Association analysis was applied to a panel of accessions of Embrapa Rice Core Collection (ERiCC) with 86 SSR and field data from two experiments. A clear subdivision between lowland and upland accessions was apparent, thereby indicating the presence of population structure. Thirty-two accessions with admixed ancestry were identified through structure analysis, these being discarded from association analysis, thus leaving 210 accessions subdivided into two panels. The association of yield and grain-quality traits with SSR was undertaken with a mixed linear model, with markers and subpopulation as fixed factors, and kinship matrix as a random factor. Eight markers from the two appraised panels showed significant association with four different traits, although only one (RM190) maintained the marker-trait association across years and cultivation. The significant association detected between amylose content and RM190 was in agreement with previous QTL analyses in the literature. Herein, the feasibility of undertaking association analysis in conjunction with germplasm characterization was demonstrated, even when considering low marker density. The high linkage disequilibrium expected in rice lines and cultivars facilitates the detection of marker-trait associations for implementing marker assisted selection, and the mining of alleles related to important traits in germplasm.

Molecular linkage maps representing the rice genome have been an important tool for breeding programs because they allow the elucidation of polygenic traits and are an efficient tool for monitoring wild introgressions in interspecific crosses. Common markers among rice genetic maps are important in defining the homology of chromosomes and the synteny between genomic target regions. We used 148 markers (expressed sequence tags, microsatellites and single nucleotide polymorphisms) to construct a molecular linkage map based on co-dominant markers for an interspecific backcross population using a wild rice (Oryza glumaepatula) from Brazil and performed a comparative analysis with other interspecific maps. The comparative analysis revealed a Spearman correlation index of 0.86 for marker order conservation to a previous map constructed for an interspecific cross using the same wild parent. Approximately 90% of markers common to other interspecific maps kept the same order. These results indicate that it will be possible to generate a unique genetic map using the wild donor and that it may be a helpful tool for breeding programs because plants derived from different interspecific populations can be rapidly scanned using markers associated with useful wild traits.

The rice (Oryza sativa) breeding program of the Rice and Bean research center of the Brazilian agricultural company Empresa Brasileira de Pesquisa Agropecuária (Embrapa) is well established and provides new cultivars every year to attend the demand for improved high yielding varieties with tolerance to biotic and abiotic stresses. However, the elite genitors used to compose new populations for selection are closely related, contributing to the yield plateau reached in the last 20 years. To overcome this limit, it is necessary to broaden the genetic basis of the cultivars using diverse germplasm such as wild relatives or traditional varieties, with the latter being more practical because they are more easily crossed with elite germplasm to accelerate the recovery of modern plant types in the breeding lines. The objective of our study was to characterize the allelic diversity of 192 traditional varieties of Brazilian rice using 12 simple sequence repeat (SSR or microsatellite) markers. The germplasm was divided into 39 groups by common name similarity. A total of 176 alleles were detected, 30 of which (from 23 accessions) were exclusive. The number of alleles per marker ranged from 6 to 22, with an average of 14.6 alleles per locus. We identified 16 accessions as a mixture of pure lines or heterozygous plants. Dendrogram analysis identified six clusters of identical accessions with different common names and just one cluster with identical accessions with the same common name, indicating that SSR markers are fundamental to determining the genetic relationship between landraces. A subset of 24 landraces, representatives of the 13 similarity groups plus the 11 accessions not grouped, was the most variable set of genotypes analyzed. These accessions can be used as genitors to increase the genetic variability available to rice breeding programs.

The ''cagaita tree'' (Eugenia dysenterica) is a plant found widespread in the Brazilian Cerrado. Its fruit is used for popular consumption and for industrial purposes. This study opens a new perspective for the generation of population genetic data and parameters estimates for devising sound collection and conservation procedures for Eugenia dysenterica. A battery of 356 primer pairs developed for Eucalyptus spp. was tested on the ''cagaita tree''. Only 10 primer pairs were found to be transferable between the two species. Using a polyacrilamide gel, an average of 10.4 alleles per locus was detected, in a sample of 116 individuals from 10 natural ''cagaita tree'' populations. Seven polymorphic loci allowed estimation of genetic parameters, including expected average heterozygosity He = 0,442, among population diversity, R ST = 0,268 and gene flow Nm = 0,680. Results indicated a potential of SSR locus transferability developed for Eucalyptus to other species of different genera, such as in the case of the ''cagaita tree''. The high genetic diversity among populations detected with SSR markers indicated that these markers are highly sensitive to detect population structure. Estimated Nm values and the existence of private alleles indicated reduced gene flow and consequently possible damage to the metapopulation structure.

Uma biblioteca genômica enriquecida para seqüências microssatélites foi construída para Magnaporthe grisea (anamorfo Pyricularia grisea), o agente causal da doença brusone do arroz. Setenta e dois clones de DNA contendo unidades repetitivas microssatélites foram isolados e seqüenciados para o desenvolvimento de uma série de novos marcadores moleculares baseados em reação de PCR, para serem utilizados na análise genética do fungo. Dos 72 clones, 24 foram selecionados para o desenho dos pares de primers para amplificação dos alelos microssatélites pela técnica de PCR. Culturas monospóricas de M. grisea isoladas de plantas de arroz e trigo no Brasil, Colômbia e China foram genotipadas utilizando-se 3 locos microssatélites. Isolados do fungo provenientes do Estado do Rio Grande do Sul foram predominantemente monomórficos nos locos microssatélites testados, indicando um baixo nível de variabilidade genética destas amostras. Contudo, 7 alelos puderam ser detectados pelo marcador MGM-1 em isolados provenientes do Estado do Tocantins e no mínimo 9 alelos puderam ser detectados com o mesmo marcador em uma amostra de isolados da Colômbia. A análise com marcadores microssatélites é uma metodologia simples e direta para se estimar a diversidade genética dos isolados de M. grisea e uma poderosa ferramenta para o estudo da genética de M. grisea.

An AG microsatellite-enriched genomic DNA library was constructed for Magnaporthe grisea (anamorph Pyricularia grisea), the causal agent of rice blast. Seventy-two DNA clones containing microsatellite repeats were isolated and sequenced in order to develop a series of new PCR-based molecular markers to be used in genetic studies of the fungus. Twenty-four of these clones were selected to design primer pairs for the PCR amplification of microsatellite alleles. Single spore cultures of M. grisea isolated from rice and wheat in Brazil, Colombia and China were genotyped at three microsatellite loci. Isolates from southern Brazil were predominantly monomorphic at the tested SSR loci, indicating a low level of genetic variability in these samples. However, seven alleles were observed at the MGM-1 locus in isolates from Central Brazil and at least nine alleles were detected at the same locus in a sample of Colombian isolates. Polymorphism analysis at SSR loci is a simple and direct approach for estimating the genetic diversity of M. grisea isolates and a powerful tool for studying M. grisea genetics.