Agro-morphological characterization of upland rice accessions

The agro-morphological characterization is fundamental in order to provide information for plant breeding programs. The aim of the present study was to characterize 146 accessions of upland rice (Oryza sativa L.), based on qualitative and quantitative agro-morphological descriptors. The experiment was conducted in Recife, state of Pernambuco, Brazil, using a randomized block design with three replicates. Polymorphism was observed among 12 of 14 qualitative characters evaluated, whereas significant differences (p < 0.05) were observed for 11 of the 14 analysed quantitative traits. Genetic variance was higher than environmental variance and the average inheritability coefficients were above 80 % for all characters, which ensures the predominance of the genetic components in the differences observed among accessions. On the cluster analysis for qualitative traits the accessions were classified in two groups with a total of 18 duplicates, whereas for the quantitative traits three groups were obtained with few subgroups. The principal component analysis for quantitative traits showed great dispersion of the accessions. The most divergent group of accessions included the genotypes Mitsukasane, Mie, Tomoe mochi, Ooba kirishima and Nourin mochi 6, which showed a higher number of spicklets per plant. There is high variability among the rice accessions from the germplasm collection studied, which presents great importance for breeding programs or for genetic studies on this species

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%, 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%, 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.Fundação de Amparo à Pesquisa no Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq

Diversidade morfológica e molecular entre genótipos de mandioca

The objective of this work was to characterize morphologically and molecularly the genetic diversity of cassava accessions, collected from different regions in Brazil. A descriptive analysis was made for 12 morphological traits in 419 accessions. Data was transformed into binary data for cluster analysis and analysis of molecular variance. A higher proportion of white or cream (71%) root cortex color was found, while flesh colors were predominantly white (49%) and cream (42%). Four accession groups were classified by the cluster analysis, but they were not grouped according to their origin, which indicates that diversity is not structured in space. The variation was greater within regions (95.6%). Sixty genotypes were also evaluated using 14 polymorphic microsatellite markers. Molecular results corroborated the morphological ones, showing the same random distribution of genotypes, with no grouping according to origin. Diversity indices were high for each region, and a greater diversity was found within regions, with: a mean number of alleles per locus of 3.530; observed and expected heterozygosity of 0.499 and 0.642, respectively; and Shannon index of 1.03. The absence of spatial structure among cassava genotypes according to their origins shows the anthropic influence in the distribution and movement of germplasm, both within and among regions.O objetivo deste trabalho foi caracterizar, morfológica e molecularmente, a diversidade genética de acessos de mandioca de diferentes regiões do Brasil. Realizou-se a análise descritiva de 12 características morfológicas em 419 acessos. Os dados foram transformados em dados binários para análise de agrupamento e análise de variância molecular. Observou-se maior proporção (71%) de cor branca ou creme do córtex da raiz, enquanto as cores da polpa foram predominantemente branca (49%) e creme (42%). Quatro grupos de acessos foram classificados pela análise de agrupamento, mas não foram agrupados de acordo com sua origem, o que indica que a diversidade não está estruturada no espaço. A maior parte da variação ocorreu dentro das populações (95,6%). Sessenta genótipos também foram avaliados com o uso de 14 marcadores microssatélites polimórficos. Os resultados moleculares corroboraram os morfológicos e mostraram a mesma distribuição aleatória dos genótipos, com ausência de agrupamento quanto ao local de origem. Os índices de diversidade foram elevados para cada região e a maior parte da diversidade foi observada dentro de regiões, com: número médio de alelos por loco de 3,530; heterozigosidade média observada de 0,499 e esperada de 0,642; e índice de Shannon de 1,03. A ausência de estrutura espacial entre os genótipos de mandioca de acordo com suas origens mostra a influência antrópica na distribuição e movimentação de germoplasma, tanto entre como dentro de regiões

Genetic diversity in Brazilian sweet potato (Ipomoea batatas (L.) Lam., Solanales, Convolvulaceae) landraces assessed with microsatellite markers

