Sugarcane for water-limited environments. Genetic variation in cane yield and sugar content in response to water stress

Regulation of an endophytic nitrogen-fixing bacteria GXS16 promoting drought tolerance in sugarcane

BACKGROUND

Drought limits crop growth and is an important issue in commercial sugarcane (Saccharum officinarum) production. Drought tolerance in sugarcane induced by endophytic nitrogen-fixing bacteria is a complex biological process that ranges from altered gene expression and cellular metabolism to changes in growth and productivity.

RESULTS

In this study, changes in physiological features and transcriptome related to drought tolerance in sugarcane conferred by the Burkholderia endophytic nitrogen-fixing bacterial strain GXS16 were investigated. Sugarcane samples inoculated with GXS16 exhibited significantly higher leaf relative water content than those without GXS16 inoculation during the drought stages. Sugarcane treated with GXS16 had lower levels of H2O2 and higher levels of abscisic acid than sugarcane not treated with GXS16 in the non-watering groups. Transcriptomic analysis of sugarcane roots identified multiple differentially expressed genes between adjacent stages under different treatments. Moreover, both trend and weighted correlation network analyses revealed that carotenoid biosynthesis, terpenoid backbone biosynthesis, starch and sucrose metabolism, and plant hormone signal transduction strongly contributed to the drought-tolerant phenotype of sugarcane induced by GXS16 treatment. Accordingly, a gene regulatory network including four differentially regulated genes from carotenoid biosynthesis (crtB, crtZ, ZEP and CYP707A) and three genes from terpenoid backbone biosynthesis (dxs, dxr, and PCME) was constructed.

CONCLUSIONS

This study provides insights into the molecular mechanisms underlying the application of GXS16 treatment to enhance drought tolerance in sugarcane, which will lay the foundation for crop development and improve productivity.

Drought and salinity stresses induced physio-biochemical changes in sugarcane: an overview of tolerance mechanism and mitigating approaches

Sugarcane productivity is being hampered globally under changing environmental scenarios like drought and salinity. The highly complex nature of the plant responses against these stresses is determined by a variety of factors such as genotype, developmental phase of the plant, progression rate and stress, intensity, and duration. These factors influence plant responses and can determine whether mitigation approaches associated with acclimation are implemented. In this review, we attempt to summarize the effects of drought and salinity on sugarcane growth, specifically on the plant's responses at various levels, viz., physiological, biochemical, and metabolic responses, to these stresses. Furthermore, mitigation strategies for dealing with these stresses have been discussed. Despite sugarcane's complex genomes, conventional breeding approaches can be utilized in conjunction with molecular breeding and omics technologies to develop drought- and salinity-tolerant cultivars. The significant role of plant growth-promoting bacteria in sustaining sugarcane productivity under drought and salinity cannot be overlooked.

Receptor-like cytoplasmic kinase ScRIPK in sugarcane regulates disease resistance and drought tolerance in Arabidopsis

Introduction

Receptor-like cytoplastic kinases (RLCKs) are known in many plants to be involved in various processes of plant growth and development and regulate plant immunity to pathogen infection. Environmental stimuli such as pathogen infection and drought restrict the crop yield and interfere with plant growth. However, the function of RLCKs in sugarcane remains unclear.

Methods and results

In this study, a member of the RLCK VII subfamily, ScRIPK, was identified in sugarcane based on sequence similarity to the rice and Arabidopsis RLCKs. ScRIPK was localized to the plasma membrane, as predicted, and the expression of ScRIPK was responsive to polyethylene glycol treatment and Fusarium sacchari infection. Overexpression of ScRIPK in Arabidopsis enhanced drought tolerance and disease susceptibility of seedlings. Moreover, the crystal structure of the ScRIPK kinase domain (ScRIPK KD) and the mutant proteins (ScRIPK-KD K124R and ScRIPK-KD S253A|T254A) were characterized in order to determine the activation mechanism. We also identified ScRIN4 as the interacting protein of ScRIPK.

Discussion

Our work identified a RLCK in sugarcane, providing a potential target for sugarcane responses to disease infection and drought, and a structural basis for kinase activation mechanisms.

A Comprehensive Identification and Expression Analysis of VQ Motif-Containing Proteins in Sugarcane (Saccharum spontaneum L.) under Phytohormone Treatment and Cold Stress

The VQ motif-containing proteins play a vital role in various processes such as growth, resistance to biotic and abiotic stresses and development. However, there is currently no report on the VQ genes in sugarcane (Saccharum spp.). Herein, 78 VQ genes in Saccharum spontaneum were identified and classified into nine subgroups (I-IX) by comparative genomic analyses. Each subgroup had a similar structural and conservative motif. These VQ genes expanded mainly through whole-genome segmental duplication. The cis-regulatory elements (CREs) of the VQ genes were widely involved in stress responses, phytohormone responses and physiological regulation. The RNA-seq data showed that SsVQ gene expression patterns in 10 different samples, including different developmental stages, revealed distinct temporal and spatial patterns. A total of 23 SsVQ genes were expressed in all tissues, whereas 13 SsVQ genes were not expressed in any tissues. Sequence Read Archive (SRA) data showed that the majority of SsVQs responded to cold and drought stress. In addition, quantitative real-time PCR analysis showed that the SsVQs were variously expressed under salicylic acid (SA), jasmonic acid (JA), abscisic acid (ABA) and cold treatment. This study conducted a full-scale analysis of the VQ gene family in sugarcane, which could be beneficial for the functional characterization of sugarcane VQ genes and provide candidate genes for molecular resistance breeding in cultivated sugarcane in the future.

