Martin Vivodík

Start codon targeted (scot) polymorphism reveals genetic diversity in european old maize (zea mays l.) Genotypes

Maize ( Zea mays L.) is one of the worlds most important crop plants following wheat and rice, which provides staple food to large number of human population in the world. It is cultivated in a wider range of environments than wheat and rice because of its greater adaptability. Molecular characterization is frequently used by maize breeders as an alternative method for selecting more promising genotypes and reducing the cost and time needed to develop hybrid combinations. In the present investigation 40 genotypes of maize from Czechoslovakia, Hungary, Poland, Union of Soviet Socialist Republics, Slovakia and Yugoslavia were analysed using 20 Start codon targeted (SCoT) markers. These primers produced total 114 fragments across 40 maize genotypes, of which 86 (76.43%) were polymorphic with an average of 4.30 polymorphic fragments per primer and number of amplified fragments ranged from 2 (SCoT 45) to 8 (SCoT 28 and SCoT 63). The polymorphic information content (PIC) value ranged from 0.374 (ScoT 45) to 0.846 (SCoT 28) with an average of 0.739. The dendrogram based on hierarchical cluster analysis using UPGMA algorithm was prepared. The hierarchical cluster analysis showed that the maize genotypes were divided into two main clusters. Unique maize genotype (cluster 1), Zuta Brzica, originating from Yugoslavia separated from others. Cluster 2 was divided into two main clusters (2a and 2b). Subcluster 2a contained one Yugoslavian genotype Juhoslavanska and subcluster 2b was divided in two subclusters 2ba and 2bb. The present study shows effectiveness of employing SCoT markers in analysis of maize, and would be useful for further studies in population genetics, conservation genetics and genotypes improvement.

Molecular characterization of rye cultivars.

14.00 The results of molecular analysis of 45 rye taxa ( Secale cereale L.) represented by agricultural varieties originated from Central Europe and the Union of Soviet Socialist Republics (SUN) are presented. The genetic diversity of rye cultivars by 6 SSR markers was evaluated. Six specific microsatellite primer pairs produced 58 polymorphic alleles with an average of 9.7 alleles per locus. The number of alleles ranged from 6 ( SCM2 ) to 14 ( SCM86 ). Genetic polymorphism was characterized based on diversity index (DI), probability of identity (PI) and polymorphic information content (PIC). The diversity index (DI) of SSR markers ranged from 0.5478 ( SCM2 ) to 0.887 ( SCM86 ) with an average of 0.778. The lowest value of polymorphic information content was recorded for SCM2 (0.484) and the highest value for SCM86 (0.885) of PIC was detected in SCM86 with an average of 0.760.The dendrogram of genetic similarity was constructed, based on UPGMA algorithm. The hierarchical cluster analysis divided rye genotypes into 4 main clusters. The first cluster of 14 genotypes was subdivided in two subclusters (1a and 1b) where 50% of genotypes were Czechoslovak origin. The second cluster contained four genotypes were three (75%) of them had Czech or Czechoslovak origin. In the third subcluster separated three rye genotypes of different origin. The rest (24) of rye genotypes in the fourth cluster were divided into two subclusters (4a and 4b) where clearly separated group of Polish (4aa) and Czech and Czechoslovak (4ab) genotypes. Two genotypes of 4aa subcluster (Wojcieszyckie and Dankowskie Nowe) from Poland were genetically the closest. In the dendrogram alle genotypes were differentiated and clustering partially reflects geographic origin of studied rye genotypes. In this experiment, SSRs markers proved to be a high informative and usefull tool in genetic diversity research for the distinguishing and characterization of close related varieties. Normal 0 21 false false false CS JA X-NONE

