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Sample records for caracteres cuantitativos qtl

  1. ESTIMACIÓN DE LA HEREDABILIDAD EN SENTIDO ANCHO A CARACTERES DE IMPORTANCIA AGRÍCOLA EVALUADOS EN UNA POBLACIÓN DE GUAYABO (Psidium guajava L.

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    Leneidy Pérez Pelea

    2013-01-01

    Full Text Available El guayabo (Psidium guajava L. es considerado como uno de los frutales tropicales y subtropicales más valiosos, pues resulta una fuente natural de vitaminas y sales minerales. A nivel mundial se han realizado muy pocos estudios relacionados con la herencia de los caracteres cuantitativos en esta especie y en nuestro país no han sido abordados hasta el momento. En la Unidad Científico Tecnológica de Base de Alquízar, perteneciente al Instituto de Investigaciones en Fruticultura Tropical, se realizó un cruzamiento entre los cultivares ‘Enana Roja Cubana’ (EEA 18-40 y ‘N6’, obteniéndose un total de 96 descendientes, los cuales se plantaron según un Diseño Completamente Aleatorizado. Se evaluaron 14 caracteres cuantitativos del fruto durante los años 2006 al 2009. Con los datos obtenidos se realizaron Análisis de Varianza Factoriales (Modelo II con el objetivo de estimar las componentes de la varianza y la heredabilidad en sentido ancho, para lo cual se empleó el programa SPSS (versión 16.0. Los caracteres ancho y largo del fruto, relación largo/ancho del fruto, diámetro de la cavidad del cáliz, relación diámetro del cá liz/fruto, número, masa total y masa promedio de las semillas/fruto mostraron valores medios de heredabilidad en sentido ancho, a diferencia del resto de los caracteres que presentaron estimados bajos. Doce de las variables evaluadas manifestaron una varianza de interacción genotipo x ambiente estadísticamente significativa, por lo que se sugiere la aplicación de modelos más refinados para el análisis de la interacción genotipo x ambiente.

  2. Localización de Instalaciones. Enfoque Cuantitativo

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    Juan Gabriel Correa Medina

    2004-01-01

    Full Text Available Aplicación de la Informática a el problema de localización de instalaciones desde un aspecto cuantitativo, tomando como base el método de centro de gravedad, utilizando tanto la técnica de la mediana simple como la de distancias euclidianas. Dicho artículo es un extracto de la tesis de grado, Ubicación de Empresas, Enfoque Cuantitativo, cuyo sustentante es el autor del presente artículo. Cabe mencionar que dicha tesis fue auspiciada por el Consejo de Ciencia y Tecnología del Estado de Aguascalientes (CONCYTEA

  3. PRINCIPIOS DEL PARADIGMA CUANTITATIVO EN LA INVESTIGACIÓN EDUCATIVA

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    Wálter Salazar Rojas

    2002-01-01

    Este artículo discute las bases históricas y filosóficas del paradigma cuantitativo en la investigación educativa. Se analiza el concepto numérico de la realidad en el marco de la filosofía griega tomando como referencia a Pitágoras y Platón. Posteriormente, se discute elconcepto de ciencia e investigación científica. Se define la variable, la taxonomía y los niveles de medición.Siguiendo los lineamientos de Campbell y Stanley se analizan los conceptos del diseño experimental, de validez inte...

  4. Discovering genes underlying QTL

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    Vanavichit, Apichart [Kasetsart University, Kamphaengsaen, Nakorn Pathom (Thailand)

    2002-02-01

    A map-based approach has allowed scientists to discover few genes at a time. In addition, the reproductive barrier between cultivated rice and wild relatives has prevented us from utilizing the germ plasm by a map-based approach. Most genetic traits important to agriculture or human diseases are manifested as observable, quantitative phenotypes called Quantitative Trait Loci (QTL). In many instances, the complexity of the phenotype/genotype interaction and the general lack of clearly identifiable gene products render the direct molecular cloning approach ineffective, thus additional strategies like genome mapping are required to identify the QTL in question. Genome mapping requires no prior knowledge of the gene function, but utilizes statistical methods to identify the most likely gene location. To completely characterize genes of interest, the initially mapped region of a gene location will have to be narrowed down to a size that is suitable for cloning and sequencing. Strategies for gene identification within the critical region have to be applied after the sequencing of a potentially large clone or set of clones that contains this gene(s). Tremendous success of positional cloning has been shown for cloning many genes responsible for human diseases, including cystic fibrosis and muscular dystrophy as well as plant disease resistance genes. Genome and QTL mapping, positional cloning: the pre-genomics era, comparative approaches to gene identification, and positional cloning: the genomics era are discussed in the report. (M. Suetake)

  5. Discovering genes underlying QTL

    International Nuclear Information System (INIS)

    A map-based approach has allowed scientists to discover few genes at a time. In addition, the reproductive barrier between cultivated rice and wild relatives has prevented us from utilizing the germ plasm by a map-based approach. Most genetic traits important to agriculture or human diseases are manifested as observable, quantitative phenotypes called Quantitative Trait Loci (QTL). In many instances, the complexity of the phenotype/genotype interaction and the general lack of clearly identifiable gene products render the direct molecular cloning approach ineffective, thus additional strategies like genome mapping are required to identify the QTL in question. Genome mapping requires no prior knowledge of the gene function, but utilizes statistical methods to identify the most likely gene location. To completely characterize genes of interest, the initially mapped region of a gene location will have to be narrowed down to a size that is suitable for cloning and sequencing. Strategies for gene identification within the critical region have to be applied after the sequencing of a potentially large clone or set of clones that contains this gene(s). Tremendous success of positional cloning has been shown for cloning many genes responsible for human diseases, including cystic fibrosis and muscular dystrophy as well as plant disease resistance genes. Genome and QTL mapping, positional cloning: the pre-genomics era, comparative approaches to gene identification, and positional cloning: the genomics era are discussed in the report. (M. Suetake)

  6. Variación de la componente genética-ambiental de caracteres continuos en poblaciones antiguas

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    Varela, Héctor Hugo

    2001-01-01

    Full Text Available La varianza fenotípica (Vp comprende la varianza genética (Vg, la varianza ambiental general (Veg y la varianza ambiental especial (Ves. Esta última puede estimarse mediante el cálculo de la repetibilidad (r2. Este valor es considerado el límite superior de la heredabilidad (h2 y representa la proporción de la Vg más la Veg con respecto a la Vp (r2= (Vg+Veg/Vp. Esta técnica permite establecer relaciones de parentesco entre grupos a partir de estimadores que maximizan la información genética contenida en los caracteres cuantitativos. Se empleó una muestra constituida por 237 individuos que habitaron durante 4000 años la costa Norte de Chile. Se midieron 6 caracteres métricos en ambos lados del cráneo. Los valores ambientales especiales (es se obtuvieron por regresión. La diferencia entre estos y los valores fenotípicos (p representan los valores genéticos más ambientales generales (g+eg. Un valor r2 promedio de 0.81, indicó que la Ves representa el 19% de la Vp. Se comprobó que la proporción de la componente (g+eg con respecto a p se mantiene estable, reflejando la evolución de un mismo grupo humano. Además, se demuestra una estrecha relación entre los modelos p y (g+eg, lo que sustenta el uso de modelos fenotípicos en la interpretación de la historia evolutiva de un determinado grupo.

  7. PRINCIPIOS DEL PARADIGMA CUANTITATIVO EN LA INVESTIGACIÓN EDUCATIVA

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    Wálter Salazar Rojas

    2002-06-01

    Full Text Available Este artículo discute las bases históricas y filosóficas del paradigma cuantitativo en la investigación educativa. Se analiza el concepto numérico de la realidad en el marco de la filosofía griega tomando como referencia a Pitágoras y Platón. Posteriormente, se discute elconcepto de ciencia e investigación científica. Se define la variable, la taxonomía y los niveles de medición.Siguiendo los lineamientos de Campbell y Stanley se analizan los conceptos del diseño experimental, de validez interna y externa, las amenazas que diversos factores le plantean a las mismas, y cuáles son los elementos de control que el método científico y los diseños de investigación tienen para contrarrestar estas amenazas: aleatorización, pretest y grupo control. Finalmente se presenta uno de los avances más relevantes de la metodología cuantitativa como es el meta-análisis, técnica para resumir y analizar resultados de grupos de investigaciones. Se enumeran sus características y los pasos que hay que realizar para completar un meta-análisis.

  8. Fine mapping of multiple QTL using combined linkage and linkage disequilibrium mapping – A comparison of single QTL and multi QTL methods

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    Meuwissen Theo HE

    2007-04-01

    Full Text Available Abstract Two previously described QTL mapping methods, which combine linkage analysis (LA and linkage disequilibrium analysis (LD, were compared for their ability to detect and map multiple QTL. The methods were tested on five different simulated data sets in which the exact QTL positions were known. Every simulated data set contained two QTL, but the distances between these QTL were varied from 15 to 150 cM. The results show that the single QTL mapping method (LDLA gave good results as long as the distance between the QTL was large (> 90 cM. When the distance between the QTL was reduced, the single QTL method had problems positioning the two QTL and tended to position only one QTL, i.e. a "ghost" QTL, in between the two real QTL positions. The multi QTL mapping method (MP-LDLA gave good results for all evaluated distances between the QTL. For the large distances between the QTL (> 90 cM the single QTL method more often positioned the QTL in the correct marker bracket, but considering the broader likelihood peaks of the single point method it could be argued that the multi QTL method was more precise. Since the distances were reduced the multi QTL method was clearly more accurate than the single QTL method. The two methods combine well, and together provide a good tool to position single or multiple QTL in practical situations, where the number of QTL and their positions are unknown.

  9. Mapeamento de QTL para conteúdos de proteína e óleo em soja Mapping QTL for protein and oil content in soybean

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    Josiane Isabela da Silva Rodrigues

    2010-05-01

    Full Text Available O objetivo deste trabalho foi detectar e mapear locos de caracteres quantitativos (QTL que afetam os conteúdos de proteína e óleo em soja (Glycine max L. Merr.. Plantas F2, derivadas do cruzamento entre a linhagem CS3032PTA276 e a variedade UFVS2012, foram cultivadas em casa de vegetação e forneceram as folhas para extração e análise de DNA. Quarenta e oito marcadores microssatélites (SSR polimórficos foram avaliados na população F2. A avaliação dos fenótipos foi realizada em 207 famílias das progênies F2:3, em um delineamento em blocos ao acaso, com três repetições, conduzido em Viçosa, MG, em 2006. Foram detectados quatro QTL associados ao conteúdo de proteína, nos grupos de ligação D1a, G, A1, e I, e três QTL associados ao conteúdo de óleo, nos grupos A1, I e O. A variação fenotípica explicada pelos QTL variou de 6,24 a 18,94% e 17,26 a 25,93%, respectivamente, para os conteúdos de proteína e óleo. Foram detectados novos QTL associados aos conteúdos de proteína e óleo, além dos previamente relatados em outros estudos. Regiões distintas das atualmente conhecidas podem estar envolvidas no controle genético do teor de proteína e óleo na soja.The objective of this study was to detect and map quantitative trait loci (QTL affecting soybean (Glycine max L. Merr. protein and oil contents. F2 plants, derived from the cross between the CS3032PTA276 line and the variety UFVS2012, were grown in a greenhouse and provided the leaves for DNA extraction and analysis. Forty-eight polymorphic microsatelite markers (SSR were evaluated in the F2 population. Evaluation of the phenotype was performed in 207 families from F2:3 progenies, in a complete block design with three replicates, carried out in Viçosa, MG, Brazil, in 2006. Four QTL associated with protein content, in linkage groups D1a, G, A1, and I, and three QTL for oil content in groups A1, I and O were identified. Phenotypic variation for protein and oil

  10. Estimación de la varianza genética y ambiental en caracteres métricos del esqueleto humano

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    Varela, Héctor Hugo

    2003-01-01

    Full Text Available En la teoría evolutiva de rasgos cuantitativos el conocimiento de la varianza genética (VG es determinante para hacer inferencias acerca del parentesco. En muchos casos no es posible estimar dicha componente sin la información obtenida a partir de la correlación entre parientes o de experimentos de selección. Por esta razón, en ausencia de datos apropiados es posible lograr una aproximación mediante el análisis de la repetibilidad de caracteres cuantitativos. En este trabajo se estima la proporción de la varianza genética máxima (VGmax o repetibilidad de medidas del cráneo y del esqueleto postcraneal, empleando la información obtenida por la Dra. Silvia Quevedo en el grupo prehistórico de Punta Teatinos (Norte Semiárido de Chile. La VG es igual a la varianza fenotípica (VP menos la varianza ambiental (VE. Esta última se puede particionar en una varianza ambiental especial (VEe y en una varianza ambiental general (VEg. Como la VEe se puede conocer por la medición de caracteres simétricos del lado derecho e izquierdo del individuo, entonces es posible calcular la varianza genética máxima de la siguiente manera, VGmax=VP-VEe. La proporción de la VGmax se obtuvo para siete variables del esqueleto postcraneano en individuos femeninos (n=56, masculinos (n=55, de ambos sexos (n=115 e infantiles (n=66, y para nueve mediciones del cráneo en un único grupo (n=54. Los resultados indican que la proporción media de la VGmax es menor en el cráneo que en el esqueleto postcraneal sugiriendo una distribución diferencial del efecto ambiental desde el punto de vista topográfico. Además, dicha cantidad es mayor en individuos infantiles que en masculinos y femeninos posiblemente por la existencia en aquellos de una mayor influencia del efecto ambiental general confundido con la VGmax.

  11. Métodos cuantitativos de organización industrial II

    OpenAIRE

    Fonollosa Guardiet, Juan Bautista; Sallán Leyes, José María; Suñé Torrents, Albert

    2002-01-01

    Esta obra constituye el material básico de estudio de la asignatura Métodos Cuantitativos en Organización Industrial II, de la carrera de segundo ciclo de Ingeniería en Organización Industrial de Terrassa (ETSEIT). En particular, pretende ser la obra de referencia para cursar dicha asignatura de modo semipresencial. En la línea de la obra anterior, se introducen técnicas de métodos cuantitativos para su aplicación en las organizaciones, muy especialmente en las actividades de planificación y ...

  12. QTL Information Table: 188 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available 30 RZ801 pha Cao, G.Q., Zhu, J., He, C.X., Gao, Y.M., and Wu, P. (2001). QTL analysis for epistatic effects ...and QTL x environment interaction effects on final height of rice (Oryza sativa L.). Yi Chuan Xue Bao 28, 135-143. ...

  13. QTL Information Table: 73 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available GS3 Morphological trait Seed small grain, CAPS A)Physical BC3F2 Minghui 63 Chuan 7 ...hang, Q. (2006). GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in

  14. Validación de métodos analíticos no cuantitativos

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    Juan Francisco Sánchez R.; María Elena Tejeda R.; Wolfhard Koch; José Luis Alfredo Mora G.; Rubén Marroquín S.; Vicente Hernández A.; Valentín Islas P.; Elizabeth Guadalupe Sánchez G.; Alfredo De León V.

    2010-01-01

    En las ciencias farmacéuticas es bien conocida la metodología para validar métodos analíticos cuantitativos, sin embargo no es muy abundante la información sobre la metodología a seguir para validar un método analítico cualitativo o no cuantitativo. En este artículo se describen los aspectos importantes sobre los métodos de análisis cualitativos, se definen los principales parámetros de calidad y se describe una metodología de trabajo, soportada matemáticamente, para validar un método analíti...

  15. Métodos cualitativos y cuantitativos: el caso de la arqueología colombiana

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    Carl Henrik Langebaek

    2003-04-01

    Full Text Available Este artículo discute el impacto de los métodos cuantitativos y cualitativos en una de las áreas de las ciencias sociales en Colombia: la arqueología. Sostiene que ninguno de ellos ha cumplido con su potencial desarrollo. Los primeros porque se han limitado a ser “herramientas”. Los segundos porque se han planteado exclusivamente como“reflexiones teóricas”. En el caso de la arqueología sólo una integración entre métodos cualitativos y cuantitativos fortalecerá la disciplina, en lugar de la predominante antí- tesis que frecuentemente se traza entre ellos. Para este fin se plantea que tanto las aproximaciones cuantitativas como las cualitativas pueden servir a propuestas hegemónicas y excluyentes. Por lo tanto ninguna puede reclamar superioridad moral sobre la otra.

  16. Aportes epistemol??gicos para vencer la polaridad antagonista cualitativo / cuantitativo

    OpenAIRE

    Oliveros, Gabriel

    2004-01-01

    En un mundo donde se impone la urgencia del dato cuantificable, antes que cualificable, como garant??a de validez y objetividad. Aun en las investigaciones sociales se desprende una preocupaci??n donde lo cualitativo intenta imponerse de forma semejante al dato cuantitativo como garante de la verdad absoluta en ciencias sociales. Planteamos dos hechos fundamentales: La imposibilidad epist??mica de separar lo cuantificable de lo cualificable, para lo cual realizaremos un breve an??lisis al len...

  17. Relações entre os caracteres de maracujazeiro-azedo Relations between variables in passion fruit

    OpenAIRE

    Alessandro Dal'Col Lúcio; Lindolfo Storck; Willian Krause; Regis Queiroz Gonçalves; Astor Henrique Nied

    2013-01-01

    O objetivo foi identificar os caracteres que mais merecem atenção em experimentos com a cultura do maracujá-azedo (Passiflora edulis Sims) e verificar suas relações com o caractere dependente principal produção total de frutos. A partir dos dados de quatro experimentos com a cultura do maracujá calculou-se a matriz de correlações entre todos os caracteres e realizou-se o diagnóstico de multicolinearidade. Em seguida foi aplicada a análise de trilha entre os caracteres restantes. Para identifi...

  18. QTL Information Table: 735 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available (2007). A Large-Effect QTL for Grain Yield under Reproductive-Stage Drought Stress in Upland Rice. Crop Sci. 47, 507-516. http://crop.scijournals.org/cgi/content/abstract/47/2/507 ...

  19. QTL Information Table: 731 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available 007). A Large-Effect QTL for Grain Yield under Reproductive-Stage Drought Stress in Upland Rice. Crop Sci. 47, 507-516. http://crop.scijournals.org/cgi/content/abstract/47/2/507 ...

  20. QTL Information Table: 733 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available 007). A Large-Effect QTL for Grain Yield under Reproductive-Stage Drought Stress in Upland Rice. Crop Sci. 47, 507-516. http://crop.scijournals.org/cgi/content/abstract/47/2/507 ...

  1. QTL Information Table: 843 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available parison between QTLs and expressed sequence tags. TAG Th... T., and Ohsugi, R. (2001). Toward the mapping of physiological and agronomic characters on a rice function map: QTL analysis and com

  2. QTL Information Table: 842 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available parison between QTLs and expressed sequence tags. TAG Th... T., and Ohsugi, R. (2001). Toward the mapping of physiological and agronomic characters on a rice function map: QTL analysis and com

  3. QTL Information Table: 850 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available and Ohsugi, R. (2001). Toward the mapping of physiological and agronomic characters on a rice function map: QTL analysis and comparis...on between QTLs and expressed sequence tags. TAG Theoret

  4. QTL Information Table: 837 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available map: QTL analysis and comparison between QTLs and expressed sequence tags. TAG T..., T., and Ohsugi, R. (2001). Toward the mapping of physiological and agronomic characters on a rice function

  5. QTL Information Table: 840 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available parison between QTLs and expressed sequence tags. TAG Th... T., and Ohsugi, R. (2001). Toward the mapping of physiological and agronomic characters on a rice function map: QTL analysis and com

  6. QTL Information Table: 845 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available map: QTL analysis and comparison between QTLs and expressed sequence tags. TAG T..., T., and Ohsugi, R. (2001). Toward the mapping of physiological and agronomic characters on a rice function

  7. QTL Information Table: 847 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available and Ohsugi, R. (2001). Toward the mapping of physiological and agronomic characters on a rice function map: QTL analysis and compari...son between QTLs and expressed sequence tags. TAG Theore

  8. QTL Information Table: 692 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available , N., Takagi, K., Ichikawa, N., Maruoka, M., and Sano, Y. (2007). A QTL Cluster for Plant Architecture and Its Ecological Significance in Asian Wild Rice. Breeding Science 57, 7-16. ...

  9. QTL Information Table: 841 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available gs. TAG Theoretical and Applied Genetics 102, 793-800. http://dx.doi.org/10.1007/s001220000467 ... ... function map: QTL analysis and comparison between QTLs and expressed sequence ta

  10. Comparación temporal del desarrollo mediante un índice cuantitativo

    OpenAIRE

    Puerta Gil, Carmen; García del Valle Irala, Teresa

    2008-01-01

    En este trabajo se presenta un índice cuantitativo que permite medir el desarrollo humano de los países y hacer comparaciones temporales.La metodología desarrollada para obtenerlo tiene unas características que la convierten en una herramienta excelente para este tipo de estudios. Es flexible en el sentido de que no se altera al cambiar el número o las variables con las que se trabaja. A las coordenadas que proporciona se les puede aplicar las técnicas de clasificación múltiple y construir gr...

  11. QTL analysis for some quantitative traits in bread wheat

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Quantitative trait loci (QTL) analysis was conducted in bread wheat for 14 important traits utilizing data from four different mapping populations involving different approaches of QTL analysis. Analysis for grain protein content (GPC) suggested that the major part of genetic variation for this trait is due to environmental interactions. In contrast, pre-harvest sprouting tolerance (PHST) was controlled mainly by main effect QTL (M-QTL) with very little genetic variation due to environmental interactions; a major QTL for PHST was detected on chromosome arm 3AL. For grain weight, one QTL each was detected on chromosome arms 1AS, 2BS and 7AS. QTL for 4 growth related traits taken together detected by different methods ranged from 37 to 40; nine QTL that were detected by single-locus as well as two-locus analyses were all M-QTL. Similarly, single-locus and two-locus QTL analyses for seven yield and yield contributing traits in two populations respectively allowed detection of 25 and 50 QTL by composite interval mapping (CIM), 16 and 25 QTL by multiple-trait composite interval mapping (MCIM) and 38 and 37 QTL by two-locus analyses. These studies should prove useful in QTL cloning and wheat improvement through marker aided selection.