A Sugarcane G-Protein-Coupled Receptor, ShGPCR1, Confers Tolerance to Multiple Abiotic Stresses

Sugarcane (Saccharum spp.) is a prominent source of sugar and serves as bioenergy/biomass feedstock globally. Multiple biotic and abiotic stresses, including drought, salinity, and cold, adversely affect sugarcane yield. G-protein-coupled receptors (GPCRs) are components of G-protein-mediated signaling affecting plant growth, development, and stress responses. Here, we identified a GPCR-like protein (ShGPCR1) from sugarcane and energy cane (Saccharum spp. hybrids) and characterized its function in conferring tolerance to multiple abiotic stresses. ShGPCR1 protein sequence contained nine predicted transmembrane (TM) domains connected by four extracellular and four intracellular loops, which could interact with various ligands and heterotrimeric G proteins in the cells. ShGPCR1 sequence displayed other signature features of a GPCR, such as a putative guanidine triphosphate (GTP)-binding domain, as well as multiple myristoylation and protein phosphorylation sites, presumably important for its biochemical function. Expression of ShGPCR1 was upregulated by drought, salinity, and cold stresses. Subcellular imaging and calcium (Ca²⁺) measurements revealed that ShGPCR1 predominantly localized to the plasma membrane and enhanced intracellular Ca²⁺ levels in response to GTP, respectively. Furthermore, constitutive overexpression of ShGPCR1 in sugarcane conferred tolerance to the three stressors. The stress-tolerance phenotype of the transgenic lines corresponded with activation of multiple drought-, salinity-, and cold-stress marker genes, such as Saccharum spp. LATE EMBRYOGENESIS ABUNDANT, DEHYDRIN, DROUGHT RESPONSIVE 4, GALACTINOL SYNTHASE, ETHYLENE RESPONSIVE FACTOR 3, SALT OVERLY SENSITIVE 1, VACUOLAR Na+/H+ ANTIPORTER 1, NAM/ATAF1/2/CUC2, COLD RESPONSIVE FACTOR 2, and ALCOHOL DEHYDROGENASE 3. We suggest that ShGPCR1 plays a key role in conferring tolerance to multiple abiotic stresses, and the engineered lines may be useful to enhance sugarcane production in marginal environments with fewer resources.

Assessing the performance of two gridded weather data for sugarcane crop simulations with a process-based model in Center-South Brazil

High-quality measured weather data (MWD) are essential for long-term and in-season crop model applications. When MWD is not available, one alternative for crop simulations is to employ gridded weather data (GWD), which needs to be evaluated a priori. Therefore, this study aimed to evaluate the impact of weather data from two GWD sources (NASA and XAVIER), in the way that they are available for end users, on simulating sugarcane crop performance within the APSIM-Sugar model at traditional sites where sugarcane is grown in Center-South Brazil, compared to simulations with MWD. Besides, this study also evaluated the impact of replacing GWD rainfall by the site-specific measured data on such simulations. A common sugarcane cropping system was repeatedly simulated between 1997 and 2015 for different combinations of climate input. Both NASA and XAVIER appear to be interesting for applications that only require temperature and solar radiation for predictions, such as crop phenology and potential yield. Nonetheless, GWD should be used with caution for crop model applications that rely on accurate estimation of crop water balance, canopy development, and biomass accumulation, at least with crop models that run at a daily time-step. The replacement of gridded rainfall with measured rainfall was pivotal for improving sugarcane simulations, as observed for cane yield, by increasing both agreement (NASA d index from 0.67 to 0.90; XAVIER d from 0.73 to 0.93) and R² (NASA from 0.35 to 0.76; XAVIER from 0.43 to 0.79) and reducing root mean square errors (RMSE) from 32.8 to 16.3 t/ha when simulated with other variables of NASA data and from 27.9 to 12.7 t/ha when having XAVIER data as input. Therefore, while using both GWD sets without any correction, it is recommended to replace gridded rainfall by measured values, whenever possible, to improve sugarcane simulations in Center-South Brazil.

