Assessing the genetic structure of Oryza glumaepatula populations with isozyme markers

To assess the genetic diversity and genetic structure parameters, nine populations of Oryza glumaepatula from the Amazon biome, four from the Pantanal biome, and one collected at Rio Xingu, Mato Grosso, totaling 14 populations and 333 individuals were studied with isozyme markers. Six loci were evaluated showing a moderate allozyme variability (A = 1.21, P = 20.7 percent, Ho = 0.005, He = 0.060). The populations from the Pantanal biome showed higher diversity levels than the Amazon biome. High genetic differentiation among the populations, expected for self-fertilizing species, was observed (F ST=0.763), with lower differentiation found among the Pantanal populations (F ST=0.501). The average apparent outcrossing rate was higher for the Pantanal populations (t a = 0.092) than for the Amazonian populations (t a = 0.003), while the average for the 14 populations was 0.047, in accordance with a self-fertilization mating system.

Utilizando marcadores isoenzimáticos, foram avaliadas nove populações de Oryza glumaepatula originárias da Amazônia, quatro do bioma do Pantanal, e uma coletada no Rio Xingu, Mato Grosso, totalizando 14 populações e 333 indivíduos, com o objetivo de avaliar a diversidade genética e a estrutura genética dessas populações. Seis locos foram avaliados, mostrando variabilidade alozímica moderada (A = 1.21, P = 20.7 por cento, Ho = 0.005, He = 0.060). As populações do bioma Pantanal apresentaram níveis de diversidade mais altos que as da Amazônia. Alta diferenciação genética entre populações, esperada para espécies autógamas, foi observada (F ST=0.763), com menor diferenciação encontrada entre populações do Pantanal (F ST=0.501). A taxa média de cruzamento aparente foi maior para as populações do Pantanal (t a = 0.092) que da Amazônia (t a = 0.003), enquanto que a taxa media para as 14 populações foi 0.047, em concordância com o sistema reprodutivo por autogamia.

Agronomic and molecular characterization of introgression lines from the interspecific cross Oryza sativa (BG90-2) x Oryza glumaepatula (RS-16)

The reduced genetic variability of modern rice varieties (Oryza sativa) is of concern because it reduces the possibilities of genetic gain in breeding programs. Introgression lines (ILs) containing genomic fragments from wild rice can be used to obtain new improved cultivars. The objective of the present study was to perform the agronomic and molecular characterizations of 35 BC2F8 ILs from the cross O. glumaepatula x O. sativa, aiming to select high-yielding ILs to be used in rice-breeding programs. All 35 ILs were field evaluated in the season 2002/2003 in three locations and the 15 best performing ones were evaluated in the season 2003/2004 in five locations. In 2003/2004, six ILs (CNAi 9934, CNAi 9931, CNAi 9930, CNAi 9935, CNAi 9936, and CNAi 9937) showed the highest yield means and were statistically superior to the controls Metica 1 and IRGA 417. Molecular characterization of the 35 ILs was performed with 92 microsatellite markers distributed on the 12 rice chromosomes and a simple regression Oriza glumaepatula-derived introgression lines quantitative trait locus analysis was performed using the phenotypic data from 2002/2003. The six high-yielding ILs showed a low proportion of wild fragment introgressions. A total of 14 molecular markers were associated with quantitative trait loci in the three locations. The six high-yielding ILs were incorporated in the Embrapa breeding program, and the line CNAi 9930 is recommended for cultivation due to additional advantages of good grain cooking and milling qualities and high yield stability. The O. glumaepatula-derived ILs proved to be a source of new alleles for the development of high-yielding rice cultivars.

Comparative linkage mapping of Oryza glumaepatula and Oryza sativa interspecific crosses based on microsatellite and expressed sequence tag markers

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 percent 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.

Elevada diversidade genética interpopulacional em Oryza glumaepatula Steud. (Poaceae) avaliada com microssatélites / High interpopulational genetic diversity of Oryza glumaepatula Steud. (Poaceae) assessed with microsatellites

Marcadores microssatélites foram usados para caracterizar a diversidade genética entre e dentro de sete populações naturais de Oryza glumaepaula. Seis dessas populações são originárias da bacia hidrográfica da Amazônia e uma do rio Paraguai no Pantanal Matogrossense. Utilizando sete locos de microssatélites, observou-se diversidade genética intrapopulacional média de 1,98 alelos por loco, 56,2 por cento de locos polimórficos, Ho = 0,026 e He = 0,241. Elevada diferenciação interpopulacional foi observada pelo índice de fixação de Wright e pelo parâmetro de divergência de Slatkin (F ST = 0,715 e R ST = 0,595, respectivamente), bem como elevado nível de endogamia total (F IT = 0,963), em grande parte influenciada pelo sistema reprodutivo (F IS = 0,858). Verificou-se que nenhuma população estava em equilíbrio de Hardy-Weinberg, devido ao predomínio da autofertilização, o que também pôde ser verificado pela taxa média aparente de cruzamentos: t a = 0,055. Consequentemente, o fluxo gênico entre populações foi praticamente nulo o que contribuiu para o elevado nível de divergência interpopulacional. De modo geral, as taxas de cruzamento foram muito baixas ou nulas nas populações da Amazônia. Entretanto, a população PG-3 do Rio Paraguai, originária do Pantanal Matogrossense, apresentou taxa de cruzamento mais elevada (13,2 por cento), indicando sistema reprodutivo misto com predomínio de autogamia. Como a diversidade intrapopulacional foi baixa, os resultados indicam que a amostragem de elevado número de populações é a estratégia mais adequada para a conservação ex situ desta espécie. Para a conservação in situ, com base na riqueza alélica, recomenda-se como prioridade as populações PG-3, TA-3, SO-17 e NE-7, originárias das bacias hidrográficas dos Rios Paraguai, Tapajós, Solimões e Negro, respectivamente.