  12. solQTL: a tool for QTL analysis, visualization and linking to genomes at SGN database

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    van der Knaap Esther

    2010-10-01

    Full Text Available Abstract Background A common approach to understanding the genetic basis of complex traits is through identification of associated quantitative trait loci (QTL. Fine mapping QTLs requires several generations of backcrosses and analysis of large populations, which is time-consuming and costly effort. Furthermore, as entire genomes are being sequenced and an increasing amount of genetic and expression data are being generated, a challenge remains: linking phenotypic variation to the underlying genomic variation. To identify candidate genes and understand the molecular basis underlying the phenotypic variation of traits, bioinformatic approaches are needed to exploit information such as genetic map, expression and whole genome sequence data of organisms in biological databases. Description The Sol Genomics Network (SGN, http://solgenomics.net is a primary repository for phenotypic, genetic, genomic, expression and metabolic data for the Solanaceae family and other related Asterids species and houses a variety of bioinformatics tools. SGN has implemented a new approach to QTL data organization, storage, analysis, and cross-links with other relevant data in internal and external databases. The new QTL module, solQTL, http://solgenomics.net/qtl/, employs a user-friendly web interface for uploading raw phenotype and genotype data to the database, R/QTL mapping software for on-the-fly QTL analysis and algorithms for online visualization and cross-referencing of QTLs to relevant datasets and tools such as the SGN Comparative Map Viewer and Genome Browser. Here, we describe the development of the solQTL module and demonstrate its application. Conclusions solQTL allows Solanaceae researchers to upload raw genotype and phenotype data to SGN, perform QTL analysis and dynamically cross-link to relevant genetic, expression and genome annotations. Exploration and synthesis of the relevant data is expected to help facilitate identification of candidate genes

  13. Conocimiento numérico cuantitativo y léxico : evidencia de doble disociación

    OpenAIRE

    Alameda Bailén, José Ramón; Salguero Alcañiz, María del Pilar; Lorca Marín, José Andrés

    2007-01-01

    El objetivo de este trabajo es determinar las implicaciones de una lesión cerebral concreta en el sistema de procesamiento numérico y el cálculo. El método empleado es el estudio de caso único, mediante la aplicación de pruebas de evaluación neuropsicológica. Los datos evidencian una doble disociación entre conocimiento numérico cuantitativo y cualitativo o léxico. Por un lado, la paciente M.C. preserva el conocimiento numérico cuantitativo tal como muestran los resultados en tare...

  14. Quantitative Phylogenetic Analysis in the 21st Century Análisis Filogenéticos Cuantitativos en el siglo XXI

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    Daniel R Brooks

    2007-12-01

    produce the same results, more data are needed.Se revisa la sistemática filogenética Hennigiana y se compara con las aproximaciones de Máxima Parsimonia, Máxima Verosimilitud y verosimilitud Bayesiana. Todos los métodos utilizan el principio de la parsimonia en alguna forma. Las aproximaciones con bases Hennigianas se justifican ontológicamente con los conceptos Darwinianos de conservacionismo filogenético y cohesión de las homologías, representados en el Principio Auxiliar de Hennig, y aplicado en la comparación con el grupo externo. La Parsimonia se utiliza como una herramienta epistemológica, aplicada a posteriori en la elección de la hipótesis más robusta cuando hay datos en conflicto. Los métodos cuantitativos utilizan la parsimonia como un criterio ontológico: los análisis de Máxima Parismonia utilizan la parsimonia sin pesaje, la Máxima Verosimilitud les asigna un peso igual a todos los caracteres que explican los datos, mientras que la verosimilitud Bayesiana depende del pesaje de cada una de las particiones de caracteres que explican los datos. Las diferencias en los resultados derivan de un muestreo insuficiente de datos, en cuyo caso cada método trata las ambigüedades de manera diferente. Todos los métodos cuantitativos producen redes. Las redes pueden convertirse en árboles al ser enraizadas. Si el enraizamiento se efectua de acuerdo con el Principio Auxiliar de Hennig, utilizando la comparación con un grupo externo, el árbol resultante puede considerarse como una hipótesis filogenética. Al incrementarse el número de datos, los métodos de verosimilitud selccionan modelos que permiten un número cada vez mayor de posibilidades a priori, convergiendo en la perspectiva Hennigiana de que nada está prohibido a priori. Por lo tanto, todos los métodos producen resultados similares independientemente del tipo de datos, especialmente cuando las redes se enraizan utilizando grupos externos. Las invocaciones a la filosofia Popperiana no

  15. MetaQTL: a package of new computational methods for the meta-analysis of QTL mapping experiments

    Directory of Open Access Journals (Sweden)

    Charcosset Alain

    2007-02-01

    Full Text Available Abstract Background Integration of multiple results from Quantitative Trait Loci (QTL studies is a key point to understand the genetic determinism of complex traits. Up to now many efforts have been made by public database developers to facilitate the storage, compilation and visualization of multiple QTL mapping experiment results. However, studying the congruency between these results still remains a complex task. Presently, the few computational and statistical frameworks to do so are mainly based on empirical methods (e.g. consensus genetic maps are generally built by iterative projection. Results In this article, we present a new computational and statistical package, called MetaQTL, for carrying out whole-genome meta-analysis of QTL mapping experiments. Contrary to existing methods, MetaQTL offers a complete statistical process to establish a consensus model for both the marker and the QTL positions on the whole genome. First, MetaQTL implements a new statistical approach to merge multiple distinct genetic maps into a single consensus map which is optimal in terms of weighted least squares and can be used to investigate recombination rate heterogeneity between studies. Secondly, assuming that QTL can be projected on the consensus map, MetaQTL offers a new clustering approach based on a Gaussian mixture model to decide how many QTL underly the distribution of the observed QTL. Conclusion We demonstrate using simulations that the usual model choice criteria from mixture model literature perform relatively well in this context. As expected, simulations also show that this new clustering algorithm leads to a reduction in the length of the confidence interval of QTL location provided that across studies there are enough observed QTL for each underlying true QTL location. The usefulness of our approach is illustrated on published QTL detection results of flowering time in maize. Finally, MetaQTL is freely available at http://bioinformatics.org/mqtl.

  16. Elementos geomorfológico-cuantitativos del piedemonte nororiental del volcán Nevado de Toluca

    OpenAIRE

    Luis Miguel Espinosa Rodríguez

    2003-01-01

    A partir de un análisis cuantitativo y morfométrico, se determina la geodinámica del piedemonte nororiental del volcán Nevado de Toluca. Se destaca la relación entre el material, las formas heredadas y la energía que dinamiza el noreste del volcán.

  17. Análisis sensorial descriptivo cuantitativo (QDA) aplicado al estudio del aroma de los vinos gallegos

    OpenAIRE

    Vilanova de la Torre, María del Mar

    2008-01-01

    Este trabajo ha pretendido establecer descriptores útiles en la identificación del aroma de los vinos jóvenes elaborados con tres de las variedades más representativas de Galicia, utilizando la metodología del análisis sensorial descriptivo cuantitativo.

  18. Advances on methods for mapping QTL in plant

    Institute of Scientific and Technical Information of China (English)

    ZHANG Yuan-Ming

    2006-01-01

    Advances on methods for mapping quantitative trait loci (QTL) are firstly summarized.Then, some new methods, including mapping multiple QTL, fine mapping of QTL, and mapping QTL for dynamic traits, are mainly described. Finally, some future prospects are proposed, including how to dig novel genes in the germplasm resource, map expression QTL (eQTL) by the use of all markers,phenotypes and micro-array data, identify QTL using genetic mating designs and detect viability loci. The purpose is to direct plant geneticists to choose a suitable method in the inheritance analysis of quantitative trait and in search of novel genes in germplasm resource so that more potential genetic information can be uncovered.

  19. Statistical properties of interval mapping methods on quantitative trait loci location: impact on QTL/eQTL analyses

    Directory of Open Access Journals (Sweden)

    Wang Xiaoqiang

    2012-04-01

    Full Text Available Abstract Background Quantitative trait loci (QTL detection on a huge amount of phenotypes, like eQTL detection on transcriptomic data, can be dramatically impaired by the statistical properties of interval mapping methods. One of these major outcomes is the high number of QTL detected at marker locations. The present study aims at identifying and specifying the sources of this bias, in particular in the case of analysis of data issued from outbred populations. Analytical developments were carried out in a backcross situation in order to specify the bias and to propose an algorithm to control it. The outbred population context was studied through simulated data sets in a wide range of situations. The likelihood ratio test was firstly analyzed under the "one QTL" hypothesis in a backcross population. Designs of sib families were then simulated and analyzed using the QTL Map software. On the basis of the theoretical results in backcross, parameters such as the population size, the density of the genetic map, the QTL effect and the true location of the QTL, were taken into account under the "no QTL" and the "one QTL" hypotheses. A combination of two non parametric tests - the Kolmogorov-Smirnov test and the Mann-Whitney-Wilcoxon test - was used in order to identify the parameters that affected the bias and to specify how much they influenced the estimation of QTL location. Results A theoretical expression of the bias of the estimated QTL location was obtained for a backcross type population. We demonstrated a common source of bias under the "no QTL" and the "one QTL" hypotheses and qualified the possible influence of several parameters. Simulation studies confirmed that the bias exists in outbred populations under both the hypotheses of "no QTL" and "one QTL" on a linkage group. The QTL location was systematically closer to marker locations than expected, particularly in the case of low QTL effect, small population size or low density of markers, i

  20. QTL Information Table: 673 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available , Xu, X., Mei, H., and Luo, L. (2007). A major QTL associated with cold tolerance at seedling stage in rice ( Oryza sativa L.). Euphytica. http://dx.doi.org/10.1007/s10681-007-9431-5 ...

  1. QTL Information Table: 641 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available ronment interaction for yield components and plant height in rice. Rice Genetics Newsletter 13, 127-129. ... ... RG13 RG573 rgn Zhuang, J.Y., Lin, H.X., Lu, J., Qian, H.R., Hittalman, S., Huang, N., and Zheng, K.L. (1996). Analysis of QTL x envi

  2. QTL Information Table: 360 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available H.C., McLaren, G., and Khush, G.S. (2003). Identification of QTL for growth- and ...Zheng, K.L., Liu, G.F., Wang, G.C., Sidhu, J.S., Srivantaneeyakul, S., Singh, V.P., Bagali, P.G., Prasanna,

  3. QTL Information Table: 823 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Resistance or Tolerance Other soil stress tolerance Plant height (Low N level, Soil... QTL × N-level interaction for plant height in rice (Oriza Sativa L.). Plant and Soil 236, 237-242. http://dx.doi.org/10.1023/A:1012787510201 ...

  4. QTL Information Table: 370 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available sd-1 Morphological trait Dwarf plant height RFLP C)Interval DHL IR64 Azucena A RZ73...l, S., and Khush, G.S. (2003). QTL x environment interactions in rice. I. heading date and plant height. Theor Appl Genet 108, 141-153. ...

  5. QTL Information Table: 820 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Resistance or Tolerance Other soil stress tolerance Plant height (High N level, Soi...QTL × N-level interaction for plant height in rice (Oriza Sativa L.). Plant and Soil 236, 237-242. http://dx.doi.org/10.1023/A:1012787510201 ...

  6. QTL Information Table: 819 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Resistance or Tolerance Other soil stress tolerance Plant height (High N level, Soi.... QTL × N-level interaction for plant height in rice (Oriza Sativa L.). Plant and Soil 236, 237-242. http://dx.doi.org/10.1023/A:1012787510201 ...

  7. QTL Information Table: 131 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available 2-3SY Physiological trait Source activity biomass yield RFLP C)Interval DHL IR64 Az...ucena A RG171 RG157 pha Liu, G.F., Yang, J., and Zhu, J. (2006). Mapping QTL for biomass yield and its components in rice (Oryza sativa L.). Yi Chuan Xue Bao 33, 607-616. ...

  8. QTL Information Table: 917 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available RIL Nekken-1 IR36 RM5586 RM3916 RM3839 pha Ochiai, K., Uemura, S., Shimizu, A., Okumoto, Y., and Matoh, T. (2008). Boron toxicity... in rice (Oryza sativa L.). I. Quantitative trait locus (QTL) analysis of tolerance to boron toxicity. Theor Appl Genet 117, 125-133. ...

  9. QTL Information Table: 290 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Physiological trait Eating quality breakdown RFLP C)Interval DHL IR64 Azucena A RZ5...90 RG214 pha Bao, J.S., Wu, Y.R., Hu, B., Wu, P., Cui, H.R., and Shu, Q.Y. (2002). QTL for rice grain quality

  10. QTL Information Table: 2 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available hr6 Physiological trait Eating quality Head rice SSR C)Interval DH from BC3F1 Caiap...C., Bergman, C., and Oard, J.H. (2004). QTL mapping of grain quality traits from the interspecific cross Oryza sativa x O. glaberrima. Theor Appl Genet 109, 630-639. ...

  11. QTL Information Table: 4 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available alk6-1 Physiological trait Eating quality Alkali-spread.score SSR C)Interval DH fro...J., Castano, C., Bergman, C., and Oard, J.H. (2004). QTL mapping of grain quality traits from the interspecific cross Oryza sativa x O. glaberrima. Theor Appl Genet 109, 630-639. ...

  12. QTL Information Table: 289 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Physiological trait Eating quality cool paste viscosity RFLP C)Interval DHL IR64 Az...ucena A RZ574 RZ284 pha Bao, J.S., Wu, Y.R., Hu, B., Wu, P., Cui, H.R., and Shu, Q.Y. (2002). QTL for rice grain quality

  13. QTL Information Table: 288 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Physiological trait Eating quality hot paste viscosity RFLP C)Interval DHL IR64 Azu...cena A RG139 RZ58 pha Bao, J.S., Wu, Y.R., Hu, B., Wu, P., Cui, H.R., and Shu, Q.Y. (2002). QTL for rice grain quality

  14. QTL Information Table: 1041 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available qST3-2 Physiological trait Eating quality stickiness SSR B)Fine F3 SL207 Koshihikar...mbe, T. (2007). QTL Detection for Eating Quality Including Glossiness, Stickiness, Taste and Hardness of Cooked Rice. Breeding Science 57, 231-242. ...

  15. QTL Information Table: 1040 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available qOE3-1 Physiological trait Eating quality overall evaluation SSR B)Fine F3 SL207 Ko...., and Imbe, T. (2007). QTL Detection for Eating Quality Including Glossiness, Stickiness, Taste and Hardness of Cooked Rice. Breeding Science 57, 231-242. ...

  16. QTL Information Table: 1042 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available qTA3 Physiological trait Eating quality taste SSR B)Fine F3 SL207 Koshihikari RM133... (2007). QTL Detection for Eating Quality Including Glossiness, Stickiness, Taste and Hardness of Cooked Rice. Breeding Science 57, 231-242. ...

  17. QTL Information Table: 1039 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available qGL3-1 Physiological trait Eating quality glossiness SSR B)Fine F3 SL207 Koshihikar...mbe, T. (2007). QTL Detection for Eating Quality Including Glossiness, Stickiness, Taste and Hardness of Cooked Rice. Breeding Science 57, 231-242. ...

  18. QTL Information Table: 720 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available DHL Yuefu IRAT109 RM253 RM314 pha Guo, Y., Mu, P., Liu, J., Lu, Y., and Li, Z. (2007). QTL mapping and QxE interactions of grain cook...ing and nutrient qualities in rice under upland and lowland environments. J Genet Genomics 34, 420-428. ...

  19. QTL Information Table: 454 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available 61 rgn Zhuang, J.Y., Fan, Y.Y., Wu, J.L., Xia, Y.W., and Zheng, K.L. (2000). Mapping major and minor QTL for rice CMS-WA fertility restoration. Rice Genetics Newsletter 17, 56-59. ...

  20. QTL Information Table: 240 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available qGB Physiological trait Eating quality grain breadth Mixture d)Co-segregated F2 Bas...sis to detect main effect QTL associated with grain quality parameters in Basmati 370/ASD 16 cross in rice O

  1. QTL Information Table: 5 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Physiological trait Eating quality Grain l/w ratio SSR C)Interval DH from BC3F1 Cai..., C., Bergman, C., and Oard, J.H. (2004). QTL mapping of grain quality traits from the interspecific cross Oryza sativa x O. glaberrima. Theor Appl Genet 109, 630-639. ...

  2. QTL Information Table: 929 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available val RIL Bala Azucena B RZ2 G1465 C189 pha Price, A.H., Steele, K.A., Moore, B.J., Barraclough, P.P., and Clark, L.J. (2000). A combin...ed RFLP and AFLP linkage map of upland rice ( Oryza sativa L.) used to identify QTL

  3. QTL Information Table: 364 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available qSD-1-2 Physiological trait Germination/dormancy RFLP d)Co-segregated CSSL Asominor...ion and analysis of QTL for seed dormancy in rice (Oryza sativa L.) using RIL and CSSL population. Yi Chuan Xue Bao 30, 453-458. ...

  4. Inter-relação entre caracteres de caupi de porte ereto e crescimento determinado

    Directory of Open Access Journals (Sweden)

    Bezerra Antonio Aécio de Carvalho

    2001-01-01

    Full Text Available Foram estudados dez caracteres em 32 genótipos de caupi [Vigna unguiculata (L.Walp.], com o objetivo de avaliar o grau de associação existente entre o rendimento de grãos e seus componentes. Oensaio foi conduzido no Campo Experimental da Embrapa-Centro de Pesquisa Agropecuária do Meio-Norte, em Teresina, PI. Utilizou-se o delineamento experimental de blocos casualizados, com seis repetições. Os dados foram coletados nas duas fileiras centrais, subtraídas das duas primeiras covas em cada extremidade. A floração inicial e o peso de 100 grãos apresentaram, com rendimento de grãos, as maiores correlações genéticas positivas e os maiores efeitos diretos em sentido favorável à seleção, e foram os caracteres mais importantes para o processo de seleção indireta. A seleção, praticada nos caracteres ângulo de inserção dos ramos laterais e número de grãos por vagem, não teve influência direta significativa sobre o rendimento de grãos.

  5. Análise de trilha em caracteres de frutos de jabuticabeira

    Directory of Open Access Journals (Sweden)

    Vanessa Padilha Salla

    2015-03-01

    Full Text Available O objetivo deste trabalho foi identificar os efeitos diretos e indiretos de caracteres dos frutos de jabuticabeira (Plinia cauliflora sobre o rendimento de polpa e o teor de antocianinas na casca. Foram coletados frutos de 36 jabuticabeiras, em cinco locais de ocorrência, na região Sudoeste do Paraná. Diferentes estratégias de análise de trilha foram utilizadas na avaliação dos seguintes caracteres dos frutos: peso e diâmetro; rendimento de polpa; percentual de sementes e casca; teores de sólidos solúveis totais, acidez titulável, antocianinas e flavonoides; e número de sementes por fruto. A estratégia de análise de trilha com regressão em crista teve melhor desempenho que a de análise com exclusão de caracteres, principalmente sob presença de multicolinearidade severa no conjunto de dados. O percentual de polpa e o teor de sólidos solúveis totais podem servir de critérios de seleção indireta no aumento do teor de antocianinas na casca da jabuticaba. O percentual de casca é a principal característica com efeito determinante no percentual de polpa de jabuticabas, e a seleção indireta para frutos com menor quantidade de casca pode ser eficaz para aumentar o rendimento de polpa.

  6. Aspectos estructurales y cuantitativos del ovario de Fulica armillata (Aves: Rallidae

    Directory of Open Access Journals (Sweden)

    Mirian Bulfon

    2012-02-01

    Full Text Available Se estudiaron los aspectos morfohistológicos y cuantitativos del ovario de Fulica armillata durante la fase de recrudescencia gonadal. Se utilizaron 5 hembras adultas. El análisis morfohistológico reveló la presencia de numerosos folículos en diferentes estadios de desarrollo y regresión. El epitelio simple de células granulosas caracterizó a los ovocitos primordiales y el pseudoestratificado a los folículos previtelogénicos, ambos tipos foliculares exhibieron un notorio cuerpo de Balbiani. En los folículos vitelogénicos blancos y amarillos (> de 1 mm se evidenció una compleja pared folicular formada por la zona radiada, el epitelio folicular estratificado y las envolturas tecales bien delimitadas, mientras que, en los vitelogénicos amarillos (> de 3 mm fue observado un epitelio simple con células cúbicas muy basófilas. Se identificaron dos tipos de atresia folicular: 1 pared folicular intacta o no bursting, la involución se realiza en el interior del folículo, comprende a la atresia lipoidal (Ovocitos primordiales y lipoglandular (folículos previtelogénicos y vitelogénicos pequeños y 2 atresia por ruptura de la pared o bursting con extrusión del contenido ovoplásmico (folículos vitelogénicos > 1 mm. El análisis cuantitativo reveló una diferencia significativa (p <0,05, entre los folículos en desarrollo (< de 2 mm y los folículos mayores e idéntica diferencia entre lo folículos atrésicos pequeños (lipoidales y lipoglandulares y los folículos bursting. Los procesos de crecimiento y diferenciación (foliculogénesis y vitelogénesis y el de atresia folicular se desarrollan normalmente durante la fase de recrudescencia gonadal, contribuyendo a la homeostasis del ovario de esta ave.

  7. Los métodos cuantitativos en distintos planes de estudio

    Directory of Open Access Journals (Sweden)

    Álvarez Martínez, P.

