Search Results (37)

Potato common scab is one of the major diseases posing a threat to potato production on a global scale. No chemical agents have been found to effectively control the occurrence of this disease, and research on the identification of resistance genes and the development of molecular markers remains relatively limited. In this study, a diploid potato variety H535, which exhibits resistance to the predominant pathogen Streptomyces scabies, was utilized as the male parent, whereas the susceptible diploid potato variety H012 served as the female parent. Building upon the resistance QTL intervals pinpointed through a genome-wide association study, two potential resistance loci were localized on chromosome 2 of the potato genome, spanning the regions between 38–38.6 Mb and 41.3–42.7 Mb. These intervals accounted for 18.03% of the total phenotypic variance and are presumed to be the primary QTLs underlying scab resistance. Building upon this foundation, we expanded the hybrid progeny population, conducted resistance assessments, selected individuals with extreme phenotypes, developed molecular markers, and conducted fine mapping of the resistance gene. A phenotypic evaluation of scab resistance was carried out using a pot-based inoculation test on 175 potato hybrid progenies to characterize the F1 generation population. Twenty lines exhibiting high resistance and thirty lines displaying high susceptibility were selected for investigations. Within the preliminary mapping interval on potato chromosome 2 (spanning 38–43 Mb), a total of 214 SSR (Simple Sequence Repeat) and 133 InDel (Insertion/Deletion) primer pairs were designed. Initial screening with parental lines identified 18 polymorphic markers (8 SSR and 10 InDel) that demonstrated stable segregation patterns. Validation using bulked segregant analysis revealed that 3 SSR markers (with 70–90% linkage) and 6 InDel markers (with 70–90% linkage) exhibited significant co-segregation with the resistance trait. A high-density genetic linkage map spanning 104.59 cm was constructed using 18 polymorphic markers, with an average marker spacing of 5.81 cm. Through linkage analysis, the resistance locus was precisely mapped to a 767 kb interval (41.33–42.09 Mb) on potato chromosome 2, flanked by SSR-2-9 and InDel-3-9. Within this refined interval, four candidate disease resistance genes were identified: RHC02H2G2507, RHC02H2G2515, PGSC0003DMG400030643, and PGSC0003DMG400030661. This study offers novel insights into the genetic architecture underlying scab resistance in potato. The high-resolution mapping results and characterized markers will facilitate marker-assisted selection (MAS) in disease resistance breeding programs, providing an efficient strategy for developing cultivars with enhanced resistance to Streptomyces scabies. Full article

Potato (Solanum tuberosum L.) is a major staple crop globally, yet its production is severely impacted by common scab, a disease caused by Streptomyces spp., leading to substantial economic losses. This study evaluated copper sulfate (CuSO₄) and zinc sulfate (ZnSO₄) as potential control agents for common scab, focusing on their antimicrobial properties and effects on potato resistance mechanisms. Both CuSO₄ and ZnSO₄ exhibited dose-dependent inhibition of Streptomyces spp., significantly reducing the production of the pathogenic toxin Thaxtomin A by 57.02% and 41.29%, respectively. Electrical conductivity assays indicated their disruptive effects on cell membrane integrity, and HPLC confirmed their suppression of toxin production. Pot experiments showed that these treatments enhanced plant growth, chlorophyll content, and defense enzyme activities (SOD, POD, CAT, PPO), while reducing malondialdehyde (MDA) levels. qPCR analysis revealed upregulation of defense-related genes (PR1, PR3, PR9, SOD1, HSF1). Field trials demonstrated disease control efficiencies of 56.58% and 59.06% for CuSO₄ and ZnSO₄, respectively, with ZnSO₄ increasing yield by 19.29%. These findings highlight CuSO₄ and ZnSO₄ as effective agents for suppressing Streptomyces spp. and enhancing potato resistance, offering practical value for sustainable potato production systems. Full article

