Biology subjects

Creste, S.

Publications and source records attributed to Creste, S..

3 recordsLinked to original sources

bioRxiv2025

Reference Gene Validation in Energy Cane Under Smut Infection and Insights into Antioxidant Gene Expression

Sporisorium scitamineum is the causal agent of smut disease affecting sugarcane and energy cane crop production. Despite the frequent use of traditional reference genes for gene expression normalization by RT-qPCR, their stability can vary across genotypes and stress conditions. Here, we evaluated the stability of seven commonly used reference genes (GAPDH, SAMDC, UBQ, 25S rRNA, TUB, SARMp1, and ACAD) and two additional candidates (EF5A-1 and SDH1-1) identified from RNA-Seq data in two contrasting energy cane genotypes (Vertix 1, smut-susceptible; Vertix 2, smut-resistant). Stability was assessed at three infection time points (12 hours post-inoculation, 48 hpi, and 5 days post-inoculation) separately and also on a combined dataset comprising all time points, under mock and smut-inoculated conditions. Gene stability, evaluated through multiple approaches (coefficient of variation, RefFinder, GeNorm) and consolidated using RankAggreg, revealed genotype and condition-dependent variability, with no universal reference gene set for most conditions. GAPDH, commonly used in sugarcane studies, showed the highest variation in our experiments, reinforcing the need for genotype and condition-specific validation. The best-ranked reference genes were used to quantify ROS-related defense responses. Vertix 2 (Vx2) exhibited coordinated induction of SOD, POX5, and CATB, whereas Vertix 1 (Vx1) showed delayed or reduced activation of these genes alongside a compensatory up-regulation of GSTt3. By validating reliable endogenous genes from literature and RNA-Seq data, this study ensures accurate gene expression quantification under biotic stress and highlights antioxidant mechanisms as contributors to smut resistance in S. scitamineum-energy cane interactions.

plant biology↗

bioRxiv2025

Soil Determines Microbial Functionality and Genotype Guides Endophytic Recruitment to Adaptability in Sugarcane Systems

Soil properties critically shape sugarcane growth and its microbiome, yet their influence on gene expression remains unclear. We investigated the combined effects of soil type (clayey and sandy loam) and sugarcane genotype (IACSP-5503 and IACSP-6007) on microbiome composition and plant transcriptional profiles. Bacterial communities from soils and stalk tissues, as well as transcriptomes of 48-hour sprouted buds grown for 10 months, were analyzed. Results showed that IACSP-5503 (adapted to low-fertility soils) and IACSP-6007 (less adapted) recruited endophytic microbiota in a soil-genotype-dependent manner. In sandy loam, IACSP-5503 promoted diverse plant growth-promoting bacteria (PGPB) (including Burkholderia, Leifsonia, and Mycobacterium), associated with nitrogen fixation, hormone production, and stress tolerance, while IACSP-6007 displayed reduced PGPB diversity and transcriptomic signatures of nutrient deficiencies. Conversely, in clayey soil, IACSP-6007 recruited more PGPBs (such as Pseudomonas, Bacillus and Klebsiella) linked to nutrient acquisition and defense responses. Both genotypes exhibited enhanced expression of defense- and antioxidant-related genes in clayey soil, suggesting priming effects. Overall, our findings reveal soil-dependent, genotype-specific microbial recruitment strategies, including a potential "cry for help" mechanism in IACSP-5503, reflecting adaptation under nutrient-poor conditions. The combined 16S metataxonomic and transcriptome data offered insights into how soil and genotype shape microbial recruitment and transcriptional plasticity in sugarcane.

genetics↗

bioRxiv2025

Multilayered Defense Responses in Sugarcane Against Pratylenchus zeae Revealed by Comparative Transcriptomics

1.The root-lesion nematode Pratylenchus zeae ranks among the most pervasive soilborne threats to global sugarcane (Saccharum spp.) production, however, the molecular basis of host resistance to this pathogen remains largely unexplored. Using comparative transcriptomics 15 days after inoculation, we profiled root response patterns of a resistant cultivar (RB966982) and a susceptible cultivar (CTC9001). Differential gene expression analysis identified 3,385 DEGs (1,426 up, 1,959 down) in the susceptible CTC9001 and 8,689 DEGs (5,334 up, 3,355 down) in the resistant RB966982 when comparing control and inoculated plants, revealing distinct genotype-specific defense strategies. The resistant genotype mounted a coordinated, multilayered defense marked by dramatic transcriptional reprogramming, including intensified glycolysis and fatty-acid biosynthesis, elevated oxidoreductase/ROS activity, and concurrent activation of jasmonic and salicylic acid associated pathways, with strong induction of multiple PR1 homologs. RB966982 also showed pre-primed and inducible resistance gene analogs and targeted cell-wall reinforcement through xyloglucan fucosylation. By contrast, CTC9001 displayed a delayed or attenuated response characterized by cell-proliferation signatures and broad activation of callose-related defenses (1,3-{beta}-D-glucan synthesis) that appear insufficient to limit nematode progression. GO enrichment analysis revealed that the resistant response was dominated by biological processes linked to carbohydrate and lipid metabolism, oxidoreductase activity, hormone signaling, and cell-wall organization, while the susceptible response was enriched in stress-related pathways lacking coordinated metabolic and structural reinforcement. Collectively, these findings indicate that durable resistance to P. zeae is unlikely to arise from a single mechanism, effective protection will require stacking complementary defense layers, including early metabolic reprogramming, robust hormone-mediated signaling, and reinforced cell-wall barriers. The candidate RGAs, PR1 homologs, and cell-wall remodeling enzymes identified here, together with the GO-enriched pathways, provide concrete targets for marker-assisted breeding and gene editing strategies aimed at developing sugarcane cultivars with durable nematode resistance.

bioinformatics↗