Qualitative Study on the Observations of Emissions, Transport, and the Influence of Climatic Factors from Sugarcane Burning: A South African Perspective

There are two methods of harvesting sugarcane—manual or mechanical. Manual harvesting requires the burning of the standing sugarcane crop. Burning of the crop results in the emission of aerosols and harmful trace gases into the atmosphere. This work makes use of a long-term dataset (1980–2019) to study (1) the atmospheric spatial and vertical distribution of pollutants; (2) the spatial distribution and temporal change of biomass emissions; and (3) the impact/influence of climatic factors on temporal change in atmospheric pollutant loading and biomass emissions over the Mpumalanga and KwaZulu Natal provinces in South Africa, where sugarcane farming is rife. Black carbon (BC) and sulfur dioxide (SO₂) are two dominant pollutants in the JJA and SON seasons due to sugarcane burning. Overall, there was an increasing trend in the emissions of BC, SO₂, and carbon dioxide (CO₂) from 1980 to 2019. Climatic conditions, such as warm temperature, high wind speed, dry conditions in the JJA, and SON season, favor the intensity and spread of the fire, which is controlled. The emitted pollutants are transported to neighboring countries and can travel over the Atlantic Ocean, as far as ~6600 km from the source site.

Genotypic variation in intrinsic transpiration efficiency correlates with sugarcane yield under rainfed and irrigated field conditions

Intrinsic transpiration efficiency (_i TE), the ratio of photosynthesis (A) to stomatal conductance (g_s ), is considered a useful trait for improving productivity; however, higher _i TE with high A is more desirable than that with low g_s . This study dissects _i TE of 20 sugarcane genotypes to understand its relationship with total dry matter (TDM) and cane yield (TCH) under irrigated and rainfed conditions. Water stress reduced mean A and g_s by 56 and 61%, and mean TDM and TCH by 55 and 59%, respectively; however, genotype × irrigation treatment interaction was smaller than genotype variance. Mean _i TE increased from 117.4 μmol mol^-1 in the irrigated treatment to 130.6 μmol mol^-1 in the rainfed treatment. In irrigated conditions, _i TE had high heritability (H² _b  = 0.67) and significant genetic correlation with TDM (r_g  = 0.58) and TCH (r_g  = 0.72). Under water stress, at g_s below 0.1 mol m^-2  s^-1 , non-stomatal limitation to A was evident and _i TE had low heritability (H² _b  = 0.2). Whereas in the g_s range of 0.1-0.4 mol m^-2  s^-1 , heritability of _i TE (H² _b  = 0.63) and its genetic correlation with TDM (r_g  = 0.78) and TCH (r_g  = 0.75) were maximised. There was significant genotypic variation in photosynthetic capacity (A_c ), and the differences were related to TDM and _i TE. Selecting genotypes with higher _i TE and A_c could offer potential for improving productivity without the unfavourable effect of low g_s .

Global direct nitrous oxide emissions from the bioenergy crop sugarcane (Saccharum spp. inter-specific hybrids)

Sugarcane is the second largest bioenergy crop in the world and it accounts for 80% of global sugar production. Grown mostly in wet and warm tropics with relatively high nitrogen (N) fertiliser input and crop residue retention, sugarcane production is a significant source of nitrous oxide (N₂O) emission. Yet, a global evaluation of research on N₂O emission from sugarcane crop is lacking. Here, we conducted a meta-analysis using data from 141 measurements compiled from 15 sugarcane field studies reported from different countries to i) quantify N₂O emissions and emission factors (EFs) globally, and for tropics and sub-tropics, and ii) identify the key factors that promote N₂O emission. Our analysis shows that the global mean total N₂O emission from sugarcane production reached 2.26 (CI: 1.93-2.62) kg N₂O-N ha^-1 yr^-1 with an estimated EF of 1.21% (CI: 0.971-1.46%). N₂O emissions increased exponentially with increase in N fertiliser rate, questioning the adequacy of Intergovernmental Panel on Climate Change (IPCC) default EF value (1%) for sugarcane N₂O emission estimation. Mean total N₂O emissions and EFs in tropics and sub-tropics did not vary significantly. Supplementing synthetic N fertiliser (SN) with organic amendments (OA) significantly increased mean N₂O emission (~1.4-fold) and EF (~2.5-fold) compared to SN. A remarkable reduction in N₂O emission (38.6%) and EF (61.5%) was evident when enhanced efficiency fertilisers (EEF) replaced SN. In contrast, crop residue removal had little impact on N₂O emission and EF, but both parameters showed an upward trend with irrigation and increased rainfall. Soil carbon content and pH were emerged as key regulators of sugarcane N₂O emission and EF. It is concluded that global sugarcane N₂O emission could be significant and that there is considerable prospect for mitigating the emission through innovative nutrient formulations and precision agriculture that help meet crop nutrient demand without compromising environmental imperatives.

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.