Potato common scab, caused by Streptomyces species, is a widespread soil-borne disease that poses a significant threat to potato cultivation globally. In this study, a Bacillus velezensis D7-8 strain was isolated from a potato. This endophytic bacterium exhibited broad-spectrum antifungal activity, and pot trials demonstrated that the D7-8 strain effectively controlled potato common scab with an efficacy of 42.07%. The complete genome sequence of the D7-8 strain was sequenced and subsequently identified as B. velezensis through multiple bioinformatic methods, primarily through structural variation analysis of whole-genome sequences. The machine learning method predicted that the expression profiles of colinear genes among closely related Bacillus species were highly consistent. Metabolite analysis of crude extracts using ultra-high-performance liquid chromatography coupled with quadrupole-Orbitrap high-resolution mass spectrometry (UPLC-Q-Exactive HRMS) revealed that D7-8 produces bioactive compounds, including surfactin and fengycin, both known for their antimicrobial properties. This study elucidates the antagonistic effect of B. velezensis D7-8 against Streptomyces acidiscabies and provides a valuable reference for future research on accurate microbial identification. Full article

This study investigates the early detection of sweet potato scab by using hyperspectral imaging and machine learning techniques. The research focuses on developing an accurate, economical, and non-destructive approach for disease detection and grading. Hyperspectral imaging experiments were conducted on two sweet potato varieties: Guangshu 87 (resistant) and Guicaishu 2 (susceptible). Data preprocessing included denoising, region of interest (ROI) selection, and average spectrum extraction, followed by dimensionality reduction using principal component analysis (PCA) and random forest (RF) feature selection. A novel dynamic grading method based on spectral-time data was introduced to classify the early stages of the disease, including the early latent and early mild periods. This method identified significant temporal spectral changes, enabling a refined disease staging framework. Key wavebands associated with sweet potato scab were identified in the near-infrared range, including 801.8 nm, 769.8 nm, 898.5 nm, 796.4 nm, and 780.5 nm. Classification models, including K-nearest neighbor (KNN), support vector machine (SVM), and linear discriminant analysis (LDA), were constructed to evaluate the effectiveness of spectral features. Among these classification models, the MSC-PCA-SVM model demonstrated the best performance. Specifically, the Susceptible Variety Disease Classification Model achieved an overall accuracy (OA) of 98.65%, while the Combined Variety Disease Classification Model reached an OA of 95.38%. The results highlight the potential of hyperspectral imaging for early disease detection, particularly for non-destructive monitoring of resistant and susceptible sweet potato varieties. This study provides a practical method for early disease classification of sweet potato scab, and future research could focus on real-time disease monitoring to enhance sweet potato crop management. Full article

For potato external defect detection, ordinary spectral technology has limitations in detail detection and processing accuracy, while the machine vision method has the limitation of a long feedback time. To realize accurate and rapid external defect detection for red-skin potatoes, a non-destructive detection method using hyperspectral imaging and a machine learning model was explored in this study. Firstly, Savitzky–Golay (SG), standard normal variate transformation (SNV), multiplicative scatter correction (MSC), the normalization algorithm, and different preprocessing algorithms combined with SG were used to preprocess the hyperspectral data. Then, principal component regression (PCR), support vector machine (SVM), partial least squares regression (PLSR), and least squares support vector machine (LSSVM) algorithms were used to establish quantitative models to find the most suitable preprocessing algorithm. The successive projections algorithm (SPA) was used to obtain various characteristic wavelengths. Finally, the qualitative models were established to detect the external defects of potatoes using the machine learning algorithms of backpropagation neural network (BPNN), k-nearest neighbors (KNN), classification and regression tree (CART), and linear discriminant analysis (LDA). The experimental results showed that the SG–SNV fusion hyperspectral data preprocessing algorithm and the KNN machine learning model were the most suitable for the detection of external defects in red-skin potatoes. Moreover, multiple external defects can be detected without multiple models. For healthy potatoes, black/green-skin potatoes, and scab/mechanical-damage/broken-skin potatoes, the detection accuracy was 93%,93%, and 83%, which basically meets the production requirements. However, enhancing the prediction accuracy of the scab/mechanical-damage/broken-skin potatoes is still a challenge. The results also demonstrated the feasibility of using hyperspectral imaging technology and machine learning technology to detect potato external defects and provided new insights for potato external defect detection. Full article

