Improvement of soil testing techniques for detecting spores of potato wart disease Synchytrium endobioticum using molecular methods

Synchytrium endobioticum (Schilb.) Percival. is a pathogen of potato wart disease and has a restricted distribution on the territory of the Russian Federation. Its main pathways are infected potato tubers and different planting material containing soil particles infected with spores of the fungus. One of the main problems is the use of toxic chemicals during detecting the disease in laboratory methods of direct soil testing to identify resting spores. This paper presents the assessment of molecular methods of soil diagnosis for detection of S. endobioticum by direct extraction of fungal DNA from soil samples using the MetaGen reagent kit. Identification was performed using the Fitoskrin. Synchytrium endobioticum-RT kit. The kit was pre-tested using DNA isolated from potato warts by various commercial kits. It was found that the optimal method of DNA isolation from the warts was using the FitoSorb-Avtomat 48 kit at the Tecan robotic station. Studies have shown that the sensitivity of the direct DNA extraction method from soil samples with various infection levels is the same as that of flotation method using carbon tetrachloride. Moreover, this method makes it possible to work with soil samples of different types, including peaty soils.

‘Vychegodsky’: a new potato cultivar for the Republic of Komi

Background. The presented information refers to the completed stage of the breeding process carried out at the Institute of Agrobiotechnologies (Syktyvkar) that led to the development of a new mid-early table potato variety – ‘Vychegodsky’. This cultivar was obtained from controlled crossing of cvs. Svitanok Kievsky × Amadeus. The new variety underwent a comprehensive assessment for the main agronomic traits and genetic screening for resistance to wart disease, nematode, and viruses X and Y.Materials and methods. In 2020, according to the results of production tests performed in 2017–2019, the description of the new cv. ‘Vychegodsky’ was finalized. The registered cv. ‘Nevsky’ was chosen as the reference. The study was conducted in the Institute’s experiment fields with a six-field crop rotation, which ensured high soil fertility without the use of mineral or organic fertilizers. The soil was soddy-podzolic. The planting scheme was 70 × 30 cm, at a depth of 8–10 cm, over the experimental plot area of 52.5 m2 (250 tubers), with four replications.Results. The mid-early cultivar ‘Vychegodsky’ is described as follows: the plant is erect, 50–65 cm in height; tubers are roundish-oval, with yellow skin color and light yellow flesh. The studies have shown that in its agronomic traits in the Republic of Komi cv. ‘Vychegodsky’ exceeds the reference cv. ‘Nevsky’. Its yield is 34.3 t/ha, and its marketable tuber weight 55.1 g; it contains 15.7% of starch, 24.1% of dry matter, and 11.2 mg% of vitamin C. The cultivar demonstrates high field resistance to major potato diseases, and genetically determined resistance to wart disease and golden potato nematode.Conclusion. Thus, a new potato cultivar has been released and included into the State Register of Selection Achievements (National List of the Russian Federation).

Transcriptome analysis of resistance mechanism to potato wart disease

To understand the molecular mechanism of the resistance to potato wart disease, we used the potato cultivar Qingshu 9 as the experimental material and prepared potato samples with different levels of disease through inoculation. The RNAs of the samples were extracted, and transcriptome analysis was performed on the samples not infected by the disease (control group) and also on the samples with different levels of disease, with the aid of high-throughput sequencing. Next, the differentially expressed genes (DEGs) associated with the resistance to potato wart disease were identified based on the analysis results. Using bioinformatic tools, the DEGs were functionally annotated, classified, and enriched in related metabolic pathways. The main results are as follows: Compared with the control group, 4 DEGs were identified in the samples with light disease, 52 were found in the samples with medium disease, and 214 were discovered in the samples with heavy disease. Potato mainly resists the wart disease by suppressing its gene expression, and the degree of suppression depends on the level of the disease; the disease resistance might be dominated by cellular nucleic acid-binding protein, AP2-like transcription factor, and E3 ubiquitin-protein ligase. This research provides new insights into the molecular mechanism of potato resistance against wart disease.

