The effect of filter cakes enriched with soluble phosphorus used as a fertilizer on the sugarcane ratoons

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Greenhouse gas balance associated with sugarcane production in South-Central Brazil, considering the management and expansion

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

A Spatial Propensity Score Matching Evaluation of the Social Impacts of Sugarcane Growing on Municipalities in Brazil

The expansion of sugarcane growing in Brazil, spurred particularly by increased demand for ethanol, has triggered the need to evaluate the economic, social, and environmental impacts of this process, both on the country as a whole and on the growing regions. Even though the balance of costs and benefits is positive from an overall standpoint, this may not be so in specific producing regions, due to negative externalities. The objective of this paper is to estimate the effect of growing sugarcane on the human development index (HDI) and its sub-indices in cane producing regions. In the literature on matching effects, this is interpreted as the effect of the treatment on the treated. Location effects are controlled by spatial econometric techniques, giving rise to the spatial propensity score matching model. The authors analyze 424 minimum comparable areas (MCAs) in the treatment group, compared with 907 MCAs in the control group. The results suggest that the presence of sugarcane growing in these areas is not relevant to determine their social conditions, whether for better or worse. It is thus likely that public policies, especially those focused directly on improving education, health, and income generation/distribution, have much more noticeable effects on the municipal HDI.

Whole-genome sequencing of the efficient industrial fuel-ethanol fermentative Saccharomyces cerevisiae strain CAT-1

The Saccharomyces cerevisiae strains widely used for industrial fuel-ethanol production have been developed by selection, but their underlying beneficial genetic polymorphisms remain unknown. Here, we report the draft whole-genome sequence of the S. cerevisiae strain CAT-1, which is a dominant fuel-ethanol fermentative strain from the sugarcane industry in Brazil. Our results indicate that strain CAT-1 is a highly heterozygous diploid yeast strain, and the similar to 12-Mb genome of CAT-1, when compared with the reference S228c genome, contains similar to 36,000 homozygous and similar to 30,000 heterozygous single nucleotide polymorphisms, exhibiting an uneven distribution among chromosomes due to large genomic regions of loss of heterozygosity (LOH). In total, 58 % of the 6,652 predicted protein-coding genes of the CAT-1 genome constitute different alleles when compared with the genes present in the reference S288c genome. The CAT-1 genome contains a reduced number of transposable elements, as well as several gene deletions and duplications, especially at telomeric regions, some correlated with several of the physiological characteristics of this industrial fuel-ethanol strain. Phylogenetic analyses revealed that some genes were likely associated with traits important for bioethanol production. Identifying and characterizing the allelic variations controlling traits relevant to industrial fermentation should provide the basis for a forward genetics approach for developing better fermenting yeast strains.

Identification of sense and antisense transcripts regulated by drought in sugarcane

Sugarcane is an important sugar and energy crop that can be used efficiently for biofuels production. The development of sugarcane cultivars tolerant to drought could allow for the expansion of plantations to sub-prime regions. Knowledge on the mechanisms underlying drought responses and its relationship with carbon partition would greatly help to define routes to increase yield. In this work we studied sugarcane responses to drought using a custom designed oligonucleotide array with 21,901 different probes. The oligoarrays were designed to contain probes that detect transcription in both sense and antisense orientation. We validated the results obtained using quantitative real-time PCR (qPCR). A total of 987 genes were differentially expressed in at least one sample of sugarcane plants submitted to drought for 24, 72 and 120 h. Among them, 928 were sense transcripts and 59 were antisense transcripts. Genes related to Carbohydrate Metabolism, RNA Metabolism and Signal Transduction were selected for gene expression validation by qPCR that indicated a validation percentage of 90 %. From the probes presented on the array, 75 % of the sense probes and 11.9 % of the antisense probes have signal above background and can be classified as expressed sequences. Our custom sugarcane oligonucleotide array provides sensitivity and good coverage of sugarcane transcripts for the identification of a representative proportion of natural antisense transcripts (NATs) and sense-antisense transcript pairs (SATs). The antisense transcriptome showed, in most cases, co-expression with respective sense transcripts.