Genetic Transformation of Sugarcane, Current Status and Future Prospects

Sugarcane (Saccharum spp.) is a tropical and sub-tropical, vegetative-propagated crop that contributes to approximately 80% of the sugar and 40% of the world's biofuel production. Modern sugarcane cultivars are highly polyploid and aneuploid hybrids with extremely large genomes (>10 Gigabases), that have originated from artificial crosses between the two species, Saccharum officinarum and S. spontaneum. The genetic complexity and low fertility of sugarcane under natural growing conditions make traditional breeding improvement extremely laborious, costly and time-consuming. This, together with its vegetative propagation, which allows for stable transfer and multiplication of transgenes, make sugarcane a good candidate for crop improvement through genetic engineering. Genetic transformation has the potential to improve economically important properties in sugarcane as well as diversify sugarcane beyond traditional applications, such as sucrose production. Traits such as herbicide, disease and insect resistance, improved tolerance to cold, salt and drought and accumulation of sugar and biomass have been some of the areas of interest as far as the application of transgenic sugarcane is concerned. Although there have been much interest in developing transgenic sugarcane there are only three officially approved varieties for commercialization, all of them expressing insect-resistance and recently released in Brazil. Since the early 1990's, different genetic transformation systems have been successfully developed in sugarcane, including electroporation, Agrobacterium tumefaciens and biobalistics. However, genetic transformation of sugarcane is a very laborious process, which relies heavily on intensive and sophisticated tissue culture and plant generation procedures that must be optimized for each new genotype to be transformed. Therefore, it remains a great technical challenge to develop an efficient transformation protocol for any sugarcane variety that has not been previously transformed. Additionally, once a transgenic event is obtained, molecular studies required for a commercial release by regulatory authorities, which include transgene insertion site, number of transgenes and gene expression levels, are all hindered by the genomic complexity and the lack of a complete sequenced reference genome for this crop. The objective of this review is to summarize current techniques and state of the art in sugarcane transformation and provide information on existing and future sugarcane improvement by genetic engineering.

Current breeding and genomic approaches to enhance the cane and sugar productivity under abiotic stress conditions

Sugarcane (Saccharum spp.) crop is vulnerable to many abiotic stresses such as drought, salinity, waterlogging, cold and high temperature due to climate change. Over the past few decades new breeding and genomic approaches have been used to enhance the genotypic performance under abiotic stress conditions. In sugarcane, introgression of genes from wild species and allied genera for abiotic stress tolerance traits plays a significant role in the development of several stress-tolerant varieties. Moreover, the genomics and transcriptomics approaches have helped to elucidate the key genes/TFs and pathways involved in abiotic stress tolerance in sugarcane. Several novel miRNAs families /proteins or regulatory elements that are responsible for drought, salinity, and cold tolerance have been identified through high-throughput sequencing. The existing sugarcane monoploid genome sequence information opens new gateways and opportunities for researchers to improve the desired traits through efficient genome editing tools, such as the clustered regularly interspaced short palindromic repeat-Cas (CRISPR/Cas) system. TALEN mediated mutations in a highly conserved region of the caffeic acid O-methyltransferase (COMT) of sugarcane significantly reduces the lignin content in the cell wall which is amenable for biofuel production from lignocellulosic biomass. In this review, we focus on current breeding with genomic approaches and their substantial role in enhancing cane production under the abiotic stress conditions, which is expected to provide new insights to plant breeders and biotechnologists to modify their strategy in developing stress-tolerant sugarcane varieties, which can highlight the future demand of cane, bio-energy, and viability of sugar industries.

Revisiting the physical mutagenesis for sugarcane improvement: a stomatal prospective

This study was conducted to investigate the influence of gamma rays on stomatal parameters and the interaction of these traits with agronomy of the sugarcane crop. Three genotypes of sugarcane (NIA-0819, NIA-98, and BL4) were exposed to four doses of gamma radiation (10, 20, 30, and 40 Gy) and then subjected to field trials. Stomatal length, width, and density were observed using scanning electron microscopy. Moreover, agronomic and sugar-related characteristics of the crop were determined at maturity. The stomatal parameters augmented at two lower doses of gamma radiation (10 and 20 Gy) and declined under higher doses (30 and 40 Gy). The maximum stomatal length was observed in NIA-0819 at 10 Gy (63.71 µm), whereas NIA-98 and BL4 demonstrated highest stomatal length under 20 Gy (54.11 and 57.40 µm, respectively), indicating a role of genetic factors in varietal response. Similar trend was noticed for stomatal width and density as well. The lowermost treatment (10 Gy) of NIA-0819 produced maximum stomatal density (115.31 stomata mm^-2 on the abaxial surface). Adaxial stomatal density was significantly lower than the abaxial one. Sugar quality attributes revealed a different tendency. Sucrose contents of BL4 increased gradually from 12.33% at control to 14.54% at 40 Gy. Yield and yield-contributing traits of genotypes indicated a strong positive correlation with the stomatal parameters. The present study suggested that gamma radiations cause variations in stomatal characteristics of sugarcane. These changes further influence the photosynthetic activity and instigate a direct impact on the agronomic performance of the crop.