Potato common scab (CS) caused by Streptomyces scabiei is a severe disease that threatens tuber quality and its market value. To date, little is known about the mechanism regulating the resistance of potato to CS. In this study, we identified a presequence translocase-associated motor 16 gene from potato (designated StPAM16-1) that is involved in the response to the phytotoxin thaxtomin A (TA) secreted by S. scabiei. The StPAM16-1 protein was localized in the mitochondria, and the expression of the gene was upregulated in potato leaves treated with TA. The suppression of StPAM16-1 in potato led to enhanced resistance to TA and S. scabiei. Protein interaction analyses revealed that StPAM16-1 interacted with the subunit 5b of the COP9 signalosome complex (StCSN5). Similar to that of StPAM16-1, the expression levels of StCSN5 significantly increased in potato leaves treated with TA. These results indicated that StPAM16-1 acted as a negative regulator and was functionally associated with StCSN5 in the immune response of potato plants against CS. Our study sheds light on the molecular mechanism by which PAM16 participates in the plant immune response. Furthermore, both StPAM16-1 and StCSN5 could be potential target genes in the molecular breeding of potato cultivars with increased resistance to CS. Full article

Most cultivated potato (Solanum tuberosum) varieties are highly susceptible to common scab (Streptomyces scabei). The disease is widespread in all major potato production areas and leads to high economic losses and food waste. Varietal resistance is seen as the most viable and sustainable long-term management strategy. However, resistant potato varieties are scarce, and their genetic architecture and resistance mechanisms are poorly understood. Moreover, diploid potato relatives to commercial potatoes remain to be fully explored. In the current study, a panel of 384 ethyl methane sulfonate (EMS)-mutagenized diploid potato clones were evaluated for common scab coverage, severity, and incidence traits under field conditions, and genome-wide association studies (GWASs) were conducted to dissect the genetic architecture of their traits. Using the GAPIT-MLM and RTM-GWAS statistical models, and Mann–Whitney non-parametric U-tests, we show that 58 QTNs/QTLs distributed on all 12 potato chromosomes were associated with common scab resistance, 52 of which had significant allelic effects on the three traits. In total, 38 of the 52 favorable QTNs/QTLs were found to be pleiotropic on at least two of the traits, while 14 were unique to a single trait and were found distributed over 3 chromosomes. The identified QTNs/QTLs showed low to high effects, highlighting the quantitative and multigenic inheritance of common scab resistance. The QTLs/QTNs associated with the three common scab traits were found to be co-located in genomic regions carrying 79 candidate genes playing roles in plant defense, cell wall component biosynthesis and modification, plant–pathogen interactions, and hormone signaling. A total of 61 potato clones were found to be tolerant or resistant to common scab. Taken together, the data show that the studied germplasm panel, the identified QTNs/QTLs, and the candidate genes are prime genetic resources for breeders and biologists in breeding and targeted gene editing. Full article

Modern potato varieties from high-input, conventional farming-focused breeding programs produce substantially (up to 45%) lower yields when grown in organic production systems, and this was shown to be primarily due to less efficient fertilization and late blight (Phytophthora infestans) control methods being used in organic farming. It has been hypothesized that the breeding of potato varieties suitable for the organic/low-input sector should (i) focus on increasing nutrient (especially N) use efficiency, (ii) introduce durable late blight resistance, and (iii) be based on selection under low-input conditions. To test this hypothesis, we used an existing long-term factorial field experiment (the NEFG trials) to assess the effect of crop management practices (rotation design, fertilization regime, and crop protection methods) used in conventional and organic farming systems on crop health, tuber yield, and mineral composition parameters in two potato varieties, Santé and Sarpo mira, that were developed in breeding programs for high and low-input farming systems, respectively. Results showed that, compared to Santé, the variety Sarpo mira was more resistant to foliar and tuber blight but more susceptible to potato scab (Streptomyces scabies) and produced higher yields and tubers with higher concentrations of nutritionally desirable mineral nutrients but lower concentrations of Cd. The study also found that, compared to the Cu-fungicides permitted for late blight control in organic production, application of synthetic chemical fungicides permitted and widely used in conventional production resulted in significantly lower late blight severity in Sante but not in Sarpo mira. Results from both ANOVA and redundancy analysis (RDA) indicate that the effects of climatic (precipitation, radiation, and temperature) and agronomic (fertilization and crop protection) explanatory variables on crop health and yield differed considerably between the two varieties. Specifically, the RDA identified crop protection as a significant driver for Santé but not Sarpo mira, while precipitation was the strongest driver for crop health and yield for Sarpo mira but not Santé. In contrast, the effect of climatic and agronomic drivers on tuber mineral and toxic metal concentrations in the two varieties was found to be similar. Our results support the hypothesis that selection of potato varieties under low agrochemical input conditions can deliver varieties that combine (i) late blight resistance/tolerance, (ii) nutrient use efficiency, and (iii) yield potential in organic farming systems. Full article