Study of polymorphism of maize using dna and protein markers

In the present investigation 40 genotypes of maize from Czechoslovakia, Hungary, Poland, Union of Soviet Socialist Republics, Slovakia and Yugoslavia were analysed using 20 start codon targeted (SCoT) markers, 10 simple sequence repeat (SSR) markers, 13 random amplified polymorphic (RAPD) markers and using SDS-PAGE markers. Twenty SCoT primers produced 114 DNA fragments with an average of 5.7 bands per primer. Out of the total of 114 amplified fragments, 86 (76.43 %) were polymorphic, with an average of 4.30 polymorphic bands per primer. Ten SSR primers revealed a total of 65 alleles ranging from 4 (UMC1060) to 8 (UMC2002 and UMC1155) alleles per locus with a mean value of 6.50 alleles per locus. 20 SCoT primers produced total 114 fragments across 40 maize genotypes, of which 86 (76.43 %) were polymorphic with an average of 4.30 polymorphic fragments per primer and number of amplified fragments ranged from 2 (SCoT 45) to 8 (SCoT 28 and SCoT 63). The number of total scorable protein bands was twentythree as a result of SDS-PAGE technique but those that were not cosistent in reproducibility and showed occasional variation in sharpness and density were not considered. Based on these bands forty accessions of maize were screened. Out of twentythree polypeptide bands, 6 (31%) were commonly present in all accessions and considered as monomorphic, while 17 (65%) showed variations and considered as polymorphic. The dendrogram of 40 old maize genotypes based on SSR, SCoT, RAPD and SDS-PAGE markers using UGMA algorithm was constructed.

Characterization of Tunisian castor bean genotypes using SDS-PAGE of total seed storage proteins

Due to the chemical and physical properties of castor oil ( Ricinus communis L.) that make it a valuable raw material for numerous industrial applications, including the production of biofuel, interest to develop more and better varieties has been increased. The objectives of this work, were to find out the level of genetic variability present in 56 Tunisian castor germplasm by using the electrophoretic profiles of total seed proteins with different molecular weights through SDS-PAGE. Fifty-six castor ( Ricinus communis L.) genotypes were used in the present study. Seeds of castor were obtained from the University of Carthage, National Institute of Research in Rural Engineering, Waters and Forests (INRGREF), Regional Station of Gabes, Tunisia. Storage proteins were extracted from individual grains by the standard reference electrophoretic method by ISTA in the presence of sodium dodecyl sulfate (SDS-PAGE). The number of total scorable protein bands was twentynine as a result of SDS-PAGE technique but those that were not cosistent in reproducibility and showed occasional variation in sharpness and density were not considered. Out of twentynine polypeptide bands, 5 (18%) were commonly present in all accessions and considered as monomorphic, while 24 (82%) showed variations and considered as polymorphic. The size of the protein bands obtained through SDS-PAGE ranged from 30 to 180 kDa. On the basis of banding profiles of proteins of different kDa, gel was divided into zones A, B and C. The major protein bands were lied in zones A and B, while minor bands were present in zones C. The dendrogram tree demonstrated the relationship among the 56 Tunisian castor genotypes according to the similarity index, using UPGMA cluster analysis. The dendrogram was divided into three main clusters. Similarly the present study of genetic variability in the seed storage polypeptide determined by SDS-PAGE technique proved that it is fruitful to identify genetic diversity among accessions of castor.

Genetic diversity and population structure in tunisian castor genotypes (Ricinus communis L.) Detected using scot markers