Isolation, characterization and expression analysis of stress responsive plant nuclear transcriptional factor subunit (NF-YB2) from commercial Saccharum hybrid and wild relative Erianthus arundinaceus

Plant nuclear factor (NF-Y) is a transcription activating factor, consisting of three subunits, and plays a key regulatory role in many stress-responsive mechanisms including drought and salinity stresses. NF-Ys function both as complex and individual subunits. Considering the importance of sugarcane as a commercial crop with high socio-economic importance and the crop being affected mostly by water deficit stress and salinity stress causing significant yield loss, nuclear transcriptional factor NF-YB2 was focused in this study. Plant nuclear factor subunit B2 from Erianthus arundinaceus (EaNF-YB2), a wild relative of sugarcane which is known for its drought and salinity stress tolerance, and commercial Saccharum hybrid Co 86032 (ShNF-YB2) was isolated and characterized. Both EaNF-YB2 and ShNF-YB2 genes are 543 bp long that encodes for a polypeptide of 180 amino acid residues. Comparison of EaNF-YB2 and ShNF-YB2 gene sequences revealed nucleotide substitutions at nine positions corresponding to three synonymous and six nonsynonymous amino acid substitutions that resulted in variations in physiochemical properties. However, multiple sequence alignment (MSA) of NF-YB2 proteins showed conservation of functionally important amino acid residues. In silico analysis revealed NF-YB2 to be a hydrophilic and intracellular protein, and EaNF-YB2 is thermally more stable than that of ShNF-YB2. Phylogenetic analysis suggested the lower rate of evolution of NF-YB2. Subcellular localization in sugarcane callus revealed NF-YB2 localization at nucleus that further evidenced it to be a transcription activation factor. Comparative RT-qPCR experiments showed a significantly higher level of NF-YB2 expression in E. arundinaceus when compared to that in the commercial Saccharum hybrid Co 86032 under drought and salinity stresses. Hence, EaNF-YB2 could be an ideal candidate gene, and its overexpression in sugarcane through genetic engineering approach might enhance tolerance to drought and salinity stresses.

Effects of Water Regime, Genotype, and Formative Stages on the Agro-Physiological Response of Sugarcane (Saccharum officinarum L.) to Drought

Drought during the formative stages of a plant's growth triggers a sequence of responses to maintain optimal growing conditions, but often at the expense of crop productivity. Two field experiments were conducted to determine the effect of drought on 10 high-yielding sugarcane genotypes at two formative stages (the tillering stage (TS) and stalk elongation (SS)), within 30 days after treatment imposition. The experiments followed a split-plot in a randomized complete block design with three replicates per genotype. Agro-physiological responses to drought were observed to compare the differences in the response of sugarcane during the two formative stages. Drought significantly reduced total chlorophyll content (Chl) and stomatal conductance (Gs) for both formative stages, while significantly increasing total scavenging activity (AOA) and electrolyte leakage (EC). A higher level of Chl was observed in the stalk elongation stage compared to the tillering stage; however, lower AOA coupled with higher EC in the stalk elongation stage suggests higher drought susceptibility. Pearson's correlation analysis revealed a stronger correlation between plant height, internode length, Chl, AOA, EC, and Gs at the tillering stage relative to the stalk elongation stage. Moreover, results from the multivariate analysis indicate the different contribution values of each parameter, supplementing the hypothesized difference in response between the two formative stages. Multivariate analysis clustered the 10 genotypes into groups based on the traits evaluated, suggesting the ability of these traits to detect differences in a sample population. The observed relationship among traits during the two formative stages of sugarcane will be significant in screening and identifying drought-susceptible and drought-tolerant genotypes for variety development studies.

High-Throughput Phenotyping of Indirect Traits for Early-Stage Selection in Sugarcane Breeding

One of the major limitations for sugarcane genetic improvement is the low heritability of yield in the early stages of breeding, mainly due to confounding inter-plot competition effects. In this study, we investigate an indirect selection index (Si), developed based on traits correlated to yield (indirect traits) that were measured using an unmanned aerial vehicle (UAV), to improve clonal assessment in early stages of sugarcane breeding. A single-row early-stage clonal assessment trial, involving 2134 progenies derived from 245 crosses, and a multi-row experiment representative of pure-stand conditions, with an unrelated population of 40 genotypes, were used in this study. Both experiments were screened at several stages using visual, multispectral, and thermal sensors mounted on a UAV for indirect traits, including canopy cover, canopy height, canopy temperature, and normalised difference vegetation index (NDVI). To construct the indirect selection index, phenotypic and genotypic variance-covariances were estimated in the single-row and multi-row experiment, respectively. Clonal selection from the indirect selection index was compared to single-row yield-based selection. Ground observations of stalk number and plant height at six months after planting made from a subset of 75 clones within the single-row experiment were highly correlated to canopy cover (rg = 0.72) and canopy height (rg = 0.69), respectively. The indirect traits had high heritability and strong genetic correlation with cane yield in both the single-row and multi-row experiments. Only 45% of the clones were common between the indirect selection index and single-row yield based selection, and the expected efficiency of correlated response to selection for pure-stand yield based on indirect traits (44%–73%) was higher than that based on single-row yield (45%). These results highlight the potential of high-throughput phenotyping of indirect traits combined in an indirect selection index for improving early-stage clonal selections in sugarcane breeding.

