QTL mapping of soybean cyst nematode race 9: a generalized linear modeling approach

The Female Index (FI) is a relative measure of host suitability of a soybean line for a particular nematode population and often shows a non-normal distribution. Moreover, most quantitative trait loci (QTL) mapping methods assume that the phenotype follows a normal distribution such as composite interval mapping (CIM). Therefore, a generalized linear modeling (GLM) approach was employed to map QTL for resistance to race 9 of the soybean cyst nematode (SCN) using a total of 83 simple sequence repeat markers (SSR). Two GLM models were tested: model 1, where the FI was treated as a continuous variable, assuming a Gamma distribution with a logarithmic link function; and model 2, where the FI was treated as a categorical trait in a five-item hierarchy, assuming a multinomial distribution with a cumulative logit link function. The FI data of 108 recombinant inbred lines (RIL) confirmed the non-normal distribution for race 9 of the SCN (Shapiro-Wilk?s w=0.86, P<0.0001, skewness=1.52 and kurtosis=2.93). Eight RIL were confirmed to be resistant (FI≤10), and 23 to be highly susceptible (FI≥100). Both GLM models identified one QTL for SCN on the molecular linkage group G, between the markers Satt275 and Satt038 at 48.4 centiMorgans (P=0.017 and 0.033, for models 1 and 2, respectively). Additionally, these results were also compared with the CIM and Bayesian interval mapping (BIM) methods, assuming experimental data with a non-normal response, to determine the robustness and statistical power of these two methods for mapping QTLs. The results make clear that generalized linear modeling approach can be used as an efficient method to map QTLs in a continuous trait with a non-Gaussian distribution. CIM and BIM were robust enough for a reliable mapping of QTLs underlying nonnormally distributed data.Fil: Arriagada, Osvin. Universidad de Talca; ChileFil: Ferreira, Marcia F. S.. Universidade Federal Do Espirito Santo; BrasilFil: Cervigni, Gerardo Domingo Lucio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Rosario. Centro de Estudios Fotosintéticos y Bioquímicos (i); ArgentinaFil: Schuster, Ivan. Central Cooperative for Agricultural Research; BrasilFil: Scapim, Carlos A.. Universidade Estadual de Maringá; BrasilFil: Mora, Freddy. Universidad de Talca; Chil

A common QTL for resistance to races 3 and 9 of soybean cyst nematode

El objetivo de este trabajo fue estudiar la asociación entre el gen rhg1 y la resistencia a las razas 3 y 9 de Heterodera glycines (Nematode del Quiste de la Soja - NQS). El cultivar resistente Hartwig fue cruzado con la línea susceptible Y23 y la respuesta a las razas 3 y 9 fue evaluada en 135 y 128 Líneas Endogámicas Recombinantes (LER), respectivamente. Los ensayos de respuesta al NQS fueron realizados en invernáculo bajo un diseño completamente aleatorizado. Ocho marcadores SSR fueron ordenados en una región genómica de 57 cM. La heredabilidad de la resistencia a las razas 3 y 9 fue 80,97 y 80,39%, respectivamente, indicando que pocos genes mayores estaban segregando en la población. Aplicando Mapeo por Intervalo Compuesto (MIC), el gen de resistencia rhg1 fue mapeado entre los marcadores SSR Satt275 y Satt038, a 2,0 y 3,0 cM del marcador Satt038, explicando el 29,11 y 20,01% de la varianza fenotípica de la resistencia a la raza 3 y 9, respectivamente. Estos marcadores serían herramientas útiles para auxiliar en la selección de genotipos resistentes al NQS y acelerar la introgresión de loci de resistencia al NQS a cultivares élite de soja.The aim of this work was to study the association between the rhg1 gene and the soybean response to races 3 and 9 of Heterodera glycines (Soybean Cyst Nematode - SCN). The resistant cv. Hartwig was crossed with the susceptible line Y23 and the response to races 3 and 9 was evaluated in 135 and 128 Recombinant Inbred Lines (RIL), respectively. Nematode assays were performed in the greenhouse using a completely randomized design. Eight SSR markers covered a genomic region of 57 cM. Estimated heritabilities of resistance to race 3 and 9 were 80.97 and 80.39%, respectively, showing that a few major genes are segregating in the population. Applying the Composite Interval Mapping (CIM) method, the rhg1 resistance gene was mapped between the SSR markers Satt275 and Satt038 at 2.0 and 3.0 cM from marker Satt038, explaining 29.11 and 20.01% of phenotypic variance in resistance to races 3 and 9, respectively. These SSR markers would be useful tools for assisting in the selection of SCN-resistant genotypes and for expediting the introgression of SCN resistance loci from cv. Hartwig to soybean elite cultivars.Facultad de Ciencias Agrarias y Forestale

QTLs for resistance to soybean cyst nematode, races 3, 9, and 14 in cultivar Hartwig.