    2005-01-01

    Full Text Available La adaptación al Espacio Europeo de Enseñanza Superior (EEES hace necesaria la modificación de los títulos universitarios y la reelaboración de sus planes de estudios a fin de armonizar y homogeneizar las carreras de las distintas universidades. De nuevo se pone sobre la mesa la distribución de créditos entre las áreas de conocimiento. En este estudio se parte de la hipótesis de que un peso adecuado de las asignaturas de métodos cuantitativos garantiza el éxito en el proceso de enseñanza- aprendizaje de los alumnos. Se van a analizar los resultados académicos de estas asignaturas en los distintos planes de estudios, a fin de comprobar si se verifica la hipótesis de partida y analizar el peso que ha de darse a estas asignaturas en los nuevos planes.

  8. QTL Information Table: 322 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available qCC-1 Physiological trait Source activity chlorophyll content of leaf RFLP C)Interval RIL Kinmaze DV85 B C122 R1012 rgn Hu, M.L., Wang, C.M., Yang, Q.H., Zhai, H.Q., and Wan, J.M. (2004). QTL analysis for traits associated with photosynthetic function in rice (Oryza sativa L.). Rice Genetics Newsletter 21, 42-44. ...

  9. QTL Information Table: 40 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available OSJNBb0074M06 RMw357 RMw353 C80 C1677 pha Wan, X.Y., Wan, J.M., Jiang, L., Wang, J.K., Zhai, H.Q., Weng, J.F., Wang,... H.L., Lei, C.L., Wang, J.L., Zhang, X., Cheng, Z.J., and Guo, X.P. (2006). QTL analysis for rice gr

  10. Advances in QTL Mapping in Pigs

    Directory of Open Access Journals (Sweden)

    Max F. Rothschild, Zhi-liang Hu, Zhihua Jiang

    2007-01-01

    Full Text Available Over the past 15 years advances in the porcine genetic linkage map and discovery of useful candidate genes have led to valuable gene and trait information being discovered. Early use of exotic breed crosses and now commercial breed crosses for quantitative trait loci (QTL scans and candidate gene analyses have led to 110 publications which have identified 1,675 QTL. Additionally, these studies continue to identify genes associated with economically important traits such as growth rate, leanness, feed intake, meat quality, litter size, and disease resistance. A well developed QTL database called PigQTLdb is now as a valuable tool for summarizing and pinpointing in silico regions of interest to researchers. The commercial pig industry is actively incorporating these markers in marker-assisted selection along with traditional performance information to improve traits of economic performance. The long awaited sequencing efforts are also now beginning to provide sequence available for both comparative genomics and large scale single nucleotide polymorphism (SNP association studies. While these advances are all positive, development of useful new trait families and measurement of new or underlying traits still limits future discoveries. A review of these developments is presented.

  11. QTL mapping for production traits in Czech Fleckvieh cattle

    DEFF Research Database (Denmark)

    Matejickova, J; Stipkova, M; Sahana, Goutam;

    2013-01-01

    The objective of this study was to find QTL for milk production traits in Czech Fleckvieh cattle on chromosomes 6, 7, 11, 14, and 23 where QTL were previously identified in other dairy cattle populations. Sixteen grandsire families were genotyped for 38 microsatellite markers on the selected...... of milk production in the Czech Fleckvieh cattle....... associated with milk production traits appeared on other studied chromosomes (BTA6, BTA7, BTA11, and BTA23). This first QTL search on five chromosomes in Czech Fleckvieh population showed several suggestive QTL that can be promising for further studies and contribute to better understanding of genetics...

  12. Análisis cuantitativo de los ciclos económicos

    Directory of Open Access Journals (Sweden)

    Álvarez Vázquez, Nelson J.

    2003-01-01

    Full Text Available El análisis clásico de series temporales asumía que la serie histórica era la suma de tendencia, ciclo regular, estacional y perturbación aleatoria, movimientos que pueden reducirse a tendencia y ciclo. La descomposición en tendencia y ciclo permitía un análisis separado de ambos tipos de movimientos. Esta aproximación suponía que el ciclo era una desviación respecto de la tendencia (determinista a largo plazo, a la cual revertían aquellos ciclos. Cualquier shock aleatorio tenía sólo un efecto transitorio que se agotaba en uno o unos pocos periodos. Este enfoque ha sido hoy abandonado y sustituido por otro de naturaleza probabilística. En particular el artículo de Nelson y Plosser (1982 habría significado el fin de una aproximación ya cuestionada. En este trabajo, los autores contrastaron la hipótesis de raíz unitaria para diversas series macroeconómicas norteamericanas, encontrando que era imposible rechazarla. Mientras que en la primitiva visión, las fluctuaciones se contemplaban como desviaciones respecto a la tendencia determinista, la existencia de raíz unitaria significa que todas las fluctuaciones representan cambios 2 permanentes en la tendencia a largo plazo, dado que el efecto de cualquier shock, permanece indefinidamente, en lugar de agotarse con el paso del tiempo. De ahí la importancia de la existencia de raíz unitaria en el análisis cuantitativo del ciclo. Sólo mediante la diferenciación se alcanzaría la estacionariedad. En caso contrario, es decir si se elimina una tendencia temporal a una serie generada por un proceso de camino aleatorio (el ejemplo paradigmático de tendencia estocástica, se obtendrán inferencias espurias sobre el ciclo (Nelson y Kang, 1981. En esta cuestión como en tantas otras, es perceptible la evolución metodológica experimentada por la econometría, que se ha desplazado desde un enfoque determinista, donde lo que importaban eran cuestiones como la obtención de la cronolog

  13. Desempenho de clones elite de batata para caracteres agronômicos e de qualidade industrial

    Directory of Open Access Journals (Sweden)

    Giovani Olegario da Silva

    2015-02-01

    Full Text Available O objetivo deste trabalho foi verificar o desempenho de clones elite de batata, em relação a caracteres agronômicos e de qualidade industrial. Os experimentos foram realizados em Pelotas, RS, Canoinhas, SC, e Londrina, PR. Foi avaliado um conjunto de clones elite, pertencentes ao Programa de Melhoramento Genético de Batata, da Embrapa. O delineamento experimental foi o de blocos casualizados, com três repetições para Pelotas e Londrina e quatro para Canoinhas. Foram avaliados os caracteres massa total de tubérculos, massa comercial de tubérculos, número de tubérculos comerciais, percentagem de massa de tubérculos comerciais, massa média de tubérculos comerciais, peso específico, cor de fritura e ciclo vegetativo. A partir dos dados obtidos foram realizadas as análises de variância para cada local e teste de agrupamento de médias para cada caráter. Para identificação de clones apropriados ao mercado 'in natura', em que é fundamental o elevado potencial produtivo e precocidade, os clones mais promissores foram F80-03-06 e CL02-05, quando comparados à cultivar testemunha Ágata. Para o processamento industrial, em que o peso específico, a cor de fritura e o rendimento de tubérculo são caracteres importantes, destacou-se o clone F81-01-06, que apesar de não apresentar os maiores rendimentos totais, apresentou tubérculos grandes, ciclo vegetativo intermediário e boa aptidão para fritura, quando comparando-se ao cultivar testemunha Asterix.

  14. Inter-relação entre caracteres de caupi de porte ereto e crescimento determinado

    OpenAIRE

    Bezerra Antonio Aécio de Carvalho; Anunciação Filho Clodoaldo José da; Freire Filho Francisco Rodrigues; Ribeiro Valdenir Queiroz

    2001-01-01

    Foram estudados dez caracteres em 32 genótipos de caupi [Vigna unguiculata (L.)Walp.], com o objetivo de avaliar o grau de associação existente entre o rendimento de grãos e seus componentes. Oensaio foi conduzido no Campo Experimental da Embrapa-Centro de Pesquisa Agropecuária do Meio-Norte, em Teresina, PI. Utilizou-se o delineamento experimental de blocos casualizados, com seis repetições. Os dados foram coletados nas duas fileiras centrais, subtraídas das duas primeiras covas em cada extr...

  15. Determinación de SNPs en el gen de la diacilglicerol O-aciltransferasa 1 (DGAT1): Primeros resultados en razas bovinas autóctonas maternales

    OpenAIRE

    Avilés, C.; Azor, P.J.; F. Álvarez; I. Fernández; J. A. Pérez; Membrillo, A.; Dorado, G; Molina Alcalá, Antonio

    2007-01-01

    El nivel de grasa intramuscular o marbling constituye uno de los principales atributos de la calidad de la carne. Los avances en genética molecular en las últimas décadas han permitido la identificación de gran cantidad de marcadores genéticos asociados a genes que afectan a caracteres de interés en producción ganadera, incluyendo genes simples con efectos importantes en el fenotipo o QTL (regiones genómicas que afectan a caracteres cuantitativos). Estas nuevas tecnologías han proporcionado h...

  16. Correlações entre caracteres quantitativos em milho pipoca Correlation among quantitative traits in popcorn maize

    OpenAIRE

    Valéria Carpentieri-Pípolo; Hideaki Wilson Takahashi; Romeu Munashi Endo; Marcos Rafael Petek; Adilson Luiz Seifert

    2002-01-01

    Em um programa de melhoramento, o conhecimento da grandeza das associações entre caracteres de interesse, é de fundamental importância na obtenção de populações melhoradas. O presente trabalho teve como objetivo determinar as correlações genotípicas, fenotípicas e ambientais entre caracteres quantitativos em milho pipoca. Foram avaliados nove genótipos de milho pipoca dispostos no campo em delineamento em blocos casualizados com oito repetições. Os genótipos UEL ZP, UEL SI e UEL PAP revelaram...

  17. Educational Software for Mapping Quantitative Trait Loci (QTL)

    Science.gov (United States)

    Helms, T. C.; Doetkott, C.

    2007-01-01

    This educational software was developed to aid teachers and students in their understanding of how the process of identifying the most likely quantitative trait loci (QTL) position is determined between two flanking DNA markers. The objective of the software that we developed was to: (1) show how a QTL is mapped to a position on a chromosome using…

  18. Cell Specific eQTL Analysis without Sorting Cells

    NARCIS (Netherlands)

    Westra, Harm-Jan; Arends, Danny; Esko, Tonu; Peters, Marjolein J.; Schurmann, Claudia; Schramm, Katharina; Kettunen, Johannes; Yaghootkar, Hanieh; Fairfax, Benjamin P.; Andiappan, Anand Kumar; Li, Yang; Fu, Jingyuan; Karjalainen, Juha; Platteel, Mathieu; Visschedijk, Marijn; Weersma, Rinse K.; Kasela, Silva; Milani, Lili; Tserel, Liina; Peterson, Part; Reinmaa, Eva; Hofman, Albert; Uitterlinden, Andre G.; Rivadeneira, Fernando; Homuth, Georg; Petersmann, Astrid; Lorbeer, Roberto; Prokisch, Holger; Meitinger, Thomas; Herder, Christian; Roden, Michael; Grallert, Harald; Ripatti, Samuli; Perola, Markus; Wood, Andrew R.; Melzer, David; Ferrucci, Luigi; Singleton, Andrew B.; Hernandez, Dena G.; Knight, Julian C.; Melchiotti, Rossella; Lee, Bernett; Poidinger, Michael; Zolezzi, Francesca; Larbi, Anis; Wang, De Yun; van den Berg, Leonard H.; Veldink, Jan H.; Rotzschke, Olaf; Makino, Seiko; Salomaa, Veikko; Strauch, Konstantin; Voelker, Uwe; van Meurs, Joyce B. J.; Metspalu, Andres; Wijmenga, Cisca; Jansen, Ritsert C.; Franke, Lude

    2015-01-01

    The functional consequences of trait associated SNPs are often investigated using expression quantitative trait locus (eQTL) mapping. While trait-associated variants may operate in a cell-type specific manner, eQTL datasets for such cell-types may not always be available. We performed a genome-envir

  19. Cell Specific eQTL Analysis without Sorting Cells

    NARCIS (Netherlands)

    H.J. Westra (Harm-Jan); D. Arends (Danny); T. Esko (Tõnu); M.J. Peters (Marjolein); C. Schurmann (Claudia); K. Schramm (Katharina); J. Kettunen (Johannes); H. Yaghootkar (Hanieh); B.P. Fairfax (Benjamin); A.K. Andiappan (Anand Kumar); Y. Li (Yang); J. Fu (Jingyuan); J. Karjalainen (Juha); I. Platteel (Inge); M. Visschedijk (Marijn); R.K. Weersma (Rinse K.); S. Kasela (Silva); L. Milani (Lili); L. Tserel (Liina); P. Peterson (Pärt); E. Reinmaa (Eva); A. Hofman (Albert); A.G. Uitterlinden (André); F. Rivadeneira Ramirez (Fernando); G. Homuth (Georg); A. Petersmann (Astrid); R. Lorbeer (Roberto); H. Prokisch (Holger); T. Meitinger (Thomas); C. Herder (Christian); M. Roden (Michael); H. Grallert (Harald); S. Ripatti (Samuli); M. Perola (Markus); A.R. Wood (Andrew); D. Melzer (David); L. Ferrucci (Luigi); A. Singleton (Andrew); D.G. Hernandez (Dena); J.C. Knight (Julian); R. Melchiotti (Rossella); B. Lee (Bernett); M. Poidinger (Michael); F. Zolezzi (Francesca); A. Larbi (Anis); D.Y. Wang (De Yun); L.H. van den Berg (Leonard); J.H. Veldink (Jan); O. Rotzschke (Olaf); S. Makino (Seiko); V. Salomaa (Veikko); K. Strauch (Konstantin); U. Völker (Uwe); J.B.J. van Meurs (Joyce); A. Metspalu (Andres); C. Wijmenga (Cisca); R.C. Jansen (Ritsert); L. Franke (Lude)

    2015-01-01

    textabstractThe functional consequences of trait associated SNPs are often investigated using expression quantitative trait locus (eQTL) mapping. While trait-associated variants may operate in a cell-type specific manner, eQTL datasets for such cell-types may not always be available. We performed a

  20. Tesauros en acceso abierto en Internet. Un análisis cuantitativo

    Directory of Open Access Journals (Sweden)

    Mochón Bezares, Gonzalo

    2010-12-01

    Full Text Available This work offers a quantitative analysis of publicly available thesauri in different European languages in order to check publication trends and their degree of adherence to thesauri construction guidelines. The following parameters were analysed: publisher’s name and location, number of terms, subject coverage, query modes, latest update, level of content in introduction and on-line help. The results reveal the prevalence of thesauri published in Western Europe; English is the most frequently used language; social sciences have the highest number of thesauri among the knowledge areas observed; only one third of the thesauri has a search engine; on average, there is a poor level of content in the introductions and in the on-line help. In conclusion, many publicly available thesauri do not take advantage offered by the Internet for querying their content and should improve their interfaces.

    Se realiza un análisis cuantitativo de tesauros de acceso abierto en diversas lenguas europeas para comprobar las tendencias en su edición, así como su grado de adaptación a las directrices de construcción de tesauros. Los parámetros analizados en cada tesauro son el nombre de la institución o persona editora y su ubicación geográfica, el número de términos, las principales materias tratadas, los modos de consulta, la última fecha de actualización, el nivel de contenido de la introducción y la ayuda en línea al usuario. Los resultados indican un predominio de los tesauros editados en Europa Occidental; que el inglés es la lengua más usada; que las ciencias sociales tienen el mayor número de tesauros entre las áreas de conocimiento observadas; que sólo una tercera parte de los tesauros dispone de un motor de búsqueda; que hay un nivel medio de contenido muy bajo en las introducciones; y ausencia de ayuda al usuario en numerosas páginas. En conclusión, gran cantidad de tesauros en acceso abierto no aprovechan las ventajas que

  1. Detection of growth-related QTL in turbot (Scophthalmus maximus

    Directory of Open Access Journals (Sweden)

    Fernández Jesús

    2011-09-01

    Full Text Available Abstract Background The turbot (Scophthalmus maximus is a highly appreciated European aquaculture species. Growth related traits constitute the main goal of the ongoing genetic breeding programs of this species. The recent construction of a consensus linkage map in this species has allowed the selection of a panel of 100 homogeneously distributed markers covering the 26 linkage groups (LG suitable for QTL search. In this study we addressed the detection of QTL with effect on body weight, length and Fulton's condition factor. Results Eight families from two genetic breeding programs comprising 814 individuals were used to search for growth related QTL using the panel of microsatellites available for QTL screening. Two different approaches, maximum likelihood and regression interval mapping, were used in order to search for QTL. Up to eleven significant QTL were detected with both methods in at least one family: four for weight on LGs 5, 14, 15 and 16; five for length on LGs 5, 6, 12, 14 and 15; and two for Fulton's condition factor on LGs 3 and 16. In these LGs an association analysis was performed to ascertain the microsatellite marker with the highest apparent effect on the trait, in order to test the possibility of using them for marker assisted selection. Conclusions The use of regression interval mapping and maximum likelihood methods for QTL detection provided consistent results in many cases, although the high variation observed for traits mean among families made it difficult to evaluate QTL effects. Finer mapping of detected QTL, looking for tightly linked markers to the causative mutation, and comparative genomics are suggested to deepen in the analysis of QTL in turbot so they can be applied in marker assisted selection programs.

  2. Detection and use of QTL for complex traits in multiple environments.

    NARCIS (Netherlands)

    Eeuwijk, van F.A.; Bink, M.C.A.M.; Chenu, K.; Chapman, S.C.

    2010-01-01

    QTL mapping methods for complex traits are challenged by new developments in marker technology, phenotyping platforms, and breeding methods. In meeting these challenges, QTL mapping approaches will need to also acknowledge the central roles of QTL by environment interactions (QEI) and QTL by trait i

  3. Genetic Dissection of QTL Associated with Grain Yield in Diverse Environments

    Directory of Open Access Journals (Sweden)

    Junli Zhang

    2014-12-01

    Full Text Available Wheat (Triticum aestivum L. breeding programs strive to increase grain yield; however, the progress is hampered due to its quantitative inheritance, low heritability, and confounding environmental effects. In the present study, a winter wheat population of 159 recombinant inbred lines (RILs was evaluated in six trials under rainfed, terminal drought, and fully-irrigated conditions, over four years. Quantitative trait locus/loci (QTL mapping was conducted for grain yield main effect (GY and the genotype × environment interaction (GEI effect. A total of 17 QTL were associated with GY and 13 QTL associated with GEI, and nine QTL were mapped in the flanking chromosomal regions for both GY and GEI. One major QTL Q.Gy.ui-1B.2, explaining up to 22% of grain yield, was identified in all six trials. Besides the additive effect of QTL associated with GY, interactions among QTL (QTL × QTL interaction, QTL × environment, and QTL × QTL × environment were also observed. When combining the interaction effects, QTL Q.Gy.ui-1B.2 along with other QTL explained up to 52% of the variation in grain yield over the six trials. This study suggests that QTL mapping of complex traits such as grain yield should include interaction effects of QTL and environments in marker-assisted selection.

  4. Dissection of Genetic Effects of Quantitative Trait Loci(QTL) in Transgenic Cotton

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    When alien DNA inserts into cotton genome in multi-copy manner,several QTL in cotton genome are disrupted,which are called dQTL in this study.Transgenic mutant line is near-isogenic to its recipient which is divergent for the dQTL from remaining QTL.So,a set of data from a transgenic

  5. CONTROVERSIAS EPISTEMOLÓGICAS Y METODOLÓGICAS ENTRE EL PARADIGMA CUALITATIVO Y CUANTITATIVO EN PSICOLOGÍA

    OpenAIRE

    Lucas Cuenya; Eliana Ruetti

    2010-01-01

    La distinción entre metodología cuantitativa y cualitativadefine dos campos de investigación que profesan postuladosparadigmáticos encontrados. El conocimiento científicose caracteriza por ser racional y objetivo, fáctico y verificable,caracterización que sintoniza, en buena medida, con losatributos del método cuantitativo. Por el contrario, el estudiocualitativo busca comprender los fenómenos dentro de suambiente usual, utilizando como datos descripciones de situaciones,eventos, personas, in...

  6. Estudio del análisis cualitativo y cuantitativo del extracto obtenido a partir de semilla de uva por HPLC

    OpenAIRE

    Sorolla, Sílvia; Flores Reyes, Antònia; Font Vallès, Joaquim; Ollé Otero, Lluís; Bacardit Dalmases, Anna

    2016-01-01

    Este trabajo tiene como principal objetivo desarrollar un análisis cualitativo y cuantitativo de los extractos tánicos como alternativa al método de análisis oficial ISO 14088 – IUC 32, de forma que se obtenga una correlación entre los dos métodos. Desde el punto de vista de la composición química, los taninos se clasifican en dos grandes grupos: i) los taninos condensados, también conocidos como flavanoles y taninos catequínicos, ii) los taninos hidrolizables, también llamados pirogáli...

  7. QTL Mapping of Chlorophyll Contents in Rice

    Institute of Scientific and Technical Information of China (English)

    SHEN Bo; ZHUANG Jie-yun; ZHANG Ke-qin; DAI Wei-min; LU Ye; FU Li-qing; DING Jia-ming; ZHENG Kang-le

    2007-01-01

    The objectives of this study were to investigate the genetic factors controlling the chlorophyll content of rice leaf using QTL analysis. A linkage map consisting of 207 DNA markers was constructed by using 247 recombinant inbred lines (RILs) derived from an indica-indica rice cross of Zhenshan97B×Milyang 46. In 2002 and 2003, the contents of chlorophyll a and b of the parents and the 247 RILs were measured on the top first leaf, top second leaf, and top third leaf, respectively. The software QTLMapper 1.6 was used to detect quantitative trait loci (QTLs), additive by environment (AE) interactions, and epistatic by environment (AAE) interactions. A total of eight QTLs in four intervals were detected to have significant additive effects on chlorophyll a and b contents at different leaf positions, with 1.96-9.77% of phenotypic variation explained by a single QTL, and two QTLs with significant AE interactions were detected. Epistasis analysis detected nine significant additive-by-additive interactions on chlorophyll a and b contents, and one pair of QTLs with significant AAE interactions was detected. On comparison with QTLs for yield traits detected in the same population, it was found in many cases that the QTLs for chlorophyll a and b contents and those for yield traits were located in the same chromosome intervals.

  8. Mapping of quantitative trait loci for thermosensitive genic male sterility in indica rice Mapeamento de controladores de caracteres quantitativos de macho-esterilidade gênica termossensível em arroz indica

    Directory of Open Access Journals (Sweden)

    Antonio Alberto Neves de Alcochete

    2005-12-01

    (14,65%, e a seleção zigótica foi apontada como causa da distorção. Não houve evidência de relação de causa-efeito entre a seleção zigótica e o controle de TGMS nesse cruzamento. Um mapa de ligação com 1.213,3 cM foi construído, baseado nos dados de segregação da população F2. Noventa e cinco marcadores microssatélites, de um total de 116 marcadores polimórficos, foram reunidos em 11 grupos de ligação, com uma média de 12,77 cM entre os locos marcadores adjacentes. Os dados fenotípicos e genotípicos permitiram a identificação de três novos locos controladores de caracteres quantitativos (QTL para a macho-esterilidade gênica termossensível em arroz indica. Dois dos QTLs foram mapeados em cromossomos que não tinham, ainda, sido associados ao controle genético da característica TGMS (cromossomos 1 e 12. O terceiro QTL foi mapeado no cromossomo 7, onde um loco TGMS (tms2 foi recentemente mapeado. Testes alélicos deverão ser realizados para verificar se as regiões mapeadas são as mesmas.

  9. Quantitative ultrasound and bone health Ultrasonido cuantitativo y salud ósea

    Directory of Open Access Journals (Sweden)

    Karen M Knapp

    2009-01-01

    Full Text Available This review of quantiative ultrasound (QUS and bone health uses the current literature to summarise the clinical and research effectiveness of QUS. QUS has been demonstrated to have the ability to predict fracture, particularly at the hip. However, the magnitude of prediction is fracture-site, measurement-site and device dependent. The correlations between dual X-ray absorptiometry (DXA and bone mineral density (BMD are weak to moderate, resulting in different subjects being identified as being at risk of fracture by the two different methods. QUS is sensitive to age and menopause-related changes and to clinical risk factors and lifestyle factors associated with osteoporosis. Whilst a limited ability of QUS to monitor therapeutic intervention has been demonstrated, this is still an area where it's poorer precision, in comparison to DXA, results in limited applicability. Whilst DXA remains the gold standard for the diagnosis of osteoporosis, QUS may be of use for the prediction of those at risk of future fracture in areas where there is limited availability of DXA.En esta revisión sobre el Ultrasonido Cuantitativo (QUS y su aplicación en la evaluación de la salud de los huesos, se analiza detalladamente la literatura disponible para conocer su papel y efectividad en la clínica cotidiana y en los programas de investigación. El QUS ha probado ser útil para predecir fracturas, especialmente de la cadera. Sin embargo, la exactitud de la predicción depende del sitio de fractura que se desea evaluar, del sitio anatómico donde se realiza la medición y de los diferentes instrumentos. La correlación que existe entre densitometría de rayos X (DXA y QUS puede ser débil a moderada, porque ambos métodos determinan diferentes componentes de la masa ósea relacionados con la presentación de las fracturas. El resultado del QUS como el del DXA también es sensible a la edad, cambios relacionados con la menopausia, a factores de riesgo clínicos y de

  10. Divergência genética em cultivares de morangueiro, baseada em caracteres morfoagronômicos

    Directory of Open Access Journals (Sweden)

    Rafael Gustavo Ferreira Morales

    2011-06-01

    Full Text Available Os caracteres morfoagronômicos são tradicionalmente usados na caracterização de cultivares e no estudo da divergência genética, contribuindo na definição de estratégias para o melhoramento genético. Este trabalho teve por objetivo avaliar a divergência genética por meio de caracteres morfoagronômicos de 11 cultivares de morangueiro (Aromas, Camarosa, Camino Real, Campinas, Diamante, Dover, Oso Grande, Sweet Charlie, Toyonoka, Tudla e Ventana, nas condições climáticas da região Centro-Sul do Paraná. Foram analisados 29 caracteres morfoagronômicos relacionados com a planta, folha, flor, fruto e aquênios do morangueiro. As similaridades genéticas foram calculadas por meio de análise multivariada e, os cultivares, agrupados com base na matriz de similaridade genética, usando-se UPGMA. Dentre os 29 caracteres morfoagronômicos avaliados, oito apresentaram diferenças não significativas (p < 0,05. A similaridade média foi de 38%, variando de 19 (aromas e camino real a 62% (Camino Real e Camarosa; Aromas e Sweet Charlie. O dendrograma alocou os cultivares em quatro grupos, contudo, essa divisão não foi coerente com a origem e genealogia dos cultivares. O cultivar Tudla apresenta elevado potencial "per se" para utilização em programas de melhoramento. O cruzamento mais promissor com base nos caracteres morfoagronômicos é entre os cultivares Camarosa e Campinas.

  11. Composite interval mapping of QTL for dynamic traits

    Institute of Scientific and Technical Information of China (English)

    GAO Huijiang; YANG Runqing

    2006-01-01

    Many economically important quantitative traits in animals and plants are measured repeatedly over time. These traits are called dynamic traits. Mapping QTL controlling the phenotypic profiles of dynamic traits has become an interesting topic for animal and plant breeders. However, statistical methods of QTL mapping for dynamic traits have not been well developed. We develop a composite interval mapping approach to detecting QTL for dynamic traits. We fit the profile of each QTL effect with Legendre polynomials. Parameter estimation and statistical test are performed on the regression coefficients of the polynomials under the maximum likelihood framework. Maximum likelihood estimates of QTL parameters are obtained via the EM algorithm. Results of simulation study showed that composite interval mapping can improve both the statistcial power of QTL detecting and the accuracy of parameter estimation relative to the simply interval mapping procedure where only one QTL is fit to each model. The method is developed in the context of an F2 mapping population, but extension to other types of mapping populations is straightforward.

  12. Evaluación de poblaciones de zapallo (Cucurbita moschata por caracteres de importancia agroindustrial

    Directory of Open Access Journals (Sweden)

    Magda Piedad Valdés Restrepo

    2010-01-01

    Full Text Available Se evaluó el potencial agroindustrial de siete poblaciones de zapallo (Cucurbita moschata derivadas de la recombinación de genotipos de alto desempeño en caracteres asociados con rendimiento y calidad de fruto. Los análisis de varianza para los resultados obtenidos en los semestres 2008-A y 2008-B permitieron detectar diferencias altamente significativas (P < 0.01 entre poblaciones, para todas las variables, con excepción de color de fruto en el semestre 2008-A. Las poblaciones 1 y 5 mostraron consistencia para el contenido de materia seca en los dos ciclos de recombinación genética.

  13. Evaluación de poblaciones de zapallo (Cucurbita moschata por caracteres de importancia agroindustrial

    Directory of Open Access Journals (Sweden)

    Vallejo Cabrera Franco Alirio

    2010-03-01

    Full Text Available Se evaluó el potencial agroindustrial de siete poblaciones de zapallo (Cucurbita moschata derivadas de la recombinación de genotipos de alto desempeño en caracteres asociados con rendimiento y calidad de fruto. Los análisis de varianza para los resultados obtenidos en los semestres 2008-A y 2008-B permitieron detectar diferencias altamente significativas (P < 0.01 entre poblaciones, para todas las variables, con excepción de color de fruto en el semestre 2008-A. Las poblaciones 1 y 5 mostraron consistencia para el contenido de materia seca en los dos ciclos de recombinación genética.

  14. mQTL-seq delineates functionally relevant candidate gene harbouring a major QTL regulating pod number in chickpea.

    Science.gov (United States)

    Das, Shouvik; Singh, Mohar; Srivastava, Rishi; Bajaj, Deepak; Saxena, Maneesha S; Rana, Jai C; Bansal, Kailash C; Tyagi, Akhilesh K; Parida, Swarup K

    2016-02-01

    The present study used a whole-genome, NGS resequencing-based mQTL-seq (multiple QTL-seq) strategy in two inter-specific mapping populations (Pusa 1103 × ILWC 46 and Pusa 256 × ILWC 46) to scan the major genomic region(s) underlying QTL(s) governing pod number trait in chickpea. Essentially, the whole-genome resequencing of low and high pod number-containing parental accessions and homozygous individuals (constituting bulks) from each of these two mapping populations discovered >8 million high-quality homozygous SNPs with respect to the reference kabuli chickpea. The functional significance of the physically mapped SNPs was apparent from the identified 2,264 non-synonymous and 23,550 regulatory SNPs, with 8-10% of these SNPs-carrying genes corresponding to transcription factors and disease resistance-related proteins. The utilization of these mined SNPs in Δ (SNP index)-led QTL-seq analysis and their correlation between two mapping populations based on mQTL-seq, narrowed down two (Caq(a)PN4.1: 867.8 kb and Caq(a)PN4.2: 1.8 Mb) major genomic regions harbouring robust pod number QTLs into the high-resolution short QTL intervals (Caq(b)PN4.1: 637.5 kb and Caq(b)PN4.2: 1.28 Mb) on chickpea chromosome 4. The integration of mQTL-seq-derived one novel robust QTL with QTL region-specific association analysis delineated the regulatory (C/T) and coding (C/A) SNPs-containing one pentatricopeptide repeat (PPR) gene at a major QTL region regulating pod number in chickpea. This target gene exhibited anther, mature pollen and pod-specific expression, including pronounced higher up-regulated (∼3.5-folds) transcript expression in high pod number-containing parental accessions and homozygous individuals of two mapping populations especially during pollen and pod development. The proposed mQTL-seq-driven combinatorial strategy has profound efficacy in rapid genome-wide scanning of potential candidate gene(s) underlying trait-associated high-resolution robust QTL(s), thereby

  15. Improving Drought Tolerance of Rice by Designed QTL Pyramiding

    Institute of Scientific and Technical Information of China (English)

    Z.K. Li; Y. Sun; L.H. Zhu; D. Dwivedi; Y.M. Gao; T.Q. Zheng; R. Lafitte; J.L. Xu; D. Mackill; B.Y. Fu; J.Domingo

    2007-01-01

    @@ Drought is the most important factor limiting rice yields in the rainfed areas of Asia. To overcome the problem, we developed a new strategy 'designed QTL pyramiding' to more efficiently develop drought tolerant (DT)rice cultivars.

  16. Relações entre os caracteres de maracujazeiro-azedo Relations between variables in passion fruit

    Directory of Open Access Journals (Sweden)

    Alessandro Dal'Col Lúcio

    2013-02-01

    Full Text Available O objetivo foi identificar os caracteres que mais merecem atenção em experimentos com a cultura do maracujá-azedo (Passiflora edulis Sims e verificar suas relações com o caractere dependente principal produção total de frutos. A partir dos dados de quatro experimentos com a cultura do maracujá calculou-se a matriz de correlações entre todos os caracteres e realizou-se o diagnóstico de multicolinearidade. Em seguida foi aplicada a análise de trilha entre os caracteres restantes. Para identificar os caracteres com maior contribuição na variabilidade total existente foi realizada uma análise de componentes principais. Os caracteres peso médio de polpa e número de frutos são os de maior correlação com o peso total de frutos de maracujá. O teor de sólidos solúveis total, o peso médio de frutos, o comprimento e o diâmetro do fruto, a espessura da casca e a percentagem de polpa tem baixa correlação com o peso total de frutos de maracujá.The aim of this research was to indentify the variables which deserve more attention in experiments with passion fruit (Passiflora edulis Sims and verify their relations with the principal dependent variable: total fruit yield. From data of four experiments with passion fruit culture it was calculated the correlation matrix between the variables and performed the diagnosis of multicollinearity, then applied the path analysis between the variables left. To identify the variables with more contribution in the total variability it was performed analysis of main components. The pulp weight and the fruit number have higher correlation with the fruits total weight. The total soluble solids rate, the average weight of fruits, length and fruit diameter, peel thickness and the pulp percentage has lower correlation with the fruit total weight of passion fruit.

  17. Seguimiento cuantitativo de reacciones de resinas epoxi mediante espectroscopia de infrarrojo cercano y métodos de resolución de curvas

    OpenAIRE

    Garrido, Mariano Enrique

    2006-01-01

    En esta Tesis doctoral que lleva por título: "Seguimiento cuantitativo de reacciones de resinas epoxi mediante espectroscopía de infrarrojo cercano y métodos de resolución de curvas" se han planteado dos objetivos generales. En el primer objetivo se ha propuesto evaluar la capacidad de la espectrosocopía de infrarrojo cercano, asistida mediante la Resolución Multivariante de Curvas basada en la optimización por Mínimos Cuadrados Alternados, para realizar el seguimiento cuantitativo reacciones...

  18. Primera aproximación a un estudio cuantitativo de la cultura y clima organizacional de un hospital público de la provincia de Buenos Aires

    OpenAIRE

    Góngora, Norberto H.; Nóbile, Cecilia

    2008-01-01

    Este trabajo es un estudio de casos que trata de describir el clima y la cultura organizacional de una entidad cuyos integrantes voluntariamente accedieron a responder un cuestionario que trata de discernir los valores, las presunciones básicas (a través de los indicadores de Hofstede) y demás características de la cultura organizacional. Es una descripción de los resultados cuantitativos. Quiere plantearse que los estudios cuantitativos de clima y cultura organizacional son limitados en c...

  19. CONTROVERSIAS EPISTEMOLÓGICAS Y METODOLÓGICAS ENTRE EL PARADIGMA CUALITATIVO Y CUANTITATIVO EN PSICOLOGÍA

    Directory of Open Access Journals (Sweden)

    Lucas Cuenya

    2010-11-01

    Full Text Available La distinción entre metodología cuantitativa y cualitativadefine dos campos de investigación que profesan postuladosparadigmáticos encontrados. El conocimiento científicose caracteriza por ser racional y objetivo, fáctico y verificable,caracterización que sintoniza, en buena medida, con losatributos del método cuantitativo. Por el contrario, el estudiocualitativo busca comprender los fenómenos dentro de suambiente usual, utilizando como datos descripciones de situaciones,eventos, personas, interacciones, documentos, etc.Este enfoque se utiliza para descubrir y refinar preguntas deinvestigación, pero solo a veces se ponen a prueba las hipótesis.En este trabajo se analizan las principales característicasde las metodologías cuantitativa y cualitativa, y se discute laimportancia de asegurar el control y la rigurosidad científicaal analizar los fenómenos complejos del comportamiento.

  20. Relações entre caracteres de cenoura para sistemas de cultivos orgânico e convencional

    Directory of Open Access Journals (Sweden)

    Giovani Olegário da Silva

    2010-10-01

    Full Text Available De acordo com a estratégia de seleção e o ganho que ela proporcionará, pode-se orientar, de maneira mais efetiva, um programa de melhoramento, bem como predizer o sucesso do esquema seletivo adotado. O objetivo deste trabalho foi verificar a estabilidade das relações entre caracteres fenotípicos a partir de populações de cenoura cultivadas em sistemas de produção orgânico e convencional. Os experimentos foram conduzidos na Embrapa Hortaliças, DF. Duas populações de cenoura em fase de melhoramento e quatro cultivares comerciais foram plantados em novembro de 2007 no campo nos dois sistemas de produção, com delineamento de blocos casualizados com quatro repetições e parcelas de 1 m², com 100 plantas por parcela. Aos 90 dias após o semeio, 20 raízes por parcela foram colhidas e avaliadas para caracteres fenotípicos. Foi realizada análise de variância com determinação da interação entre tratamentos e sistemas de produção, correlações fenotípicas, análise de trilha e os ganhos com as seleções direta e correlacionada. Observouse que a quase totalidade das correlações medianas acima de 0,30, bem como os maiores efeitos diretos da análise de trilha e os maiores ganhos diretos e indiretos estimados, foi repetida nos dois sistemas, indicando que eles foram muito semelhantes na expressão da relação entre os caracteres. Assim, o melhoramento visando aos caracteres avaliados não precisa ser realizado em ambas as áreas de cultivos orgânico e convencional.

  1. Wheat kernel dimensions: how do they contribute to kernel weight at an individual QTL level?

    Indian Academy of Sciences (India)

    Fa Cui; Anming Ding; Jun Li; Chunhua Zhao; Xingfeng Li; Deshun Feng; Xiuqin Wang; Lin Wang; Jurong Gao; Honggang Wang

    2011-12-01

    Kernel dimensions (KD) contribute greatly to thousand-kernel weight (TKW) in wheat. In the present study, quantitative trait loci (QTL) for TKW, kernel length (KL), kernel width (KW) and kernel diameter ratio (KDR) were detected by both conditional and unconditional QTL mapping methods. Two related F8:9 recombinant inbred line (RIL) populations, comprising 485 and 229 lines, respectively, were used in this study, and the trait phenotypes were evaluated in four environments. Unconditional QTL mapping analysis detected 77 additive QTL for four traits in two populations. Of these, 24 QTL were verified in at least three trials, and five of them were major QTL, thus being of great value for marker assisted selection in breeding programmes. Conditional QTL mapping analysis, compared with unconditional QTL mapping analysis, resulted in reduction in the number of QTL for TKW due to the elimination of TKW variations caused by its conditional traits; based on which we first dissected genetic control system involved in the synthetic process between TKW and KD at an individual QTL level. Results indicated that, at the QTL level, KW had the strongest influence on TKW, followed by KL, and KDR had the lowest level contribution to TKW. In addition, the present study proved that it is not all-inclusive to determine genetic relationships of a pairwise QTL for two related/causal traits based on whether they were co-located. Thus, conditional QTL mapping method should be used to evaluate possible genetic relationships of two related/causal traits.

  2. Incertidumbre doble cuadrática y asociación entre caracteres.

    Directory of Open Access Journals (Sweden)

    López Menéndez, Ana Jesús

    2003-01-01

    Full Text Available Las medidas de información proporcionan un contexto adecuado para el estudio de la asociación entre dos o más características. Algunos autores como C. Rajski (1961, 1964, P. Gil (1981, N. Muñoz y M. Alvargonzález (1991, 1992, entre otros, han definido indicadores de asociación entre caracteres basados en medidas de incertidumbre, incertidumbre útil e inquietud. A partir de la medida de incertidumbre doble cuadrática se define un coeficiente de asociación entre dos atributos y se estudian sus propiedades. A continuación se extiende la medida al caso de más de dos características, definiendo una medida de dependencia múltiple y medidas de asociación parcial. El estudio concluye con una aplicación de las medidas presentadas al análisis de la asociación a partir de información proporcionada por la Encuesta de Población Activa (EPA.

  3. QTL and QTL x Environment Effects on Agronomic and Nitrogen Acquisition Traits in Rice

    Institute of Scientific and Technical Information of China (English)

    Senapathy Senthilvel; Kunnummal Kurungara Vinod; Palaniappan Malarvizhi; Marappa Maheswaran

    2008-01-01

    Agricultural environments deteriorate due to excess nitrogen application.Breeding for low nitrogen responsive genotypes can reduce soil nitrogen input.Rice genotypes respond variably to soil available nitrogen.The present study attempted quantification of genotype x nitrogen level interaction and mapping of quantitative trait loci (QTLs) associated with nitrogen use efficiency (NUE) and other associated agronomic traits.Twelve parameters were observed across a set of 82 double haploid (DH) lines derived from IR64/Azucena.Three nitrogen regimes namely,native (0 kg/ha; no nitrogen applied),optimum (100 kg/ha) and high (200 kg/ha) replicated thrice were the environments.The parents and DH lines were significantly varying for all traits under different nitrogen regimes.All traits except plant height recorded significant genotype x environment interaction.Individual plant yield was positively correlated with nitrogen use efficiency and nitrogen uptake.Sixteen QTLs were detected by composite interval mapping.Eleven QTLs showed significant QTL x environment interactions.On chromosome 3,seven QTLs were detected associated with nitrogen use,plant yield and associated traits.A QTL region between markers RZ678,RZ574 and RZ284 was associated with nitrogen use and yield.This chromosomal region was enriched with expressed gene sequences of known key nitrogen assimilation genes.

  4. Capacidade de combinação de genitores de batata para caracteres de aparência e rendimento de tubérculos

    Directory of Open Access Journals (Sweden)

    Giovani Olegário da Silva

    2013-08-01

    Full Text Available O objetivo deste trabalho foi estimar as capacidades de combinação de genitores de batata, em gerações iniciais de seleção. Os experimentos foram realizados em Pelotas e Canoinhas. Foram estudadas 12 famílias, derivadas de dois grupos de genitores, cruzados em esquema dialelo parcial (3 x 4 'Eliza', 'C-1730-7-94' e 'C-1742-8-95'; 'Shepody', 'Asterix', 'White Lady' e 'Caesar'. As famílias foram avaliadas, na geração de plântula e na primeira geração de campo, para caracteres componentes de aparência e rendimento de tubérculos. Os dados foram submetidos às análises de variância e dialélica parcial. No conjunto de caracteres avaliados, verificou-se superioridade de efeitos significativos para a capacidade geral de combinação, em relação à capacidade específica de combinação, indicando predominância de efeitos aditivos dos genes, no controle dos caracteres. Em relação à capacidade geral de combinação, 'White Lady' é o genitor mais destacado positivamente, contribuindo com genes de ação aditiva para a melhoria, tanto dos caracteres que compõem a aparência dos tubérculos, quanto dos caracteres de rendimento. Quanto à capacidade específica de combinação, o cruzamento ('C1730-7-94' x 'White Lady' é o mais indicado para a geração de famílias superiores quanto a caracteres de aparência e a caracteres componentes do rendimento de tubérculos.

