South African Sugarcane Research Institute

Cryopreservation for sugarcane ( Saccharum spp. hybrids) germplasm conservation is well established. Virus elimination using droplet-vitrification (D-V) and cryo- or osmo-therapy has only been recently reported for sugarcane mosaic virus (SCMV). In this study, exposing large (3 mm) in vitro shoot tips of cultivars N12, N19, N58, and NCo376 infected with sugarcane yellow leaf virus (SCYLV) and NCo376 co-infected with SCMV and SCYLV were tested for virus elimination using both of the above-mentioned techniques. Cryo-therapy involved the exposure of infected in vitro shoot tips to the D-V protocol followed by recording recovery and virus-free shoot tips 16 wk after treatment. Osmo-therapy, consisting of the same treatment as cryo-therapy without immersion in liquid nitrogen (LN), was included for comparative purposes. Cryo-therapy resulted in 100% of the recovered shoots being SCYLV-free in cultivars N19, N58, and NCo376 and 83% in N12 when compared with untreated material. Osmo-therapy showed 58% (N12), 91% (N19 and N58), and 100% (NCo376) of shoots being clear of SCYLV when compared with untreated in vitro control plants (0 to 8%). Both techniques reduced the regrowth levels of treated shoot tips (22 to 57% recovery) when compared with untreated controls (92 to 97%). A novel finding of the study was that NCo376 co-infected with SCMV and SCYLV showed 100% virus-free recovered shoots after cryo-therapy and 92 to 100% of healthy shoots after osmo-therapy, compared with controls, which had 17 to 42% virus-free shoots. Plants from all cultivars that were re-tested 4 mo after hardening maintained their virus-free status. The described techniques for virus eradication offer a promising solution for the provision of clean vegetative planting propagules and safer germplasm exchange.

Background The Nuclear Factor Y (NF-Y) transcription factor (TF) gene family plays a crucial role in plant development and response to stress. Limited information is available on this gene family in sugarcane. Objectives To identify sugarcane NF-Y genes through bioinformatic analysis and phylogenetic association and investigate the expression of these genes in response to abiotic and biotic stress. Methods Sugarcane NF-Y genes were identified using comparative genomics from functionally annotated Poaceae and Arabidopsis species. Quantitative PCR and transcriptome analysis assigned preliminary functional roles to these genes in response to water deficit, cold and African sugarcane borer ( Eldana saccharina ) infestation. Results We identify 21 NF-Y genes in sugarcane. Phylogenetic analysis revealed three main branches representing the subunits with potential discrepancies present in the assignment of numerical names of some NF-Y putative orthologs across the different species. Gene expression analysis indicated that three genes, ShNF-YA1, A3 and B3 were upregulated and two genes, NF-YA4 and A7 were downregulated, while three genes were upregulated, ShNF-YB2, B3 and C4, in the plants exposed to water deficit and cold stress, respectively. Functional involvement of NF-Y genes in the biotic stress response were also detected where three genes, ShNF-YA6, A3 and A7 were downregulated in the early resistant (cv. N33) response to Eldana infestation whilst only ShNF-YA6 was downregulated in the susceptible (cv. N11) early response. Conclusions Our research findings establish a foundation for investigating the function of ShNF-Ys and offer candidate genes for stress-resistant breeding and improvement in sugarcane.

Indirect selection for yield in sugarcane (Saccharum officinarum L.) production can be achieved by identifying and selecting for plant traits that are correlated to yield. This study aimed to identify and quantify sugarcane traits that are associated with ratooning ability to generate information for varieties' selection. Data sourced from three variety trials established at three sites, comprising eight varieties, and collected over six successive crops (plant cane and five ratoons) were used for this study. The data were subjected to linear mixed model, Spearman's correlation, and biplot analyses. Stalk height, stalk population, stalk mass, and stalk sucrose mass were significantly correlated with cane and sucrose yield across all ratoon crops, suggesting that varieties that combine these traits over multiple crops will have higher ratoon cane and sucrose yields. Significant correlation between brix and sucrose content suggested that brix can be used to indirectly select for sucrose content. Measuring brix is easier, cheaper, and faster than measuring sucrose content. Significant site and variety effects on ratoon crop yields indicated the existence of opportunities to identify good ratooning varieties that are specifically and or broadly adapted to different growing conditions. ARTICLE HISTORY