A Novel Stress-Induced Sugarcane Gene Confers Tolerance to Drought, Salt and Oxidative Stress in Transgenic Tobacco Plants

Background: Drought is a major abiotic stress that affects crop productivity worldwide. Sugarcane can withstand periods of water scarcity during the final stage of culm maturation, during which sucrose accumulation occurs. Meanwhile, prolonged periods of drought can cause severe plant losses. Methodology/Principal Findings: In a previous study, we evaluated the transcriptome of drought-stressed plants to better understand sugarcane responses to drought. Among the up-regulated genes was Scdr1 (sugarcane drought-responsive 1). The aim of the research reported here was to characterize this gene. Scdr1 encodes a putative protein containing 248 amino acids with a large number of proline (19%) and cysteine (13%) residues. Phylogenetic analysis showed that ScDR1is in a clade with homologs from other monocotyledonous plants, separate from those of dicotyledonous plants. The expression of Scdr1 in different varieties of sugarcane plants has not shown a clear association with drought tolerance. Conclusions/Significance: The overexpression of Scdr1 in transgenic tobacco plants increased their tolerance to drought, salinity and oxidative stress, as demonstrated by increased photosynthesis, water content, biomass, germination rate, chlorophyll content and reduced accumulation of ROS. Physiological parameters, such as transpiration rate (E), net photosynthesis (A), stomatal conductance (gs) and internal leaf CO2 concentration, were less affected by abiotic stresses in transgenic Scdr1 plants compared with wild-type plants. Overall, our results indicated that Scdr1 conferred tolerance to multiple abiotic stresses, highlighting the potential of this gene for biotechnological applications.

A novel linkage map of sugarcane with evidence for clustering of retrotransposon-based markers

Background: The development of sugarcane as a sustainable crop has unlimited applications. The crop is one of the most economically viable for renewable energy production, and CO2 balance. Linkage maps are valuable tools for understanding genetic and genomic organization, particularly in sugarcane due to its complex polyploid genome of multispecific origins. The overall objective of our study was to construct a novel sugarcane linkage map, compiling AFLP and EST-SSR markers, and to generate data on the distribution of markers anchored to sequences of scIvana_1, a complete sugarcane transposable element, and member of the Copia superfamily. Results: The mapping population parents ('IAC66-6' and 'TUC71-7') contributed equally to polymorphisms, independent of marker type, and generated markers that were distributed into nearly the same number of co-segregation groups (or CGs). Bi-parentally inherited alleles provided the integration of 19 CGs. The marker number per CG ranged from two to 39. The total map length was 4,843.19 cM, with a marker density of 8.87 cM. Markers were assembled into 92 CGs that ranged in length from 1.14 to 404.72 cM, with an estimated average length of 52.64 cM. The greatest distance between two adjacent markers was 48.25 cM. The scIvana_1-based markers (56) were positioned on 21 CGs, but were not regularly distributed. Interestingly, the distance between adjacent scIvana_1-based markers was less than 5 cM, and was observed on five CGs, suggesting a clustered organization. Conclusions: Results indicated the use of a NBS-profiling technique was efficient to develop retrotransposon-based markers in sugarcane. The simultaneous maximum-likelihood estimates of linkage and linkage phase based strategies confirmed the suitability of its approach to estimate linkage, and construct the linkage map. Interestingly, using our genetic data it was possible to calculate the number of retrotransposonscIvana_1 (similar to 60) copies in the sugarcane genome, confirming previously reported molecular results. In addition, this research possibly will have indirect implications in crop economics e. g., productivity enhancement via QTL studies, as the mapping population parents differ in response to an important fungal disease.