We used simple sequence repeat (SSR) markers to investigate the genetic diversity of 78 sweet potato (Ipomoea batatas) accessions (58 landraces and 20 putative clones) from traditional agricultural households from 19 local communities in the Vale do Ribeira, São Paulo, Brazil. Eight SSR loci were assessed using 6% (w/v) polyacrylamide gels stained with silver nitrate and the accessions genotyped considering the presence or absence of bands. The results were subjected to analysis of molecular variance (AMOVA), and cluster and principal coordinate analyses. Spatial structure was assessed using Mantel's test to compare genetic and geographic distances. Each primer pair generated between three and ten clearly scorable polymorphic fragments. Cluster analyses showed a Jaccard's index from 0.3 to 1.0, indicating high genetic and intravarietal diversity. Accessions from all 19 communities were not spatially structured (r = 0.15, p < 0.054), with AMOVA indicating that most of the variability (58.2%) was distributed within households and only 18.1% of the variability was distributed between households within communities. The outcrossing mating system of sweet potato, and anthropic factors such as selection of different varieties and their maintenance within household small plots and home gardens, as well as an extensive exchange system between agriculturists, may all be contributing to these results.FAPESPCNP

Variabilidade isoenzimática de acessos de mandioca de diferentes regiões do Brasil

A mandioca (Manihot esculenta Crantz) pertence à família Euphorbiaceae, gênero Manihot, cultivada em todo o país. É a única do gênero utilizada na alimentação. O presente trabalho teve como objetivo o estudo da variabilidade isoenzimática de 200 acessos de mandioca obtidos junto ao banco de germoplasma da Embrapa Amazônia Oriental. Os acessos foram agrupados de acordo com o local de origem, obtendo-se desta forma sete grupos: 1-Amazonas, 2-Amapa, 3-Bahia, 4-Para, 5-Rondonia, 6-Diversos, incluindo-se neste grupo os acessos que se apresentavam em pequena quantidade por local de origem (um ou no máximo dois indivíduos), e 7- Acessos de origem desconhecida. Os acessos foram também avaliados como um todo. Para a corrida eletroforética, foram utilizadas amostras de folhas jovens em gel de amido a 12%. Foram avaliados oito sistemas isoenzimáticos: glutamato desidrogenase (GTDH), fosfatase ácida (ACP), leucina aminopeptidase (LAP), isocitrato desidrogenase (IDH), xiquimato desidrogenase (SKDH), enzima málica (ME), malato desidrogenase (MDH) e glucose-6-fosfato desidrogenase (G6PDH). A análise revelou um loco polimórfico por sistema. O material avaliado apresentou grande variabilidade isoenzimática. O número médio de alelos por loco variou de 2,3 a 2,5, a heterozigosidade média observada (;) variou de 0,381 a 0,615, e o índice de diversidade de 0,479 a 0,559. Observou-se maior variabilidade genética dentro dos grupos do que entre grupos, sugerindo um padrão de distribuição de variabilidade genética semelhante ao esperado para populações naturais de espécies alógamas.Cassava (Manihot esculenta Crantz) belongs to the Euphorbiaceae family, and is widely cultivated in Brazil. The objective of this study was to evaluate the isoenzymatic variability of 200 cassava accessions from the germplasm bank of Embrapa Amazonia Oriental. Seven groups were formed according to their origin: 1-Amazonas, 2-Amapa, 3-Bahia, 4-Para, 5-Rondonia, 6-Various, for accessions with a maximum of three individuals per place of origin, and 7 - Accessions of indefinite origin. The accessions were also evaluated as a whole. For the electrophoretic analyses, samples of young leaves were used in a 12% starch gel. Eight isoenzymatic systems were evaluated: acid phosphatase (ACP), leucine aminopeptidase (LAP), glucose-6-phosphate dehydrogenase (G6PDH), malate dehydrogenase (MDH), shikimate dehydrogenase (SKDH), malic enzyme (ME), glutamate dehydrogenase (GTDH) and isocitrate dehydrogenase (IDH). Analysis revealed a polymorphic locus for each system and high isoenzymatic variability among accessions. The average number of alleles per locus varied from 2.3 to 2.5. Average observed heterozigosity varied from 0.381 to 0.615 and the diversity index varied from 0.479 to 0.559. Genetic variability within groups was greater than among groups, suggesting a distribution pattern similar to what can be expected for natural populations of outcrossing plants