Eldana saccharina Walker is a problematic sugarcane stalk borer pest in South Africa. Twenty-eight sugarcane genotypes ( Saccharum spp. hybrids) and seven different species of host plants of E. saccharina were surveyed for the presence of endophytic Beauveria bassiana sensu lato ( s.l. ). Collectively, 326 plant samples (roots, stems, or leaves) were collected from five locations in sugarcane-producing areas (KwaZulu-Natal; South Africa). Following plant surface disinfection, 128 fungal colonies morphologically resembling Beauveria spp. were isolated from internal plant tissues. The sequence analysis of the internal transcribed spacer region confirmed that 13 representative isolates were B. bassiana. s.l . Eight B. bassiana isolates were recovered from E. saccharina natural host plants, and 120 from different sugarcane stem parts (top node, top internodes, bottom node, and bottom internode). Endophytic B. bassiana isolates were recovered from 22 of 28 sugarcane genotypes surveyed. The number of B. bassiana isolates obtained from different sugarcane parts differed significantly, with more B. bassiana isolates obtained from the top than the bottom internodes. Furthermore, sugarcane genotypes N31 and N41 yielded B. bassiana from all plant parts sampled, while five sugarcane genotypes harbored no B. bassiana isolates. This study demonstrates for the first time the natural occurrence of endophytic B. bassiana strains in sugarcane plants and E. saccharina host plants in South Africa.

Sugarcane varieties differ in their ratooning ability (RA), and it is hypothesized that soil types and harvest seasons impact varieties' RA. However, the effects of these factors on varieties' RA remain unclear. This study aimed to assess the RA of different commercial sugarcane varieties (NCo376, N19, N23, N25, and N36), and establish the effects of soils and seasons on ratoon yields of these varieties in Eswatini. Fifteen years data on tons cane per ha per annum (TCHA) and tons sucrose per ha per annum (TSHA) achieved by plant cane and seven ratoon crops were collected from four commercial growers and analysed using linear regression models. The varieties significantly differed in RA. Variety N25, which had the highest plant cane yields (121.3 TCHA and 16.7 TSHA), had the sharpest yield decline over ratoon crops (-2.74 TCHA and −0.33 TSHA), suggesting that this variety is more suitable for short crop cycles. Variety N36 had second highest plant cane yields (111.7 TCHA and 16.4 TSHA) and a lower ratoon yield decline (-1.38 TCHA and −0.16 TSHA) than N25, suggesting that it is suitable for longer ratoon crop cycles. While soil type and harvest season significantly affected the relative yields of varieties, they did not significantly impact their RA, indicating that differences in varieties' RA were driven by genotype and were relatively stable across environments. This suggests that tests to assess the adaptability of varieties should be conducted in multiple environments, while testing the RA of varieties may be conducted in fewer environments.

The term ‘regenerative agriculture’ describes a rehabilitation and conservation approach to farming, which aims to enhance the sustainability of production. The approach consists of an array of practices that focus on the maintenance and rehabilitation of soil health. In the South African sugar industry, major soil related problems include: (a) soil erosion; (b) compaction; (c) acidification; and (d) soil salinity/sodicity. While regenerative practices to guide growers have been developed at the South African Sugarcane Research Institute (SASRI), the remediation of poor soil health in the industry has generally been hampered by low levels of adoption of these practices. The importance of the small-scale grower (SSG) sector to economic development has been recognised as a key element of the South African Sugarcane Value Chain Master Plan to 2030, which aims to ensure the long-term sustainability of the industry. To understand the barriers to adoption, SASRI conducted a survey of a small-scale grower community. This revealed that conventional knowledge exchange methods were ineffective with SSGs. Consequently, SASRI is developing and implementing knowledge exchange approaches which are founded on: (a) networks of demonstration plots where regenerative practices can be showcased and (b) participative research methodologies which aim to empower SSGs in discovering their own practical solutions to production challenges. Complementing these is an initiative to upskill extension specialists and agricultural advisors in soil health regenerative practices supported by regular radio broadcasts and newsletters. In the short term, the impact of these knowledge exchange tactics is being monitored through analysis of SSG production and economic data by SASRI, in collaboration with stakeholders from the local grower associations and mills. To date, data from the small-scale grower community study indicated that the implementation of the demonstration plot methodology focused on matching variety to soil type has had a positive impact on SSG livelihoods.