Hydrothermal pretreatment of sugarcane bagasse using response surface methodology improves digestibility and ethanol production by SSF

Sugarcane bagasse was characterized as a feedstock for the production of ethanol using hydrothermal pretreatment. Reaction temperature and time were varied between 160 and 200A degrees C and 5-20 min, respectively, using a response surface experimental design. The liquid fraction was analyzed for soluble carbohydrates and furan aldehydes. The solid fraction was analyzed for structural carbohydrates and Klason lignin. Pretreatment conditions were evaluated based on enzymatic extraction of glucose and xylose and conversion to ethanol using a simultaneous saccharification and fermentation scheme. SSF experiments were conducted with the washed pretreated biomass. The severity of the pretreatment should be sufficient to drive enzymatic digestion and ethanol yields, however, sugars losses and especially sugar conversion into furans needs to be minimized. As expected, furfural production increased with pretreatment severity and specifically xylose release. However, provided that the severity was kept below a general severity factor of 4.0, production of furfural was below an inhibitory concentration and carbohydrate contents were preserved in the pretreated whole hydrolysate. There were significant interactions between time and temperature for all the responses except cellulose digestion. The models were highly predictive for cellulose digestibility (R (2) = 0.8861) and for ethanol production (R (2) = 0.9581), but less so for xylose extraction. Both cellulose digestion and ethanol production increased with severity, however, high levels of furfural generated under more severe pretreatment conditions favor lower severity pretreatments. The optimal pretreatment condition that gave the highest conversion yield of ethanol, while minimizing furfural production, was judged to be 190A degrees C and 17.2 min. The whole hydrolysate was also converted to ethanol using SSF. To reduce the concentration of inhibitors, the liquid fraction was conditioned prior to fermentation by removing inhibitory chemicals using the fungus Coniochaeta ligniaria.

Long-term decomposition of sugarcane harvest residues in Sao Paulo state, Brazil

Crop residues returned to the soil are important to preserve fertility and sustainability. This research addressed the long-term decomposition of sugarcane post-harvest residues (trash) under reduced tillage, therefore field renewal was performed with herbicide followed by subsoiling and ratoons were deprived of interrow scarification. The trial was conducted in the northern Sao Paulo State, Brazil during four consecutive crops (2005-2008) where litter bags containing N-15-labeled trash were disposed in the field attempting to simulate two distinct situations: the previous crop trash (PCT) or residues incorporated in the field after tillage, and post-harvest trash (PHT) or the remains of plant-cane harvest. Decomposition rates regarding dry matter (DM), carbon (C), root growth, plant nutrients (N, P, K, Ca, Mg and S), lignin (LIG) cellulose (CEL) and hemicellulose (HCEL) contents were assessed for PCT (2005 ndash;2008) and for PHT (2006-2008). There were significant reductions on DM and C:N ratio due to C losses and root growth within the litter bags over time. The DM from PCT and PHT decreased 96% and 73% after four and three crops, respectively, and the higher nutrients release were found for K, Ca and N. The LIG, CEL and HCEL concentrations in PCT decreased 60%, 29%, 70% after four crops and 47%, 35%, 70% from PHT after three crops, respectively. Trash decomposition was driven mainly by residues biochemical composition, root growth within the trash blanket and the climatic conditions during the crop cycles. (C) 2012 Elsevier Ltd. All rights reserved.

A biophysical model of Sugarcane growth

Scientists predict that global agricultural lands will expand over the next few decades due to increasing demands for food production and an exponential increase in crop-based biofuel production. These changes in land use will greatly impact biogeochemical and biogeophysical cycles across the globe. It is therefore important to develop models that can accurately simulate the interactions between the atmosphere and important crops. In this study, we develop and validate a new process-based sugarcane model (included as a module within the Agro-IBIS dynamic agro-ecosystem model) which can be applied at multiple spatial scales. At site level, the model systematically under/overestimated the daily sensible/latent heat flux (by -10.5% and 14.8%, H and E, respectively) when compared against the micrometeorological observations from southeast Brazil. The model underestimated ET (relative bias between -10.1% and 12.5%) when compared against an agro-meteorological field experiment from northeast Australia. At the regional level, the model accurately simulated average yield for the four largest mesoregions (clusters of municipalities) in the state of Sao Paulo, Brazil, over a period of 16 years, with a yield relative bias of -0.68% to 1.08%. Finally, the simulated annual average sugarcane yield over 31 years for the state of Louisiana (US) had a low relative bias (-2.67%), but exhibited a lower interannual variability than the observed yields.

