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

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

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

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

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

Explorando os efeitos da sincronização do segundo estro e flushing alimentar sobre a incidência de cistos ovarianos em marrãs utilizando gonadotrofinas exógenas

Estrus stimulation by exogenous gonadotropins (EG) in association with dietary flushing is an important tool for the improvement of gilt reproductive performance. However, there is evidence associating both flushing and EG with a disturbance in the endocrine balance that could lead to increased ovarian cysts. The aim of this study was to evaluate whether flushing or EG might affect the ovulation rate and the incidence of ovarian cysts. Seventy-one gilts were randomly distributed into 2x2 factorial design with four treatments: flushing and hormone (wFwH); no flushing and hormone (nFwH); flushing without hormone (wFnH); and neither flushing nor hormone (nFnH). Gilts were slaughtered for macroscopic and histopathological ovary examination approximately five days after AI. The characterization of these cysts was performed by optical microscopy in the following: follicular cysts (FC), luteinized cysts (LC) or cystic corpora lutea (CCL). The number of ovulations did not differ between treatments. There was no interaction between the factors in any analyzed variable. The frequency of gilts with CCL and LC was not affected by flushing and EG. No difference was found in the incidence of FC, with 12.5% and 5.88% in gilts from wFwH and nFwH treatments, respectively. There were no differences in the proportion of CCL between FC and LC (9.85 vs. 4.22 and 4.22%, respectively). In conclusion, the use of exogenous gonadotropins for second estrus synchronization in gilts, either alone or in association with dietary flushing, does not increase the incidence of ovarian cysts, nor does it decrease the ovulation rate.A estimulação do estro por gonadotrofinas exógenas (GE) associada ao flushing alimentar é uma ferramenta importante na melhoria do desempenho reprodutivo de marrãs. Contudo, há evidência da associação do flushing com GE levando ao desequilíbrio no sistema endócrino que poderia levar ao aumento de cistos ovarianos. O objetivo deste estudo foi avaliar se o flushing ou GE pode afetar a taxa de ovulação e a incidência de cistos ovarianos. Setenta e uma marrãs foram distribuídas aleatoriamente em arranjo fatorial 2x2 com quatro tratamentos: flushing e hormônio (cFcH); sem flushing e com hormônio (sFcH); com flushing e sem hormônio (cFsH) e sem flushing e hormônio (sFsH). Marrãs foram abatidas para exame macroscópico e histopatológico dos ovários, aproximadamente cinco dias após IA. A caracterização desses cistos foi realizada por microscopia óptica: cistos foliculares (CF), cistos luteinizados (CL) ou corpos lúteos císticos (CCL). O número de ovulações não diferiu entre os tratamentos. Não houve interação entre os fatores em qualquer variável analisada. A frequência de leitoas com CCL e CL não foi afetada pelo flushing e GE. Não houve diferença na incidência de CF, com 12,5% e 5,88 % em leitoas dos tratamentos cFcH e sFcH, respectivamente. Não foram obtidas diferenças na proporção de CCL entre CF e CL (9,85 vs. 4,22 e 4,22%, respectivamente). Em conclusão, a utilização de gonadotrofinas exógenas para sincronização do segundo estro de marrãs, isoladamente ou em associação com o flushing, não aumenta a incidência de cistos ovarianos e não diminui a taxa de ovulação

Polygenic risk score for attention-deficit/hyperactivity disorder and brain functional networks segregation in a community-based sample

Neuroimaging studies suggest that brain development mechanisms might explain at least some behavioural and cognitive attention-deficit/hyperactivity disorder (ADHD) symptoms. However, the putative mechanisms by which genetic susceptibility factors influence clinical features via alterations of brain development remain largely unknown. Here, we set out to integrate genomics and connectomics tools by investigating the associations between an ADHD polygenic risk score (ADHD-PRS) and functional segregation of large-scale brain networks. With this aim, ADHD symptoms score, genetic and rs-fMRI (resting-state functional magnetic resonance image) data obtained in a longitudinal community-based cohort of 227 children and adolescents were analysed. A follow-up was conducted approximately 3 years after the baseline, with rs-fMRI scanning and ADHD likelihood assessment in both stages. We hypothesised a negative correlation between probable ADHD and the segregation of networks involved in executive functions, and a positive correlation with the default-mode network (DMN). Our findings suggest that ADHD-PRS is correlated with ADHD at baseline, but not at follow-up. Despite not surviving for multiple comparison correction, we found significant correlations between ADHD-PRS and segregation of cingulo-opercular networks and DMN at baseline. ADHD-PRS was negatively correlated with the segregation level of cingulo-opercular networks but positively correlated with the DMN segregation. These directions of associations corroborate the proposed counter-balanced role of attentional networks and DMN in attentional processes. However, the association between ADHD-PRS and brain networks functional segregation was not found at follow-up. Our results provide evidence for specific influences of genetic factors on development of attentional networks and DMN. We found significant correlations between polygenic risk score for ADHD (ADHD-PRS) and segregation of cingulo-opercular networks and default-mode network (DMN) at baseline. ADHD-PRS was negatively correlated with the segregation level of cingulo-opercular networks but positively correlated with the DMN segregation