Zsolt Polgár

Efficiency of Arbitrarily Amplified Dominant Markers (SCOT, ISSR and RAPD) for Diagnostic Fingerprinting in Tetraploid Potato

Three molecular markering techniques: start codon targeted (SCOT), inter-simple sequence repeat (ISSR) and random amplified polymorphic DNA (RAPD) markers were compared for fingerprinting of 24 varieties and a segregating population of tetraploid potato. The number of scoreable and polymorphic bands produced using the SCOT, ISSR and RAPD primers for varieties was more than that of genotypes. SCOTs markers were more informative, followed by ISSRs marker, than other markers for the assessment of varieties based on polymorphism information content (PIC). There were no significant differences among these markers in terms of the evaluation of genotypes. All marker techniques individually illustrated that Diversity Index and Marker Index for varieties were higher than that of genotypes, and SCOT had superiority to other markers. The resolving power (Rp) of the SCOT, ISSR and RAPD techniques was 71.25, 46.62 and 30.63 for varieties and 21.38, 18.83 and 18.87 for genotypes, respectively. Standard Jaccard’s similarity coefficient of each marker technique revealed that similarity among varieties was less than that of the genotypes. Overall the Shannon index showed that relative genetic diversity of the varieties was high when SCOT markers were used but it was fairly similar when ISSR and RAPD markers were applied. The results of Analysis of Molecular Variance (AMOVA) revealed that variation within groups of varieties of a country was significantly higher than among groups. These results suggest that efficiency of SCOT, ISSR and RAPD markers was relatively the same in fingerprinting of genotypes but SCOT analysis is more effective in fingerprinting of potato varieties. Overall, our results indicate that SCOT, ISSR and RAPD fingerprinting could be used to detect polymorphism for genotypes and for varieties of potato.ResumenSe compararon tres técnicas de marcadores moleculares para caracterizar molecularmente 24 variedades y a una población segregante de papa tetraploide: enfocado a codón de inicio (SCOT), repetición de secuencia inter-simple (ISSR) y amplificación al azar de ADN polimórfico (RAPD). El número de bandas polimórficas registrables producidas usando iniciadores para SCOT, ISSR y RAPD, fue mayor para las variedades que el de los genotipos. Los marcadores SCOT fueron más informativos, seguidos por los de ISSR, más que otros marcadores para el análisis de variedades con base al contenido de información del polimorfismo (PIC). No hubo diferencias significativas entre estos marcadores en términos de la evaluación de genotipos. Todas las técnicas de marcación ilustraron individualmente que el Índice de Diversidad y el índice de marcador para las variedades fue mayor que el de los genotipos, y SCOT tuvo superioridad sobre otros marcadores. El poder de resolución (Rp) de las técnicas SCOT, ISSR y RAPD fue de 71.25, 46.62 y 30.63 para las variedades y de 21.38, 18.83 y 18.87 para los genotipos, respectivamente. El coeficiente estándar de similitud de Jaccard de cada técnica de marcador reveló que la similitud entre variedades era menor que la de los genotipos. En general, el índice Shannon mostró que la diversidad genética relativa de las variedades era alta cuando se usaban los marcadores SCOT, pero era muy similar cuando se aplicaban los marcadores ISSR y RAPD. Los resultados del Análisis de Varianza Molecular (AMOVA) revelaron que la variación dentro de grupos de variedades de un país era significativamente más alta que entre grupos. Estos resultados sugieren que la eficiencia de los marcadores SCOT, ISSR y RAPD fue relativamente la misma en la caracterización de los genotipos, pero el análisis SCOT es más efectivo en la caracterización molecular de las variedades. En general, nuestros resultados indican que la caracterización SCOT, ISSR y RAPD puede usarse para detectar el polimorfismo para genotipos y para variedades de papa.

Development of intron targeting (IT) markers for potato and cross-species amplification in Solanum nigrum (Solanaceae).

UNLABELLED PREMISE OF THE STUDY Intron Targeting (IT) primers were developed for potato using expressed sequence tags (EST) and NCBI database records to study genetic diversity. • METHODS AND RESULTS Twenty-nine polymorphic intron targeting (IT) markers were generated and characterized from 30 samples of potato and 22 samples of Solanum nigrum to detect polymorphism. The number of alleles (A) per locus ranged from 2 to 7 in the analyzed populations, and the observed heterozygosity (H(O)) and expected heterozygosity (H(E)) from 0 to 0.833 and 0.750, respectively. All of the primers also amplified in the related species S. nigrum. • CONCLUSIONS The developed markers will provide valuable tools for genetic diversity analysis, genetic mapping, and marker-assisted breeding of potato and related Solanum species.

A GC–MS-based metabolomics study on the tubers of commercial potato cultivars upon storage

Using gas chromatography-mass spectrometry (GC-MS) as a system for the detection of amino acids, organic acids, sugars, sugar alcohols, and fatty acids, we characterised six commercial potato cultivars (Hópehely, Katica, Lorett, Somogyi kifli, Vénusz Gold, and White Lady) with different pedigrees, starch contents, cooking types, and dormancy periods, in five developmental stages from harvest to sprouting. The tubers were stored at 20-22°C in the dark. The metabolite data were subjected to principal component analysis. No correlation between metabolite contents of freshly harvested tubers and starch content or cooking type of the cultivars was detected. The storage decreased the fructose and sucrose and increased the proline concentrations of tubers. Irrespective of the length of dormancy a substantial difference in metabolite composition at each time point upon storage was detected in each cultivar except Somogyi kifli, the only cultivar amongst those tested with a pure Solanum tuberosum origin and A cooking type.