In South Africa, the stalk borer Eldana saccharina is an indigenous pest that significantly reduces sugarcane yield. Severe economic losses due to E. saccharina in the South African sugarcane industry are estimated at approximately US$60 million annually. Researchers at the South African Sugarcane Research Institute (SASRI) have researched this topic for many years to develop tools to enable sugarcane growers to manage this pest sustainably according to integrated pest management principles, with the sterile insect technique (SIT) being one of these tools. For more than three decades, the SIT has been used in area-wide integrated pest management (AW-IPM) programmes to manage pests of agricultural crops. SIT-based research has been conducted to control dipteran pests; however, controlling lepidopterans has been difficult because of their resistance to irradiation used to sterilize moths. Nevertheless, recent research on the application of SIT has proven successful in controlling lepidopteran pests. This paper provides an overview of the SIT background and studies conducted in South Africa on the SIT programme to control this key pest in sugarcane.

The primary objective of sugarcane (Saccharum spp.) variety testing programs is to identify cultivars that have high cane yields and good ratooning ability (RA). The purpose of this study was to evaluate the usefulness of six RA indices to estimate RA among sugarcane varieties and to identify an index well suited to predict RA in long‐term ratoon crop cycles. The six indices were as follows: ratoon crops yield means, second ratoon to plant cane yield ratio, final ratoon crop to plant cane yield ratio, mean of ratoon crops to plant cane yield ratio (RP), linear regression, and quadratic regression. Data from four variety trials consisting of eight post‐release varieties plus a control, harvested early, mid, and late in the cropping season for over six crop cycles, were used to estimate the RA indices. To identify indices that can predict RA in long‐term ratoon crop cycles, simple linear regression analyses were used to compare the RA indices derived from 6‐year crop cycles and similar indices derived from data from 111 commercial fields harvested over 11 successive crops. Coefficient of determination (R²) values plotted against their respective ratoon crop numbers were used to determine the minimum number of ratoon crops required to accurately predict RA indices for the 11‐year crop cycle. The six indices varied in their rankings of the RA of varieties, emphasizing the importance of identifying the most appropriate indices for different ratooning practices. Based on its highest R² value of 0.92, the RP index was identified as the most accurate index to predict RA in long‐term ratoon crop cycles requiring a minimum of five successive crops.

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

Testing sugarcane varieties for ratooning ability (RA) prerelease happens over fewer ratoon crops than those achieved commercially due to inadequate resources and the need to release varieties quicker. The purpose of this study was to model yield potential and RA of sugarcane varieties. To achieve this, yield (cane yield, TCH; sucrose yield, TSH; stalk weight, STM) and quality (sucrose content, SUC%) data for eight test varieties and a control planted on different soil types (good draining and poor draining), harvesting seasons (early, mid and late), and harvested over six successive crops, were subjected to linear mixed model and regression models. The results indicated varieties had significantly different RA suggesting existence of opportunities to identify varieties with good RA. Soil types and harvesting seasons did not have any significant effect on varieties’ RA for yield traits, but were significant for SUC% with seasons having a higher impact than soils. M1176/77 was identified as the most preferred for both TCH and TSH due to high yield potential and RA. Varieties M1400/86, M695/69 and M1551/80 were suitable for SUC%. A positive relationship between TCH and STM was observed which needs to be explored further to inform breeding efforts.

