Sugarcane smut, caused by Sporisorium scitamineum, is a globally prevalent disease that severely impacts sugarcane yield and quality. The most cost-effective and sustainable approach to disease control is breeding for smut-resistant varieties. In this study, we conducted a genome-wide association study (GWAS) using a panel of core sugarcane parents and their derived lines to elucidate the genetic basis of smut resistance across seven different environments. We identified 68 new loci significantly associated with smut resistance across all the chromosomes. Based on functional annotations and genomic positions, 164 candidate genes were identified, many of which are related to enzymatic systems, resistance genes, transcription factors, and other pathways implicated in smut defense. Using resistance ratings and associated SNPs, we further selected ten elite parents and derivatives as potential donors for marker-assisted selection (MAS). This study provides a valuable reservoir of genetic resources for improving smut resistance in sugarcane.

Northern corn leaf blight (NCLB), caused by Exserohilum turcicum, is a devastating disease in China. To better understand this disease, its temporal progress and spatial patterns were investigated in this study. A susceptible corn cultivar was planted in a field in Beijing in 2016 and 2017, and NCLB lesions on each plant were counted twice a week. In addition, temporal disease progress was monitored weekly in 3 commercial fields in each of 4 districts of Beijing in 2017, and the spatial patterns of diseased plants and NCLB lesion counts were assessed in 3 commercial fields in Yanqing District. The results demonstrated that a logistic model could describe the temporal progress of NCLB incidence. The initial disease incidence was the key factor affecting disease epidemics in the four districts of Beijing. The higher the initial incidence of NCLB, the higher the final incidence. Thus, the earlier NCLB incidence attained 1%, the higher was the final disease incidence. Greater than 1.0 variance-to-mean ratios suggested that the leaf lesions of NCLB tended to be aggregated on a plant. According to results from join-counts, variance of moving window averages and semivariogram analysis, diseased corn plants and lesion numbers per plant were aggregated in the field. The clustered pattern of NCLB lesions and infected plants suggested that conidia produced locally on diseased plants were important for disease spread within the field. The aggregated pattern of diseased plants implied that plants should be sampled from more sites to accurately estimate NCLB incidence in a field.

Sugarcane smut, caused by Sporisorium scitamineum, is a devastating fungal disease of sugarcane. Sexual mating/filamentation of opposite mating types is a key step in the infection and pathogenicity of S. scitamineum, yet its regulation remains unclear. In this study, we identified a cytochrome P450 enzyme-encoding gene, SsCYP64, which plays an important role in oxidative stress and maintaining cell membrane stability in S. scitamineum. Further investigations revealed that deletion of SsCYP64 leads to a decrease in the transcriptional level of SsPRF1, a key transcription factor regulating the sexual mating of S. scitamineum. Subsequently, the constitutive expression of SsPRF1 restored the defect in sexual mating/filamentation of the SsCYP64 deletion mutant, indicating that SsCyp64 regulates the sexual reproduction of S. scitamineum by mediating the transcriptional level of SsPRF1. In addition, metabolomic analysis revealed that the fatty alcohol metabolite γ-linolenyl alcohol significantly decreased in the SsCYP64 deletion mutant, whereas exogenous supplementation with γ-linolenyl alcohol increased the transcriptional level of SsPRF1 and partially restored the sexual mating/filamentation of the SsCYP64 deletion mutant. In conclusion, our results indicated that SsCyp64 mediated the transcription of SsPRF1 by modulating γ-linolenyl alcohol levels, thereby regulating the formation of dikaryotic hyphae in S. scitamineum. These findings provide new insights into the role of cytochrome P450 enzymes in the pathogenic process of plant pathogenic fungi.

Photosynthesis is the ultimate source of energy for crop productivity, and leaf morphology as well as chlorophyll content are traditional, indirectly related traits of photosynthesis. However, the genetic basis of these traits remains unexplored in sugarcane. In this study, we conducted genome-wide association studies (GWAS) to identify loci controlling nine photosynthesis-related traits, including four leaf morphological traits (leaf length, leaf width, leaf ratio, and leaf area) and five chlorophyll-related traits (chlorophyll a, chlorophyll b, chlorophyll a/b ratio, total chlorophyll, and SPAD value). The analysis was performed using whole-genome resequencing data from 219 elite, globally diverse sugarcane materials evaluated at two locations across two years (four environments). Based on 5,964,084 high-quality single nucleotide polymorphisms (SNPs), we identified 308 GWAS-significant SNPs (p ≤ 1.5 × 10⁻⁶) that were consistently detected in two or more environments, defining 97 GWAS-associated intervals across 30 chromosomes. Within these intervals, 98 putative genes were predicted, of which 20 genes in 16 intervals were potentially associated with leaf photosynthesis based on functional annotation and literature mining. These candidates are primarily involved in pathways related to ADP-ribosylation factors, ATP-dependent Clp protease proteolytic subunits, protein kinases, F-box proteins, MYB and WRKY transcription factors, UVR8, pentatricopeptide repeat-containing (PPR) proteins, Aux/IAA proteins, monogalactosyldiacylglycerol (MGDG) synthase, Orange (OR) proteins, PsbP domain-containing (PPD) proteins, and chloroplast stem-loop binding proteins of 41 kDa b (CSP41b). Ten genes were prioritized for future functional validation. Notably, these photosynthesis-related structural and pigment traits represent a different regulatory layer from direct gas exchange parameters (e.g., net photosynthetic rate), and their associations with actual photosynthetic efficiency require further validation. Nevertheless, this study provides novel candidate genes and molecular markers to assist marker-assisted breeding aimed at improving the photosynthetic structure and light-harvesting capacity of sugarcane.