  5. Regeneração in vitro de anteras de arroz irrigado (Oryza sativa L. e mapeamento de QTL associado

    Directory of Open Access Journals (Sweden)

    Lannes Sérgio Dias

    2004-01-01

    Full Text Available A baixa taxa de regeneração in vitro de alguns cultivares de arroz da subespécie indica limita a utilização de técnicas de cultura de anteras como ferramenta para o desenvolvimento de novos cultivares. A identificação de regiões genômicas associadas à formação de calos e regeneração de plantas, a partir do cultivo de anteras, poderá permitir a transferência do caráter por seleção assistida. Duas populações de retrocruzamento foram utilizadas para o mapeamento genético e estudo destes caracteres, sendo Taipei 309// BRS 7 "Taim"/Taipei 309 (53 genótipos e BRS 7 "Taim"// BRS 7 "Taim"/Taipei 309 (74 genótipos. Duzentas anteras imaturas de cada genótipo utilizado no estudo foram inoculadas em meio NL líquido e, após 40 dias, os calos formados foram transferidos para o meio MS sólido para regeneração de plantas. Todas as plantas doadoras de anteras foram usadas na extração de DNA genômico e sete primers RAPD foram utilizados na geração de marcadores para a construção dos mapas de ligação dos retrocruzamentos estudados. A taxa de formação de calos variou de 2,27 a 3,36% e a taxa de regeneração de plantas 1,38 a 1,82%, não se diferenciando significativamente. Seis grupos de ligação foram obtidos, três em cada população. Um QTL com LOD 3,10 foi detectado para o caráter formação de calos na população Taipei 309 // BRS 7 "Taim" / Taipei 309. Nenhum QTL foi detectado para a característica regeneração de plantas.

  6. Consistent effects of a major QTL for thermal resistance in field-released Drosophila melanogaster

    DEFF Research Database (Denmark)

    Loeschcke, Volker; Kristensen, Torsten Nygård; Norry, Fabian M

    2011-01-01

    Molecular genetic markers can be used to identify quantitative trait loci (QTL) for thermal resistance and this has allowed characterization of a major QTL for knockdown resistance to high temperature in Drosophila melanogaster. The QTL showed trade-off associations with cold resistance under lab...

  7. Linear models for joint association and linkage QTL mapping

    Directory of Open Access Journals (Sweden)

    Fernando Rohan L

    2009-09-01

    Full Text Available Abstract Background Populational linkage disequilibrium and within-family linkage are commonly used for QTL mapping and marker assisted selection. The combination of both results in more robust and accurate locations of the QTL, but models proposed so far have been either single marker, complex in practice or well fit to a particular family structure. Results We herein present linear model theory to come up with additive effects of the QTL alleles in any member of a general pedigree, conditional to observed markers and pedigree, accounting for possible linkage disequilibrium among QTLs and markers. The model is based on association analysis in the founders; further, the additive effect of the QTLs transmitted to the descendants is a weighted (by the probabilities of transmission average of the substitution effects of founders' haplotypes. The model allows for non-complete linkage disequilibrium QTL-markers in the founders. Two submodels are presented: a simple and easy to implement Haley-Knott type regression for half-sib families, and a general mixed (variance component model for general pedigrees. The model can use information from all markers. The performance of the regression method is compared by simulation with a more complex IBD method by Meuwissen and Goddard. Numerical examples are provided. Conclusion The linear model theory provides a useful framework for QTL mapping with dense marker maps. Results show similar accuracies but a bias of the IBD method towards the center of the region. Computations for the linear regression model are extremely simple, in contrast with IBD methods. Extensions of the model to genomic selection and multi-QTL mapping are straightforward.

  8. IDENTIFICACIÓN DE QTLs ASOCIADOS A CARACTERES DE ARQUITECTURA VEGETAL EN YUCA (Manihot esculenta

    Directory of Open Access Journals (Sweden)

    Camilo López

    2015-11-01

    Full Text Available RESUMENLa yuca (Manihot esculenta es el cuarto cultivo en importancia a nivel mundial como fuente de calorías para la población humana después del arroz, el azúcar y el maíz, posicionándose por esta razón como un cultivo primordial para la seguridad alimentaria. Su arquitectura ha sido considerada como un factor clave que subyace a la fisiología del rendimiento, relacionando características morfológicas con productividad. En este trabajo se evaluaron diferentes características de arquitectura vegetal en yuca. Los caracteres fueron evaluados en una población F1 compuesta por 133 hermanos completos (familia K sembrados en dos lugares biogeográficamente diferentes: La Vega (Cundinamarca y Arauca (Arauca en Colombia. Las características evaluadas relacionadas con la arquitectura vegetal fueron altura de la planta (AT, número de brotes (NB, longitud entrenudos (LE, número de raíces (NR, peso de raíces (PR, pigmentación del peciolo (PP, área de la hoja (AH y tipo de hoja (TH. A partir de los datos obtenidos y empleando un mapa genético de alta densidad basado en SNPs (Single Nucleotide Polymorphisms se llevó a cabo un análisis de QTLs (Quantitative Trait Loci. Se lograron identificar tres QTLs para La Vega asociados con los caracteres altura total, número de brotes y área de la hoja. Para Arauca se detectaron tres QTLs asociados con altura total, longitud de entrenudos y número de brotes. Los QTLs se distribuyeron en cuatro grupos de ligamiento y explicaron entre 18,93 y 41,92 % de la variación genética.ABSTRACTCassava (Manihot esculenta is the fourth most important crop worldwide as a source of calories for the human population after rice, sugar and corn and therefore it is considered as a staple crop. Cassava’s architecture has been considered as a key factor underlying the physiology of yield, relating morphological traits with productivity. In this work different characteristics of plant architecture were evaluated in

  9. Variabilidade e correlações entre caracteres agronômicos em caupi (Vigna unguiculata

    Directory of Open Access Journals (Sweden)

    Lopes Ângela Celis de Almeida

    2001-01-01

    Full Text Available O caupi (Vigna unguiculata (L. Walp é um alimento básico das populações do Nordeste brasileiro, devendo merecer atenção com vistas a melhoria da qualidade de grãos, resistência a doenças e pragas e aumento de produtividade. Este trabalho teve por objetivo estudar a variabilidade e o potencial genético de 28 linhagens, escolhidas após uma seleção para cor, tamanho de grãos e resistência a viroses. A produtividade apresentou coeficiente de variação genético de 23,90%, e o valor agronômico, de 3,56%. O número de vagens por pedúnculo apresentou a menor estimativa do coeficiente de determinação genético (4,51%, e o peso de 100 grãos, a maior (81,74%. O coeficiente de determinação genético da produtividade foi de 34,15%. As maiores estimativas de ganho genético foram as do peso de 100 grãos (21,73% e da produtividade (19,77%. As correlações genotípicas foram superiores às fenotípicas e às de ambiente, destacando-se as correlações entre número de ramos secundários e produtividade (68,13%, e valor agronômico e produtividade (100%. Estes resultados mostram amplas possibilidades de seleção entre as linhagens com relação à maioria dos caracteres estudados.

  10. Tesis doctorales defendidas por las profesoras de la Universidad de Granada (1975-1990: análisis cuantitativo

    Directory of Open Access Journals (Sweden)

    Muñoz Muñoz, Ana María

    2004-12-01

    Full Text Available This paper studies the doctoral dissertations read by the lecturers at the University of Granada from 1975-1990 from a gender perspective. Starting from a quantitative analysis their production is examined by disciplines, areas of knowledge and year. Aspects related to the distribution, direction or co-direction of the doctoral theses are also studied. This paper attempts to answer two questions: Who has directed the female lecturers dissertations? And whose theses have they directed once they have become doctors?

    Se estudian las tesis doctorales defendidas por las profesoras de la Universidad de Granada durante el periodo 1975-1990 desde una perspectiva de género. A partir de un análisis cuantitativo se analiza su producción por disciplinas, áreas de conocimiento y años. También se estudian los aspectos de difusión y dirección o codirección de las tesis. El trabajo pretende dar respuesta a dos preguntas: ¿Quiénes han dirigido las tesis de las profesoras?, y ¿A quiénes han dirigido éstas una vez que han sido doctoras?

  11. Reciprocidad y convergencia de los enfoques cuantitativo y cualitativo: Una experiencia de investigación en salud

    Directory of Open Access Journals (Sweden)

    Alexis Romero Salazar

    1997-12-01

    Full Text Available En este ensayo se comentan los cambios ocurridos en el paradigma clásico de la ciencia -de orientacion cuantitativa- y se presentan algunas ideas en relación con sus implicaciones para la investigación social. Al respecto, se discuten los señalamientos en torno a la insuficiencia de aquel y se expone una estrategia metodológica en la que convergen los enfoques cuantitativo y cualitativo. El estudio de la representación social brinda tal posibilidad, en virtud de la naturaleza de sus elementos constitutivos, que pueden ser abordados, unos desde fuera y a partir de su consideración estadística y otros desde adentro, asumiendo su formulación en el habla. El primer acercamiento, entonces, se concreta en el número que es la entidad mediante la cual se hace el análisis; en el segundo, la aproximación se produce a través de la palabra.

  12. Joint QTL analyses for partial resistance to Phytophthora sojae using six nested inbred populations with heterogeneous conditions

    Science.gov (United States)

    Partial resistance to Phytophthora sojae in soybean is controlled by multiple quantitative trait loci (QTL). With traditional QTL mapping approaches, power to detect these QTL, frequently of small effect, can be limited by population size. Joint linkage QTL analysis of nested recombinant inbred li...

  13. Identifying QTL for fur quality traits in mink (Neovison vison)

    DEFF Research Database (Denmark)

    Thirstrup, Janne Pia; Anistoroaei, Razvan Marian; Guldbrandtsen, Bernt;

    2012-01-01

    Mapping of quantitative trait loci (QTL) affecting fur quality traits (guard hair length, guard hair thikness, and density of woll) was performed in a 3-generation population (F2-design). In the parental generation, Nordic wild mink were crossed reciprocally with American short nap mink. Twenty one...... wade on all genotyped mink by Kopenhagen Fur. The QTL analyses were performed by least square regression implemented in the software Grid QTL. Evidence was found for QTL for the fur quality on eight autosomal chromosomes (LOD score >3.0). QTL were detected for guard hair thickness on chromosomes 1, 2...

  14. Mapping Isoflavone QTL with Main, Epistatic and QTL × Environment Effects in Recombinant Inbred Lines of Soybean

    OpenAIRE

    Yan Wang; Yingpeng Han; Xue Zhao; Yongguang Li; Weili Teng; Dongmei Li; Yong Zhan; Wenbin Li

    2015-01-01

    Soybean (Glycine max (L.) Merr.) isoflavone is important for human health and plant defense system. To identify novel quantitative trait loci (QTL) and epistatic QTL underlying isoflavone content in soybean, F5:6, F5:7 and F5:8 populations of 130 recombinant inbred (RI) lines, derived from the cross of soybean cultivar 'Zhong Dou 27' (high isoflavone) and 'Jiu Nong 20' (low isoflavone), were analyzed with 95 new SSR markers. A new linkage map including 194 SSR markers and covering 2,312 cM wi...

  15. Mapping carcass and meat quality QTL on Sus Scrofa chromosome 2 in commercial finishing pigs

    Directory of Open Access Journals (Sweden)

    van Kampen Tony A

    2009-01-01

    Full Text Available Abstract Quantitative trait loci (QTL affecting carcass and meat quality located on SSC2 were identified using variance component methods. A large number of traits involved in meat and carcass quality was detected in a commercial crossbred population: 1855 pigs sired by 17 boars from a synthetic line, which where homozygous (A/A for IGF2. Using combined linkage and linkage disequilibrium mapping (LDLA, several QTL significantly affecting loin muscle mass, ham weight and ham muscles (outer ham and knuckle ham and meat quality traits, such as Minolta-L* and -b*, ultimate pH and Japanese colour score were detected. These results agreed well with previous QTL-studies involving SSC2. Since our study is carried out on crossbreds, different QTL may be segregating in the parental lines. To address this question, we compared models with a single QTL-variance component with models allowing for separate sire and dam QTL-variance components. The same QTL were identified using a single QTL variance component model compared to a model allowing for separate variances with minor differences with respect to QTL location. However, the variance component method made it possible to detect QTL segregating in the paternal line (e.g. HAMB, the maternal lines (e.g. Ham or in both (e.g. pHu. Combining association and linkage information among haplotypes improved slightly the significance of the QTL compared to an analysis using linkage information only.

  16. Mapping multiple QTL using linkage disequilibrium and linkage analysis information and multitrait data

    Directory of Open Access Journals (Sweden)

    Goddard Mike E

    2004-05-01

    Full Text Available Abstract A multi-locus QTL mapping method is presented, which combines linkage and linkage disequilibrium (LD information and uses multitrait data. The method assumed a putative QTL at the midpoint of each marker bracket. Whether the putative QTL had an effect or not was sampled using Markov chain Monte Carlo (MCMC methods. The method was tested in dairy cattle data on chromosome 14 where the DGAT1 gene was known to be segregating. The DGAT1 gene was mapped to a region of 0.04 cM, and the effects of the gene were accurately estimated. The fitting of multiple QTL gave a much sharper indication of the QTL position than a single QTL model using multitrait data, probably because the multi-locus QTL mapping reduced the carry over effect of the large DGAT1 gene to adjacent putative QTL positions. This suggests that the method could detect secondary QTL that would, in single point analyses, remain hidden under the broad peak of the dominant QTL. However, no indications for a second QTL affecting dairy traits were found on chromosome 14.

  17. QTL list - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us PGD...nism name, papers and trait. Data file File name: pgdbj_dna_marker_linkage_map_pl...ant_qtl_list.zip File URL: ftp://ftp.biosciencedbc.jp/archive/pgdbj-dna-marker-linkage-map/LATEST/pgdbj_dna_...marker_linkage_map_plant_qtl_list.zip File size: 22.6 KB Simple search URL http://togodb.biosciencedbc.jp/togodb/view/pgd...Policy | Contact Us QTL list - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive ...

  18. Simultaneous QTL detection and genomic breeding value estimation using high density SNP chips

    Directory of Open Access Journals (Sweden)

    Veerkamp Roel F

    2010-03-01

    Full Text Available Abstract Background The simulated dataset of the 13th QTL-MAS workshop was analysed to i detect QTL and ii predict breeding values for animals without phenotypic information. Several parameterisations considering all SNP simultaneously were applied using Gibbs sampling. Results Fourteen QTL were detected at the different time points. Correlations between estimated breeding values were high between models, except when the model was used that assumed that all SNP effects came from one distribution. The model that used the selected 14 SNP found associated with QTL, gave close to unity correlations with the full parameterisations. Conclusions Nine out of 18 QTL were detected, however the six QTL for inflection point were missed. Models for genomic selection were indicated to be fairly robust, e.g. with respect to accuracy of estimated breeding values. Still, it is worthwhile to investigate the number QTL underlying the quantitative traits, before choosing the model used for genomic selection.

  19. Comunicar en 140 caracteres. Cómo usan Twitter los comunicadores en España

    Directory of Open Access Journals (Sweden)

    Miguel de Aguilera Moyano

    2016-01-01

    Full Text Available La irrupción de Twitter parece estar cambiando las prácticas informativas. De ahí que bastantes investigaciones recientes partan de su popularidad entre los comunicadores para concluir que sirve para aumentar la interactividad con los lectores. Pero ¿hasta qué punto es cierta su contribución a un periodismo más abierto a la ciudadanía? Este trabajo busca sobre todo contribuir a clarificar dos cuestiones principales: qué usos concretos dan a Twitter los periodistas y hasta qué punto se mantiene esa interacción ?de ida y vuelta? con la ciudadanía gracias a este medio. Se basa en el análisis cuantitativo de una muestra de casi cinco millones de tuits correspondientes a 1.504 comunicadores de medios españoles; probablemente, la mayor muestra estudiada hasta ahora. El análisis constata la existencia de un Twitter a dos velocidades (con una minoría de comunicadores muy influyente y una mayoría con escaso impacto, pero una interacción con los seguidores prácticamente nula. Salvo excepciones, los comunicadores establecen en Twitter relaciones muy endogámicas, respondiendo, retuiteando y mencionando a colegas, desaprovechando así las potencialidades multidireccionales que ofrece esta plataforma. Esta investigación amplía la base empírica con la que pensar y discutir el alcance y los límites de la participación de los usuarios en los fenómenos informativos, que tantos autores han teorizado, quizá, con demasiado entusiasmo y, sin duda, con una perspectiva en cierta medida utópica.

  20. Implementation of SNPs in pig genetics: LD and QTL analysis

    NARCIS (Netherlands)

    Jungerius, B.J.

    2004-01-01

    The aim of this thesis was the implementation and application of SNP markers in animal breeding and genetics. The emphasis was on the analysis of fatness traits in pigs, in particular of the imprinted QTL region on SSC2p. Several aspects of the implemetation of SNP markers in genetic analysis of

  1. Influence of outliers on QTL mapping for complex traits

    Institute of Scientific and Technical Information of China (English)

    Yousaf HAYAT; Jian YANG; Hai-ming XU; Jun ZHU

    2008-01-01

    A method was proposed for the detection of outliers and influential observations in the framework of a mixed linear model, prior to the quantitative trait locus (QTL) mapping analysis. We investigated the impact of outliers on QTL mapping for complex traits in a mouse BXD population, and observed that the dropping of outliers could provide the evidence of additional QTL and epistatic loci affecting the 1 stBrain-OB and the 2ndBrain-OB in a cross of the abovementioned population. The results could also reveal a remarkable increase in estimating heritabilities of QTL in the absence of outliers. In addition, simulations were conducted to investigate the detection powers and false discovery rates (FDRs) of QTLs in the presence and absence of outliers. The results suggested that the presence of a small proportion of outliers could increase the FDR and hence decrease the detection power of QTLs. A drastic increase could be obtained in the estimates of standard errors for position, additive and additivex environment interaction effects of QTLs in the presence of outliers.

  2. Bayesian multi-QTL mapping for growth curve parameters

    DEFF Research Database (Denmark)

    Heuven, Henri C M; Janss, Luc L G

    2010-01-01

    segregating QTL using a Bayesian algorithm. Results For each individual a logistic growth curve was fitted and three latent variables: asymptote (ASYM), inflection point (XMID) and scaling factor (SCAL) were estimated per individual. Applying an 'animal' model showed heritabilities of approximately 48...

  3. Biphasic survival analysis of trypanotolerance QTL in mice

    NARCIS (Netherlands)

    Koudante, O.D.; Thomson, P.C.; Bovenhuis, H.; Iraqi, F.; Gibson, J.P.; Arendonk, van J.A.M.

    2008-01-01

    A marker-assisted introgression (MAI) experiment was conducted to transfer trypanotolerance quantitative trait loci (QTL) from a donor mouse strain, C57BL/6, into a recipient mouse strain, A/J. The objective was to assess the effect of three previously identified chromosomal regions on mouse chromos

  4. DISPONIBILIDAD LÉXICA MATEMÁTICA: ANALISIS CUANTITATIVO Y CUALITATIVO LEXICAL AVAILABILITY IN MATHEMATICS: A QUANTITATIVE AND QUALITATIVE ANALYSIS

    Directory of Open Access Journals (Sweden)

    PAULA URZÚA C

    2006-12-01

    Full Text Available Se aplicó una prueba de disponibilidad léxica a tres grupos de estudiantes de la carrera Ingeniería Civil Matemática de la Universidad de Concepción y a un grupo de docentes de dicha carrera con el objeto de conocer cuánto y cuál es el léxico disponible que poseen profesores y alumnos en el área de las matemáticas. Igualmente interesa saber si existe algún tipo de crecimiento léxico en los alumnos a medida que aumentan sus años de estudio. La investigación se alejó de los parámetros tradicionales de los estudios de disponibilidad léxica en lo que respecta a los centros de interés, pues hubo que crear centros llamados específicos que fueran capaces de extraer el léxico disponible del área en cuestión: la matemática. Los resultados mostraron que tanto los análisis cuantitativos tradicionales como los biplots descriptivos apoyaron las hipótesis de trabajoA test of lexical availability was applied to students and Faculty members of the Mathematical Engineering School at the University of Concepción, Chile, in order to find out how much and which specific lexicon belonging to mathematical disciplines is handled by them. It is expected that lexical availability increases according to the number of years of study and also that the vocabulary becomes more specific and pertinent as the subjects get close to their graduation. Quantitative analyses as well as descriptive biplots support the hypotheses suggested at the beginning of the research

  5. Discapacidad y pobreza en las villas de la ciudad de Buenos Aires. Reflexiones a partir de algunos datos cuantitativos

    Directory of Open Access Journals (Sweden)

    Liliana Pantano

    2015-09-01

    Full Text Available Antecedentes. Este artículo se encuadra en una investigación sobre las villas de la ciudad de Buenos Aires llevada a cabo en la Universidad Católica Argentina y orientada a indagaciones epistemológicas y empíricas referidas a la relación entre la pobreza y la existencia de discapacidad en los sectores más pobres entre 2011-2012, y como reflejo de los efectos de la creciente urbanización que caracteriza a América Latina. Objetivo. El objetivo central de este artículo ha sido conocer cómo afectan estos entornos urbanos fragmentados, altamente carenciados y con restringidas oportunidades de participación, la vida de las personas con discapacidad y de sus hogares. Materiales y métodos. Se trabajó con datos cuantitativos de fuentes primarias y secundarias, siendo la principal unidad de análisis los hogares con al menos un miembro con discapacidad. Resultados. Se compararon hogares con y sin presencia de discapacidad, estableciéndose semejanzas y diferencias, y se obtuvieron resultados en relación al clima educativo y a la educación, a la atención de la salud, a la vivienda, al saneamiento, a factores referidos al hambre, la violencia y las adicciones, el rechazo y la discriminación, así como a la ayuda prestada por distintas organizaciones. Conclusión. Se concluyó en el señalamiento de tendencias diferenciales por edad en la manifestación de la discapacidad asociada a la pobreza y algunas consideraciones referidas a la investigación social en este campo.

  6. ASOCIACIÓN DE CARACTERES EN GENOTIPOS DE ARROZ (Oryza sativa L. SELECCIONADOS PARA TOLERANCIA A LAS BAJAS TEMPERATURAS

    Directory of Open Access Journals (Sweden)

    R. Morejón

    2006-01-01

    Full Text Available En áreas de la Estación Experimental del Arroz Los Palacios, perteneciente al Instituto Nacional de Ciencias Agrícolas, se desarrolló el presente trabajo, con el objetivo de realizar un análisis de asociación de 12 caracteres evaluados en siembra temprana de frío, a un grupo de genotipos seleccionados para tolerancia a las bajas temperaturas. Para el análisis estadístico de los datos se utilizaron las técnicas estadísticas multivariadas de Componentes Principales y Conglomerados. Las mejores asociaciones estuvieron dadas por la longitud de la panícula, granos llenos por panícula y rendimiento, así como entre la altura a los 20 y 30 días después de la germinación (ddg. Además, junto a las variables anteriores, los granos vanos y el número de hijos a los 60 ddg fueron los caracteres de mayor importancia para el análisis, constituyendo las asociaciones descritas una información esencial, para la selección de materiales tolerantes a las bajas temperaturas en los programas de mejoramiento genético en el cultivo del arroz.

  7. Valor genético estimado y qtl que afecta el porcentaje de sólidos totales en la raza bovina gyr

    Directory of Open Access Journals (Sweden)

    Ariosto Ardila Silva

    2010-12-01

    Full Text Available Además de todos los progresos que ha representado el mejoramiento genético animal clásico, este presenta algunas limitaciones como en algunos casos donde el fenotipo no se expresa en el individuo. Con el advenimiento de las enzimas de restricción, del secuenciamiento y de la amplificación del ADN, fue posible el uso de marcadores moleculares asociados con loci de características cuantitativas (QTL, como herramienta que auxilia y perfecciona el mejoramiento genético animal por medio de la selección asistida por marcadores (MAS, lo que aumenta el mérito genético para características de difícil medida, baja heredabilidad y limitadas por el sexo. La raza bovina gyr se caracteriza por su rusticidad y adaptación al trópico, y presenta una buena producción de leche para los países tropicales, por lo que es fundamental en la conformación de la raza gyrholando (5/8holstein y 3/8 gyr. El propósito del presente estudio fue complementar el análisis cuantitativo con la genética molecular, en el mejoramiento genético de la característica porcentaje de sólidos totales en la razagyr en Brasil. Catorce familias (toros gyr con 657 hijas fueron analizadas, siendo el promedio 0,095 % y la desviación estándar 0,1923 del valor genético estimadopara porcentaje de sólidos totales. Al utilizar 27 marcadores microsatélites en el análisis a travésde las 14 familias para porcentaje de sólidos totales en el cromosoma 6, un QTL fue identificado con P< 0,05 y F = 2,34 en la posición 58 cm, próximo al marcador MNB-208 (60,21 cm. Al emplear las familias3 y 4, las más significativas, el mismo QTL fue identificado con P < 0,01 y F = 7,61, pero en la posición 58 cm, próximo al marcador MNB-208.

  8. UN ESTUDIO DESCRIPTIVO CUANTITATIVO

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    María Soledad Aguilera

    2015-01-01

    Full Text Available Este artículo presenta resultados de una investigación transeccional descriptiva, sobre las metas de aprendizaje que eligen estudiantes secundarios avanzados. Se pretendió conocer y describir las eleccion es motivacionales de alumnos en diferentes situaciones pedagógicas de aula. Los datos se obtuvieron implementando una Encuesta de Relatos Motivacionales, administrada a 126 alumnos de cuatro escuelas públicas de la ciudad de Río Cuarto, Argentina. Los resultados se sistematizaron mediante estadística descriptiva y muestran que: 1 la meta de ‘aprendizaje’ fue elegida principalmente, para describir las acciones más frecuentes orientadas a obtener mejores notas, y para la manera más adecuada de resolver una m ateria especialmente difícil; 2 la meta de ‘no complicarse la vida’ fue seleccionada para caracterizar el mejor modo de enfrentar los aprendizajes, y para describir el propio comportamiento dentro del aula; 3 la meta de la ‘desesperanza aprendida’ fue elegida para describir la historia más frecuente en clases, y para el mejor modo de revolver una asignatura particularmente fácil. Dichas metas aluden a motivos, intereses, razones, creencias y deseos que se proponen los alumnos para orientar su comportamiento dentro del aula, en tanto dicho espacio configura las elecciones que realizan los estudiantes en él. Ellos persiguen diversas metas en función de las condiciones contextuales pedagógicas, optando por distintos modos de relacionarse con las tareas y los contenidos de enseñanza. Por ello, el compromiso, la dedicación y las valoraciones que realizan los alumnos sobre su propio desempeño son altamente situacionales, dependiendo del propósito personal hacia el aprendizaje.

  9. Identification of unconditional and conditional QTL for oil, protein and starch content in maize

    Institute of Scientific and Technical Information of China (English)

    Yuqiu; Guo; Xiaohong; Yang; Subhash; Chander; Jianbing; Yan; Jun; Zhang; Tongming; Song; Jiansheng; Li

    2013-01-01

    Oil, protein and starch are key chemical components of maize kernels. A population of 245 recombinant inbred lines(RILs) derived from a cross between a high-oil inbred line, By804, and a regular inbred line, B73, was used to dissect the genetic interrelationships among oil, starch and protein content at the individual QTL level by unconditional and conditional QTL mapping. Combined phenotypic data over two years with a genetic linkage map constructed using 236 markers, nine, five and eight unconditional QTL were detected for oil, protein and starch content, respectively. Some QTL for oil, protein and starch content were clustered in the same genomic regions and the direction of their effects was consistent with the sign of their correlation. In conditional QTL mapping, 37(29/8) unconditional QTL were not detected or showed reduced effects, four QTL demonstrated similar effects under unconditional and conditional QTL mapping, and 17 additional QTL were identified by conditional QTL mapping. These results imply that there is a strong genetic relationship among oil, protein and starch content in maize kernels. The information generated in the present investigation could be helpful in marker-assisted breeding for maize varieties with desirable kernel quality traits.

  10. Analysis of digenic epistatic effects and QE interaction effects QTL controlling grain weight in rice

    Institute of Scientific and Technical Information of China (English)

    高用明; 朱军; 宋佑胜; 何慈信; 石春海; 邢永忠

    2004-01-01

    Immortalized F2 population of rice (Oryza sativa L.) was developed by randomly mating F1 among recombinant inbred (RI) lines derived from (Zhenshan 97B×Minghui 63),which allowed replications within and across environments.QTL (quantitative trait loci) mapping analysis on kilo-grain weight of immortalized F2 population was performed by using newly developed software for QTL mapping,QTL Mapper 2.0. Eleven distinctly digenic epistatic loci included a total of 15 QTL were located on eight chromosomes.QTL main effects of additive,dominance,and additive×additive,additive×dominance,and dominance×dominance interactions were estimated.Interaction effects between QTL main effects and environments (QE) were predicted.Less than 40% of single effects,most of which were additive effects,for identified QTL were significant at 5% level.The directional difference for QTL main effects suggested that these QTL were distributed in parents in the repulsion phase.This should make it feasible to improve kilo-grain weight of both parents by selecting appropriate new recombinants. Only few of the QE interaction effects were significant.Application prospect for QTL mapping achievements in genetic breeding was discussed.

  11. Evaluation and Bulked Segregant Analysis of Major Yield QTL qtl12.1 Introgressed into Indigenous Elite Line for Low Water Availability under Water Stress

    Institute of Scientific and Technical Information of China (English)

    N.Manikanda BOOPATHI; Gat SWAPNASHRI; P.KAVITHA; S.SATHISH; R.NITHYA; Wickneswari RATNAM; Arvind KUMAR

    2013-01-01

    Near isogenic lines carrying large-effect QTL (qtl12.1),which has a consistent influence on grain yield under upland drought stress conditions in a wide range of environments,were evaluated under water stress in the fields.The line which gave higher yield under drought was crossed with a local elite line,PMK3,and forwarded to F2:3 generation.Significant variation was found among the F2:3 lines for agronomic traits under water stress in the fields.Low to high broad sense heritability (H) for investigated traits was also found.Water stress indicators such as leaf rolling and leaf drying were negatively correlated with plant height,biomass and grain yield under stress.Bulked segregant analysis (BSA) was performed with the markers in the vicinity of qtl12.1,and RM27933 was found to be segregated perfectly well in individual components of drought resistant and drought susceptible bulks which were bulked based on yield under water stress among F2:3 lines.Hence,this simple and breeder friendly marker,RM27933,may be useful as a potentially valuable candidate marker for the transfer of the QTL qtl12.1 in the regional breeding program.Bioinformatic analysis of the DNA sequence of the qtl12.1 region was also done to identify and analyze positional candidate genes associated with this QTL and to ascertain the putative molecular basis of qtl12.1.

  12. Identification of expression QTL (eQTL of genes expressed in porcine M. longissimus dorsi and associated with meat quality traits

    Directory of Open Access Journals (Sweden)

    Schellander Karl

    2010-10-01

    Full Text Available Abstract Background Genetic analysis of transcriptional profiles is a promising approach for identifying and dissecting the genetics of complex traits like meat performance. Accordingly, expression levels obtained by microarray analysis were taken as phenotypes in a linkage analysis to map eQTL. Moreover, expression levels were correlated with traits related to meat quality and principle components with high loadings of these traits. By using an up-to-date annotation and localization of the respective probe-sets, the integration of eQTL mapping data and information of trait correlated expression finally served to point to candidate genes for meat quality traits. Results Genome-wide transcriptional profiles of M. longissimus dorsi RNAs samples of 74 F2 animals of a pig resource population revealed 11,457 probe-sets representing genes expressed in the muscle. Linkage analysis of expression levels of these probe-sets provided 9,180 eQTL at the suggestive significance threshold of LOD > 2. We mapped 653 eQTL on the same chromosome as the corresponding gene and these were designated as 'putative cis-eQTL'. In order to link eQTL to the traits of interest, probe-sets were addressed with relative transcript abundances that showed correlation with meat quality traits at p ≤ 0.05. Out of the 653 'putative cis-eQTL', 262 transcripts were correlated with at least one meat quality trait. Furthermore, association of expression levels with composite traits with high loadings for meat quality traits generated by principle component analysis were taken into account leading to a list of 85 genes exhibiting cis-eQTL and trait dependent expression. Conclusion Holistic expression profiling was integrated with QTL analysis for meat quality traits. Correlations between transcript abundance and meat quality traits, combined with genetic positional information of eQTL allowed us to prioritise candidate genes for further study.

  13. HOT ROLLING OF A FERRITIC STAINLESS STEEL IN A STECKEL MILL: THERMOMECHANICAL AND MICROSTRUCTURAL CARACTERIZATION AND MATHEMATICAL MODELLING OF THE EVOLUTION OF RECRYSTALLIZED VOLUME FRACTION OF FERRITE

    OpenAIRE

    Willy Schuwarten Júnior; Ronaldo Antônio Neves Marques Barbosa

    2013-01-01

    A thermomechanical and a microstructure caracterization and a mathematical model of the evolution of the recrystallized volume fraction of ferrite in hot rolling in a Steckel mill have been carried out here. The proposed model is able to reasonably predict the observed in hot rolling, that is, there is 100% recrystallization of ferrite after roughing and partial recrystallization only after finishing

  14. HOT ROLLING OF A FERRITIC STAINLESS STEEL IN A STECKEL MILL: THERMOMECHANICAL AND MICROSTRUCTURAL CARACTERIZATION AND MATHEMATICAL MODELLING OF THE EVOLUTION OF RECRYSTALLIZED VOLUME FRACTION OF FERRITE

    Directory of Open Access Journals (Sweden)

    Willy Schuwarten Júnior

    2013-10-01

    Full Text Available A thermomechanical and a microstructure caracterization and a mathematical model of the evolution of the recrystallized volume fraction of ferrite in hot rolling in a Steckel mill have been carried out here. The proposed model is able to reasonably predict the observed in hot rolling, that is, there is 100% recrystallization of ferrite after roughing and partial recrystallization only after finishing

  15. CARACTERE SPECIFICE VINOVĂŢIEI – CONDIŢIE A RĂSPUNDERII JURIDICE CIVILE

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    Eugenia COJOCARI

    2015-11-01

    Full Text Available În acest articol autorii şi-au propus scopul să analizeze particularităţile caracterelor specifice vinovăţiei – condiţie a răspunderii juridice civile în ambele ei forme din cadrul dreptului civil, pentru a determina rolul şi importanţa acesteia în aplicarea răspunderii civile şi repararea prejudiciului. Pentru realizarea acestui scop şi determinarea rolului, importanţei şi particularităţilor caracterelor specifice ale vinovăţiei din dreptul civil, autorii au analizat legislaţia în vigoare a Republicii Moldova, a altor state, precum şi doctrina. Ei au caracterizat noţiunea de vinovăţie, caracterele ei specifice, propunând o definiţie proprie, specificul căreia constă în faptul că apare şi ca noţiune de culpă, greşală, prin care se subînţelege atitu-dinea persoanei faţă de fapta săvârşită, toate având un caracter subiectiv. Sunt evidenţiate şi analizate următoarele caractere specifice vinovăţiei civile: intelectiv, volitiv, exterioritiv. Pentru a formula unele concluzii şi recomandări proprii, autorii au analizat în aspect de drept comparat Codul civil al Republicii Moldova, ale altor state cu referire la subiect, precum şi doctrina. În rezultatul cercetărilor efectuate sunt formulate concluzii şi înaintate recomandări, principala fiind că vino-văţia – condiţie a răspunderii juridice civile – este nu doar necesară, dar ar fi bine ca la aplicarea răspunderii juridice civile, la determinarea valorii prejudiciului cauzat să se ţină cont de formele şi de gradele acesteia, aşa ca în dreptul penal.SPECIFIC CHARACTERS GUILT – CONDITION OF LIABILITY CIVIL LEGALIn this article the authors aimed to analyze the peculiarities of specific characters guilt - condition of civil liability in both its forms of civil law to determine the role and importance in the application of liability and compensation. In achieving this goal and determining the role, importance and

  16. Dissection of Genetic Effects of Quantitative Trait Loci (QTL) in Transgenic Cotton

    Institute of Scientific and Technical Information of China (English)

    ZHANG Yong-shan

    2008-01-01

    @@ When alien DNA inserts into cotton genome in multi-copy manner,several QTL in cotton genome are disrupted,which are called dQTL in this study.Transgenic mutant line is near-isogenic to its recipient which is divergent for the dQTL from remaining QTL.So,a set of data from a transgenic QTL mutant line produced by Agrobacterium-mediated transformation,30074,its recipient,their F1 hybrids between them,and three elite lines were analyzed under a modified additive-dominance model with genotype by environment interactions in three different environments to dissect the genetic effects due to dQTL from the whole genome based genetic effects.

  17. Fine Mapping QTL for mastitis resistance on BTA9 in three Nordic red cattle breeds

    DEFF Research Database (Denmark)

    Sahana, G; Lund, M S; Andersson-Eklund, L;

    2008-01-01

    A QTL affecting clinical mastitis and/or somatic cell score (SCS) has been reported previously on chromosome 9 from studies in 16 families from the Swedish Red and White (SRB), Finnish Ayrshire (FA) and Danish Red (DR) breeds. In order to refine the QTL location, 67 markers were genotyped over...... mastitis to be mapped to a small interval (BM4208 and INRA084. This QTL showed a pleiotropic effect on SCS in the DR and SRB breeds. Haplotypes associated with variations in mastitis resistance were identified. The haplotypes were predictive in the general population and can be used in marker......-assisted selection. Pleiotropic effects of the mastitis QTL were studied for three milk production traits and eight udder conformation traits. This QTL was also associated with yield traits in DR but not in FA or SRB. No QTL were found for udder conformation traits on chromosome 9...

  18. Contribuição de caracteres agronômicos para a produtividade de grãos em pinhão-manso

    Directory of Open Access Journals (Sweden)

    Paulo Eduardo Teodoro

    2016-03-01

    Full Text Available RESUMO O conhecimento da associação entre os caracteres que compõem a produtividade é importante para a seleção de plantas superiores, principalmente para garantir que o ganho genético ocorra para os diversos caracteres favoráveis. No pinhão-manso, a produtividade de grãos é o principal alvo do programa de melhoramento, porém existem outros caracteres importantes que impactam na produção. Diante desse contexto, o objetivo deste trabalho foi estimar, por meio de análise de trilha, os efeitos diretos e indiretos de caracteres vegetativos sobre a produtividade de grãos de pinhão-manso. Aos 18 meses após o plantio, foram mensurados os caracteres altura de plantas, diâmetro do caule, número de ramos por planta, projeção da copa na linha, projeção da copa na entrelinha e produtividade de grãos. Foram estimadas as correlações fenotípicas entre os caracteres avaliados, sendo essas correlações desdobradas, por meio da análise de trilha, em efeitos diretos e indiretos, considerando-se o caráter produtividade de grãos como a variável dependente principal. Observou-se que 76% da variação em produtividade foi explicada pelas variáveis explicativas, valor este superior ao observado em outros estudos e adequado para explorar os ganhos com a seleção direta e indireta em pinhão-manso. Os caracteres diâmetro do caule, massa de cem sementes e projeção da copa na entrelinha influenciam diretamente a produtividade de grãos, sendo indicados para seleção direta, assim como para a seleção indireta de progênies superiores de pinhão-manso para produtividade de grãos.

  19. Contribuição de caracteres agronômicos para a produtividade de grãos em pinhão-manso

    Directory of Open Access Journals (Sweden)

    Paulo Eduardo Teodoro

    2015-01-01

    Full Text Available RESUMO O conhecimento da associação entre os caracteres que compõem a produtividade é importante para a seleção de plantas superiores, principalmente para garantir que o ganho genético ocorra para os diversos caracteres favoráveis. No pinhão-manso, a produtividade de grãos é o principal alvo do programa de melhoramento, porém existem outros caracteres importantes que impactam na produção. Diante desse contexto, o objetivo deste trabalho foi estimar, por meio de análise de trilha, os efeitos diretos e indiretos de caracteres vegetativos sobre a produtividade de grãos de pinhão-manso. Aos 18 meses após o plantio, foram mensurados os caracteres altura de plantas, diâmetro do caule, número de ramos por planta, projeção da copa na linha, projeção da copa na entrelinha e produtividade de grãos. Foram estimadas as correlações fenotípicas entre os caracteres avaliados, sendo essas correlações desdobradas, por meio da análise de trilha, em efeitos diretos e indiretos, considerando-se o caráter produtividade de grãos como a variável dependente principal. Observou-se que 76% da variação em produtividade foi explicada pelas variáveis explicativas, valor este superior ao observado em outros estudos e adequado para explorar os ganhos com a seleção direta e indireta em pinhão-manso. Os caracteres diâmetro do caule, massa de cem sementes e projeção da copa na entrelinha influenciam diretamente a produtividade de grãos, sendo indicados para seleção direta, assim como para a seleção indireta de progênies superiores de pinhão-manso para produtividade de grãos.

  20. Correlações entre caracteres quantitativos em milho pipoca Correlation among quantitative traits in popcorn maize

    Directory of Open Access Journals (Sweden)

    Valéria Carpentieri-Pípolo

    2002-12-01

    Full Text Available Em um programa de melhoramento, o conhecimento da grandeza das associações entre caracteres de interesse, é de fundamental importância na obtenção de populações melhoradas. O presente trabalho teve como objetivo determinar as correlações genotípicas, fenotípicas e ambientais entre caracteres quantitativos em milho pipoca. Foram avaliados nove genótipos de milho pipoca dispostos no campo em delineamento em blocos casualizados com oito repetições. Os genótipos UEL ZP, UEL SI e UEL PAP revelaram maiores capacidades de expansão (27,50; 27,15 e 24,40 respectivamente e número de grãos por volume (244,75; 248,50 e 248,75 respectivamente. A capacidade de expansão revelou correlação fenotípica positiva com o tamanho da pipoca e com o número de grãos por volume, e correlação negativa com massa de grãos por planta. Os caracteres massa de grãos por planta e peso total da espiga revelaram correlações fenotípicas e genotípicas positivas entre si, o que possibilita a utilização de um ou outro na seleção, optando-se pelo que melhor convier aos propósitos do programa de melhoramento.Knowledge of the size of the association among traits of interest is of fundamental importance in a breeding program to allow genetic progress. The genotypic, phenotypic and environment correlation were studied among quantitative traits of popcorn maize. Nine popcorn maize genotypes were assessed. A randomized complete block design with eight replications was used. The UEL ZP, UEL SI and UEL PAP. genotypes which had greatest expansion capacity (27.50; 27.15 and 24.20, respectively, also had the greatest values for the number of grains per volume (244.75; 248.50 and 248.75, respectively. The expansion capacity correlated positively with the popcorn size and with number of grains per volume and negatively with plant yield. The traits plant yield, and total ear weight showed positive phenotypic and genotypic correlation that permits the choice of

  1. Mapping Quantitative Trait Loci (QTL) in sheep. III. QTL for carcass composition traits derived from CT scans and aligned with a meta-assembly for sheep and cattle carcass QTL.

    Science.gov (United States)

    Cavanagh, Colin R; Jonas, Elisabeth; Hobbs, Matthew; Thomson, Peter C; Tammen, Imke; Raadsma, Herman W

    2010-09-16

    An (Awassi × Merino) × Merino single-sire backcross family with 165 male offspring was used to map quantitative trait loci (QTL) for body composition traits on a framework map of 189 microsatellite loci across all autosomes. Two cohorts were created from the experimental progeny to represent alternative maturity classes for body composition assessment. Animals were raised under paddock conditions prior to entering the feedlot for a 90-day fattening phase. Body composition traits were derived in vivo at the end of the experiment prior to slaughter at 2 (cohort 1) and 3.5 (cohort 2) years of age, using computed tomography. Image analysis was used to gain accurate predictions for 13 traits describing major fat depots, lean muscle, bone, body proportions and body weight which were used for single- and two-QTL mapping analysis. Using a maximum-likelihood approach, three highly significant (LOD ≥ 3), 15 significant (LOD ≥ 2), and 11 suggestive QTL (1.7 ≤ LOD < 2) were detected on eleven chromosomes. Regression analysis confirmed 28 of these QTL and an additional 17 suggestive (P < 0.1) and two significant (P < 0.05) QTL were identified using this method. QTL with pleiotropic effects for two or more tissues were identified on chromosomes 1, 6, 10, 14, 16 and 23. No tissue-specific QTL were identified.A meta-assembly of ovine QTL for carcass traits from this study and public domain sources was performed and compared with a corresponding bovine meta-assembly. The assembly demonstrated QTL with effects on carcass composition in homologous regions on OAR1, 2, 6 and 21.