Microsatellite markers were used to characterize the genetic diversity within and among seven natural populations of Oryza glumaepaula. Six of these populations originated from the hydrographic basin of the Amazon and one from Rio Paraguay in the Pantanal Matogrossense. Using seven microsatellite loci, the following intrapopulation genetic diversity parameters were estimated on average: 1.98 alleles per locus, 56.2 percent polymorphic loci, Ho = 0.026 and He = 0.241. High interpopulational differentiation was noticed by examining Wright's fixation index and Slatkin's divergence parameter (F ST = 0.715 and R ST = 0.595, respectively), as well as a high level of total inbreeding (F IT = 0.963), greatly influenced by the mating system (F IS = 0.858). No population was in Hardy-Weinberg equilibrium, due to the prevailing autogamic mating behavior, as also indicated by the average apparent outcrossing rate observed: t a = 0.055. Consequently, among populations gene flow was practically absent, which has contributed to the high interpopulational genetic divergence. In general, very low or null outcrossing rates were found in the Amazonian populations. However, population PG-3 from Rio Paraguay, originated from Pantanal Matogrossense, showed a higher outcrossing rate (13.2 percent), indicating a mixed mating system with the predominance of self-fertilization. Since intrapopulation diversity was low, results indicate that sampling a large number of populations is the most appropriate strategy for the ex situ conservation of this species. For in situ conservation, taking in consideration the allelic richness, the following populations are indicated as priority: PG-3, TA-3, SO-17, and NE-7, from the hydrographic basins of the rivers Paraguay, Tapajos, Solimoes and Negro, respectively.

Variation of biometric parameters and C, N, and P concentrations of Oryza glumaepatula at different depths of an amazonian lake impacted by bauxite tailings (Lake Batata, Pará, Brazil)

Lake Batata is a typical Amazonian clear water lake which has undergone anthropogenic impacts. Thirty percent of its total area has been covered with bauxite tailings. Thus, it is possible to distinguish two areas in this ecosystem: the impacted and the natural. The goal of this research was to study C, N, and P content variation and the values of biomass, length, density, and culm diameter of Oryza glumaepatula at different depths in the natural and impacted areas of Lake Batata. The results obtained in this research suggest that the availability of P and N, in both water and sediment, is lower at the shallow site when compared to the deeper sites. On the other hand, C concentrations decreased as P and N concentrations increased. This may be explained by the structural function of C in aquatic macrophytes. At shallower sites, due to the reduced water column, individuals invest in supporting structures that display high C concentrations. The higher density and biomass of O. glumaepatula at the intermediate site indicate that this area presents the best conditions for germination and establishment of individuals of this species. The chemical composition and biometric parameters of O. glumaepatula have shown that this population has higher spatial variation in the natural area. In the impacted area, the absence of significant variations in N and P concentrations in O. glumaepatula among the three sampled sites promotes higher homogeneity in the stands. The high C:P and N:P ratios indicate that, in the impacted area, P is more limiting to the development of O. glumaepatula than it is in the natural area. The reduced values of biomass and density of O. glumaepatula in the impacted area suggest that the bauxite tailings limit the development of this population.

O Lago Batata é um típico lago amazônico de águas claras que sofreu impactos antropogênicos. De sua área total, 30% foi recoberta com rejeito de bauxita. Desta forma, pode-se distinguir duas áreas nesse ecossistema: impactada e natural. O objetivo desta pesquisa foi estudar a variação de C, N e P e os valores de biomassa, comprimento, densidade e diâmetro do colmo de Oryza glumaepatula em diferentes profundidades, nas áreas impactada e natural, do Lago Batata. Os resultados obtidos na pesquisa sugerem que as disponibilidades de P e N, tanto na água como no sedimento, são menores no ponto raso quando comparado com os pontos mais profundos. Por outro lado, as concentrações de C diminuíram à medida que as concentrações de P e N aumentaram. Isto pode ser explicado pela função estrutural do C em macrófitas aquáticas. Nos pontos mais rasos, devido à reduzida coluna d'água, indivíduos investem em estruturas de suporte com elevadas concentrações de C. A elevada densidade e biomassa de O. glumaepatula no ponto intermediário indica que essa área apresenta as melhores condições para germinação e estabelecimento de indivíduos dessa espécie. A composição química e os parâmetros biométricos de O. glumaepatula mostraram que essa população possui elevada variação espacial na área natural. Na área impactada, a menor variação nas concentrações de N e P nos três pontos de amostragem promove alta homogeneidade nos estandes. As altas razões C:P e N:P indicam que, na área impactada, o P é mais limitante para o desenvolvimento de O. glumaepatula do que na área natural. Os reduzidos valores de biomassa e densidade de O. glumaepatula na área impactada sugerem que o rejeito de bauxita limita o desenvolvimento dessa população.