A pathogen strain responsible for sweet potato stem and foliage scab disease was isolated from sweet potato stems. Through a phylogenetic analysis based on the rDNA internal transcribed spacer (ITS) region, combined with morphological methods, the isolated strain was identified as Elsinoë batatas. To comprehensively analyze the pathogenicity of the isolated strain from a genetic perspective, the whole-genome sequencing of E. batatas HD-1 was performed using both the PacBio and Illumina platforms. The genome of E. batatas HD-1 is about 26.31 Mb long in 167 scaffolds, with a GC content of 50.81%, and 7898 protein-coding genes, 131 non-coding RNAs, and 1954 interspersed repetitive sequences were predicted. Functional annotation revealed that 408 genes encode virulence factors involved in plant disease (DFVF—Plant). Notably, twenty-eight of these virulence genes encode secretory carbohydrate-active enzymes (CAZymes), including two endo-1,4-β-xylanase genes and seven cutinase genes, which suggested that endo-1,4-β-xylanase and cutinase play a vital role in the pathogenicity of E. batatas HD-1 within sweet potato. In total, twelve effectors were identified, including five LysM effectors and two CDIP effectors, suggesting that LysM and CDIP effectors play significant roles in the interaction between E. batatas HD-1 and sweet potato. Additionally, our analysis of biosynthetic gene clusters (BGCs) showed that two gene clusters are involved in melanin and choline metabolism. This study enriches the genomic resources of E. batatas and provides a theoretical foundation for future investigations into the pathogenic mechanisms of its infection in sweet potatoes, as well as potential targets for disease control. Full article

Cropping systems incorporating soil health management practices such as longer rotations, cover crops and green manures, and organic amendments have been shown to improve soil and crop health. However, long-term trials are needed to fully assess the impacts and effects of these systems over time. Crop varieties may also respond differently to cropping practices or systems. In field trials originally established in 2004, three different 3-year potato cropping systems focused on management goals of soil conservation (SC), soil improvement (SI), and disease suppression (DS) were evaluated and compared to a standard 2-year rotation (SQ) and a nonrotation control (PP). Results compiled over a 4-year period (2019–2022) using two different potato varieties showed that the SI system (with a history of compost amendments) improved soil properties, including organic matter and nutrient contents, aggregate stability, and microbial activity relative to other systems. The SI system also had higher total and marketable tuber yields (by 22–28%) relative to the standard SQ system. The DS system, which included a disease-suppressive green manure rotation crop, also improved yield (by 12%) and reduced soilborne diseases (black scurf and common scab). Variety Caribou Russet, a newer variety with improved characteristics, produced higher marketable yields and larger tuber size, as well as lower severity of common scab than the standard Russet Burbank variety. These results demonstrate that improved cropping systems can substantially enhance productivity relative to standard cropping systems, as well as provide greater sustainability through long-term improvements in soil health. Full article

The prolonged practice of continuous potato cropping, coupled with inadequate field management, disrupts the soil bacterial community equilibrium. Such disturbances compromise the resilience of the soil ecosystem, predisposing it to an increased incidence of potato diseases. However, the effects of the phosphorus fertiliser application rate on the rhizosphere soil bacterial community composition of potatoes and the occurrence of potato common scab (CS) have not been adequately studied. Here, diseased field soils from Dingxi and Huidong Counties were collected for potting tests, and field tests were conducted in Huidong County for validation. An examination of the relationship between the bacterial community composition in the potato rhizosphere soil and potato CS under different phosphate fertiliser treatments was conducted using 16S rRNA high-throughput sequencing. The results show that a lower phosphorus fertiliser application rate was more conducive to maintaining soil bacterial community diversity under different phosphorus fertiliser treatments in different habitats. In addition, the relative abundance of the txtA gene increased significantly (p < 0.05) with the increase in the phosphate fertiliser application rate. Field trials conducted in Huidong revealed that treatments F1, F2, and F3 had respective CS incidence rates of 28.33%, 46.67%, and 59.44%, while their corresponding disease severity indices were 7.67, 17.33, and 29.44. Further analysis revealed that the relative abundance of antagonistic genera of pathogenic S. scabies decreased significantly (p < 0.05) with increases in the phosphorus fertiliser application rate. In summary, the correlation between potato CS and changes in the bacterial community of rhizosphere soil was used to determine the optimal phosphorus application rate during potato production, which can provide a scientific basis for the management of phosphorus fertiliser in potato farmland. Full article