Due to the chemical and physical properties of castor oil ( Ricinus communis L.) that make it a valuable raw material for numerous industrial applications, including the production of biofuel, interest to develop more and better varieties has been increased. In the present study, the representatives of the genus castor collected from 12 different parts of Tunisia were differentiated by the DNA fingerprinting patterns using 37 SCoT primers. PCR amplification of DNA using 37 primers for SCoT analysis produced 268 DNA fragments that could be scored in all 56 genotypes of Tunisian castor. The number of amplified fragments varied from 4 (SCoT 45, SCoT 31 and ScoT 17) to 10 (SCoT 3, SCoT 11, SCoT 14, SCoT 18 and SCoT 12). Of the 268 amplified bands 230 were polymorphic, with an average of 6.22 polymorphic bands per primer. To determine the level of polymorphism in the analysed group of Tunisian castor genotypes polymorphic information content (PIC) was calculated. The lowest values of polymorphic information content were recorded for SCoT 17 (0.411) and the the highest PIC values were detected for SCoT 14 (0.868) with an average of 0.751. A dendrogram was constructed from a genetic distance matrix based on profiles of the 37 SCoT primers using the unweighted pair-group method with the arithmetic average (UPGMA). According to analysis, the collection of 56 Tunisian castor genotypes were clustered into two main clusters (1 and 2). Of the 56 genotypes of Tunisian castor, 2 unique genotypes were separated (BA-5 and K-4). Genetically the closest were two genotypes from Tunisian region Souassi (S-2 and S-5) in subclaster 2bc. Results showed the utility of SCoT markers for estimation of genetic diversity of castor genotypes leading to genotype identification.

Molecular analysis of buckwheat using gene specific markers

Buckwheat ( Fagopyrium esculentum ) is a pseudo-cereal which has spread troughout the world and nowadays it represents cultural, economic and nutritionally important pseudocereal . It´s enviromentally friendly, characterized by high fiber, routine, protein and B vitamins, and is general-purpose. The goal of the present study was to analyze 17 genotypes of buckwheat by using 7 SCoT markers. In total, 52 fragments were detected, of which 38 were polymorphic. The average number of polymorphic fragments was 5.43. The most polymorphic fragments were detected in SCoT 26 and SCoT 29 markers, and the average percentage of polymorphism was 73.36 %. SCoT 29 reached the highest percentage of polymorphism (87.5 %) and SCoT 36 was lowest (60 %). The DI values ​​ranged from 0.625 (SCoT 36) to 0.887 (SCoT 26) and the average DI value was 0.749. The average PIC value was 0.729 with PIC values ranging from 0.386 (SCoT 36) to 0.831 (SCoT 26). To determine the genetic diversity of 17 genotypes of the buckwheat, a dendrogram was created using the hierarchical cluster analysis. The genotypes were divided into two major clusters (I and II). Cluster I was divided into three other subgroups. Sixteen genotypes were included in cluster I and the genotype of Madawaska (USA) was genetically the farthest in cluster II. Genetically the closest were the varieties of Ballada (Russia) and Bamby (Austria). Used SCoT markers were sufficiently polymorphic, were able identify and differentiate chosen set of buckwheat genotypes.

Genetic variation of european maize genotypes (zea mays l.) Detected using ssr markers

The SSR molecular markers were used to assess genetic diversity in 40 old European maize genotypes. Ten SSR primers revealed a total of 65 alleles ranging from 4 (UMC1060) to 8 (UMC2002 and UMC1155) alleles per locus with a mean value of 6.50 alleles per locus. The PIC values ranged from 0.713 (UMC1060) to 0.842 (UMC2002) with an average value of 0.810 and the DI value ranged from 0.734 (UMC1060) to 0.848 (UMC2002) with an average value of 0.819. 100% of used SSR markers had PIC and DI values higher than 0.7 that means high polymorphism of chosen markers used for analysis. Probability of identity (PI) was low ranged from 0.004 (UMC1072) to 0.022 (UMC1060) with an average of 0.008. A dendrogram was constructed from a genetic distance matrix based on profiles of the 10 maize SSR loci using the unweighted pair-group method with the arithmetic average (UPGMA). According to analysis, the collection of 40 diverse accessions of maize was clustered into four clusters. The first cluster contained nine genotypes of maize, while the second cluster contained the four genotypes of maize. The third cluster contained 5 maize genotypes. Cluster 4 contained five genotypes from Hungary (22.73%), two genotypes from Poland (9.10%), seven genotypes of maize from Union of Soviet Socialist Republics (31.81%), six genotypes from Czechoslovakia (27.27%), one genotype from Slovak Republic (4.55%) and one genotype of maize is from Yugoslavia (4.55%). We could not distinguish 4 maize genotypes grouped in cluster 4, (Voroneskaja and Kocovska Skora) and 2 Hungarian maize genotypes - Feheres Sarga Filleres and Mindszentpusztai Feher, which are genetically the closest.

