Mauricio Marini Kopp

SSR Locator: Tool for Simple Sequence Repeat Discovery Integrated with Primer Design and PCR Simulation

Microsatellites or SSRs (simple sequence repeats) are ubiquitous short tandem duplications occurring in eukaryotic organisms. These sequences are among the best marker technologies applied in plant genetics and breeding. The abundant genomic, BAC, and EST sequences available in databases allow the survey regarding presence and location of SSR loci. Additional information concerning primer sequences is also the target of plant geneticists and breeders. In this paper, we describe a utility that integrates SSR searches, frequency of occurrence of motifs and arrangements, primer design, and PCR simulation against other databases. This simulation allows the performance of global alignments and identity and homology searches between different amplified sequences, that is, amplicons. In order to validate the tool functions, SSR discovery searches were performed in a database containing 28 469 nonredundant rice cDNA sequences.

IRAP and REMAP assessments of genetic similarity in rice.

Rice is a model genome for cereal research, providing important information about genome structure and evolution. Retrotransposons are common components of grass genomes, showing activity at transcription, translation and integration levels. Their abundance and ability to transpose make them good potential markers. In this study, we used 2 multilocus PCR-based techniques that detect retrotransposon integration events in the genome: IRAP (inter-retrotransposon amplified polymorphism) and REMAP (retrotransposon-microsatellite amplified polymorphism). Markers derived fromTos17, a copia-like endogenous retrotransposon of rice, were used to identify genetic similarity among 51 rice cultivars (Oryza sativa L.). Genetic similarity analysis was performed by means of the Dice coefficient, and dendrograms were developed by using the average linkage distance method. A cophenetic correlation coefficient was also calculated. The clustering techniques revealed a good adjustment between matrices, with correlation coefficients of 0.74 and 0.80, or lower (0.21) but still significant, between IRAP and REMAP-based techniques. Consistent clusters were found for Japanese genotypes, while a subgroup clustered the irrigated Brazilian genotypes.

Association between genetic distances in wheat (Triticum aestivum L.) as estimated by AFLP and morphological markers

Molecular and morphological data analyses matrices are very informative tools for the estimation of genetic distances. We used AFLP markers, morphological traits and combined analysis to estimate the genetic distances between wheat genotypes and ascertain any associations between the two techneques. Nineteen wheat (Triticum aestivum L.) genotypes were analyzed using amplified fragment length polymorphism (AFLP) markers and field evaluated for two years. The matrices obtained by morphological and molecular marker data analyses revealed a significant but moderate correlation (r = 0.47), indicating that such techniques sample distinct genome regions. The combined analysis was found to be highly correlated with AFLP (r = 0.97) and moderately correlated with morphological (r = 0.59) markers. A possible explanation for such results is a bias caused by the much higher number of AFLP (229) than morphological (17) markers. Thus, it is evident that the combined analysis is not efficient when a very dissimilar number of markers are used in each isolated technique. Therefore, to obtain a better knowledge of the degree of divergence among genotypes it is necessary to consider each analysis separately.

Absorção de P, Mg, Ca e K e tolerância de genótipos de arroz submetidos a estresse por alumínio em sistemas hidropônicos

Soils with high aluminum (Al3+) concentrations can affect the development and nutrient absorption of rice plants. The goals of this study were to evaluate the absorption of P, Mg, Ca and K in 18 rice genotypes and their overall performance when subjected to Al3+ stress in hydroponic systems. The experimental design was randomized blocks with 3 replications and four Al3+ levels (0, 10, 20 and 30mg L-1). Plantlets were treated for 20 days and evaluated for root length (CR) and P, Mg, Ca and K contents. All variables presented significant reductions in their values, and the genotypes presented different performance in nutrient absorption when facing different treatments, with an exception for Mg absorption response in which all genotypes evaluated were similar. Based on the variable CR, the genotypes Felune and Taim were considered the most tolerant and sensitive to Al3+, respectively. Regarding nutrient absorption, the genotypes presented variable responses to each evaluated nutrient, nevertheless the genotype Felune presented also high absorption levels. All the variables presented significant correlations to each other.

Dissimilaridade genética em mutantes de aveia tolerantes e sensíveis a ácidos orgânicos

ABSTRACT GENETIC DISSIMILARITY IN OAT ( AVENA SATIVA L.) TOLERANT AND SENSITIVEMUTANTS TO ORGANIC ACIDS In order to cultivate oats ( Avena sativa L.) as an economically alternative in low lands, it is necessaryto use cultivars tolerant to the main organic acids produced by organic matter decomposition resultingfrom no tillage systems. The objectives of this work were estimate genetic dissimilarity among M 3 mutantfamilies and the oat cultivar UFRGS 14 using ISSR markers; and to detect genomic regions associatedwith organic acids toxicity. Thirty M 3 mutant families from the Plant Genomic Center of the College ofAgronomy “Eliseu Maciel”, derived from the cultivar UFRGS 14 irradiated with gamma ray (Co 60 ) at400 Gy dosage were used. The genetic characterization was carried out using the ISSR marker technique.The results indicated that UBC 854, 855 and 811 primers allowed the identification of genomic regionsrelated to organic acid toxicity tolerance, while UBC 850 and 826 primers of genomic regions associatedto organic acid sensitivity.

