcomes from the screened substrates, a series of experiments were performed by varying the concentration of RS and SB, with 1% w/w DM. It is worth noting that the highest protein content of 32.76 ± 0.38 mg g-1 was obtained along with the total yield of 702.56 ± 2.9 g kg-1 of mushroom when the ratio of RS:SB was 0.7:0.3. © 2024 Society of Chemical Industry.

Towards a dynamic photosynthesis model to guide yield improvement in C4 crops.

The most productive C4 food and biofuel crops, such as Saccharum officinarum (sugarcane), Sorghum bicolor (sorghum) and Zea mays (maize), all use NADP-ME-type C4 photosynthesis. Despite high productivities, these crops fall well short of the theoretical maximum solar conversion efficiency of 6%. Understanding the basis of these inefficiencies is key for bioengineering and breeding strategies to increase the sustainable productivity of these major C4 crops. Photosynthesis is studied predominantly at steady state in saturating light. In field stands of these crops light is continually changing, and often with rapid fluctuations. Although light may change in a second, the adjustment of photosynthesis may take many minutes, leading to inefficiencies. We measured the rates of CO2 uptake and stomatal conductance of maize, sorghum and sugarcane under fluctuating light regimes. The gas exchange results were combined with a new dynamic photosynthesis model to infer the limiting factors under non-steady-state conditions. The dynamic photosynthesis model was developed from an existing C4 metabolic model for maize and extended to include: (i) post-translational regulation of key photosynthetic enzymes and their temperature responses; (ii) dynamic stomatal conductance; and (iii) leaf energy balance. Testing the model outputs against measured rates of leaf CO2 uptake and stomatal conductance in the three C4 crops indicated that Rubisco activase, the pyruvate phosphate dikinase regulatory protein and stomatal conductance are the major limitations to the efficiency of NADP-ME-type C4 photosynthesis during dark-to-high light transitions. We propose that the level of influence of these limiting factors make them targets for bioengineering the improved photosynthetic efficiency of these key crops.

An insight to rhizosphere bacterial community composition and structure of consecutive winter-initiated sugarcane ratoon crop in Southern China.

BACKGROUND: Ratooning in sugarcane is a crucial strategy for ensuring the long-term sustainability of the sugarcane industry. Knowledge gap relating to the interaction between rhizosphere microbiome and ratooning crop, particularly the impact of different sugarcane cultivars on the rhizosphere microbiome in consecutive ratooning, requires additional research. The response of two different sugarcane cultivars, viz ZZ-1 and ZZ-13, were evaluated in consecutive ratooning towards the rhizosphere microbial community and cane morphological characters. RESULTS: Significant changes in the rhizosphere microbiome were observed in the second ratooning over the years. Several important genera were observed in high abundance during the second ratooning, including Burkholderia, Sphingomonas, Bradyzhizobium, and Acidothermus. Cultivar ZZ-13 caused more alterations in the rhizosphere microbiome than ZZ-1, resulting in a more favorable rhizosphere environment for sugarcane growth. The genotypes also varied in terms of nutrients and enzyme activity over the years. There were significant differences between the genotypes and year for number of stalks and yield was significant for genotypes, years and genotype × year. CONCLUSION: This finding will help to understand thorough interactions between rhizosphere microorganisms and ratoon sugarcane and lay the foundation for promoting and maximizing yield as far as possible. In the future, this work can serve as guidance in sugarcane husbandry, mainly in Guangxi, China.

Chromosome behavior during meiosis in pollen mother cells from Saccharum officinarum × Erianthus arundinaceus F1 hybrids.

BACKGROUND: In recent years, sugarcane has attracted increasing attention as an energy crop. Wild resources are widely used to improve the narrow genetic base of sugarcane. However, the infertility of F1 hybrids between Saccharum officinarum (S. officinarum) and Erianthus arundinaceus (E. arundinaceus) has hindered sugarcane breeding efforts. To discover the cause of this infertility, we studied the hybridization process from a cytological perspective. RESULTS: We examined the meiotic process of pollen mother cells (PMCs) in three F1 hybrids between S. officinarum and E. arundinaceus. Cytological analysis showed that the male parents, Hainan 92-77 and Hainan 92-105, had normal meiosis. However, the meiosis process in F1 hybrids showed various abnormal phenomena, including lagging chromosomes, micronuclei, uneven segregation, chromosome bridges, and inability to form cell plates. Genomic in situ hybridization (GISH) showed unequal chromatin distribution during cell division. Interestingly, 96.70% of lagging chromosomes were from E. arundinaceus. Furthermore, fluorescence in situ hybridization (FISH) was performed using 45S rDNA and 5S rDNA as probes. Either 45S rDNA or 5S rDNA sites were lost during abnormal meiosis, and results of unequal chromosomal separation were also clearly observed in tetrads. CONCLUSIONS: Using cytogenetic analysis, a large number of meiotic abnormalities were observed in F1. GISH further confirmed that 96.70% of the lagging chromosomes were from E. arundinaceus. Chromosome loss was found by further investigation of repeat sequences. Our findings provide insight into sugarcane chromosome inheritance to aid innovation and utilization in sugarcane germplasm resources.

Strategies and considerations for implementing genomic selection to improve traits with additive and non-additive genetic architectures in sugarcane breeding.

KEY MESSAGE: Simulations highlight the potential of genomic selection to substantially increase genetic gain for complex traits in sugarcane. The success rate depends on the trait genetic architecture and the implementation strategy. Genomic selection (GS) has the potential to increase the rate of genetic gain in sugarcane beyond the levels achieved by conventional phenotypic selection (PS). To assess different implementation strategies, we simulated two different GS-based breeding strategies and compared genetic gain and genetic variance over five breeding cycles to standard PS. GS scheme 1 followed similar routines like conventional PS but included three rapid recurrent genomic selection (RRGS) steps. GS scheme 2 also included three RRGS steps but did not include a progeny assessment stage and therefore differed more fundamentally from PS. Under an additive trait model, both simulated GS schemes achieved annual genetic gains of 2.6-2.7% which were 1.9 times higher compared to standard phenotypic selection (1.4%). For a complex non-additive trait model, the expected annual rates of genetic gain were lower for all breeding schemes; however, the rates for the GS schemes (1.5-1.6%) were still greater than PS (1.1%). Investigating cost-benefit ratios with regard to numbers of genotyped clones showed that substantial benefits could be achieved when only 1500 clones were genotyped per 10-year breeding cycle for the additive genetic model. Our results show that under a complex non-additive genetic model, the success rate of GS depends on the implementation strategy, the number of genotyped clones and the stage of the breeding program, likely reflecting how changes in QTL allele frequencies change additive genetic variance and therefore the efficiency of selection. These results are encouraging and motivate further work to facilitate the adoption of GS in sugarcane breeding.

Accuracy of genomic prediction of complex traits in sugarcane.

KEY MESSAGE: Complex traits in sugarcane can be accurately predicted using genome-wide DNA markers. Genomic single-step prediction is an attractive method for genomic selection in commercial breeding programs. Sugarcane breeding programs have achieved up to 1% genetic gain in key traits such as tonnes of cane per hectare (TCH), commercial cane sugar (CCS) and Fibre content over the past decades. Here, we assess the potential of genomic selection to increase the rate of genetic gain for these traits by deriving genomic estimated breeding values (GEBVs) from a reference population of 3984 clones genotyped for 26 K SNP. We evaluated the three different genomic prediction approaches GBLUP, genomic single step (GenomicSS), and BayesR. GenomicSS combining pedigree and SNP information from historic and recent breeding programs achieved the most accurate predictions for most traits (0.3-0.44). This method is attractive for routine genetic evaluation because it requires relatively little modification to the existing evaluation and results in breeding value estimates for all individuals, not only those genotyped. Adding information from early-stage trials added up to 5% accuracy for CCS and Fibre, but 0% for TCH, reflecting the importance of competition effects for TCH. These GEBV accuracies are sufficiently high that, combined with the right breeding strategy, a doubling of the rate of genetic gain could be achieved. We also assessed the flowering traits days to flowering, gender and pollen viability and found high heritabilities of 0.57, 0.78 and 0.72, respectively. The GEBV accuracies indicated that genomic selection could be used to improve these traits. This could open new avenues for breeders to manage their breeding programs, for example, by synchronising flowering time and selecting males with high pollen viability.

Protoplast-mediated transformation in Sporisorium scitamineum facilitates visualization of in planta developmental stages in sugarcane.

BACKGROUND: Sporisorium scitamineum is the causative agent of smut disease in sugarcane. The tricky life cycle of S. scitamineum consists of three distinct growth stages: diploid teliospores, haploid sporidia and dikaryotic mycelia. Compatible haploid sporidia representing opposite mating types (MAT-1 and MAT-2) of the fungus fuse to form infective dikaryotic mycelia in the host tissues, leading to the development of a characteristic whip shaped sorus. In this study, the transition of distinct stages of in vitro life cycle and in planta developmental stages of S. scitamineum are presented by generating stable GFP transformants of S. scitamineum. METHODS AND RESULTS: Haploid sporidia were isolated from the teliospores of Ss97009, and the opposite mating types (MAT-1 and MAT-2) were identified by random mating assay and mating type-specific PCR. Both haploid sporidia were individually transformed with pNIIST plasmid, harboring an enhanced green fluorescent protein (eGFP) gene and hygromycin gene by a modified protoplast-based PEG-mediated transformation method. Thereafter, the distinct in vitro developmental stages including fusion of haploid sporidia and formation of dikaryotic mycelia expressing GFP were demonstrated. To visualize in planta colonization, transformed haploids (MAT-1gfp and MAT-2gfp) were fused and inoculated onto the smut susceptible sugarcane cultivar, Co 97009 and examined microscopically at different stages of colonization. GFP fluorescence-based analysis presented an extensive fungal colonization of the bud surface as well as inter- and intracellular colonization of the transformed S. scitamineum in sugarcane tissues during initial stages of disease development. Noticeably, the GFP-tagged S. scitamineum led to the emergence of smut whips, which established their pathogenicity, and demonstrated initial colonization, active sporogenesis and teliospore maturation stages. CONCLUSION: Overall, for the first time, an efficient protoplast-based transformation method was employed to depict clear-cut developmental stages in vitro and in planta using GFP-tagged strains for better understanding of S. scitamineum life cycle development.

Effect of crop residue management on damage by Diatraea saccharalis (Lepidoptera: Crambidae), its egg parasitoids and the ants associated with sugarcane.

In the American continent, the sugarcane borer Diatraea saccharalis (F.) is the main pest in sugarcane producing areas. The objective of this study was to assess the effect of crop residue management on damage by D. saccharalis, its egg parasitoids and the ants associated with sugarcane. The study was carried out during 2011-2012, 2012-2013 and 2013-2014 crop cycles, in three commercial fields located in different regions of Tucumán state, Argentina. Two types of crop residue management (= treatments) were compared: conservation of trash at the soil surface (CT) and trash burning (TB). In 'trash conservation' treatment, crop residue was allowed to remain over the soil surface during the whole sugarcane growing season, while the second treatment consisted of complete burning of trash blanket approximately 2 weeks after harvest. The injury level was measured by recording the number of stalks bored and internodes bored. Parasitism was estimated by counting the total number of eggs and number of black eggs (which indicates the occurrence of egg parasitoids). Ants (Formicidae) richness was calculated by two estimators; abundance-based coverage estimator and incidence-based coverage estimator, using the non-parametric richness estimators: Chao 2 and Jackknife. Finally, the indicator value was estimated through the measurement of specificity and fidelity. In all the parameters studied no significant difference was found between TB and CT treatments.

Silicon enhancement for endorsement of Xanthomonas albilineans infection in sugarcane.

Silicon (Si) is considered to be a plant growth and development regulator element as well as provide the regulatory response against various biotic stressors. However, the potential mechanism of Si enhancement to regulate plant disease resistance remains to be studied. Therefore, the current study evaluated the effects of Si application on the performance of sugarcane against Xanthomonas albilineans (Xa) infection. Si was applied exogenously (0, 3.85 and 7.70 g Si/kg soil) and the results show that plant height, stem circumference and leaf width of siliconized sugarcane have been improved, which effectively reduced the disease index (0.17-0.21) and incidence (58.2%-69.1%) after Xa infection. Lowest values of MDA (348.5 nmol g-1 FW) and H2O2 (3539.4 mmol/L) were observed in 7.70 g Si/kg soil followed by in 3.85 g Si/kg soil (MDA: 392.6 nmol g-1 FW and H2O2: 3134.6 mmol/L) than that of the control. Whereas, PAL enzyme activity (50.8 mmol/L), JA (230.2 mmol/L) and SA (2.7 ug mL-1) contents were significantly higher in 7.70 g Si/kg soil followed by in 3.85 g Si/kg soil (PAL: 46.3 mmol/L, JA: 182.7 mmol/L and SA: 2.4 ug mL-1) as compared to control. The lower MDA, H2O2 level and higher enzymatic activities were associated with the highest expression levels of their metabolic pathway associated genes i.e., ShMAPK1, ShLOX, ShPAL, ShAOS, ShAOC, ShC4H, ShCAT, Sh4CL and ShNPR1 (22.08, 15.56, 10.42, 3.35, 2.54, 2.14, 1.82, 1.67 and 1.22 folds, respectively) in 7.70 g Si/kg soil as compared to other experimental units and control. Overall, the results of current study indicates that siliconized sugarcane more actively regulates disease resistance through modulation of growth and MDA, H2O2, SA and JA associated metabolic pathways.

Sugarcane/peanut intercropping system improves the soil quality and increases the abundance of beneficial microbes.

Sugarcane/peanut intercropping is a highly efficient planting pattern in South China. However, the effects of sugarcane/peanut intercropping on soil quality need to be clarified. This study characterized the soil microbial community and the soil quality in sugarcane/peanut intercropping systems by the Illumina MiSeq platform. The results showed that the intercropping sugarcane (IS) system significantly increased the total N (TN), available N (AN), available P (AP), pH value, and acid phosphatase activity (ACP), but it had little effect on the total P (TP), total K (TK), available K (AK), organic matter (OM), urease activity, protease activity, catalase activity, and sucrase activity, compared with those in monocropping sugarcane (MS) and monocropping peanut (MP) systems. Both intercropping peanut (IP) and IS soils contained more bacteria and fungi than soils in the MP and MS fields, and the microbes identified were mainly Chloroflexi and Acidobacteria, respectively. Intercropping significantly increased the number of unique microbes in IS soils (68 genera), compared with the numbers in the IP (14), MS (17), and MP (16) systems. The redundancy analysis revealed that the abundances of culturable Acidobacteriaceae subgroup 1, nonculturable DA111, and culturable Acidobacteria were positively correlated with the measured soil quality in the intercropping system. Furthermore, the sugarcane/peanut intercropping significantly increased the economic benefit by 87.84% and 36.38%, as compared with that of the MP and MS, respectively. These results suggest that peanut and sugarcane intercropping increases the available N and P content by increasing the abundance of rhizospheric microbes, especially Acidobacteriaceae subgroup 1, DA111, and Acidobacteria.

Genome-wide identification and expression analysis of AP2/ERF transcription factors in sugarcane (Saccharum spontaneum L.).

BACKGROUND: APETALA2/ETHYLENE RESPONSIVE FACTOR (AP2/ERF) transcription factors play essential roles in plant growth, development, metabolism, and responses to biotic and abiotic stresses. However, few studies concerning AP2/ERF genes in sugarcane which are the most critical sugar and energy crops worldwide. RESULTS: A total of 218 AP2/ERF genes were identified in the Saccharum spontaneum genome. Phylogenetic analysis showed that these genes could be divided into four groups, including 43 AP2s, 160 ERFs and Dehydration-responsive element-binding (DREB) factors, 11 ABI3/VPs (RAV), and four Soloist genes. These genes were unevenly distributed on 32 chromosomes. The structural analysis of SsAP2/ERF genes showed that 91 SsAP2/ERFs lacked introns. Sugarcane and sorghum had a collinear relationship between 168 SsAP2/ERF genes and sorghum AP2/ERF genes that reflected their similarity. Multiple cis-regulatory elements (CREs) present in the SsAP2/ERF promoter were related to abiotic stresses, suggesting that SsAP2/ERF activity could contribute to sugarcane adaptation to environmental changes. The tissue-specific analysis showed spatiotemporal expression of SsAP2/ERF in the stems and leaves of sugarcane at different development stages. In ten sugarcane samples, 39 SsAP2/ERFs were not expressed, whereas 58 SsAP2/ERFs were expressed in all samples. Quantitative PCR experiments showed that SsERF52 expression was up-regulated under salt stress, but suppressed under dehydration stress. SsSoloist4 had the most considerable upregulation in response to treatment with the exogenous hormones ABA and GA. Within 3 h of ABA or PEG6000 treatment, SsSoloist4 expression was up-regulated, indicating that this gene could play a role in the responses to ABA and GA-associated dehydration stress. Analysis of AP2/ERF gene expression patterns under different treatments indicated that SsAP2/ERF genes played an essential role in dehydration and salt stress responses of S. spontaneum. CONCLUSIONS: In this study, a total of 218 members of the AP2 / ERF superfamily were identified in sugarcane, and their genetic structure, evolution characteristics, and expression patterns were studied and analyzed. The results of this study provide a foundation for future analyses to elucidate the importance of AP2/ERF transcription factors in the function and molecular breeding of sugarcane.

Differential expression in leaves of Saccharum genotypes contrasting in biomass production provides evidence of genes involved in carbon partitioning.

BACKGROUND: The development of biomass crops aims to meet industrial yield demands, in order to optimize profitability and sustainability. Achieving these goals in an energy crop like sugarcane relies on breeding for sucrose accumulation, fiber content and stalk number. To expand the understanding of the biological pathways related to these traits, we evaluated gene expression of two groups of genotypes contrasting in biomass composition. RESULTS: First visible dewlap leaves were collected from 12 genotypes, six per group, to perform RNA-Seq. We found a high number of differentially expressed genes, showing how hybridization in a complex polyploid system caused extensive modifications in genome functioning. We found evidence that differences in transposition and defense related genes may arise due to the complex nature of the polyploid Saccharum genomes. Genotypes within both biomass groups showed substantial variability in genes involved in photosynthesis. However, most genes coding for photosystem components or those coding for phosphoenolpyruvate carboxylases (PEPCs) were upregulated in the high biomass group. Sucrose synthase (SuSy) coding genes were upregulated in the low biomass group, showing that this enzyme class can be involved with sucrose synthesis in leaves, similarly to sucrose phosphate synthase (SPS) and sucrose phosphate phosphatase (SPP). Genes in pathways related to biosynthesis of cell wall components and expansins coding genes showed low average expression levels and were mostly upregulated in the high biomass group. CONCLUSIONS: Together, these results show differences in carbohydrate synthesis and carbon partitioning in the source tissue of distinct phenotypic groups. Our data from sugarcane leaves revealed how hybridization in a complex polyploid system resulted in noticeably different transcriptomic profiles between contrasting genotypes.

Metabolic Regulation and Development of Energy Cane Setts upon Auxin Stimulus.

Energy cane is a bioenergy crop with an outstanding ability to bud sprouting and increasing yield in ratoon cycles even in marginal lands. Bud fate control is key to biomass production and crop profits due to vegetative propagation and tiller dependency, as well as phenotype plasticity to withstand harsh environmental conditions. During the establishment stage (plant cane cycle), energy cane has a tendency for low root:shoot ratio, which might hamper the ability to cope with stress. Auxin is known to modulate bud sprouting and stimulate rooting in sugarcane. Hence, we treated a slow and a fast bud sprouting energy cane cultivars with auxin or controls (with and without water soaking) for 6 h prior to planting and evaluate plant growth parameters and metabolic profiling using two techniques (gas chromatography with time-of-flight mass spectrometer and nuclear magnetic resonance) to characterize the effect and identify metabolite markers associated with bud inhibition and outgrowth. Auxin inhibited bud burst and promote rooting in setts changing the root:shoot ratio of plantlets. Metabolome allowed the identification of lactate, succinate and aspartate family amino acids as involved in bud fate control through the potential modulation of oxygen and energy status. Investigating environmental and biochemical factors that regulate bud fate can be incremental to other monocot species. Our study provides new insights into bud quiescence and outgrowth in cane hybrids, with the potential to leverage our understanding of yield-related traits, crop establishment and adaptation to global climate change.

