Efficient Exact Maximum a Posteriori Computation for Bayesian SNP Genotyping in Polyploids

The problem of genotyping polyploids is extremely important for the creation of genetic maps and assembly of complex plant genomes. Despite its significance, polyploid genotyping still remains largely unsolved and suffers from a lack of statistical formality. In this paper a graphical Bayesian model for SNP genotyping data is introduced. This model can infer genotypes even when the ploidy of the population is unknown. We also introduce an algorithm for finding the exact maximum a posteriori genotype configuration with this model. This algorithm is implemented in a freely available web-based software package SuperMASSA. We demonstrate the utility, efficiency, and flexibility of the model and algorithm by applying them to two different platforms, each of which is applied to a polyploid data set: Illumina GoldenGate data from potato and Sequenom MassARRAY data from sugarcane. Our method achieves state-of-the-art performance on both data sets and can be trivially adapted to use models that utilize prior information about any platform or species

Seleção recorrente fenotípica para melhoramento da qualidade protéica em populações de milho não opaco

A proteína do milho (Zea mays L.) é considerada como de baixa qualidade, pois apresenta nível reduzido dos aminoácidos essenciais lisina e triptofano. Uma alternativa para contornar esse problema consiste na introdução do gene opaco-2, que eleva a quantidade desses aminoácidos, embora apresente efeitos pleiotrópicos negativos em caracteres agronômicos relacionados à produtividade. O objetivo deste trabalho foi verificar a viabilidade de melhorar a qualidade protéica do milho com uso de Seleção Recorrente Fenotípica (SRF), sem introdução do gene opaco. Foram realizados quatro ciclos de SRF em duas populações, IG-1 e IG-2, para o teor de triptofano nos grãos, com 20% de intensidade. Os quatro ciclos seletivos e as populações originais foram avaliados para caracteres agronômicos em três locais. Para avaliação da qualidade protéica, foi conduzido um experimento com controle da polinização, para se evitar o efeito de xênia. Houve pequeno aumento nos níveis de triptofano para IG-1 (cerca de 0,70% por ciclo) e ausência de alteração em IG-2. Ocorreu aumento na relação triptofano/proteína para IG-1 (1,26% por ciclo) e os teores de proteína não se alteraram para as duas populações. A qualidade protéica da testemunha ESALQ VD2-opaco foi superior a das populações mesmo após a realização dos quatro ciclos. Como resposta correlacionada à seleção, houve redução na produção de grãos (2,50% por ciclo), prolificidade, altura da planta e altura da espiga. O baixo ganho, associado às alterações desfavoráveis em caracteres agronômicos, indica que este método de seleção possivelmente não é eficiente para elevar a qualidade protéica.Maize (Zea mays L.) protein is considered to be of low quality due to low levels of the essential lysine and tryptophan amino acids. An alternative to solve this problem is to use the opaque-2 gene, which improves the level of these amino acids, but has negative pleiotropic effects on agronomic characters. A phenotypic recurrent selection scheme was carried out in two non-opaque maize populations to verify the possibility of improving their protein quality without using this gene. Four cycles were completed and a 20% selection intensity for tryptophan content in the kernels was used in two populations, IG-1 and IG-2. The original and the four-cycle populations were evaluated in three locations for agronomic traits. For protein and tryptophan content, a separated trial was carried out because plants of the plots were hand-pollinated. No increase in tryptophan content was observed in the IG-2 population, whereas IG-1 presented a small increase (0.70% per cycle). The ratio tryptophan/protein increased 1.26% per cycle in IG-1 and the protein content did not increase in both populations. The ESALQ-VD2-opaque check was superior in relation to both populations for protein quality, as expected, even after completion of four selection cycles. The kernel yield (2.5% per cycle) prolificacy, plant and ear heights, decreased with selection cycles, as a correlated response to selection. Phenotypic recurrent selection in non-opaque maize was not able to increase, at reasonable rates, the protein quality of maize kernels

Characterization of rust, early and late leaf spot resistance in wild and cultivated peanut germplasm