Chemical ripening is a promising technology at Metahara and Kessem sugarcane plantations where conditions are not optimal for natural ripening in the early and late period of sugarcane processing. However, the harvest age at which sucrose yield could be maximized with application of ripeners has not been established. Thus, field experiments were conducted to determine the effects of harvest age and chemical ripeners on yield and juice quality of sugarcane. The experiments were conducted in the late period (June) harvesting at Metahara, and in the early (October) and late period (June) harvesting at Kessem. A split plot design with three replications was used where the main plot treatments were two sugarcane varieties, viz. B52-298 and SP70-1284, and the sub-plot treatment consisted of combinations of four harvest ages (10, 12, 14 and 16 months) and two ripener treatments [Moddus™ at 250 g ai ha−1 + Fusilade Forte™ (M + FF) at 25.6 g ai ha−1 combination sequentially sprayed and unsprayed control]. The results showed significant difference between the varieties for stalk height and stalk weight in early period study at Kessem with variety SP70-1284 being superior as compared to variety B52-298. Furthermore, harvest age and ripener combination significantly affected all yield and quality parameters, while there was a significant cane and sucrose yield response at Kessem at both sites and seasons. The highest cane yield was recorded in the unsprayed 16-month harvest age treatment, while the highest sucrose yield was recorded in the M + FF ripener combination 12-month harvest age treatment in all the studies. The economic analysis showed the highest marginal rate of return and net revenue in the M + FF ripener combination 12-month harvest age treatment and represents the best cane quality management practice for varieties B52-298 and SP70-1284 at these plantations.

Reliable fertilizer recommendations should account for factors influencing nutrient supply, including non-exchangeable potassium (K) reserves and fixation capacity, to ensure optimum crop yields. The combined effects of non-exchangeable K reserves and fixation capacity of soils on crop response to K application has not been evaluated. This study evaluated the response of sugarcane yields to K application on two soils with contrasting combinations of non-exchangeable K reserves and fixation capacity. Potassium was applied at 0, 120, and 240 kg K ha −1 at the commencement of the field trials and after each harvest on an umbric Acrisol, which had low non-exchangeable K reserves and medium K fixation capacity, and a cutanic Acrisol, which had 'very high' non-exchangeable K reserves and fixation capacity. Sugarcane stalk and sucrose yield, leaf, and exchangeable K were measured for each season. In the umbric Acrisol, a lower sucrose yield was measured in the 240 kg K ha −1 treatment compared to the control for the plant crop, but this application rate had higher yields for the second ratoon. In contrast, there was no yield response to K application in cutanic Acrisol. This study indicated the importance of non-exchangeable K reserves and fixation capacity when calculating K requirements and conducting field calibration studies.

Cultivar genetic gains quantify the increase in productivity from release of cultivars and measure genetic improvements from plant breeding. The objectives of this study were to evaluate the genetic gains from sugarcane coastal cultivars and evaluate their contribution to productivity. Data were derived from replicated plant breeding and post-release variety evaluation trials conducted by the South Africa Sugarcane Research Institute (SASRI) from 1996 to 2020. There were significant cultivar differences for cane yield, sucrose content, sugar yield, fibre % and purity %. Significant analyses of cultivar by location, cultivar by crop-year and cultivar by location by crop-year indicate further optimisation of cultivar disposition is needed to increase productivity. Cultivar genetic gains were found for cane yield (0.19–0.48 t ha⁻¹), sucrose content (0.01–0.02%), sugar yield (0.03–0.07 t ha⁻¹ per year), fibre % cane (0.04–0.06%) and purity % (0.02–0.04%), highlighting the increased yield and quality from genetic improvement. The best cultivars produced 8–22% higher sugar yields than popular cultivars indicating that planting high yield cultivars did increase yields. Sugar cane production declined at a slower rate than area planted, also showing the benefit of high yield cultivars. Increasing the area planted to new, higher yielding cultivars will increase sugar yields for coastal regions of South Africa.