A Hitchhiker’s guide to the potato wart disease resistance galaxy

Key message Two novel major effect loci (Sen4 and Sen5) and several minor effect QTLs for potato wart disease resistance have been mapped. The importance of minor effect loci to bring full resistance to wart disease was investigated. Using the newly identified and known wart disease resistances, a panel of potato breeding germplasm and Solanum wild species was screened. This provided a state-of-the-art “hitch-hikers-guide” of complementary wart disease resistance sources. Abstract Potato wart disease, caused by the obligate biotrophic soil-born fungus Synchytrium endobioticum, is the most important quarantine disease of potato. Because of its huge impact on yield, the lack of chemical control and the formation of resting spores with long viability, breeding for resistant varieties combined with strict quarantine measures are the only way to efficiently and durably manage the disease. In this study, we set out to make an inventory of the different resistance sources. Using a Genome-Wide Association Study (GWAS) in the potato breeding genepool, we identified Sen4, associated with pathotypes 2, 6 and 18 resistance. Associated SNPs mapped to the south arm of chromosome 12 and were validated to be linked to resistance in one full-sib population. Also, a bulked segregant analysis combined with a Comparative Subsequence Sets Analysis (CoSSA) resulted in the identification of Sen5, associated with pathotypes 2, 6 and 18 resistance, on the south arm of chromosome 5. In addition to these two major effect loci, the GWAS and CoSSA allowed the identification of several quantitative trait loci necessary to bring full resistance to certain pathotypes. Panels of varieties and Solanum accessions were screened for the presence of Sen1, Sen2, Sen3, Sen4 and Sen5. Combined with pedigree analysis, we could trace back some of these genes to the ancestral resistance donors. This analysis revealed complementary resistance sources and allows elimination of redundancy in wart resistance breeding programs.

Distribution of P1(D1) wart disease resistance in potato germplasm and GWAS identification of haplotype-specific SNP markers

Key message A Genome-Wide Association Study using 330 commercial potato varieties identified haplotype specific SNP markers associated with pathotype 1(D1) wart disease resistance. Abstract Synchytrium endobioticum is a soilborne obligate biotrophic fungus responsible for wart disease. Growing resistant varieties is the most effective way to manage the disease. This paper addresses the challenge to apply molecular markers in potato breeding. Although markers linked to Sen1 were published before, the identification of haplotype-specific single-nucleotide polymorphisms may result in marker assays with high diagnostic value. To identify hs-SNP markers, we performed a genome-wide association study (GWAS) in a panel of 330 potato varieties representative of the commercial potato gene pool. SNP markers significantly associated with pathotype 1 resistance were identified on chromosome 11, at the position of the previously identified Sen1 locus. Haplotype specificity of the SNP markers was examined through the analysis of false positives and false negatives and validated in two independent full-sib populations. This paper illustrates why it is not always feasible to design markers without false positives and false negatives for marker-assisted selection. In the case of Sen1, founders could not be traced because of a lack of identity by descent and because of the decay of linkage disequilibrium between Sen1 and flanking SNP markers. Sen1 appeared to be the main source of pathotype 1 resistance in potato varieties, but it does not explain all the resistance observed. Recombination and introgression breeding may have introduced new, albeit rare haplotypes involved in pathotype 1 resistance. The GWAS approach, in such case, is instrumental to identify SNPs with the best possible diagnostic value for marker-assisted breeding.

Analisis Algoritma Klasifikasi C 4.5 Untuk Memprediksi Keberhasilan Immunotherapy Pada Penyakit Kutil

Maintaining skin health is one thing that is also needed. Not only health from inside, health from the outside must also be considered. There are so many skin problems that arise in the human body. Wart disease is characterized by small bumps on the surface of the skin which are generally caused by the Human Papiloma Virus (HPV) virus. One technique for treating wart disease is immunotherapy, this method is a treatment by increasing the immune system to deal with wart disease. Clinical predictions are growing very rapidly by adopting computer science and information technology in managing health and drug data, this clinical prediction can be produced from processing using data mining methods. Data mining is a popular method used to explore patterns or knowledge from large data stacks. C 4.5 algorithm which is one of the decision tree induction algorithms is also a method of data mining algorithms used to classify. This study aims to predict the success rate of immunotherapy treatment methods on wart disease with algorithm C 4.5 using RapidMiner. From the study it was known that the accuracy rate for processing immunotherapy data on wart disease to predict its success using the C 4.5 algorithm of 74.07%.