Genetic diversity in Brazilian sweet potato (Ipomoea batatas (L.) Lam., Solanales, Convolvulaceae) landraces assessed with microsatellite markers

We used simple sequence repeat (SSR) markers to investigate the genetic diversity of 78 sweet potato (Ipomoea batatas) accessions (58 landraces and 20 putative clones) from traditional agricultural households from 19 local communities in the Vale do Ribeira, São Paulo, Brazil. Eight SSR loci were assessed using 6% (w/v) polyacrylamide gels stained with silver nitrate and the accessions genotyped considering the presence or absence of bands. The results were subjected to analysis of molecular variance (AMOVA), and cluster and principal coordinate analyses. Spatial structure was assessed using Mantel's test to compare genetic and geographic distances. Each primer pair generated between three and ten clearly scorable polymorphic fragments. Cluster analyses showed a Jaccard's index from 0.3 to 1.0, indicating high genetic and intravarietal diversity. Accessions from all 19 communities were not spatially structured (r = 0.15, p < 0.054), with AMOVA indicating that most of the variability (58.2%) was distributed within households and only 18.1% of the variability was distributed between households within communities. The outcrossing mating system of sweet potato, and anthropic factors such as selection of different varieties and their maintenance within household small plots and home gardens, as well as an extensive exchange system between agriculturists, may all be contributing to these results313725733CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICO - CNPQFUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULO - FAPESPsem informaçã

Genetic diversity of American wild rice species

Studies on genetic diversity and genetic structure of natural populations are important in order to define strategies for in situ and ex situ conservation actions and for plant pre-breeding programs. Aiming to assess the genetic diversity and genetic structure of three wild American Oryza species with isozyme markers, 14 populations of the diploid O. glumaepatula (AglAgl), 11 populations of the tetraploid O. grandiglumis (CCDD) and five populations of the also tetraploid O. latifolia (CCDD) were studied. They were all originated from Rio Paraguay hydrographic basin and the Amazon. Four enzymes were used and they gave 40 polymorphic bands. The most polymorphic species was O. glumaepatula, followed by O. latifolia and O. grandiglumis. A cluster analysis with the Jaccard similarity coefficient separated the diploid from the two tetraploid species, and also the two tetraploid species. This separation was also evident on a scatter plot from a principal component analysis, suggesting that they should be treated as two separate species, although further studies are necessary to provide support for this affirmative. The AMOVA analyses showed a high intrapopulational variability for O. latifolia (67.6%) and O. grandiglumis (52.2%), when compared to their interpopulational variability (32.4% and 47.8%, respectively), which suggests the hypothesis of a higher degree of outcrossing events within these species. When studying the correlation between the Jaccard dissimilarity coefficient and geographic distances, a spatial genetic structure was observed for O. glumaepatula only. These results are important for defining strategies of both in situ and ex situ conservation.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq

Fenologia e diversidade morfológica de etnovariedades de batata-doce (Ipomoea batatas) do Vale do Ribeira

