New Genes in Traditional Seed Systems: Diffusion, Detectability and Persistence of Transgenes in a Maize Metapopulation

Gene flow of transgenes into non-target populations is an important biosafety concern. The case of genetically modified (GM) maize in Mexico has been of particular interest because of the country’s status as center of origin and landrace diversity. In contrast to maize in the U.S. and Europe, Mexican landraces form part of an evolving metapopulation in which new genes are subject to evolutionary processes of drift, gene flow and selection. Although these processes are affected by seed management and particularly seed flow, there has been little study into the population genetics of transgenes under traditional seed management. Here, we combine recently compiled data on seed management practices with a spatially explicit population genetic model to evaluate the importance of seed flow as a determinant of the long-term fate of transgenes in traditional seed systems. Seed flow between farmers leads to a much wider diffusion of transgenes than expected by pollen movement alone, but a predominance of seed replacement over seed mixing lowers the probability of detection due to a relative lack of homogenization in spatial frequencies. We find that in spite of the spatial complexities of the modeled system, persistence probabilities under positive selection are estimated quite well by existing theory. Our results have important implications concerning the feasibility of long term transgene monitoring and control in traditional seed systems

New Genes in Traditional Seed Systems: Diffusion, Detectability and Persistence of Transgenes in a Maize Metapopulation

Gene flow of transgenes into non-target populations is an important biosafety concern. The case of genetically modified (GM) maize in Mexico has been of particular interest because of the country’s status as center of origin and landrace diversity. In contrast to maize in the U.S. and Europe, Mexican landraces form part of an evolving metapopulation in which new genes are subject to evolutionary processes of drift, gene flow and selection. Although these processes are affected by seed management and particularly seed flow, there has been little study into the population genetics of transgenes under traditional seed management. Here, we combine recently compiled data on seed management practices with a spatially explicit population genetic model to evaluate the importance of seed flow as a determinant of the long-term fate of transgenes in traditional seed systems. Seed flow between farmers leads to a much wider diffusion of transgenes than expected by pollen movement alone, but a predominance of seed replacement over seed mixing lowers the probability of detection due to a relative lack of homogenization in spatial frequencies. We find that in spite of the spatial complexities of the modeled system, persistence probabilities under positive selection are estimated quite well by existing theory. Our results have important implications concerning the feasibility of long term transgene monitoring and control in traditional seed systems

Tetramer formation in Arabidopsis MADS domain proteins: analysis of a protein-protein interaction network

Background: MADS domain proteins are transcription factors that coordinate several important developmental processes in plants. These proteins interact with other MADS domain proteins to form dimers, and it has been proposed that they are able to associate as tetrameric complexes that regulate transcription of target genes. Whether the formation of functional tetramers is a widespread property of plant MADS domain proteins, or it is specific to few of these transcriptional regulators remains unclear. Results: We analyzed the structure of the network of physical interactions among MADS domain proteins in Arabidopsis thaliana. We determined the abundance of subgraphs that represent the connection pattern expected for a MADS domain protein heterotetramer. These subgraphs were significantly more abundant in the MADS domain protein interaction network than in randomized analogous networks. Importantly, these subgraphs are not significantly frequent in a protein interaction network of TCP plant transcription factors, when compared to expectation by chance. In addition, we found that MADS domain proteins in tetramer-like subgraphs are more likely to be expressed jointly than proteins in other subgraphs. This effect is mainly due to proteins in the monophyletic MIKC clade, as there is no association between tetramer-like subgraphs and co-expression for proteins outside this clade. Conclusions: Our results support that the tendency to form functional tetramers is widespread in the MADS domain protein-protein interaction network. Our observations also suggest that this trend is prevalent, or perhaps exclusive, for proteins in the MIKC clade. Because it is possible to retrodict several experimental results from our analyses, our work can be an important aid to make new predictions and facilitates experimental research on plant MADS domain proteins

Close relationship between diameters at 30cm height and at breast height (DBH) Relações entre diametros a 30 cm de altura e à altura do peito (DAP)

This paper proposes the establishment of a second diameter measuring standard at 30cm shoot extension ('diam30') as input variable for allometric biomass estimation of small and mid-sized plant shoots. This diameter standard is better suited than the diameter at breast height (DBH, i.e. diameter at 1.30m shoot extension) for adequate characterization of plant dimensions in low bushy vegetation or in primary forest undergrowth. The relationships between both diameter standards are established based on a dataset of 8645 tree, liana and palm shoots in secondary and primary forests of central Amazonia (ranging from 1-150mm dbh). Dbh can be predicted from the diam(30) with high precision, the error introduced by diameter transformation is only 2-3% for trees and palms, and 5% for lianas. This is well acceptable for most field study purposes. Relationships deviate slightly from linearity and differ between growth forms. Relationships were markedly similar for different vegetation types (low secondary regrowth vs. primary forests), soils, and selected genera or species. This points to a general validity and applicability of diameter transformations for other field studies. This study provides researchers with a tool for the allometric estimation of biomass in low or structurally heterogeneous vegetation. Rather than applying a uniform diameter standard, the measuring position which best represents the respective plant can be decided on shoot-by-shoot. Plant diameters measured at 30cm height can be transformed to dbh for subsequent allometric biomass estimation. We recommend the use of these diameter transformations only for plants extending well beyond the theoretical minimum shoot length (i.e., >2m height). This study also prepares the ground for the comparability and compatability of future allometric equations specifically developed for small- to mid-sized vegetation components (i.e., bushes, undergrowth) which are based on the diam(30) measuring standard.<br>Este estudo propõe o estabelecimento de um segundo padrão de medição de diâmetro a 30 cm de extensão do tronco ('diam30') para a estimativa alométrica da biomassa de plantas de pequeno até médio porte. Considera-se este padrão de diâmetro mais adequado do que o diâmetro à altura do peito ('DAP', a 1,30m de extensão do tronco) para a caracterização das dimensões de plantas em vegetação baixa ou no sub-bosque da mata primária. O presente trabalho investiga as relações entre os dois padrões de diâmetro, baseado em 8645 troncos de árvores, cipós e palmeiras arbóreas (com diâmetros entre 1 e 150mm DAP) em capoeiras e mata primária da Amazônia Central. Conclui-se que se pode estimar o DAP do diam30 com alta precisão, o erro causado pela transformação dos diâmetros é somente 2-3% para árvores e palmeiras e 5% para os cipós, níveis bem aceitáveis para a maioria dos estudos de campo. As relações entre os diâmetros desviaram levemente da linearidade e são diferentes para os três hábitos de crescimento. No entanto, as equações são bastante similares entre os diferentes tipos de vegetação (capoeira baixa vs. mata primária), solos e gêneros ou espécies, indicando sua aplicabilidade e validade geral para outros estudos de campo. Esse trabalho fornece ao pesquisador de campo uma ferramenta para a estimativa alométrica da biomassa de vegetação baixa ou estruturalmente heterogênea. Em vez de utilizar um único padrão uniforme de diâmetro pode-se escolher livremente e individualmente qual posição de diâmetro melhor representa cada tronco. Os diâmetros a 30 cm de extensão do tronco podem ser transformados para o dap para uma subseqüente estimação alométrica da sua biomassa. Recomenda-se o uso destas transformações de diâmetros somente acima de uma extensão mínima do tronco (>2m de altura). Os resultados do presente trabalho também preparam a base para a comparabilidade e compatibilidade de futuras equações alométricas baseadas no diam(30) para uma melhor estimação da biomassa dos componentes de vegetação baixa e média (arbustos, sub-bosque da mata primária)