The objective of this work was to identify major and minor?effect quantitative trait loci (QTL) for resistance to races 3, 9, and 14 of soybean cyst nematode (SCN) in Hartwig cultivar; to map new resistance QTLs for these races; and to check for the existence of epistatic interactions between QTLs. Cultivar Hartwig is an important resistance source to SCN. Recombinant inbred lines (RIL) obtained from a cross between 'Hartwig' (resistant) and Y23 (susceptible) were evaluated regarding resistance to the three races. New genomic regions for resistance to SCN were identified by microsatellites. Four QTLs, which explained between 12 and 34% of phenotypic variance, were detected for resistance to race 3 in linkage groups (LG) A2, G, J, and M. The QTL in LG G is also important for resistance to race 9. Epistatic interactions were detected between loci, which indicate resistance to races 9 and 14. There are high and low? effect resistance QTLs to SCN. QTLs de resistência ao nematoide do cisto da soja, raças 3, 9 e 14 na cultivar Hartwig: O objetivo deste trabalho foi identificar locos associados a características quantitativas (QTL) de efeito maior e menor para a resistência às raças 3, 9 e 14 do nematoide do cisto da soja (NCS) na cultivar Hartwig, mapear novos QTLs de resistência para estas raças e verificar a existência de interações epistáticas entre QTLs. A cultivar Hartwig é uma importante fonte de resistência ao NCS. Linhagens endogâmicas recombinantes (LER) obtidas do cruzamento entre 'Hartwig' (resistente) e Y23 (suscetível) foram avaliadas quanto à resistência às três raças. Novas regiões genômicas de resistência ao NCS foram identificadas por microssatélites. Quatro QTLs, que explicaram entre 12 e 34% da variância fenotípica, foram detectados para a resistência à raça 3 nos grupos de ligação (GL) A2, G, J e M. O QTL no GL G também é importante para a resistência à raça 9. Interações epistáticas foram detectadas entre loci, o que indica resistência às raças 9 e 14. Há QTLs de maior e menor efeito para a resistência ao NCS

Inheritance of resistance to soybean cyst nematode races 3 and 14 in soybean RIL and F2 populations.

The objective of this work was to evaluate the soybean inheritance of resistance to cyst nematode races 3 and 14. The following populations where evaluated: one population of recombinant inbred lines (RILs) [Hartwig (resistant) x Y23 (susceptible line)] for races 3, 14 and 9; one population of families F2:3 [M-SOY 8001 (resistant) x MB/BR 46 -Conquista (susceptible)] for race 3; and one population of families F2:3 [(S5995 (resistant) x BRSMG Renascença (susceptible)] for race 14. In RIL populations, four epistatic genes were identified which conditioned resistance to race 14, and three epistatic ones for resistance to races 3 and 9. The lack of one gene provided moderate resistance under all situations. The highest number of genes for resistance to race 14 points out that genes responsible for lower effects might be involved. In population F2:3 from M-SOY 8001 x MB/BR 46 - Conquista, one recessive gene for moderate resistance and two recessive genes complete resistance to race 3 were identified. Two recessive genes conditioning moderate resistance to race 14 were identified in population F2:3 from the crossing S5995 x BRSMG Renascença. These results will be useful in designing crossings, involving these parentals, with higher possibility to accumulating genes that provide resistance to several SCN races

QTLs for resistance to soybean cyst nematode, races 3, 9, and 14 in cultivar Hartwig.

The objective of this work was to identify major and minor-effect quantitative trait loci (QTL) for resistance to races 3, 9, and 14 of soybean cyst nematode (SCN) in Hartwig cultivar; to map new resistance QTLs for these races; and to check for the existence of epistatic interactions between QTLs. Cultivar Hartwig is an important resistance source to SCN. Recombinant inbred lines (RIL) obtained from a cross between 'Hartwig' (resistant) and Y23 (susceptible) were evaluated regarding resistance to the three races. New genomic regions for resistance to SCN were identified by microsatellites. Four QTLs, which explained between 12 and 34% of phenotypic variance, were detected for resistance to race 3 in linkage groups (LG) A2, G, J, and M. The QTL in LG G is also important for resistance to race 9. Epistatic interactions were detected between loci, which indicate resistance to races 9 and 14. There are high and low-effect resistance QTLs to SCN.Título em português: QTLs de resistência ao nematoide do cisto da soja, raças 3, 9 e 14 na cultivar Hartwig