Groundnut (Arachis hypogaea) has an AB genome and is one of the most important oil crops in the world. The main constraints of crop management in Brazil are fungal diseases. Several species of the genus Arachis are resistant to pests and diseases. The objective of our experiments was to identify wild species belonging to the taxonomic section Arachis with either A or B (or " non-A" ) genomes that are resistant to early leaf spot (Cercospora arachidicola), late leaf spot (Cercosporidium personatum) and rust (Puccinia arachidis). For the identification of genotypes resistant to fungal diseases, bioassays with detached leaves were done in laboratory conditions, with artificial inoculation, a controlled temperature of 25ºC and a photoperiod of 10 h light/14 h dark, for 20-42 days, depending on the fungi species. Most of the accessions of wild species were more resistant than accessions of A. hypogaea for one, two or all three fungi species studied. Arachis monticola, considered to be a possible tetraploid ancestor or a derivative of A. hypogaea, was also more susceptible to Cercosporidium personatum and Puccinia arachidis, as compared to most of the wild species. Therefore, wild germplasm accessions of both genome types are available to be used for the introgression of resistance genes against three fungal diseases of peanut.O amendoim (Arachis hypogaea) possui genoma AB e é uma das mais importantes culturas oleaginosas em todo o mundo. Os principais problemas da cultura no Brasil são as doenças fúngicas. Várias espécies do gênero Arachis são resistentes a pragas e doenças. Este trabalho visou a identificar espécies silvestres pertencentes à seção Arachis associadas aos genomas A ou B (ou " não-A" ) do amendoim que são resistentes à mancha castanha (Cercospora arachidicola), mancha preta (Cercosporidium personatum) e ferrugem (Puccinia arachidis). Para a identificação de genótipos resistentes a doenças fúngicas, bioensaios utilizando folhas destacadas foram realizados em condições de laboratório, com inoculação artificial, temperatura controlada de 25ºC e fotoperíodo de 10h luz/14h escuro, por 20-42 dias, de acordo com a espécie fúngica. A maioria dos acessos das espécies silvestres foram mais resistentes que os acessos de A. hypogaea para uma, duas ou todas as espécies fúngicas estudadas. Arachis monticola, considerada como o possível ancestral tetraplóide ou como um derivativo de A. hypogaea, também mostrou-se mais suscetível a Cercosporidium personatum e Puccinia arachidis, quando comparado à maioria das espécies silvestres. Portanto, acessos de germoplasma silvestre com genoma A ou B estão disponíveis para serem utilizados na introgressão de genes de resistência a doenças fúngicas no amendoim

Comparison of similarity coefficients used for cluster analysis with dominant markers in maize (Zea mays L)

The objective of this study was to evaluate whether different similarity coefficients used with dominant markers can influence the results of cluster analysis, using eighteen inbred lines of maize from two different populations, BR-105 and BR-106. These were analyzed by AFLP and RAPD markers and eight similarity coefficients were calculated: Jaccard, Sorensen-Dice, Anderberg, Ochiai, Simple-matching, Rogers and Tanimoto, Ochiai II and Russel and Rao. The similarity matrices obtained were compared by the Spearman correlation, cluster analysis with dendrograms (UPGMA, WPGMA, Single Linkage, Complete Linkage and Neighbour-Joining methods), the consensus fork index between all pairs of dendrograms, groups obtained through the Tocher optimization procedure and projection efficiency in a two-dimensional space. The results showed that for almost all methodologies and marker systems, the Jaccard, Sorensen-Dice, Anderberg and Ochiai coefficient showed close results, due to the fact that all of them exclude negative co-occurrences. Significant alterations in the results for the Simple Matching, Rogers and Tanimoto, and Ochiai II coefficients were not observed either, probably due to the fact that they all include negative co-occurrences. The Russel and Rao coefficient presented very different results from the others in almost all the cases studied and should not be used, because it excludes the negative co-occurrences in the numerator and includes them in the denominator of their expression. Due to the fact that the negative co-occurrences do not necessarily mean that the regions of the DNA are identical, the use of coefficients that do not include negative co-occurrences was suggested.8391Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES