Development of a dense SNP-based linkage map of an apple rootstock progeny using the Malus Infinium whole genome genotyping array

Background A whole-genome genotyping array has previously been developed for Malus using SNP data from 28 Malus genotypes. This array offers the prospect of high throughput genotyping and linkage map development for any given Malus progeny. To test the applicability of the array for mapping in diverse Malus genotypes, we applied the array to the construction of a SNPbased linkage map of an apple rootstock progeny. Results Of the 7,867 Malus SNP markers on the array, 1,823 (23.2 %) were heterozygous in one of the two parents of the progeny, 1,007 (12.8 %) were heterozygous in both parental genotypes, whilst just 2.8 % of the 921 Pyrus SNPs were heterozygous. A linkage map spanning 1,282.2 cM was produced comprising 2,272 SNP markers, 306 SSR markers and the S-locus. The length of the M432 linkage map was increased by 52.7 cM with the addition of the SNP markers, whilst marker density increased from 3.8 cM/marker to 0.5 cM/marker. Just three regions in excess of 10 cM remain where no markers were mapped. We compared the positions of the mapped SNP markers on the M432 map with their predicted positions on the ‘Golden Delicious’ genome sequence. A total of 311 markers (13.7 % of all mapped markers) mapped to positions that conflicted with their predicted positions on the ‘Golden Delicious’ pseudo-chromosomes, indicating the presence of paralogous genomic regions or misassignments of genome sequence contigs during the assembly and anchoring of the genome sequence. Conclusions We incorporated data for the 2,272 SNP markers onto the map of the M432 progeny and have presented the most complete and saturated map of the full 17 linkage groups of M. pumila to date. The data were generated rapidly in a high-throughput semi-automated pipeline, permitting significant savings in time and cost over linkage map construction using microsatellites. The application of the array will permit linkage maps to be developed for QTL analyses in a cost-effective manner, and the identification of SNPs that have been assigned erroneous positions on the ‘Golden Delicious’ reference sequence will assist in the continued improvement of the genome sequence assembly for that variety.

A maize bacterial artificial chromosome (BAC) library from the European flint inbred line F2

We report here the construction and characterisation of a BAC library from the maize flint inbred line F2, widely used in European maize breeding programs. The library contains 86,858 clones with an average insert size of approximately 90 kb, giving approximately 3.2-times genome coverage. High-efficiency BAC cloning was achieved through the use of a single size selection for the high-molecular-weight genomic DNA, and co-transformation of the ligation with yeast tRNA to optimise transformation efficiency. Characterisation of the library showed that less than 0.5% of the clones contained no inserts, while 5.52% of clones consisted of chloroplast DNA. The library was gridded onto 29 nylon filters in a double-spotted 8 × 8 array, and screened by hybridisation with a number of single-copy and gene-family probes. A 3-dimensional DNA pooling scheme was used to allow rapid PCR screening of the library based on primer pairs from simple sequence repeat (SSR) and expressed sequence tag (EST) markers. Positive clones were obtained in all hybridisation and PCR screens carried out so far. Six BAC clones, which hybridised to a portion of the cloned Rp1-D rust resistance gene, were further characterised and found to form contigs covering most of this complex resistance locus.

Non-concordance between genetic profiles of olive oil and fruit: a cautionary note to the use of DNA markers for provenance testing.

To investigate the contribution of paternal alleles to the DNA content of olive oil, genetic analyses of olive DNA samples from fruits, leaves, and oil derived from the same tree (cv. Leccino) were carried out. DNA extracted from maternal tissues--leaves and flesh--from different fruits showed identical genetic profiles using a set of DNA markers. Additional simple sequence repeat (SSR) alleles, not found in the maternal samples, were amplified in the embryos (stone), and they were also detected in DNA extracted from the paste obtained by crushing whole fruits and from the oil pressed from this material. These results demonstrate that the DNA profile obtained from olive oil is likely to represent a composite profile of the maternal alleles juxtaposed with alleles contributed by various pollen donors. Therefore, care needs to be taken in the interpretation of DNA profiles obtained from DNA extracted from oil for resolving provenance and authenticity issues.

Polynomial-based noise variance estimation for MIMO-SCBT systems

In this paper, we present a polynomial-based noise variance estimator for multiple-input multiple-output single-carrier block transmission (MIMO-SCBT) systems. It is shown that the optimal pilots for noise variance estimation satisfy the same condition as that for channel estimation. Theoretical analysis indicates that the proposed estimator is statistically more efficient than the conventional sum of squared residuals (SSR) based estimator. Furthermore, we obtain an efficient implementation of the estimator by exploiting its special structure. Numerical results confirm our theoretical analysis.

Modelled and observed changes in aerosols and surface solar radiation over Europe between 1960 and 2009

Substantial changes in anthropogenic aerosols and precursor gas emissions have occurred over recent decades due to the implementation of air pollution control legislation and economic growth. The response of atmospheric aerosols to these changes and the impact on climate are poorly constrained, particularly in studies using detailed aerosol chemistry–climate models. Here we compare the HadGEM3-UKCA (Hadley Centre Global Environment Model-United Kingdom Chemistry and Aerosols) coupled chemistry–climate model for the period 1960–2009 against extensive ground-based observations of sulfate aerosol mass (1978–2009), total suspended particle matter (SPM, 1978–1998), PM10 (1997–2009), aerosol optical depth (AOD, 2000–2009), aerosol size distributions (2008–2009) and surface solar radiation (SSR, 1960–2009) over Europe. The model underestimates observed sulfate aerosol mass (normalised mean bias factor (NMBF) = −0.4), SPM (NMBF = −0.9), PM10 (NMBF = −0.2), aerosol number concentrations (N30 NMBF = −0.85; N50 NMBF = −0.65; and N100 NMBF = −0.96) and AOD (NMBF = −0.01) but slightly overpredicts SSR (NMBF = 0.02). Trends in aerosol over the observational period are well simulated by the model, with observed (simulated) changes in sulfate of −68 % (−78 %), SPM of −42 % (−20 %), PM10 of −9 % (−8 %) and AOD of −11 % (−14 %). Discrepancies in the magnitude of simulated aerosol mass do not affect the ability of the model to reproduce the observed SSR trends. The positive change in observed European SSR (5 %) during 1990–2009 ("brightening") is better reproduced by the model when aerosol radiative effects (ARE) are included (3 %), compared to simulations where ARE are excluded (0.2 %). The simulated top-of-the-atmosphere aerosol radiative forcing over Europe under all-sky conditions increased by > 3.0 W m−2 during the period 1970–2009 in response to changes in anthropogenic emissions and aerosol concentrations.

Differentiation in populations of the apple scab fungus Venturia inaequalis on cultivars in a mixed orchard remains over time

The ascomycete Venturia inaequalis causes annual epidemics of apple scab worldwide. Scab development is reduced in mixed cultivar orchards compared with monocultures. To use mixtures in commercial production, we need to understand how the population of scab changes in a mixed orchard and how likely a super race, with virulence factors overcoming multiple resistance factors in the mixed orchard, is to emerge and become dominant. We used short sequence repeat (SSR) markers to investigate the temporal change of scab populations in two mixed cultivar orchards in the UK to infer the likelihood of emergence of a scab super race. There were no significant differences between the populations at the two sampling times (six or seven years apart) in either of the two mixed orchards. In one of the orchards apple scab populations on different cultivars were significantly different and the differences did not diminish over time. These results suggest that it is not inevitable that a super race of V. inaequalis will become dominant during the lifetime of a commercial apple orchard.

Analysis of the genetic diversity and structure across a wide range of germplasm reveals prominent gene flow in apple at the European level

Abstract Background: The amount and structure of genetic diversity in dessert apple germplasm conserved at a European level is mostly unknown, since all diversity studies conducted in Europe until now have been performed on regional or national collections. Here, we applied a common set of 16 SSR markers to genotype more than 2,400 accessions across 14 collections representing three broad European geographic regions (North+East, West and South) with the aim to analyze the extent, distribution and structure of variation in the apple genetic resources in Europe. Results: A Bayesian model-based clustering approach showed that diversity was organized in three groups, although these were only moderately differentiated (FST=0.031). A nested Bayesian clustering approach allowed identification of subgroups which revealed internal patterns of substructure within the groups, allowing a finer delineation of the variation into eight subgroups (FST=0.044). The first level of stratification revealed an asymmetric division of the germplasm among the three groups, and a clear association was found with the geographical regions of origin of the cultivars. The substructure revealed clear partitioning of genetic groups among countries, but also interesting associations between subgroups and breeding purposes of recent cultivars or particular usage such as cider production. Additional parentage analyses allowed us to identify both putative parents of more than 40 old and/or local cultivars giving interesting insights in the pedigree of some emblematic cultivars. Conclusions: The variation found at group and sub-group levels may reflect a combination of historical processes of migration/selection and adaptive factors to diverse agricultural environments that, together with genetic drift, have resulted in extensive genetic variation but limited population structure. The European dessert apple germplasm represents an important source of genetic diversity with a strong historical and patrimonial value. The present work thus constitutes a decisive step in the field of conservation genetics. Moreover, the obtained data can be used for defining a European apple core collection useful for further identification of genomic regions associated with commercially important horticultural traits in apple through genome-wide association studies.

Hot och våld i socialarbetares yrkesutövning : Threats and violence in the socialwelfare secretary occupation.

2004, the SSR, Akademikerförbundet, made a study on the threats and violence as a social secretary in the municipal social services are exposed in their occupation of the "social secretary of threats and violence at work" (T-110192), conducted by Temo ab. We have chosen to use the study on a smaller scale and then made contact with five municipalities in the middle of Sweden to investigate social secretaries experiences of threats and violence. Using the cross-sectional design and a convenience sample, we have gained access to data from 56 people. From a sociological perspective, we have chosen to use Norbert Elias theory of universal configuration and interdependence, and Michel Foucault’s theories concerning power search explanation for the existence of threats and violent situations in the contact between social workers and their clients.

Changes in sedentary behavior among adolescent girls: a 2.5-Year prospective cohort study

Purpose: To describe longitudinal changes in leisure-time sedentary behavior among girls, during early to mid-adolescence. Methods: A 2.5-year prospective cohort study, comprising 5 data collections, 6 months apart, between 2000 and 2002. Girls aged 12–15 years (n = 200) from 8 high schools located in Sydney, Australia, self-reported the usual time spent each week in a comprehensive range of sedentary behaviors.  Results: Retention rate for the study was 82%. Girls aged 12.8 years spent approximately 45% of their discretionary time in sedentary behavior, which increased to 63% at age 14.9 years. Watching TV, videos, and playing video games (small screen recreation; SSR) was the most popular sedentary pastime, accounting for 33% of time spent in sedentariness, followed by homework and reading (25%). Sedentary behavior increased 1.4 and 3.3 hours on week and weekend days, respectively. On weekdays, increased time was spent on hobbies (27 min/day) and on weekend days, increased time was spent sitting around talking with friends (60 min/day), computer use (37 min/day), and television viewing (34 min/day). Conclusions: Among girls, the transition between early and mid-adolescence was accompanied by a significant increase in leisure-time sedentary behavior. Interventions to reduce sedentariness among adolescent girls are best to focus on weekend behaviors. Studies seeking to examine the association between inactivity and the development of chronic health problems need to examine a diverse range of activities that comprehensively measure sedentariness. This information will provide a better understanding of inactivity patterns among adolescent girls.

Comparing the small sample properties of two break Lagrange Multiplier unit root tests

In this note, we examine the size and power properties and the break date estimation accuracy of the Lee and Strazicich (LS, 2003) two break endogenous unit root test, based on two different break date selection methods: minimising the test statistic and minimising the sum of squared residuals (SSR). Our results show that the performance of both Models A and C of the LS test are superior when one uses the minimising SSR procedure.

Semi-supervised classification based on subspace sparse representation

Graph plays an important role in graph-based semi-supervised classification. However, due to noisy and redundant features in high-dimensional data, it is not a trivial job to construct a well-structured graph on high-dimensional samples. In this paper, we take advantage of sparse representation in random subspaces for graph construction and propose a method called Semi-Supervised Classification based on Subspace Sparse Representation, SSC-SSR in short. SSC-SSR first generates several random subspaces from the original space and then seeks sparse representation coefficients in these subspaces. Next, it trains semi-supervised linear classifiers on graphs that are constructed by these coefficients. Finally, it combines these classifiers into an ensemble classifier by minimizing a linear regression problem. Unlike traditional graph-based semi-supervised classification methods, the graphs of SSC-SSR are data-driven instead of man-made in advance. Empirical study on face images classification tasks demonstrates that SSC-SSR not only has superior recognition performance with respect to competitive methods, but also has wide ranges of effective input parameters.

Mapeamento de QTLs para tolerância ao frio e características de importância agronômica em arroz

A temperatura baixa é um estresse comum na cultura do arroz em regiões temperadas, portanto a tolerância ao frio é uma característica altamente desejável em genótipos brasileiros de arroz cultivados no sul do país, onde as temperaturas baixas prejudicam o estabelecimento da lavoura e diminuem o redimento de grãos. O mapeamento molecular é uma estratégia promissora para o estudo e compreensão de de características com controle complexo, tais como a tolerância ao frio em arroz. Com base nisso, os objetivos deste trabalho foram estudar a herança e herdabilidade das características de tolerância ao frio e das características de importância agronômica a serem maepadas, desenvolver um mapa molecular a partir da população segregante F2 proveniente do cruzamento IRGA 417 (Índica) x Quilla 66304 (Japônica) e identificar locos de características quantitativas (QTLs) para a tolerância ao frio no período de germinação e vegetativo e características agronômicas que diferenciam estas duas subespécies. Por fim, investigar a possibilidade de obter indivíduos recombinantes com caracteristicas agronômicas desejáveis e toleância ao frio em uma população F2 do cruzamento entre IRGA 417 x Quilla 66304. As análises das distrbuições de freqüências da geração F2 evidenciaram a dificuldade de estimar o número de genes que controlam as características analisadas, sendo que todas elas apresentam distribuição contínua e segregação transgressiva em relação aos genitores. O mapa foi construído com base em oito marcadores SSR e 42 marcadores do tipo AFLP com uma densidade média de marcador a cada 38,8 cM, sendo o comprimento total do mapa de 581,6 cM. Foram identificados cinco QTLs, sendo que um deles confere tolerância ao frio no período de germinação, e explica 15,9% da variação fenotípica deste caráteer. O outros quatro QTLs identificados foram para largura do grgão (21,3%), esterilidade de espiguetas (61,6%), estatura das plantas (34, 5%) e comprimento do grão (21,9%). A detecção de um QTL associado à tolerância ao frio no período de germinação, e outros QTLs associados à demais características a viabilidade deste tipo de análise. Entretanto, um mapa de ligação enriquecido é nceessário para permitir a detecção de outros QTLs associados às características estudadas. Plantas recombinantes com alto recrescimento de coleóptilo e outrras caracteristicas agronômicas desejáveis foram encontradas, o que evidencia o potencial da população proveniente de IRGA 417 x Quilla 66304 para o melhoramento da tolerância ao frio de genótipos de arroz adaptados ao Sul do Brasil.

Caracterização morfológica, citogenética e molecular de uma população de tangerineiras híbridas de 'Clementina fina' (Citrus clementina Hort. ex Tan.) e 'Montenegrina' (Citrus deliciosa Ten.)