Plant disease identification is a crucial issue in agriculture, and with the advancement of deep learning techniques, early and accurate identification of plant diseases has become increasingly critical. In recent years, the rise of vision transformers has attracted significant attention from researchers in various vision-based application areas. We designed a model with an encoder–decoder architecture to efficiently classify plant diseases using a transfer learning approach, which effectively recognizes a large number of plant diseases in multiple crops. The model was tested on the “PlantVillage”, “FGVC8”, and “EMBRAPA” datasets, which contain leaf information from crops such as apples, soybeans, tomatoes, and potatoes. These datasets cover diseases caused by fungi, including rust, spot, and scab, as well as viral diseases such as leaf curl. The model’s performance was rigorously evaluated on datasets, and the results demonstrated its high accuracy. The model achieved 99.9% accuracy on the “PlantVillage” dataset, 97.4% on the “EMBRAPA” dataset, and 91.5% on the “FGVC8” dataset, showcasing its competitiveness with other state-of-the-art models. This study provides a robust and reliable solution for plant disease classification and contributes to the advancement of precision agriculture. Full article

Potatoes (Solanum tuberosum L.) represent an important food in the country’s gastronomy due to their cost, nutritional contribution, and versatility. However, many plant diseases such as the common scab—caused by Streptomyces species—reduce its yield and quality. This study aims to determine Streptomyces species being the causal agent of common scabs in a commercial potato field in the Yaqui Valley, Mexico, while identifying Bacillus strains as a biological control method to mitigate the impact of this disease under field conditions. Thus, three Streptomyces strains were selected from symptomatic samples, and then they were morphologically and molecularly (through sequencing recA and rpoB genes) identified as Streptomyces caniscabiei. After pathogenicity tests, the three strains were found to be pathogenic to potato tubers. In screening assays to identify biocontrol bacteria, strain TSO2^T (Bacillus cabrialesii subsp. tritici) and TE3^T_UV25 (Bacillus subtilis) had the best in vitro biocontrol effect against S. caniscabiei. Then, a field experiment (1 ha per treatment), under commercial conditions, was carried out to analyze the effectivity of these biocontrol bacteria to mitigate the common scabs on potato crops. After four months, the inoculation of this bacterial consortium decreased common scab incidence from 31% to 21% and increased the potato yield up to almost 5 tons/ha vs. the un-inoculated treatment. These findings demonstrate the effectiveness of the studied bacterial consortium as a potential biological control strategy to control common scabs of potato caused by Streptomyces caniscabiei, as well as increase the potato yield in the Yaqui Valley, Mexico. Full article

Research conducted at the Plant Breeding and Acclimatization Institute—NIR in Poland in 2020–2022 assessed the commercial quality of potato tubers depending on the production system (organic, conventional), variety, and weather conditions prevailing in the years of research. The tuber size distribution and the share of tuber defects was assessed. It was found that all tested factors influenced the commercial quality of the yield but to different extents. The production system had the greatest influence on most of the examined features, followed by weather conditions and the least influential factor being the variety. The production system had the greatest impact on such features as: tuber size distribution (all fractions), pest damage, scab infection, tuber deformations, and share of green tubers. Weather conditions had the greatest impact on scab infection, pest damage, deformation, cracks and share of large tubers. The variety factor had the greatest influence on such features as: deformations, cracks, green tubers, black scarf, and share of the smallest (non-commercial) tubers. In the conventional system, a significantly better tuber yield distribution was found. The share of tuber defects varied depending on the production system. In the organic system, a greater share of defects such as scab (68.3 and 41.3) and pest damage was found (6.8 and 0.2), while in the conventional system, a greater share of deformations (9.2 and 4.9), cracks (5.4 and 2.4), and rust spots (0.61 and 0.06) occurred. Full article