A common QTL for resistance to races 3 and 9 of soybean cyst nematode

El objetivo de este trabajo fue estudiar la asociación entre el gen rhg1 y la resistencia a las razas 3 y 9 de Heterodera glycines (Nematode del Quiste de la Soja - NQS). El cultivar resistente Hartwig fue cruzado con la línea susceptible Y23 y la respuesta a las razas 3 y 9 fue evaluada en 135 y 128 Líneas Endogámicas Recombinantes (LER), respectivamente. Los ensayos de respuesta al NQS fueron realizados en invernáculo bajo un diseño completamente aleatorizado. Ocho marcadores SSR fueron ordenados en una región genómica de 57 cM. La heredabilidad de la resistencia a las razas 3 y 9 fue 80,97 y 80,39%, respectivamente, indicando que pocos genes mayores estaban segregando en la población. Aplicando Mapeo por Intervalo Compuesto (MIC), el gen de resistencia rhg1 fue mapeado entre los marcadores SSR Satt275 y Satt038, a 2,0 y 3,0 cM del marcador Satt038, explicando el 29,11 y 20,01% de la varianza fenotípica de la resistencia a la raza 3 y 9, respectivamente. Estos marcadores serían herramientas útiles para auxiliar en la selección de genotipos resistentes al NQS y acelerar la introgresión de loci de resistencia al NQS a cultivares élite de soja.The aim of this work was to study the association between the rhg1 gene and the soybean response to races 3 and 9 of Heterodera glycines (Soybean Cyst Nematode - SCN). The resistant cv. Hartwig was crossed with the susceptible line Y23 and the response to races 3 and 9 was evaluated in 135 and 128 Recombinant Inbred Lines (RIL), respectively. Nematode assays were performed in the greenhouse using a completely randomized design. Eight SSR markers covered a genomic region of 57 cM. Estimated heritabilities of resistance to race 3 and 9 were 80.97 and 80.39%, respectively, showing that a few major genes are segregating in the population. Applying the Composite Interval Mapping (CIM) method, the rhg1 resistance gene was mapped between the SSR markers Satt275 and Satt038 at 2.0 and 3.0 cM from marker Satt038, explaining 29.11 and 20.01% of phenotypic variance in resistance to races 3 and 9, respectively. These SSR markers would be useful tools for assisting in the selection of SCN-resistant genotypes and for expediting the introgression of SCN resistance loci from cv. Hartwig to soybean elite cultivars.Facultad de Ciencias Agrarias y Forestale

Optimizing the two-step floating catchment area method for measuring spatial accessibility to medical clinics in Montreal

<p>Abstract</p> <p>Background</p> <p>Reducing spatial access disparities to healthcare services is a growing priority for healthcare planners especially among developed countries with aging populations. There is thus a pressing need to determine which populations do not enjoy access to healthcare, yet efforts to quantify such disparities in spatial accessibility have been hampered by a lack of satisfactory measurements and methods. This study compares an optimised and the conventional version of the two-step floating catchment area (2SFCA) method to assess spatial accessibility to medical clinics in Montreal.</p> <p>Methods</p> <p>We first computed catchments around existing medical clinics of Montreal Island based on the shortest network distance. Population nested in dissemination areas were used to determine potential users of a given medical clinic. To optimize the method, medical clinics (supply) were weighted by the number of physicians working in each clinic, while the previous year's medical clinic users were computed by ten years age group was used as weighting coefficient for potential users of each medical clinic (demand).</p> <p>Results</p> <p>The spatial accessibility score (SA) increased considerably with the optimisation method. Within a distance of 1 Km, for instance, the maximum clinic accessible for 1,000 persons is 2.4 when the conventional method is used, compared with 27.7 for the optimized method. The t-test indicates a significant difference between the conventional and the optimized 2SFCA methods. Also, results of the differences between the two methods reveal a clustering of residuals when distance increases. In other words, a low threshold would be associated with a lack of precision.</p> <p>Conclusion</p> <p>Results of this study suggest that a greater effort must be made ameliorate spatial accessibility to medical clinics in Montreal. To ensure that health resources are allocated in the interest of the population, health planners and the government should consider a strategy in the sitting of future clinics which would provide spatial access to the greatest number of people.</p

ATLAS FTK : Fast Track Trigger

A track reconstruction system for the trigger of the ATLAS detector at the Large Hadron Collider is described. The Fast Tracker is a highly parallel hardware system designed to operate at the Level-1 trigger output rate. It will provide high-quality tracks reconstructed over the entire inner detector by the start of processing in the Level-2 trigger. The system is based on associative memories for pattern recognition and fast FPGA's for track reconstruction. Its design and expected performance under instantaneous luminosities up to 3 x 10^34 / cm^2 / s are discussed