Next generation sequencing based development of intron-targeting markers in tetraploid potato and their transferability to other Solanum species.

Intron-targeting (IT) markers were developed from next generation sequencing (NGS) derived transcript sequencing data from the potato cultivar White Lady. The applicability of the IT markers was analyzed in other potato genotypes, and their transferability was studied in other Solanum species: section Archaesolanum (5 species), sect. Solanum (6 species) and a Solanum nigrum population (11 genotypes). Out of 250 randomly chosen transcript sequences, 144 intron harboring loci could be identified for which primer pairs were designed on exons flanking the putative introns. The usefulness of the IT primers was experimentally analyzed on a subset of 40 randomly chosen loci. Statistical analysis of diversity parameters was performed using the ATETRA and POPGENE software packages. By localizing the detected 17 polymorphic loci 11 of the 12 potato chromosomes could be identified. Specificity of the designed IT primers was tested by sequence analysis of amplified IT fragments in a randomly chosen locus. The results revealed the efficiency of NGS derived IT marker development and indicated their utility in diverse molecular analyses including their applicability for cross-species studies.

Stability Analysis of Agronomic Traits in Potato Cultivars of Different Origin

Potato (Solanum tuberosum ssp. tuberosum) cultivars are expected to express a stable level for traits important for growers and consumers. To investigate how this expectation was met by a set of 21 cultivars bred in Hungary, Poland and Spain, 2-year field experiments were carried out in these countries for the evaluation of tuber yield, starch content and yield, and occurrence of secondary growth of tubers. Stability in an agronomic sense was evaluated by the analysis of genotype by environment interaction (GE) using the Scheffé-Caliński mixed model. Unstable trait expression was indicated by the statistically significant share of GE in the variability contributed by a specific cultivar. This instability could lead to either complete or partial unpredictability. Stable trait expression was observed for 6–11 cultivars, depending on the trait. A significant genetic factor, which indicates broad adaptation, was rarely found. Stable expression of tuber yield occurred together with stable or predictable expression of both starch content and yield. Unstable expressions of tuber and starch yield were also associated. The stability or instability of secondary growth was not associated with stability or instability of the other measured traits. Analysis of GE interaction was useful for identifying stable or unstable responses and revealed the presence of incomplete stability or partial unpredictability as intermediate types of reaction.ResumenSe esperaría que las variedades de papa (Solanum tuberosum spp. tuberosum) expresen un nivel estable de caracteres importantes para productores y consumidores. Para investigar como esta expectativa pudiera darse en un juego de 21 variedades de Hungría, Polonia y España, se llevaron a cabo experimentos de campo durante dos años en estos países para la evaluación de rendimiento de tubérculo, rendimiento y contenido de almidón, y la presencia de crecimiento secundario de tubérculos. Se evaluó la estabilidad, en un sentido agronómico, mediante el análisis de la interacción genotipo-medio ambiente (GE), usando el modelo de la mezcla Scheffé-Caliński. La expresión de un carácter inestable se indicó por la significancia estadística de GE en la variabilidad proporcionada por una variedad específica. Esta inestabilidad podría conducir ya fuera para imprevisibilidad completa o parcial. La expresión de un carácter estable se observó en 6–11 variedades, dependiendo del carácter. Raramente se encontró un factor genético significativo que indicara amplia adaptación. La expresión estable de rendimiento de tubérculo se presentó junto con la expresión estable o predecible tanto con el contenido como con el rendimiento de almidón. También se asociaron expresiones inestables de rendimiento de tubérculo y almidón. La estabilidad o inestabilidad de crecimiento secundario no se asoció con estabilidad o inestabilidad de los otros caracteres medidos. El análisis de la interacción GE fue útil para la identificación de respuestas estables o inestables y reveló la presencia de estabilidad incompleta o imprevisibilidad parcial como tipos intermedios de reacción.

Development of Molecular Tools for Distinguishing Between the Highly Similar Rx1 and Rx2 PVX Extreme Resistance Genes in Tetraploid Potato

The Rx1 and Rx2 are extreme resistance genes, which have been introgressed from different species into potato cultivars and breeding lines. These two genes have a 98% and 96% sequence similarity at the nucleotide as well as at the amino acid level, respectively. Except one extra amino acid in the Rx2 gene, the high variations of the amino acid chain are due to single and double nucleotide variations, which are scattered throughout the coding regions. The high level of sequence similarity makes it complicated to identify these genes and to distinguish them from other highly similar genes, like the Gpa2 or from paralogous sequences by a single polymerase chain reaction (PCR). Here, we report the development of markers for the simple and rapid identification of the Rx1 as well as the Rx2 gene. Further, a multiplex PCR reaction is recommended for the simultaneous detection of both genes in a single reaction. Since these genes reside on different chromosomes, following their inheritance by the multiplex PCR method could help the easy incorporation of both genes into breeding lines. The detection method shown here could be routinely used in marker-assisted selection for Potato virus X extreme resistance and could enhance the effectiveness of potato breeding programs. Besides potato breeding, this method could also be effectively applied to mapping experiments as well as in research studies of resistance.