The phenotypic diversity of sweet potato (Ipomoea batatas) landraces was assessed using morphological traits, verifying how this diversity is distributed among the households and settlements of the Vale do Ribeira, Brazil. A total of 74 accessions, involving 53 landraces, collected from 30 households distributed among 18 settlements that practice traditional agriculture in the municipalities of Iguape, Ilha Comprida, and Cananeia, as well as four commercial varieties acquired in markets of Iguape and Piracicaba, were evaluated under an ex situ experimental condition in Piracicaba, SP, Brazil. Nine phenological and floral descriptors, nine morphological vegetative aerial descriptors and five storage root traits were recorded. The 14 aerial vegetative and root descriptors were evaluated as binary data, totaling 74 attributes. Cluster analyses were made using the Jaccard similarity index and the UPGMA (unweighted pair group method with arithmetic mean) agglomerative method. Binary data was also submitted to a variance analysis (AMOVA). No defined groups were observed, indicating that the diversity of the landraces is not structured in space, but considerable morphological variation was found in this area (Jaccard similarity index varying from 0.12 to 1.0). Most of the variability occurred within households (64.4%), followed by the distribution among households within settlements (27.1%) and among settlements (8.4%). Thus, the traditional agriculturists of Vale do Ribeira maintain a high morphological diversity for sweet potato within their households, which can be assumed to be produced by the outcrossing mating system of this species and somatic mutation events, as well as the exchange system at local and regional levels.Avaliou-se a diversidade fenotípica de etnovariedades de batata-doce através de descritores morfológicos, visando verificar como esta diversidade está distribuída em nível de roças e comunidades do Vale do Ribeira, SP, Brasil. Foram avaliados, no total, 74 acessos, envolvendo 53 etnovariedades, coletadas em 30 roças, distribuídas em 18 comunidades de agricultores que praticam agricultura tradicional nos municípios de Iguape, Ilha Comprida e Cananéia, somadas a quatro variedades comerciais adquiridas em varejões de Iguape e Piracicaba. A avaliação foi realizada em condições experimentais ex situ em Piracicaba, SP. Foram avaliados nove descritores fenológicos e florais, nove descritores morfológicos da parte aérea e cinco da raiz. Os 14 descritores de parte aérea e raiz foram transformados em dados binários, totalizando 74 atributos. Foi realizada uma análise de agrupamento, empregando-se o coeficiente de similaridade de Jaccard e o método aglomerativo UPGMA (unweighted pair group method with arithmetic mean). Os dados binários foram também submetidos a uma análise de variância (AMOVA). Não se detectou formação de grupos definidos, indicando que não há estruturação espacial da diversidade para as etnovariedades, mas observou-se grande variação morfológica (índice de Jaccard variando de 0,12 a 1,0) na região estudada. A maior parte da variabilidade encontra-se distribuída dentro de roças (64,4%), seguida pela distribuição entre roças dentro de comunidades (27,1%) e entre comunidades (8,4%). Portanto, os agricultores tradicionais no Vale do Ribeira cultivam em suas roças grande diversidade morfológica de batata-doce, cuja origem pode ter sido gerada pelo sistema reprodutivo da espécie por alogamia, por eventuais mutações somáticas e pelo amplo sistema de trocas entre agricultores em âmbito local e regional

Métodos CTAB de extração de DNA para a análise de microssatélites em batata-doce

Os marcadores microssatélites são úteis para a análise da diversidade genética de variedades tradicionais de batata-doce (Ipomoea batatas). Para estes estudos, métodos práticos de extração de DNA precisam ser estabelecidos para assegurar uma boa qualidade e quantidade de DNA extraído. Assim, foi comparada a eficiência de três metodologias para extração de DNA usando o tampão de extração CTAB, todas com modificações. Para verificar a quantidade e pureza na quantificação de DNA, bem como o padrão de bandas de microssatélites para as três metodologias utilizaram-se seis etnovariedades de batata-doce. Os testes mostraram que as três metodologias apresentaram resultados satisfatórios. Uma das metodologias baseada em tecido foliar macerado em nitrogênio líquido mostrou-se a mais adequada devido à simplicidade e menor custo. Entretanto, o método baseado em tecido foliar seco foi o mais vantajoso devido à praticidade na aquisição da planta e no processo de secagem, principalmente quando a coleção encontra-se em condições in situ, e pela possibilidade do armazenamento refrigerado das amostras secas e maceradas para futuras extrações de DNA.Microsatellite markers have proved to be useful in genetic diversity assessments of sweetpotato (Ipomoea batatas) but practical DNA extraction methods to ensure good quality and quantity DNA for these studies are yet to be established. This study compares the efficiency of three modified methodologies for DNA extraction of six sweetpotato landraces using the CTAB extraction buffer in regard to quantity and purity of DNA quantification and microsatellite band patterns. All methodologies yielded satisfactory results, but the method based in leaf tissue macerated in liquid nitrogen was deemed more adequate because of its simplicity and lower cost. However, the method based in dry leaf tissue was considered more advantageous, first because elicits practicability in the plant acquisition and drying process, especially when the collection is performed in situ, and also because its simplicity makes possible the cold storage of the dry, ground samples for future DNA extractions