Sustainable sugarcane production in areas prone to frequent and severe drought can be achieved by creating resilient sugarcane varieties. In this study, a unique mutant line, M9.2, was generated from a drought susceptible commercial sugarcane cultivar, N19, through the exposure of callus cells to the ethyl methanesulfonate mutagen and subsequent in vitro osmotic selection on polyethylene glycol. The study aimed to characterise the M9.2 mutant, in comparison with the parental genotype, in terms of its physiological and biochemical performance and proteome profile when exposed to moderate (14 days without water) and severe (21 days without water) water deficit stress in glasshouse pot trials. In comparison to the parental counterparts, the mutant plants were able to sustain the quantum efficiency of photosystem II (Fv/Fm) throughout the stress. Under mild stress, the mutant plants displayed elevated stomatal conductance, high concentrations of proline, accumulated less H2O2 and phenotypically displayed limited wilting and no visible signs of leaf senescence. Under severe stress, the mutant plants accumulated less malondialdehyde and more antioxidant enzymes (superoxide dismutase and catalase) than the parental line. Differential protein expression was also observed according to two‐dimensional difference gel electrophoresis patterns of proteins expressed in the M9.2 mutant versus the parental plants during moderate stress. Analysis revealed proteins related to photosynthesis (pyruvate orthophosphate dikinase, un‐fragmented ribulose‐1,5‐bisphosphate carboxylase/oxygenase large subunit and chlorophyll a/b‐binding protein 3) and carbohydrate metabolism (sucrose synthase) were up‐regulated in the mutant. Differentially expressed proteins were further linked to energy metabolism, methylation homeostasis and DNA repair. This study characterises the new M9.2 mutant with beneficial drought‐tolerant traits which have the potential to be exploited in future sugarcane breeding programmes.

Spatial information on crop productivity and resource use is required to enable efficient sugarcane production with limited resources and under a changing climate. The objective of this study was to estimate biomass, sugar and ethanol yields for high-sucrose (HS) and high-fibre (HF) sugarcane cultivars for current and future climate in water limited South Africa. An upgraded version of the Canegro sugarcane model, calibrated for a HS and HF cultivar, was used to simulate biomass component yields for 1,986 agro-climatic zones. Ethanol yields were calculated from simulated biomass fractions and theoretical conversion efficiencies. Historical daily weather data for 1971–1990 were used to represent the baseline climate, while daily weather data generated from three global circulation models for 1971–1990 and 2046–2065 were used to project future changes in climate. Simulations show that the HF cultivar produced higher (15–35%) biomass and ethanol yields than the HS cultivar, but also used slightly more (~ 4%) water. Climate change is projected to increase dryland yields for both cultivar types (8–19%) Irrigated yields will not change much in current high potential areas (1–5%), given adequate water supply, while yields could increase substantially in current cool areas (~ 20%). Water and irrigation requirements are expected to increase (9–15%) under a future climate. New areas could be become suitable for irrigated and dryland production. The information produced in this study can be used to assist decision-making for: (1) optimizing production and processing processes and (2) the development of sustainable greenfield projects in marginal areas of South Africa.

The present study evaluated the drought tolerance potential of ten epimutants generated in vitro via 5-Azacytidine (Azac) demethylation, followed by re-methylation in the presence of imidacloprid (IMI), both under polyethylene glycol (PEG) osmotic pressure and heat stress. Ex vitro chimera dissolution involved four rounds of repeated drought stress in the glasshouse. Most epimutant lines had significantly high Fv/Fm values (up to 0.46, 0.76, and 0.78 respectively for V2, V3 and V4 stress rounds) when compared with the stressed parent cultivar N41 control (S N41) with 0.12, 0.21, and 0.59 ratios respectively. Significant rapid growth rates (0.25 cm height increase per day) were observed in the GP4, MP1, MP5, and SP5 lines while S N41 had 0.10 cm stalk height gain per day during stress. Moreover, the percent green leaf area (GLA) values were higher (57.2–73.0%) for the epimutant lines than drought sensitive MP6 (12.4%) and S N41 (47.3%) during stress. The GP1, MP5 and SP5 lines maintained high relative water content (43–51%) than S N41 (38%) under drought conditions. Principal component and cluster analyses of morpho-physiological traits separated trait indices data and revealed that the epimutants with highest drought stress tolerance were the MP2, MP5, GP2, GP4, GP5, and SP5, and these same lines recuperated rapidly from stress. This study has laid a foundation for an alternative method of assessing sugarcane phenotypes for drought tolerance using morpho-physiological traits.