Diversity of nitrogen-fixing rhizobacteria associated with sugarcane: a comprehensive study of plant-microbe interactions for growth enhancement in Saccharum spp.

BACKGROUND: Nitrogen is an essential element for sugarcane growth and development and is generally applied in the form of urea often much more than at recommended rates, causing serious soil degradation, particularly soil acidification, as well as groundwater and air pollution. In spite of the importance of nitrogen for plant growth, fewer reports are available to understand the application and biological role of N2 fixing bacteria to improve N2 nutrition in the sugarcane plant. RESULTS: In this study, a total of 350 different bacterial strains were isolated from rhizospheric soil samples of the sugarcane plants. Out of these, 22 isolates were selected based on plant growth promotion traits, biocontrol, and nitrogenase activity. The presence and activity of the nifH gene and the ability of nitrogen-fixation proved that all 22 selected strains have the ability to fix nitrogen. These strains were used to perform 16S rRNA and rpoB genes for their identification. The resulted amplicons were sequenced and phylogenetic analysis was constructed. Among the screened strains for nitrogen fixation, CY5 (Bacillus megaterium) and CA1 (Bacillus mycoides) were the most prominent. These two strains were examined for functional diversity using Biolog phenotyping, which confirmed the consumption of diverse carbon and nitrogen sources and tolerance to low pH and osmotic stress. The inoculated bacterial strains colonized the sugarcane rhizosphere successfully and were mostly located in root and leaf. The expression of the nifH gene in both sugarcane varieties (GT11 and GXB9) inoculated with CY5 and CA1 was confirmed. The gene expression studies showed enhanced expression of genes of various enzymes such as catalase, phenylalanine-ammonia-lyase, superoxide dismutase, chitinase and glucanase in bacterial-inoculated sugarcane plants. CONCLUSION: The results showed that a substantial number of Bacillus isolates have N-fixation and biocontrol property against two sugarcane pathogens Sporisorium scitamineum and Ceratocystis paradoxa. The increased activity of genes controlling free radical metabolism may at least in part accounts for the increased tolerance to pathogens. Nitrogen-fixation was confirmed in sugarcane inoculated with B. megaterium and B. mycoides strains using N-balance and 15N2 isotope dilution in different plant parts of sugarcane. This is the first report of Bacillus mycoides as a nitrogen-fixing rhizobacterium in sugarcane.

Identification of genes from the general phenylpropanoid and monolignol-specific metabolism in two sugarcane lignin-contrasting genotypes.

The phenylpropanoid pathway is an important route of secondary metabolism involved in the synthesis of different phenolic compounds such as phenylpropenes, anthocyanins, stilbenoids, flavonoids, and monolignols. The flux toward monolignol biosynthesis through the phenylpropanoid pathway is controlled by specific genes from at least ten families. Lignin polymer is one of the major components of the plant cell wall and is mainly responsible for recalcitrance to saccharification in ethanol production from lignocellulosic biomass. Here, we identified and characterized sugarcane candidate genes from the general phenylpropanoid and monolignol-specific metabolism through a search of the sugarcane EST databases, phylogenetic analysis, a search for conserved amino acid residues important for enzymatic function, and analysis of expression patterns during culm development in two lignin-contrasting genotypes. Of these genes, 15 were cloned and, when available, their loci were identified using the recently released sugarcane genomes from Saccharum hybrid R570 and Saccharum spontaneum cultivars. Our analysis points out that ShPAL1, ShPAL2, ShC4H4, Sh4CL1, ShHCT1, ShC3H1, ShC3H2, ShCCoAOMT1, ShCOMT1, ShF5H1, ShCCR1, ShCAD2, and ShCAD7 are strong candidates to be bona fide lignin biosynthesis genes. Together, the results provide information about the candidate genes involved in monolignol biosynthesis in sugarcane and may provide useful information for further molecular genetic studies in sugarcane.