A new high-throughput assay for determining soluble sugar in sorghum internode-extracted juice

A high-throughput method combining liquid handling system and 96-well microplate pipetting format was developed for total sugar determination. With this new method, we characterized diverse sugar accumulation in sorghum varieties. Sweet sorghum accumulates large amounts of sucrose in its stalk and, therefore, has emerged as one important bioenergy crop. The commonly used sugar measurement, Brix, limits the characterization of internode variation of the sugar concentrations due to its low throughput. Here we developed a low-cost, high-throughput method to determine profiles of total sugars in sorghum internodes with a liquid handling system-based sample preparation and a phenol-sulfuric acid assay in 96-well microplate format. The present method generates results highly correlated with commonly used Brix measurements (r = 0.922). The inter-assay coefficient of variation ranged from 4.8 to 7.6%. The present method can reliably estimate mixed sugars composed of 80% sucrose. We characterized the profiles of 35 sorghum accessions and identified 21 accessions with significantly different sugar concentrations between internodes either due to dried-up internodes or concentration differences. As a high-throughput alternative to Brix measurements, the new method makes it possible to phenotype total sugars from large numbers of internode samples and, therefore, will be useful for genetic and breeding purposes.

ScGAI is a key regulator of culm development in sugarcane

Sugarcane contributes more than 70% of sugar production and is the second largest feedstock for ethanol production globally. Since sugar accumulates in sugarcane culms, culm biomass and sucrose content are the most commercially important traits. Despite extensive breeding, progress in both cane yield and sugar content remains very slow in most countries. We hypothesize that manipulating the genetic elements controlling culm growth will alter source-sink regulation and help break down the yield barriers. In this study, we investigate the role of sugarcane ScGAI, an ortholog of SLR1/D8/RHT1/GAI, on culm development and source-sink regulation through a combination of molecular techniques and transgenic strategies. We show that ScGAI is a key molecular regulator of culm growth and development. Changing ScGAI activity created substantial culm growth and carbon allocation changes for structural molecules and storage. ScGAI regulates spatio-temporal growth of sugarcane culm and leaf by interacting with ScPIF3/PIF4 and ethylene signaling elements ScEIN3/ScEIL1, and its action appears to be regulated by SUMOylation in leaf but not in the culm. Collectively, the remarkable culm growth variation observed suggests that ScGAI could be used as an effective molecular breeding target for breaking the slow yield gain in sugarcane.

Physiological Plasticity Is Important for Maintaining Sugarcane Growth under Water Deficit

The water availability at early phenological stages is critical for crop establishment and sugarcane varieties show differential performance under drought. Herein, we evaluated the relative importance of morphological and physiological plasticity of young sugarcane plants grown under water deficit, testing the hypothesis that high phenotypic plasticity is associated with drought tolerance. IACSP95-5000 is a high yielding genotype and IACSP94-2094 has good performance under water limiting environments. Plants were grown in rhizotrons for 35 days under three water availabilities: high (soil water matric potential [Ψ_m] higher than -20 kPa); intermediate (Ψ_m reached -65 and -90 kPa at the end of experimental period) and low (Ψ_m reached values lower than -150 kPa). Our data revealed that morphological and physiological responses of sugarcane to drought are dependent on genotype and intensity of water deficit. In general, IACSP95-5000 showed higher physiological plasticity given by leaf gas exchange and photochemical traits, whereas IACSP94-2094 showed higher morphological plasticity determined by changes in leaf area (LA) and specific LA. As IACSP94-2094 accumulated less biomass than IACSP95-5000 under varying water availability, it is suggested that high morphological plasticity does not always represent an effective advantage to maintain plant growth under water deficit. In addition, our results revealed that sugarcane varieties face water deficit using distinct strategies based on physiological or morphological changes. When the effectiveness of those changes in maintaining plant growth under low water availability is taken into account, our results indicate that the physiological plasticity is more important than the morphological one in young sugarcane plants.

Physiological Plasticity Is Important for Maintaining Sugarcane Growth under Water Deficit

The water availability at early phenological stages is critical for crop establishment and sugarcane varieties show differential performance under drought. Herein, we evaluated the relative importance of morphological and physiological plasticity of young sugarcane plants grown under water deficit, testing the hypothesis that high phenotypic plasticity is associated with drought tolerance. IACSP95-5000 is a high yielding genotype and IACSP94-2094 has good performance under water limiting environments. Plants were grown in rhizotrons for 35 days under three water availabilities: high (soil water matric potential [Ψ_m] higher than -20 kPa); intermediate (Ψ_m reached -65 and -90 kPa at the end of experimental period) and low (Ψ_m reached values lower than -150 kPa). Our data revealed that morphological and physiological responses of sugarcane to drought are dependent on genotype and intensity of water deficit. In general, IACSP95-5000 showed higher physiological plasticity given by leaf gas exchange and photochemical traits, whereas IACSP94-2094 showed higher morphological plasticity determined by changes in leaf area (LA) and specific LA. As IACSP94-2094 accumulated less biomass than IACSP95-5000 under varying water availability, it is suggested that high morphological plasticity does not always represent an effective advantage to maintain plant growth under water deficit. In addition, our results revealed that sugarcane varieties face water deficit using distinct strategies based on physiological or morphological changes. When the effectiveness of those changes in maintaining plant growth under low water availability is taken into account, our results indicate that the physiological plasticity is more important than the morphological one in young sugarcane plants.

Sugarcane Water Stress Tolerance Mechanisms and Its Implications on Developing Biotechnology Solutions

Sugarcane is a unique crop with the ability to accumulate high levels of sugar and is a commercially viable source of biomass for bioelectricity and second-generation bioethanol. Water deficit is the single largest abiotic stress affecting sugarcane productivity and the development of water use efficient and drought tolerant cultivars is an imperative for all major sugarcane producing countries. This review summarizes the physiological and molecular studies on water deficit stress in sugarcane, with the aim to help formulate more effective research strategies for advancing our knowledge on genes and mechanisms underpinning plant response to water stress. We also overview transgenic studies in sugarcane, with an emphasis on the potential strategies to develop superior sugarcane varieties that improve crop productivity in drought-prone environments.

Salt stress induces changes in the proteomic profile of micropropagated sugarcane shoots

Salt stress is one of the most common stresses in agricultural regions worldwide. In particular, sugarcane is affected by salt stress conditions, and no sugarcane cultivar presently show high productivity accompanied by a tolerance to salt stress. Proteomic analysis allows elucidation of the important pathways involved in responses to various abiotic stresses at the biochemical and molecular levels. Thus, this study aimed to analyse the proteomic effects of salt stress in micropropagated shoots of two sugarcane cultivars (CB38-22 and RB855536) using a label-free proteomic approach. The mass spectrometry proteomics data are available via ProteomeXchange with identifier PXD006075. The RB855536 cultivar is more tolerant to salt stress than CB38-22. A quantitative label-free shotgun proteomic analysis identified 1172 non-redundant proteins, and 1160 of these were observed in both cultivars in the presence or absence of NaCl. Compared with CB38-22, the RB855536 cultivar showed a greater abundance of proteins involved in non-enzymatic antioxidant mechanisms, ion transport, and photosynthesis. Some proteins, such as calcium-dependent protein kinase, photosystem I, phospholipase D, and glyceraldehyde-3-phosphate dehydrogenase, were more abundant in the RB855536 cultivar under salt stress. Our results provide new insights into the response of sugarcane to salt stress, and the changes in the abundance of these proteins might be important for the acquisition of ionic and osmotic homeostasis during exposure to salt stress.

Sugarcane Water Stress Tolerance Mechanisms and Its Implications on Developing Biotechnology Solutions

Sugarcane is a unique crop with the ability to accumulate high levels of sugar and is a commercially viable source of biomass for bioelectricity and second-generation bioethanol. Water deficit is the single largest abiotic stress affecting sugarcane productivity and the development of water use efficient and drought tolerant cultivars is an imperative for all major sugarcane producing countries. This review summarizes the physiological and molecular studies on water deficit stress in sugarcane, with the aim to help formulate more effective research strategies for advancing our knowledge on genes and mechanisms underpinning plant response to water stress. We also overview transgenic studies in sugarcane, with an emphasis on the potential strategies to develop superior sugarcane varieties that improve crop productivity in drought-prone environments.

Genetic variation in transpiration efficiency and relationships between whole plant and leaf gas exchange measurements in Saccharum spp. and related germplasm

Fifty-one genotypes of sugarcane (Saccharum spp.) or closely related germplasm were evaluated in a pot experiment to examine genetic variation in transpiration efficiency. Significant variation in whole plant transpiration efficiency was observed, with the difference between lowest and highest genotypes being about 40% of the mean. Leaf gas exchange measurements were made across a wide range of conditions. There was significant genetic variation in intrinsic transpiration efficiency at a leaf level as measured by leaf internal CO2 (Ci) levels. Significant genetic variation in Ci was also observed within subsets of data representing narrow ranges of stomatal conductance. Ci had a low broad sense heritability (Hb = 0.11) on the basis of single measurements made at particular dates, because of high error variation and genotype × date interaction, but broad sense heritability for mean Ci across all dates was high (Hb = 0.81) because of the large number of measurements taken at different dates. Ci levels among genotypes at mid-range levels of conductance had a strong genetic correlation (-0.92 ± 0.30) with whole plant transpiration efficiency but genetic correlations between Ci and whole plant transpiration efficiency were weaker or not significant at higher and lower levels of conductance. Reduced Ci levels at any given level of conductance may result in improved yields in water-limited environments without trade-offs in rates of water use and growth. Targeted selection and improvement of lowered Ci per unit conductance via breeding may provide longer-term benefits for water-limited environments but the challenge will be to identify a low-cost screening methodology.

Sugarcane for water-limited environments. Variation in stomatal conductance and its genetic correlation with crop productivity

Stomatal conductance (g(s)) and canopy temperature have been used to estimate plant water status in many crops. The behaviour of g(s) in sugarcane indicates that the internal leaf water status is controlled by regular opening and closing of stomata. A large number of g(s) measurements obtained across varying moisture regimes, locations, and crop cycles with a diverse sugarcane germplasm composed of introgression, and commercial clones indicated that there is a high genetic variation for g(s) that can be exploited in a breeding programme. Regardless of the environmental influences on the expression of this trait, moderate heritability was observed across 51 sets of individual measurements made on replicated trials over 3 years. The clone×water status interaction (G×E) variation was smaller than the clone (G) variation on many occasions. A wide range of genetic correlations (r(g)= -0.29 to 0.94) between g(s) and yield were observed across test environments in all three different production regions used. Canopy conductance (g(c)) based on g(s) and leaf area index (LAI) showed a stronger genetic correlation than the g(s) with cane yield (tonnes of cane per hectare; TCH) at 12 months (mature crop). The regression analysis of input weather data for the duration of measurements showed that the predicted values of r(g) correlated with the maximum temperature (r=0.47) during the measurements and less with other environmental variables. These results confirm that the g(c) could have potential as a criterion for early-stage selection of clones in sugarcane breeding programmes.

Full-length enriched cDNA libraries and ORFeome analysis of sugarcane hybrid and ancestor genotypes

Sugarcane is a major crop used for food and bioenergy production. Modern cultivars are hybrids derived from crosses between Saccharum officinarum and Saccharum spontaneum. Hybrid cultivars combine favorable characteristics from ancestral species and contain a genome that is highly polyploid and aneuploid, containing 100–130 chromosomes. These complex genomes represent a huge challenge for molecular studies and for the development of biotechnological tools that can facilitate sugarcane improvement. Here, we describe full-length enriched cDNA libraries for Saccharum officinarum, Saccharum spontaneum, and one hybrid genotype (SP803280) and analyze the set of open reading frames (ORFs) in their genomes (i.e., their ORFeomes). We found 38,195 (19%) sugarcane-specific transcripts that did not match transcripts from other databases. Less than 1.6% of all transcripts were ancestor-specific (i.e., not expressed in SP803280). We also found 78,008 putative new sugarcane transcripts that were absent in the largest sugarcane expressed sequence tag database (SUCEST). Functional annotation showed a high frequency of protein kinases and stress-related proteins. We also detected natural antisense transcript expression, which mapped to 94% of all plant KEGG pathways; however, each genotype showed different pathways enriched in antisense transcripts. Our data appeared to cover 53.2% (17,563 genes) and 46.8% (937 transcription factors) of all sugarcane full-length genes and transcription factors, respectively. This work represents a significant advancement in defining the sugarcane ORFeome and will be useful for protein characterization, single nucleotide polymorphism and splicing variant identification, evolutionary and comparative studies, and sugarcane genome assembly and annotation.

Induced over-expression of AtDREB2A CA improves drought tolerance in sugarcane

Drought is one of the most challenging agricultural issues limiting sustainable sugarcane production and, in some cases, yield losses caused by drought are nearly 50%. DREB proteins play vital regulatory roles in abiotic stress responses in plants. The transcription factor DREB2A interacts with a cis-acting DRE sequence to activate the expression of downstream genes that are involved in drought-, salt- and heat-stress response in Arabidopsis thaliana. In the present study, we evaluated the effects of stress-inducible over-expression of AtDREB2A CA on gene expression, leaf water potential (ΨL), relative water content (RWC), sucrose content and gas exchanges of sugarcane plants submitted to a four-days water deficit treatment in a rhizotron-grown root system. The plants were also phenotyped by scanning the roots and measuring morphological parameters of the shoot. The stress-inducible expression of AtDREB2A CA in transgenic sugarcane led to the up-regulation of genes involved in plant response to drought stress. The transgenic plants maintained higher RWC and ΨL over 4 days after withholding water and had higher photosynthetic rates until the 3rd day of water-deficit. Induced expression of AtDREB2A CA in sugarcane increased sucrose levels and improved bud sprouting of the transgenic plants. Our results indicate that induced expression of AtDREB2A CA in sugarcane enhanced its drought tolerance without biomass penalty.