Detection genetic variability of secale cereale L. by scot markers

Rye (Secale cereale L.) is our traditional cereal used for baking. The genetic variability of grown rye has been reduced by modern agronomic practices, which subsequently prompted the importance of search for species that could be useful as a gene pool for the improving of flour quality for human consumption or for other industrial uses. Therefore, the aim of this study was to detect genetic variability among the set of 45 rye genotypes using 8 SCoT markers. Amplification of genomic DNA of 45 genotypes, using SCoT analysis, yielded 114 fragments, with an average of 14.25 polymorphic fragments per primer. The most polymorphic primer was SCoT 36, where 21 polymorphic amplification products were detected. In contract the lowest polymorphic primer was SCoT 45 with 5 polymorphic products. Genetic polymorphism was characterized based on diversity index (DI), probability of identity (PI) and polymorphic information content (PIC). The hierarchical cluster analysis showed that the rye genotypes were divided into 2 main clusters. One rye genotype Motto, origin from Poland formed a separate subcluster (1b). Subscluster 2a included only genotype Valticke (CSK). In this experiment, SCoT proved to be a rapid, reliable and practicable method for revealing of polymorphism in the rye cultivars. Normal 0 21 false false false EN-GB X-NONE X-NONE

Characterization Of Slovak Castor Genotypes (Ricinus Communis L.) Using Molecular Markers

The aim of this work was to detect genetic variability among the set of 30 castor genotypes using 6 RAPD markers. Amplification of genomic DNA of 30 genotypes, using RAPD analysis, yielded 42 fragments, with an average of 7.00 polymorphic fragments per primer. Number of amplified fragments ranged from 5 to 9, with the size of amplicons ranging from 100 to 1,200 bp. The polymorphic information content (PIC) value ranged from 0.662 to 0.855 with an average of 0.780 and diversity index (DI) value ranged from 0.669 to 0.857 with an average of 0.785. The dendrogram based on hierarchical cluster analysis using UPGMA algorithm was prepared. Knowledge on the genetic diversity of castor can be used for future breeding programs for increased oil production to meet the ever increasing demand of castor oil for industrial uses as well as for biodiesel production.

Separation Of Rye Secalins By A-Page

The aim of our study was to evaluate the electrophoretic profiles of secalins of fifteen genotypes of rye (Secale cereale L.), which were obtained by polyacrylamide gel electrophoresis in the presence at pH 3.1 (A-PAGE). Electrophoretic separation of storage proteins was conducted according to the methodology recommended by an international organization ISTA, with some own modifications. Fractions from the preparative separation were pooled in such a way that no components from one pool were present in the others. Doc-It LS software was used to detect and to calculate variability of genotypes within individual rye species.Preparative electrophoresis at low pH allowed a simple separation of γ75k-secalins, ω-secalins and γ40k-secalins from the crude material under non-denaturing conditions. The content of γ75k-secalins varied in analyzed collection of rye from 22.86% (variety Čerkascanka tetra) to 53.93% (genotype Valtické) with an average 39.27%. The proportion of ω-secalins in our samples was in an average 39.27%. The largest percent representation of ω-secalins was proved in variety České (58.68%) and the lowest part of this subunits was detected in variety Radomske (25.83%). Our results showed that average representation of γ40k-secalins was 22.05%, with the highest content in variety Vígľašské (32.44%) overleaf with the lowest part of this fraction was detected in Valtické (8.28%). The variety of wheat Chinese spring and Marquis were used as standards. Storage proteins consist of three fractions, which are the main part of grain proteins and are used as a marker not only for genetic variability investigation, but also for characterization of genotypes. These pooled fractions could be used as starting material for single polypeptide purification.