Evaluation of Rice Genotypes under Propionate Stress

Abstract The objective of the present work was to evaluate the response of 25 rice genotypes to propionate, a compound largely produced in low‐drainage and high‐organic matter‐content soils. The work was performed in hydroponics with four doses and a random block design with three replications. The variables measured were root (RL) and shoot (SL) length, number of roots (NR), and root (RDM) and shoot (SDM) dry matter. Analyses of variance, relative performance, and regression fitting were performed, showing significance for most variables. The variable RL was the most affected by propionate, and the use of this variable for screening genotypes indicated 6 tolerant and 19 sensitive genotypes. Most tolerant genotypes belonged to irrigated japonica.

Caracterização de famílias mutantes de arroz para tolerância ao frio nos períodos vegetativo e reprodutivo

Low temperatures that occur during the cultivation of rice in the Southern region of Brazil cause reductions in to the yield and quality of the rice grain. Genotypes tolerant to low temperatures would be an alternative to minimize these problems. In the present work cold tolerance was evaluated in rice families (M4 generation) in the vegetative and reproductive phases, in order to identify possible genetic variability. For the evaluation in the vegetative stage, 10 seeds from each family were placed in cell trays and kept at 13 oC for 10 days in controlled chamber with 12 hour day light. The evaluation at the reproductive stage consisted of the application of low temperature at anthesis, by a stress of 15 oC for 7 days. The results suggest that in the vegetative phase, 6 families presented 0-20% reduction in stature, showing a high degree of tolerance. For the reproductive phase there were no families showing higher tolerance than the tolerant control.

Evaluation of Aluminum Tolerance in Rice

Abstract The objectives of the present work were to adjust the method for identifying genetic variability in rice through the use of minimal solution in hydroponic culture, and to identify the most important level and character for the study. The experiment consisted of the response evaluation of 18 rice genotypes to three levels of aluminum treatment. Five variables obtained from root and shoot lengths were evaluated. The data were subjected to the clustering methods of Tocher and nearest neighbor to evaluate the dissimilarity and the most adequate aluminum level. The results indicated that the 2 mg L−1 concentration and the difference between first and second measures of root length were the most useful for evaluating Al tolerance. Based on the results, it was possible to identify tolerant and sensitive cultivars to aluminum.

Análise da germinação de cultivares de arroz submetidas a estresse por ácido acético

The objective of this research was to evaluate the germination of 12 rice genotypes under acetic acid stress, a phytotoxic compound produced in low drainage soils with high organic matter content. The tests were conducted with the first count of germination (PCG) and germination (G) of the genotypes subjected to 0mM, 4mM, 8mM and 12mM acetic acid concentrations. The seed of each genotype was placed in germitest paper that was embedded with treatment solutions and packaged in individual bags. The germination was performed at 25°C and the counts were carried out at 7 (PCG) and 14 days (G). A factorial random block design was performed with four replications of 50 seeds per genotype. The regressions set for the variables showed three genotypes with germination stability under acetic acid stress.

Polimorfismo do fungo simbionte de formigas cortadeiras submetido à luz ultravioleta

O presente trabalho teve por objetivo verificar o efeito de diferentes periodos de luz ultravioleta sobre a similaridade genetica do fungo simbionte de formigas cortadeiras pertencentes as especies Acromyrmex ambiguus, Acromyrmex crassispinus e Acromyrmex lundi, atraves da tecnica AFLP. Os fungos foram inoculados em meio de cultura Pagnocca e mantidos em câmaras climatizadas a temperatura de 25 + 1°C e escotofase de 24h, por um periodo de 15 dias. Posteriormente, foram expostos a luz ultravioleta por periodos de: 0, 5, 10, 15, 20, 25 e 30 minutos. Aos 45 dias apos o tratamento, foi realizada a extracao do DNA e padronizacao, realizando-se as reacoes de PCR por meio de 24 combinacoes de primers AFLP, das quais quatro foram selecionadas por apresentarem maior polimorfismo e consistencia. Os dados moleculares foram transformados em matriz binaria e analisados pelo programa estatistico NTSYS v. 2.1. As quatro combinacoes de primers utilizadas geraram 152 bandas polimorficas. As populacoes de fungos originarias de diferentes especies de Acromyrmex apresentaram uma similaridade genetica media de 37%, sendo que a inducao de mutacao atraves da luz ultravioleta permitiu obter isolados mais dissimilares.