  2. Major QTL Conferring Resistance to Rice Bacterial Leaf Streak

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Bacterial leaf streak (BLS) is one of the important limiting factors to rice production in southern China and other tropical and sub-tropical areas in Asia. Resistance to BLS was found to be a quantitative trait and no major resistant gene was located in rice until date. In the present study, a new major quantitative trait locus (QTL) conferring resistance to BLS was identified from a highly resistant variety Dular by the employment of Dular/Balilla (DB) and Dular/IR24 (DI) segregation populations and was designated qBLSR-11-1. This QTL was located between the simple sequence repeat (SSR) markers RM120 and RM441 on chromosome 11 and could account for 18.1-21.7% and 36.3% of the variance in DB and DI populations, respectively. The genetic pattern of rice resistance to BLS was discussed.

  3. Cell Specific eQTL Analysis without Sorting Cells.

    Directory of Open Access Journals (Sweden)

    Harm-Jan Westra

    2015-05-01

    Full Text Available The functional consequences of trait associated SNPs are often investigated using expression quantitative trait locus (eQTL mapping. While trait-associated variants may operate in a cell-type specific manner, eQTL datasets for such cell-types may not always be available. We performed a genome-environment interaction (GxE meta-analysis on data from 5,683 samples to infer the cell type specificity of whole blood cis-eQTLs. We demonstrate that this method is able to predict neutrophil and lymphocyte specific cis-eQTLs and replicate these predictions in independent cell-type specific datasets. Finally, we show that SNPs associated with Crohn's disease preferentially affect gene expression within neutrophils, including the archetypal NOD2 locus.

  4. Fine mapping of fatness QTL on porcine chromosome X and analyses of three positional candidate genes

    OpenAIRE

    Ma, Junwu; Gilbert, Hélène; Iannuccelli, Nathalie; Duan, Yanyu; Guo, Beili; Huang, Weibing; Ma, Huanban; Riquet, Juliette; Bidanel, Jean Pierre

    2013-01-01

    Background: Porcine chromosome X harbors four QTL strongly affecting backfat thickness (BFT), ham weight (HW), intramuscular fat content (IMF) and loin eye area (LEA). The confidence intervals (CI) of these QTL overlap and span more than 30 cM, or approximately 80 Mb. This study therefore attempts to fine map these QTL by joint analysis of two large-scale F2 populations (Large White × Meishan and White Duroc × Erhualian constructed by INRA and JXAU respectively) and furthermore, to determine ...

  5. Multi-QTL Mapping for Quantitative Traits Using Epistatic Distorted Markers

    OpenAIRE

    Xie, Shang-Qian; Wen, Jia; Zhang, Yuan-Ming

    2013-01-01

    The interaction between segregation distortion loci (SDL) has been often observed in all kinds of mapping populations. However, little has been known about the effect of epistatic SDL on quantitative trait locus (QTL) mapping. Here we proposed a multi-QTL mapping approach using epistatic distorted markers. Using the corrected linkage groups, epistatic SDL was identified. Then, these SDL parameters were used to correct the conditional probabilities of QTL genotypes, and these corrections were ...

  6. An Efficient Hierarchical Generalized Linear Mixed Model for Mapping QTL of Ordinal Traits in Crop Cultivars

    OpenAIRE

    Feng, Jian-Ying; Zhang, Jin; Zhang, Wen-Jie; Wang, Shi-Bo; Han, Shi-Feng; Zhang, Yuan-Ming

    2013-01-01

    Many important phenotypic traits in plants are ordinal. However, relatively little is known about the methodologies for ordinal trait association studies. In this study, we proposed a hierarchical generalized linear mixed model for mapping quantitative trait locus (QTL) of ordinal traits in crop cultivars. In this model, all the main-effect QTL and QTL-by-environment interaction were treated as random, while population mean, environmental effect and population structure were fixed. In the est...

  7. Sire design power calculation for QTL mapping experiments

    OpenAIRE

    Elsen Jean-Michel; Carta Antonello

    1999-01-01

    Estimates of sire design power for QTL mapping experiments obtained using three different methods of algebraic approximation were analysed by comparing them with the results of data simulations. Even when the binomial probability that any number of sires out of the total number of sires are jointly heterozygous at the marker and the QT loci was taken into consideration, the algebraic approximations overestimated powers. However, they could be used to rank designs differing in the number...

  8. Salt tolerance in Solanum pennellii: antioxidant response and related QTL

    Directory of Open Access Journals (Sweden)

    Şığva Hasan Ö

    2010-04-01

    Full Text Available Abstract Background Excessive soil salinity is an important problem for agriculture, however, salt tolerance is a complex trait that is not easily bred into plants. Exposure of cultivated tomato to salt stress has been reported to result in increased antioxidant content and activity. Salt tolerance of the related wild species, Solanum pennellii, has also been associated with similar changes in antioxidants. In this work, S. lycopersicum M82, S. pennellii LA716 and a S. pennellii introgression line (IL population were evaluated for growth and their levels of antioxidant activity (total water-soluble antioxidant activity, major antioxidant compounds (phenolic and flavonoid contents and antioxidant enzyme activities (superoxide dismutase, catalase, ascorbate peroxidase and peroxidase under both control and salt stress (150 mM NaCl conditions. These data were then used to identify quantitative trait loci (QTL responsible for controlling the antioxidant parameters under both stress and nonstress conditions. Results Under control conditions, cultivated tomato had higher levels of all antioxidants (except superoxide dismutase than S. pennellii. However, under salt stress, the wild species showed greater induction of all antioxidants except peroxidase. The ILs showed diverse responses to salinity and proved very useful for the identification of QTL. Thus, 125 loci for antioxidant content under control and salt conditions were detected. Eleven of the total antioxidant activity and phenolic content QTL matched loci identified in an independent study using the same population, thereby reinforcing the validity of the loci. In addition, the growth responses of the ILs were evaluated to identify lines with favorable growth and antioxidant profiles. Conclusions Plants have a complex antioxidant response when placed under salt stress. Some loci control antioxidant content under all conditions while others are responsible for antioxidant content only under

  9. Identification of seed-related QTL in Brassica rapa

    Directory of Open Access Journals (Sweden)

    H. Bagheri

    2013-10-01

    Full Text Available To reveal the genetic variation, and loci involved, for a range of seed-related traits, a new F2 mapping population was developed by crossing Brassica rapa ssp. parachinensis L58 (CaiXin with B. rapa ssp. trilocularis R-o-18 (spring oil seed, both rapid flowering and self-compatible. A linkage map was constructed using 97 AFLPs and 21 SSRs, covering a map distance of 757 cM with an average resolution of 6.4 cM, and 13 quantitative trait loci (QTL were detected for nine traits. A strong seed colour QTL (LOD 26 co-localized with QTL for seed size (LOD 7, seed weight (LOD 4.6, seed oil content (LOD 6.6, number of siliques (LOD 3 and number of seeds per silique (LOD 3. There was only a significant positive correlation between seed colour and seed oil content in the yellow coloured classes. Seed coat colour and seed size were controlled by the maternal plant genotype. Plants with more siliques tended to have more, but smaller, seeds and higher seed oil content. Seed colour and seed oil content appeared to be controlled by two closely linked loci in repulsion phase. Thus, it may not always be advantageous to select for yellow-seededness when breeding for high seed oil content in Brassicas.

  10. A General Method for QTL Mapping in Multiple Related Populations Derived from Multiple Parents

    Institute of Scientific and Technical Information of China (English)

    AO Yan; HU Zhi-qiu; TANG Zai-xiang; WANG Xue-feng; XU Chen-wu

    2009-01-01

    It's well known that incorporating some existing populations derived from multiple parents may improve QTL mapping and QTL-based breeding programs. However, no general maximum likelihood method has been available for this strategy. Based on the QTL mapping in multiple related populations derived from two parents, a maximum likelihood estimation method was proposed, which can incorporate several populations derived from three or more parents and also can be used to handle different mating designs. Taking a circle design as an example, we conducted simulation studies to study the effect of QTL heritability and sample size upon the proposed method. The results showed that under the same heritability, enhanced power of QTL detection and more precise and accurate estimation of parameters could be obtained when three F2 populations were jointly analyzed, compared with the joint analysis of any two F2 populations. Higher heritability, especially with larger sample sizes, would increase the ability of QTL detection and improve the estimation of parameters. Potential advantages of the method are as follows: firstly, the existing results of QTL mapping in single population can be compared and integrated with each other with the proposed method, therefore the ability of QTL detection and precision of QTL mapping can be improved. Secondly, owing to multiple alleles in multiple parents, the method can exploit gene resource more adequately, which will lay an important genetic groundwork for plant improvement.

  11. A comparison of bivariate and univariate QTL mapping in livestock populations

    Directory of Open Access Journals (Sweden)

    Sorensen Daniel

    2003-11-01

    Full Text Available Abstract This study presents a multivariate, variance component-based QTL mapping model implemented via restricted maximum likelihood (REML. The method was applied to investigate bivariate and univariate QTL mapping analyses, using simulated data. Specifically, we report results on the statistical power to detect a QTL and on the precision of parameter estimates using univariate and bivariate approaches. The model and methodology were also applied to study the effectiveness of partitioning the overall genetic correlation between two traits into a component due to many genes of small effect, and one due to the QTL. It is shown that when the QTL has a pleiotropic effect on two traits, a bivariate analysis leads to a higher statistical power of detecting the QTL and to a more precise estimate of the QTL's map position, in particular in the case when the QTL has a small effect on the trait. The increase in power is most marked in cases where the contributions of the QTL and of the polygenic components to the genetic correlation have opposite signs. The bivariate REML analysis can successfully partition the two components contributing to the genetic correlation between traits.

  12. Multi-QTL mapping for quantitative traits using epistatic distorted markers.

    Directory of Open Access Journals (Sweden)

    Shang-Qian Xie

    Full Text Available The interaction between segregation distortion loci (SDL has been often observed in all kinds of mapping populations. However, little has been known about the effect of epistatic SDL on quantitative trait locus (QTL mapping. Here we proposed a multi-QTL mapping approach using epistatic distorted markers. Using the corrected linkage groups, epistatic SDL was identified. Then, these SDL parameters were used to correct the conditional probabilities of QTL genotypes, and these corrections were further incorporated into the new QTL mapping approach. Finally, a set of simulated datasets and a real data in 304 mouse F2 individuals were used to validate the new method. As compared with the old method, the new one corrects genetic distance between distorted markers, and considers epistasis between two linked SDL. As a result, the power in the detection of QTL is higher for the new method than for the old one, and significant differences for estimates of QTL parameters between the two methods were observed, except for QTL position. Among two QTL for mouse weight, one significant difference for QTL additive effect between the above two methods was observed, because epistatic SDL between markers C66 and T93 exists (P = 2.94e-4.

  13. Identification of QTL for dorso-caudal chronic pleuritis in 12 crossbred porcine families

    DEFF Research Database (Denmark)

    Gregersen, V R; Sørensen, K K; Christensen, O F;

    2010-01-01

    loci (QTL) or markers associated with the prevalence of CP should be identified. In this study, 7470 pigs from crosses between 12 Danish Duroc boars and 604 sows (Danish Landrace × Danish Large White) were evaluated for CP located on the dorso-caudal part of the lungs. Quantitative trait loci were...... identified within boar families using both a Binomial logistic regression method and a chi-square test of association. Significant QTL for CP were detected on Sus scrofa chromosomes (SSC) 2, 8, 12, 13, 14 and 18 using both methods. One QTL on SSC 8 was also detected across families. For the QTL identified...

  14. The bovine QTL viewer: a web accessible database of bovine Quantitative Trait Loci

    Directory of Open Access Journals (Sweden)

    Xavier Suresh R

    2006-06-01

    Full Text Available Abstract Background Many important agricultural traits such as weight gain, milk fat content and intramuscular fat (marbling in cattle are quantitative traits. Most of the information on these traits has not previously been integrated into a genomic context. Without such integration application of these data to agricultural enterprises will remain slow and inefficient. Our goal was to populate a genomic database with data mined from the bovine quantitative trait literature and to make these data available in a genomic context to researchers via a user friendly query interface. Description The QTL (Quantitative Trait Locus data and related information for bovine QTL are gathered from published work and from existing databases. An integrated database schema was designed and the database (MySQL populated with the gathered data. The bovine QTL Viewer was developed for the integration of QTL data available for cattle. The tool consists of an integrated database of bovine QTL and the QTL viewer to display QTL and their chromosomal position. Conclusion We present a web accessible, integrated database of bovine (dairy and beef cattle QTL for use by animal geneticists. The viewer and database are of general applicability to any livestock species for which there are public QTL data. The viewer can be accessed at http://bovineqtl.tamu.edu.

  15. Partial Dominance, Overdominance, Epistasis and QTL by Environment Interactions Contribute to Heterosis in Two Upland Cotton Hybrids.

    Science.gov (United States)

    Shang, Lianguang; Wang, Yumei; Cai, Shihu; Wang, Xiaocui; Li, Yuhua; Abduweli, Abdugheni; Hua, Jinping

    2016-03-01

    Based on two recombinant inbred line (RIL) populations, two corresponding backcross (BC) populations were constructed to elucidate the genetic basis of heterosis in Upland cotton (Gossypium hirsutum L.). The yield, and yield components, of these populations were evaluated in three environments. At the single-locus level, 78 and 66 quantitative trait loci (QTL) were detected using composite interval mapping in RIL and BC populations, respectively, and 29 QTL were identified based on mid-parental heterosis (MPH) data of two hybrids. Considering all traits together, a total of 50 (64.9%) QTL with partial dominance effect, and 27 (35.1%) QTL for overdominance effect were identified in two BC populations. At the two-locus level, 120 and 88 QTL with main effects (M-QTL), and 335 and 99 QTL involved in digenic interactions (E-QTL), were detected by inclusive composite interval mapping in RIL and BC populations, respectively. A large number of QTL by environment interactions (QEs) for M-QTL and E-QTL were detected in three environments. For most traits, average E-QTL explained a larger proportion of phenotypic variation than did M-QTL in two RIL populations and two BC populations. It was concluded that partial dominance, overdominance, epistasis, and QEs all contribute to heterosis in Upland cotton, and that partial dominance resulting from single loci and epistasis play a relatively more important role than other genetic effects in heterosis in Upland cotton. PMID:26715091

  16. Los caracteres morfológicos del controvertido Neobatrachia arborícola Allophryne ruthveni Gaige, 1926

    Directory of Open Access Journals (Sweden)

    Fabrezi, Marissa

    2000-07-01

    Full Text Available Allophtyne ruthveni es un anuro neotropical arborícola asignado a una familia monotípica. Aunque sus afinidades con otros taxa permanecen sin precisar, durante mucho tiempo se lo relacionó con los anuros arborícolas neotropicales, aún cuando la ausencia de dientes, característica de los Bufonidae, fue el primer argumento para establecer alguna relación con estos. En el presente trabajo, presentamos un re-análisis de caracteres esqueléticos y miológicos de A. ruthveni a partir del cual encontramos ausencia de elementos intercalares, típicos de formas arborícolas; algunos rasgos compartidos con los bufónidos; y numerosos caracteres presentes en distintos neobatracios que deberían ser discutidos sobre la base de un análisis filogenético. Finalmente, consideramos dos características distintivas de las extremidades de A. ruthveni. Allophryne ruthveni is a neotropical arboreous frog assigned to a monotypical family. Although A. ruthveni's relationships remain poorly known, most of authors searched relationships with neotropical treefrogs in spite of the absence of teeth was an early evidence to relate it with bufonids. Herein, we presented a new analysis of osteological and some myological traits of A. ruthveni. Intercallary elements, related to the arboreal life style similar lo that present in neotropical treefrogs such as hylids, is very different in A. ruthveni; some cranial features of A. ruthveni represent traits shared with bufonids, and many morphological characters also are present among neobatracians. However, they can not be interpreted without a phylogenetic analysis. Finally, we considered two specific limb features of A. ruthveni.

  17. Migrantes internacionales en la Aglomeración Gran Buenos Aires: un análisis cuantitativo de su distribución espacial

    OpenAIRE

    Mariana Marcos; Gabriela Mera

    2015-01-01

    El presente trabajo se propone estudiar la distribución espacial de los migrantes internacionales en la Aglomeración Gran Buenos Aires (AGBA) desde un abordaje cuantitativo que combina una escala macrosocial, en tanto abarca a la AGBA en su totalidad; y microespacial, en la medida que permite visualizar diferencias que se producen a nivel intraurbano. Para ello se realiza un análisis estadístico-cartográfico que toma como fuente de datos el Censo Nacional de Población, Hogares y Viviendas 201...

  18. El discurso de la conciliación: análisis cuantitativo de las intervenciones de gustavo rojas pinilla entre 1952 y 1959

    OpenAIRE

    Cesar Augusto Ayala Diago

    2012-01-01

    A partir de la elaboración de unas categorías y del análisis cuantitativo de la composición de cada categoría (indicadores de la categoría) se explica el ideario de Rojas Pinilla y la evolución de su "Discurso de la Conciliación". De esta manera se quiere restituir su pensamiento político, que ha sido deformado por la historiografía tradicional.

  19. 基于 SNP 标记的 QTL 组合定位方法%Combined QTL Mapping Method based on SNP Markers

    Institute of Scientific and Technical Information of China (English)

    王倩雯; 郭茂祖; 王春宇; 刘晓燕

    2014-01-01

    QTL 的精确定位对数量性状遗传机制的研究及应用具有重要意义。随着分子生物技术和遗传学的发展,产生了大量可用于 QTL 定位的遗传标记和分析方法。然而,多数方法只能将 QTL 定位到一个区间而非具体位置,且具有较高的假阳性。为此,提出利用全基因组上的 SNP 标记,通过 emBayesB 方法和性状-标记回归区间分析相结合的组合方法进行 QTL 定位研究。组合方法能够筛选出与 QTL 存在较强关联的 SNP 标记,具有较高的计算速度和计算效率;通过性状-标记区间检测,能够较为精确地计算出 QTL 的位置。方法中考虑到染色体上其它标记的背景遗传信息,提高定位成功率和可信度。%Search the precise position of QTL ,is very significant for understanding the genetic mechanisms of quantitative traits and its application.The development of molecular biology and genetics results in a large number of genetic markers and analytical methods can be used for QTL mapping.However,most methods can only map QTL to a interval rather than a specific location with a high false positive.This paper proposes that the use of genome -wide SNP markers and combina-tion strategy which combining emBayesB methods and traits - mark regression interval analysis conducted QTL mapping studies.Combination strategy could screen out SNP markers which associated with QTL in the presence of strong,and hav-ing a high computing speed and efficiency;through trait -mark interval detection,the location of the QTL can be calculat-ed more accurately.The method takes into account the background genetic information of other genetic markers on the chro-mosome,achieves higher position success rate,and improves the positioning reliability.

  20. Using transcriptome profiling to characterize QTL regions on chicken chromosome 5

    Directory of Open Access Journals (Sweden)

    Demeure Olivier

    2009-12-01

    Full Text Available Abstract Background Although many QTL for various traits have been mapped in livestock, location confidence intervals remain wide that makes difficult the identification of causative mutations. The aim of this study was to test the contribution of microarray data to QTL detection in livestock species. Three different but complementary approaches are proposed to improve characterization of a chicken QTL region for abdominal fatness (AF previously detected on chromosome 5 (GGA5. Results Hepatic transcriptome profiles for 45 offspring of a sire known to be heterozygous for the distal GGA5 AF QTL were obtained using a 20 K chicken oligochip. mRNA levels of 660 genes were correlated with the AF trait. The first approach was to dissect the AF phenotype by identifying animal subgroups according to their 660 transcript profiles. Linkage analysis using some of these subgroups revealed another QTL in the middle of GGA5 and increased the significance of the distal GGA5 AF QTL, thereby refining its localization. The second approach targeted the genes correlated with the AF trait and regulated by the GGA5 AF QTL region. Five of the 660 genes were considered as being controlled either by the AF QTL mutation itself or by a mutation close to it; one having a function related to lipid metabolism (HMGCS1. In addition, a QTL analysis with a multiple trait model combining this 5 gene-set and AF allowed us to refine the QTL region. The third approach was to use these 5 transcriptome profiles to predict the paternal Q versus q AF QTL mutation for each recombinant offspring and then refine the localization of the QTL from 31 cM (100 genes at a most probable location confidence interval of 7 cM (12 genes after determining the recombination breakpoints, an interval consistent with the reductions obtained by the two other approaches. Conclusion The results showed the feasibility and efficacy of the three strategies used, the first revealing a QTL undetected using the

  1. Joint QTL linkage mapping for multiple-cross mating design sharing one common parent.

    Directory of Open Access Journals (Sweden)

    Huihui Li

    Full Text Available BACKGROUND: Nested association mapping (NAM is a novel genetic mating design that combines the advantages of linkage analysis and association mapping. This design provides opportunities to study the inheritance of complex traits, but also requires more advanced statistical methods. In this paper, we present the detailed algorithm of a QTL linkage mapping method suitable for genetic populations derived from NAM designs. This method is called joint inclusive composite interval mapping (JICIM. Simulations were designed on the detected QTL in a maize NAM population and an Arabidopsis NAM population so as to evaluate the efficiency of the NAM design and the JICIM method. PRINCIPAL FINDINGS: Fifty-two QTL were identified in the maize population, explaining 89% of the phenotypic variance of days to silking, and nine QTL were identified in the Arabidopsis population, explaining 83% of the phenotypic variance of flowering time. Simulations indicated that the detection power of these identified QTL was consistently high, especially for large-effect QTL. For rare QTL having significant effects in only one family, the power of correct detection within the 5 cM support interval was around 80% for 1-day effect QTL in the maize population, and for 3-day effect QTL in the Arabidopsis population. For smaller-effect QTL, the power diminished, e.g., it was around 50% for maize QTL with an effect of 0.5 day. When QTL were linked at a distance of 5 cM, the likelihood of mapping them as two distinct QTL was about 70% in the maize population. When the linkage distance was 1 cM, they were more likely mapped as one single QTL at an intermediary position. CONCLUSIONS: Because it takes advantage of the large genetic variation among parental lines and the large population size, NAM is a powerful multiple-cross design for complex trait dissection. JICIM is an efficient and specialty method for the joint QTL linkage mapping of genetic populations derived from the NAM design.