A produção citrícola se encontra dispersa por todos os continentes e no Brasil, os citros são a produção frutícola de maior volume de produção. A produção de citros de mesa, como as tangerinas, possibilita ao produtor obter maior valor pelo seu produto. O mercado consumidor é ávido por novas variedades e para tanto, um programa de melhoramento deve estar sempre em busca de genótipos que atendam ao mercado consumidor, bem como a cadeia produtiva. Na Estação Experimental Agronômica da Universidade Federal do Rio Grande do Sul, está localizada uma população de tangerineiras híbridas oriundas do cruzamento da tangerineira ‘Clementina Fina’ (Citrus clementina Hort. ex Tan.) e ‘Montenegrina’ (Citrus deliciosa Ten.) a qual foi caracterizada neste estudo, avaliando-se características morfológicas de acordo com os descritores propostos pelo International Board for Plant Genetic Resources, além da identificação da época de maturação, viabilidade de pólen, número cromossômico e caracterização molecular, utilizando marcadores do tipo microssatélites. Através da análise morfológica foi possível distinguir todas as 96 plantas avaliadas, porém não foi possível agrupar a F1 em grupos distintos de cada um dos genitores. A época de maturação de frutos das plantas se concentra entre a primeira quinzena de abril até a primeira quinzena de agosto. Todas as plantas analisadas apresentaram um alto grau de viabilidade de pólen, variando entre 79,04 e 98,08 %. Todas as plantas avaliadas são diplóides com um número cromossômico de 2n=18. Utilizando 12 pares de primers de microssatélites foi possível diferenciar 90 acessos do estudo, e agrupar a F1 em indivíduos mais próximos do genitor feminino e do genitor masculino. O PIC (Conteúdo de Informação de Polimorfismo) dos primers variou de 0,27 a 0,65. Não foi possível estabelecer uma relação entre a caracterização utilizando marcadores morfológicos e a caracterização utilizando marcadores moleculares.

Herança da tolerância à toxidade ao alumínio (Al³+) em milho e identificação de regiões cromossomicas associadas ao caráter

A toxicidade por alumínio é uma das principais limitações para produção de plantas em áreas cultiváveis, incluindo a cultura do milho. Existe elevada variabilidade genética para o caráter tolerância ao alumínio nesta espécie, porém, a seleção é trabalhosa devido à dificuldade de avaliação a campo. Os objetivos do presente trabalho foram caracterizar a tolerância à toxicidade ao alumínio em cinco linhagens de milho e identificar marcadores moleculares ligados aos genes que determinam essa tolerância. Foi realizado um experimento dialélico entre três linhagens tolerantes e duas sensíveis ao alumínio utilizando o método de recrescimento da raiz principal (DIF). Houve superioridade das populações híbridas em relação aos genitores e, pelo desdobramento dos efeitos de heterose, houve significância nos efeitos de heterose de variedade e heterose específica. As linhagens L06 e L09 obtiveram maior capacidade geral de combinação e o cruzamento L10xL08 foi a melhor combinação específica. Para fenotipagem, realizada em famílias F3 dos cruzamentos L09xL06 e L10xL08 foi utilizado DIF e o método coloração com hematoxilina (HEM). Para análise molecular foram utilizados marcadores SSR. Foram obtidos 37 marcadores polimórficos. A análise de regressão mostrou significância em marcadores localizados nos cromossomos 4, 5, 6, 8 e 10. Os QTLs identificados explicaram 41% e 37% da variação para as variáveis DIF e HEM, respectivamente. Foi encontrada associação entre os experimentos a campo e trabalhos realizados em solução mínima para os híbridos testemunha, entretanto não houve correlação nos dados gerados pelas famílias F3 dos cruzamentos estudados. Os resultados sugerem o envolvimento de diversos genes, tratando-se de uma característica de herança complexa determinada por efeitos genéticos aditivos e nãoaditivos.

Relação hepatosomática e esplenosomática em peixes teleósteos de cultivo intensivo

The mean values of hepatosomatic relation (HSR), splenosomatic relation (SSR) and relative condition factor (Kn) in Nile tilapia (Oreochromis nilolicus Trewavas, 1983); pacu (Piaractus mesopolamicus Holmberg, 1887); piauçu (Lepori-nus macrocephalus Garavello & Britski, 1988) and tambacu hybrid (P. mesopotamicus male x Colossoma macropomum Cuvier, 1818 female) are described. The experiment was carried out from feefishing farm situated in Franca, São Paulo State, Brazil. Nile tilapia showed the greatest HSR compared to pacu, piauçu and tambacu. Although, in the last three fishes the relation was similar. The SSR between tilapia and piausu was similar, but smaller than observed in pacu and tambacu. Nevertheless, SSR in pacu and tambacu was different. The hepatic weight/body weigth relation and hepatic weight/body length relation presented positive correlation in ali studied fishes. The splenic weight/body weigth relation and splenic weight/body length relation were not significam (P>0.05) in Nile tilapia, pacu and tambacu, but highly significant in piauçu (PO.01).