Analysis of NDVI time series using cross-correlation and forecasting methods for monitoring sugarcane fields in Brazil

Brazil is the largest sugarcane producer in the world and has a privileged position to attend to national and international market places. To maintain the high production of sugarcane, it is fundamental to improve the forecasting models of crop seasons through the use of alternative technologies, such as remote sensing. Thus, the main purpose of this article is to assess the results of two different statistical forecasting methods applied to an agroclimatic index (the water requirement satisfaction index; WRSI) and the sugarcane spectral response (normalized difference vegetation index; NDVI) registered on National Oceanic and Atmospheric Administration Advanced Very High Resolution Radiometer (NOAA-AVHRR) satellite images. We also evaluated the cross-correlation between these two indexes. According to the results obtained, there are meaningful correlations between NDVI and WRSI with time lags. Additionally, the adjusted model for NDVI presented more accurate results than the forecasting models for WRSI. Finally, the analyses indicate that NDVI is more predictable due to its seasonality and the WRSI values are more variable making it difficult to forecast.

Sugarwin: A Sugarcane Insect-Induced Gene with Antipathogenic Activity

In sugarcane fields, colonization of the stalk by opportunistic fungi usually occurs after the caterpillar Diatraea saccharalis attacks the sugarcane plant. Plants respond to insect attack by inducing and accumulating a large set of defense proteins. Two homologues of a barley wound-inducible protein (BARWIN), sugarcane wound-inducible proteins SUGARWIN1 and SUGARWIN2, have been identified in sugarcane by an in silico analysis. Antifungal properties have been described for a number of BARWIN homologues. We report that a SUGARWIN:green fluorescent protein fusion protein is located in the endoplasmic reticulum and in the extracellular space of sugarcane plants. The induction of sugarwin transcripts occurs in response to mechanical wounding, D. saccharalis damage, and methyl jasmonate treatment. The accumulation of transcripts is late induced and is restricted to the site of the wound. Although the transcripts of sugarwin genes were strongly increased following insect attack, the protein itself did not show any effect on insect development; rather, it altered fungal morphology, leading to the apoptosis of the germlings. These results suggest that, in the course of evolution, sugarwin-encoding genes were recruited by sugarcane due to their antipathogenic activity. We rationalize that sugarcane is able to induce sugarwin gene expression in response to D. saccharalis feeding as a concerted plant response to the anticipated invasion by the fungi that typically penetrate the plant stalk after insect damage.

Microcollinearity between autopolyploid sugarcane and diploid sorghum genomes

Abstract Background Sugarcane (Saccharum spp.) has become an increasingly important crop for its leading role in biofuel production. The high sugar content species S. officinarum is an octoploid without known diploid or tetraploid progenitors. Commercial sugarcane cultivars are hybrids between S. officinarum and wild species S. spontaneum with ploidy at ~12×. The complex autopolyploid sugarcane genome has not been characterized at the DNA sequence level. Results The microsynteny between sugarcane and sorghum was assessed by comparing 454 pyrosequences of 20 sugarcane bacterial artificial chromosomes (BACs) with sorghum sequences. These 20 BACs were selected by hybridization of 1961 single copy sorghum overgo probes to the sugarcane BAC library with one sugarcane BAC corresponding to each of the 20 sorghum chromosome arms. The genic regions of the sugarcane BACs shared an average of 95.2% sequence identity with sorghum, and the sorghum genome was used as a template to order sequence contigs covering 78.2% of the 20 BAC sequences. About 53.1% of the sugarcane BAC sequences are aligned with sorghum sequence. The unaligned regions contain non-coding and repetitive sequences. Within the aligned sequences, 209 genes were annotated in sugarcane and 202 in sorghum. Seventeen genes appeared to be sugarcane-specific and all validated by sugarcane ESTs, while 12 appeared sorghum-specific but only one validated by sorghum ESTs. Twelve of the 17 sugarcane-specific genes have no match in the non-redundant protein database in GenBank, perhaps encoding proteins for sugarcane-specific processes. The sorghum orthologous regions appeared to have expanded relative to sugarcane, mostly by the increase of retrotransposons. Conclusions The sugarcane and sorghum genomes are mostly collinear in the genic regions, and the sorghum genome can be used as a template for assembling much of the genic DNA of the autopolyploid sugarcane genome. The comparable gene density between sugarcane BACs and corresponding sorghum sequences defied the notion that polyploidy species might have faster pace of gene loss due to the redundancy of multiple alleles at each locus.

A non-coding genomic duplication at the HMX1 locus is associated with crop ears in highland cattle.

Highland cattle with congenital crop ears have notches of variable size on the tips of both ears. In some cases, cartilage deformation can be seen and occasionally the external ears are shortened. We collected 40 cases and 80 controls across Switzerland. Pedigree data analysis confirmed a monogenic autosomal dominant mode of inheritance with variable expressivity. All affected animals could be traced back to a single common ancestor. A genome-wide association study was performed and the causative mutation was mapped to a 4 Mb interval on bovine chromosome 6. The H6 family homeobox 1 (HMX1) gene was selected as a positional and functional candidate gene. By whole genome re-sequencing of an affected Highland cattle, we detected 6 non-synonymous coding sequence variants and two variants in an ultra-conserved element at the HMX1 locus with respect to the reference genome. Of these 8 variants, only a non-coding 76 bp genomic duplication (g.106720058_106720133dup) located in the conserved region was perfectly associated with crop ears. The identified copy number variation probably results in HMX1 misregulation and possible gain-of-function. Our findings confirm the role of HMX1 during the development of the external ear. As it is sometimes difficult to phenotypically diagnose Highland cattle with slight ear notches, genetic testing can now be used to improve selection against this undesired trait.

Determination of the uptake and translocation of nitrogen applied at different growth stages of a melon crop (Cucumis melo L.) using 15N isotope.

In order to establish a rational nitrogen (N) fertilisation and reduce groundwater contamination, a clearer understanding of the N distribution through the growing season and its dynamics inside the plant is crucial. In two successive years, a melon crop (Cucumis melo L. cv. Sancho) was grown under field conditions to determine the uptake of N fertiliser, applied by means of fertigation at different stages of plant growth, and to follow the translocation of N in the plant using 15N-labelled N. In 2006, two experiments were carried out. In the first experiment, labelled 15N fertiliser was supplied at the female-bloom stage and in the second, at the end of fruit ripening. Labelled 15N fertiliser was made from 15NH415NO3 (10 at.% 15N) and 9.6 kg N ha−1 were applied in each experiment over 6 days (1.6 kg N ha−1 d−1). In 2007, the 15N treatment consisted of applying 20.4 kg N ha−1 as 15NH415NO3 (10 at.% 15N) in the middle of fruit growth, over 6 days (3.4 kg N ha−1 d−1). In addition, 93 and 95 kg N ha−1 were supplied daily by fertigation as ammonium nitrate in 2006 and 2007, respectively. The results obtained in 2006 suggest that the uptake of N derived from labelled fertiliser by the above-ground parts of the plants was not affected by the time of fertiliser application. At the female-flowering and fruit-ripening stages, the N content derived from 15N-labelled fertiliser was close to 0.435 g m−2 (about 45% of the N applied), while in the middle of fruit growth it was 1.45 g m−2 (71% of the N applied). The N application time affected the amount of N derived from labelled fertiliser that was translocated to the fruits. When the N was supplied later, the N translocation was lower, ranging between 54% at female flowering and 32% at the end of fruit ripening. Approximately 85% of the N translocated came from the leaf when the N was applied at female flowering or in the middle of fruit growth. This value decreased to 72% when the 15N application was at the end of fruit ripening. The ammonium nitrate became available to the plant between 2 and 2.5 weeks after its application. Although the leaf N uptake varied during the crop cycle, the N absorption rate in the whole plant was linear, suggesting that the melon crop could be fertilised with constant daily N amounts until 2–3 weeks before the last harvest.