  2. Conditional QTL mapping of protein content in wheat with respect to grain yield and its components

    Indian Academy of Sciences (India)

    Lin Wang; Fa Cui; Jinping Wang; Li Jun; Anming Ding; Chunhua Zhao; Xingfeng Li; Deshun Feng; Jurong Gao; Honggang Wang

    2012-12-01

    Grain protein content in wheat (Triticum aestivum L.) is generally considered a highly heritable character that is negatively correlated with grain yield and yield-related traits. Quantitative trait loci (QTL) for protein content was mapped using data on protein content and protein content conditioned on the putatively interrelated traits to evaluate possible genetic interrelationships between protein content and yield, as well as yield-related traits. Phenotypic data were evaluated in a recombinant inbred line population with 302 lines derived from a cross between the Chinese cultivar Weimai 8 and Luohan 2. Inclusive composite interval mapping using IciMapping 3.0 was employed for mapping unconditional and conditional QTL with additives. A strong genetic relationship was found between protein content and grain yield, and yield-related traits. Unconditional QTL mapping analysis detected seven additive QTL for protein content, with additive effects ranging in absolute size from 0.1898% to 0.3407% protein content, jointly accounting for 43.45% of the trait variance. Conditional QTL mapping analysis indicated two QTL independent from yield, which can be used in marker-assisted selection for increasing yield without affecting grain protein content. Three additional QTL with minor effects were identified in the conditional mapping. Of the three QTLs, two were identified when protein content was conditioned on yield, which had pleiotropic effects on those two traits. Conditional QTL mapping can be used to dissect the genetic interrelationship between two traits at the individual QTL level for closely correlated traits. Further, conditional QTL mapping can reveal additional QTL with minor effects that are undetectable in unconditional mapping.

  3. Dynamic QTL and epistasis analysis on seedling root traits in upland cotton.

    Science.gov (United States)

    Liang, Qingzhi; Li, Pengbo; Hu, Cheng; Hua, Hua; Li, Zhaohu; Rong, Yihua; Wang, Kunbo; Hua, Jinping

    2014-04-01

    Roots are involved in acquisition of water and nutrients, as well as in providing structural support to plant. The root system provides a dynamic model for developmental analysis. Here, we investigated quantitative trait loci (QTL), dynamic conditional QTL and epistatic interactions for seedling root traits using an upland cotton F2 population and a constructed genetic map. Totally, 37 QTLs for root traits, 35 dynamic conditional QTLs based on the net increased amount of root traits (root tips, forks, length, surface area and volume) (i) after transplanting 10 days compared to 5 days, and (ii) after transplanting 15 days to 10 days were detected. Obvious dynamic characteristic of QTL and dynamic conditional QTL existed at different developmental stages of root because QTL and dynamic conditional QTL had not been detected simultaneously. We further confirmed that additive and dominance effects of QTL qRSA-chr1-1 in interval time 5 to 10 DAT (days after transplant) offset the effects in 10 to 15 DAT. Lots of two-locus interactions for root traits were identified unconditionally or dynamically, and a few epistatic interactions were only detected simultaneously in interval time of 5-10 DAT and 10-15 DAT, suggesting different interactive genetic mechanisms on root development at different stages. Dynamic conditional QTL and epistasis effects provide new attempts to understand the dynamics of roots and provide clues for root architecture selection in upland cotton. PMID:24840824

  4. Bayesian Variable Selection to identify QTL affecting a simulated quantitative trait

    NARCIS (Netherlands)

    Schurink, A.; Janss, L.L.G.; Heuven, H.C.M.

    2012-01-01

    Background Recent developments in genetic technology and methodology enable accurate detection of QTL and estimation of breeding values, even in individuals without phenotypes. The QTL-MAS workshop offers the opportunity to test different methods to perform a genome-wide association study on simulat

  5. Bayesian Variable Selection to identify QTL affecting a simulated quantitative trait

    NARCIS (Netherlands)

    Schurink, A.; Janss, L.L.G.; Heuven, H.C.M.

    2012-01-01

    Abstract Background: Recent developments in genetic technology and methodology enable accurate detection of QTL and estimation of breeding values, even in individuals without phenotypes. The QTL-MAS workshop offers the opportunity to test different methods to perform a genome-wide association study

  6. QTL mapping in new Arabidopsis thaliana advanced intercross-recombinant inbred lines.

    Directory of Open Access Journals (Sweden)

    Sureshkumar Balasubramanian

    Full Text Available BACKGROUND: Even when phenotypic differences are large between natural or domesticated strains, the underlying genetic basis is often complex, and causal genomic regions need to be identified by quantitative trait locus (QTL mapping. Unfortunately, QTL positions typically have large confidence intervals, which can, for example, lead to one QTL being masked by another, when two closely linked loci are detected as a single QTL. One strategy to increase the power of precisely localizing small effect QTL, is the use of an intercross approach before inbreeding to produce Advanced Intercross RILs (AI-RILs. METHODOLOGY/PRINCIPAL FINDINGS: We present two new AI-RIL populations of Arabidopsis thaliana genotyped with an average intermarker distance of 600 kb. The advanced intercrossing design led to expansion of the genetic map in the two populations, which contain recombination events corresponding to 50 kb/cM in an F(2 population. We used the AI-RILs to map QTL for light response and flowering time, and to identify segregation distortion in one of the AI-RIL populations due to a negative epistatic interaction between two genomic regions. CONCLUSIONS/SIGNIFICANCE: The two new AI-RIL populations, EstC and KendC, derived from crosses of Columbia (Col to Estland (Est-1 and Kendallville (Kend-L provide an excellent resource for high precision QTL mapping. Moreover, because they have been genotyped with over 100 common markers, they are also excellent material for comparative QTL mapping.

  7. Use of maternal information for QTL detection in a (granddaughter design

    Directory of Open Access Journals (Sweden)

    Boichard Didier

    2002-05-01

    Full Text Available Abstract In a (granddaughter design, maternal information is often neglected because the number of progeny per dam is limited. The number of dams per maternal grandsire (MGS, however, could be large enough to contribute to QTL detection. But dams and MGS usually are not genotyped, there are two recombination opportunities between the MGS and the progeny, and at a given location, only half the progeny receive a MGS chromosomal segment. A 3-step procedure was developed to estimate: (1 the marker phenotypes probabilities of the MGS; (2 the probability of each possible MGS haplotype; (3 the probabilities that the progeny receives either the first, or second MGS segment, or a maternal grandam segment. These probabilities were used for QTL detection in a linear model including the effects of sire, MGS, paternal QTL, MGS QTL and maternal grandam QTL. Including the grandam QTL effect makes it possible to detect QTL in the grandam population, even when MGS are not informative. The detection power, studied by simulation, was rather high, provided that MGS family size was greater than 50. Using maternal information in the French dairy cattle granddaughter design made it possible to detect 23 additional QTL genomewise significant.

  8. Detection and modelling of time-dependent QTL in animal populations

    DEFF Research Database (Denmark)

    Lund, Mogens S; Sørensen, Peter; Madsen, Per;

    2008-01-01

    A longitudinal approach is proposed to map QTL affecting function-valued traits and to estimate their effect over time. The method is based on fitting mixed random regression models. The QTL allelic effects are modelled with random coefficient parametric curves and using a gametic relationship...

  9. Multi-environment QTL mixed models for drought stress adaptation in wheat

    NARCIS (Netherlands)

    Mathews, K.L.; Malosetti, M.; Chapman, S.; McIntyre, L.; Reynolds, M.; Shorter, R.; Eeuwijk, van F.A.

    2008-01-01

    Many quantitative trait loci (QTL) detection methods ignore QTL-by-environment interaction (QEI) and are limited in accommodation of error and environment-specific variance. This paper outlines a mixed model approach using a recombinant inbred spring wheat population grown in six drought stress tria

  10. Concordance analysis for QTL detection in dairy cattle: a case study of leg morphology

    DEFF Research Database (Denmark)

    van den Berg, Irene; Rodrigue; Fritz, Sebastien;

    2014-01-01

    The present availability of sequence data gives new opportunities to narrow down from QTL (quantitative trait locus) regions to causative mutations. Our objective was to decrease the number of candidate causative mutations in a QTL region. For this, a concordance analysis was applied for a leg co...

  11. QTL alleles on chromosome 7 from fatty Meishan pigs reduce fat deposition

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    For detecting QTL in the whole swine genome, 1068 pigs from three F2 populations constructed by crossing European Wild boar and Pietrain (WxP), Meishan and Pietrain (M×P),and Wild Boar and Meishan (W×M) were genotyped for genetic markers evenly spaced at approximately 20 cM intervals. A QTL analysis was performed using a least-squares method. Here the results of the QTL analysis on the porcine chromosome 7 are presented. QTL for carcass composition (e.g. head weight, carcass length, backfat depth, abdominal fat and bacon meat) were mapped in the chromosomal region CYPA/CYPD-TNFB-S0102 in M×P and W×M, but not in W×P.The QTL explained 5.3%-27.2% of the F2 phenotypic variance in the two F2 populations. Most traits affected by the mapped QTL were related to carcass fatness. The mode of gene action of QTL was additive. Surprisingly, in contrast to the parental phenotype, the QTL alleles from fatty Meishan were associated with thinner backfat than Pietrain and Wild Boar alleles, suggesting that the genome of the fatty Meishan pig contains genes which can reduce fat content of carcass substantially.

  12. Across Breed QTL Detection and Genomic Prediction in French and Danish Dairy Cattle Breeds

    DEFF Research Database (Denmark)

    van den Berg, Irene; Guldbrandtsen, Bernt; Hozé, C;

    Our objective was to investigate the potential benefits of using sequence data to improve across breed genomic prediction, using data from five French and Danish dairy cattle breeds. First, QTL for protein yield were detected using high density genotypes. Part of the QTL detected within breed was...

  13. Expression QTL modules as functional components underlying higher-order phenotypes.

    Directory of Open Access Journals (Sweden)

    Lei Bao

    Full Text Available Systems genetics studies often involve the mapping of numerous regulatory relations between genetic loci and expression traits. These regulatory relations form a bipartite network consisting of genetic loci and expression phenotypes. Modular network organizations may arise from the pleiotropic and polygenic regulation of gene expression. Here we analyzed the expression QTL (eQTL networks derived from expression genetic data of yeast and mouse liver and found 65 and 98 modules respectively. Computer simulation result showed that such modules rarely occurred in randomized networks with the same number of nodes and edges and same degree distribution. We also found significant within-module functional coherence. The analysis of genetic overlaps and the evidences from biomedical literature have linked some eQTL modules to physiological phenotypes. Functional coherence within the eQTL modules and genetic overlaps between the modules and physiological phenotypes suggests that eQTL modules may act as functional units underlying the higher-order phenotypes.

  14. Pedigree transmission disequilibrium test for QTL mapping of threshold trait

    Institute of Scientific and Technical Information of China (English)

    DING Xiangdong; ZHANG Qin; XU Ruhai; WANG Yachun

    2004-01-01

    With biological and economic importance,threshold traits are discrete in phenotype but have the same polygenic genetic basis as quantitative traits. The traditional linkage analysis for quantitative traits is invalid for threshold traits due to their special characters. The transmission disequilibrium test (TDT) has received great attention recently in localizing human disease genes due to its simplicity and powerfulness. But TDT only deals with data from independent nuclear families and it will lose information about extended pedigree that incorporates information not only from parents and siblings but also from other relatives. The pedigree disequilibrium test (PDT) proposed by Martin in 2001 can be used to analyze the extended pedigree in human.In this study, PDT was introduced into the QTL mapping of threshold traits for farm animals, and was modified in order to accommodate the pedigree structures of farm animals.The modified PDT was renamed pedigree transmission disequilibrium test (PTDT) and its power and type I error were investigated and compared with that of PDT by Monte Carlo simulation. It was shown that PTDT is a robust and valid approach to mapping QTL of threshold trait. When the parental information is complete, PTDT and PDT are almost the same in terms of power and type I error. However, if the parental information is missing to a certain extent, PTDT is higher in power and lower in type I error than PDT. These results imply that PTDT can be a novel approach to QTL fine mapping of threshold traits based on the existing coarse mapping information.

  15. QTL Mapping for Quality Traits of Chinese Dry Noodle

    Institute of Scientific and Technical Information of China (English)

    ZHAO Jing-lan; CHEN Min-sheng; MA Yan-ming; LI Rui-jun; REN Yong-pan; SUN Qing-quan; LI Si-shen

    2009-01-01

    The QTLs for quality traits of Chinese dry noodle(CDN)were mapped based on a population of recombinant inbred lines(RILs)derived from the cross between two Chinese winter wheat varieties,Chuan 35050 and Shannong 483.Sensory quality traits of CDN were tested according to the standard of Ministry of Commerce of P.R.China(SB/T10137-93),and the textural property traits were detected using a texture analyser(TA.XTplus).We have obtained 8 putative QTLs for 6 sensory quality traits and 2 QTLs for textural property of CDN with a single QTL explainning 4.07-75.67% of phenotypic variations on chromosomes 1A,1D,3D,4A,and 6D.A duster of 3 QTLs for palate,elasticity and smoothness of CDN was found near the Glu-D1 locus on chromosome 1D with high contributions.The increasing effect come from Chuan 35050,and the relationship between the QTLs were positive.On chromosome 4A,co-location QTLs for stickiness and total score were detected in the region of Xwmc420-Xswes620-Xswes615.Their contributions were high and the increasing effects come from Shannong 483.A taste QTL QStas.sdau-4A.1 was obtained in Xsrap18-Xswes624c-Xissr25b-Xissr23b on chromosome 4A with the highest contribution of 75.67%.This QTL was a major gene and the increasing effects come from Shannong 483.

  16. Biphasic survival analysis of trypanotolerance QTL in mice.

    Science.gov (United States)

    Koudandé, O D; Thomson, P C; Bovenhuis, H; Iraqi, F; Gibson, J P; van Arendonk, J A M

    2008-04-01

    A marker-assisted introgression (MAI) experiment was conducted to transfer trypanotolerance quantitative trait loci (QTL) from a donor mouse strain, C57BL/6, into a recipient mouse strain, A/J. The objective was to assess the effect of three previously identified chromosomal regions on mouse chromosomes 1 (MMU1), 5 (MMU5) and 17 (MMU17) in different genetic backgrounds on the survival pattern following infection with Trypanosoma congolense. An exploratory data analysis revealed a biphasic pattern of time to death, with highly distinct early and late mortality phases. In this paper, we present survival analysis methods that account for the biphasic mortality pattern and results of reanalyzing the data from the MAI experiment. The analysis with a Weibull mixture model confirmed the biphasic pattern of time to death. Mortality phase, an unobserved variable, appears to be an important factor influencing survival time and is modeled as a binary outcome variable using logistic regression analysis. Accounting for this biphasic pattern in the analysis reveals that a previously observed sex effect on average survival is rather an effect on proportion of mice in the two mortality phases. The C57BL/6 (donor) QTL alleles on MMU1 and MMU17 act dominantly in the late mortality phase while the A/J (recipient) QTL allele on MMU17 acts dominantly in the early mortality phase. From this study, we found clear evidence for a biphasic survival pattern and provided models for its analysis. These models can also be used when studying defense mechanisms against other pathogens. Finally, these approaches provide further information on the nature of gene actions. PMID:18253157

  17. Functional screening of an asthma QTL in YAC transgenic mice

    Energy Technology Data Exchange (ETDEWEB)

    Symula, Derek J.; Frazer, Kelly A.; Ueda, Yukihiko; Denefle, Patrice; Stevens, Mary E.; Wang, Zhi-En; Locksley, Richard; Rubin, Edward M.

    1999-07-02

    While large numbers of quantitative trait loci (QTLs) contributing to genetically complex conditions have been discovered, few causative genes have been identified. This is mainly due to the large size of QTLs and the subtle connection between genotype and quantitative phenotype associated with these conditions. While large numbers of quantitative trait loci (QTLs) contributing to genetically complex conditions have been discovered, few causative genes have been identified. This is mainly due to the large size of QTLs and the subtle connection between genotype and quantitative phenotype associated with these conditions. To screen for genes contributing to an asthma QTL mapped to human chromosome 5q33, the authors characterized a panel of large-insert 5q31 transgenics based on studies demonstrating that altering gene dosage frequently affects quantitative phenotypes normally influenced by that gene. This panel of human YAC transgenics, propagating a one megabase interva2048 chromosome 5q31 containing 23 genes, was screened for quantitative changes in several asthma-associated phenotypes. Multiple independent transgenic lines with altered IgE response to antigen treatment shared a 180 kb region containing 5 genes, including human interleukin 4 (IL4) and interleukin 13 (IL13), which induce IgE class switching in B cells5. Further analysis of these mice and mice transgenic for only murine Il4 and Il13 demonstrated that moderate changes in murine Il4 and Il13 expression affect asthma-associated phenotypes in vivo. This functional screen of large-insert transgenics enabled them to sift through multiple genes in the 5q3 asthma QTL without prior consideration of assumed individual gene function and identify genes that influence the QTL phenotype in vivo.

  18. QTL mapping of powdery mildew resistance in WI 2757 cucumber (Cucumis sativus L.).

    Science.gov (United States)

    He, Xiaoming; Li, Yuhong; Pandey, Sudhakar; Yandell, Brain S; Pathak, Mamta; Weng, Yiqun

    2013-08-01

    Powdery mildew (PM) is a very important disease of cucumber (Cucumis sativus L.). Resistant cultivars have been deployed in production for a long time, but the genetic mechanisms of PM resistance in cucumber are not well understood. A 3-year QTL mapping study of PM resistance was conducted with 132 F2:3 families derived from two cucumber inbred lines WI 2757 (resistant) and True Lemon (susceptible). A genetic map covering 610.4 cM in seven linkage groups was developed with 240 SSR marker loci. Multiple QTL mapping analysis of molecular marker data and disease index of the hypocotyl, cotyledon and true leaf for responses to PM inoculation identified six genomic regions in four chromosomes harboring QTL for PM resistance in WI 2757. Among the six QTL, pm1.1 and pm1.2 in chromosome 1 conferred leaf resistance. Minor QTL pm3.1 (chromosome 3) and pm4.1 (chromosome 4) contributed to disease susceptibility. The two major QTL, pm5.1 and pm5.2 were located in an interval of ~40 cM in chromosome 5 with each explaining 21.0-74.5 % phenotypic variations. Data presented herein support two recessively inherited, linked major QTL in chromosome 5 plus minor QTL in other chromosomes that control the PM resistance in WI 2757. The QTL pm5.2 for hypocotyl resistance plays the most important role in host resistance. Multiple observations in the same year revealed the importance of scoring time in the detection of PM resistance QTL. Results of this study provided new insights into phenotypic and genetic mechanisms of powdery mildew resistance in cucumber. PMID:23689747

  19. Evolution of the polymorphism at molecular markers in QTL and non-QTL regions in selected chicken lines (Open Access publication

    Directory of Open Access Journals (Sweden)

    Bijma Piter

    2008-11-01

    Full Text Available Abstract We investigated the joint evolution of neutral and selected genomic regions in three chicken lines selected for immune response and in one control line. We compared the evolution of polymorphism of 21 supposedly neutral microsatellite markers versus 30 microsatellite markers located in seven quantitative trait loci (QTL regions. Divergence of lines was observed by factor analysis. Five supposedly neutral markers and 12 markers in theQTL regions showed Fst values greater than 0.15. However, the non-significant difference (P > 0.05 between matrices of genetic distances based on genotypes at supposedly neutral markers on the one hand, and at markers in QTL regions, on the other hand, showed that none of the markers in the QTL regions were influenced by selection. A supposedly neutral marker and a marker located in the QTL region on chromosome 14 showed temporal variations in allele frequencies that could not be explained by drift only. Finally, to confirm thatmarkers located inQTL regions on chromosomes 1, 7 and 14were under the influence of selection, simulations were performed using haplotype dropping along the existing pedigree. In the zone located on chromosome 14, the simulation results confirmed that selection had an effect on the evolution of polymorphism of markers within the zone.

  20. QTL-mapping in mink (Neovison vison) shows evidence for QTL for guard hair thickness, guard hair length and skin length

    DEFF Research Database (Denmark)

    Thirstrup, Janne Pia; Labouriau, Rodrigo; Guldbrandtsen, Bernt;

    2011-01-01

    Fur quality in mink (Neovison vison) is a composite trait, consisting of e.g. guard hair length, guard hair thickness and density of wool. A genome wide QTL search was performed to detect QTL for fur quality traits in mink. Here we present the results of QTL analyses for guard hair length, guard...... hair thickness and density of wool. Data from an F2-cross was analysed across fourteen chromosomes using 100 microsatellites as markers with a spacing of approximately 20 cM. The two lines used for the F2-cross were Nordic wild mink and American short nap mink. In total 1,083 animals (21 wild type, 25...... short nap, 103 F1 and 934 F2) were marker typed and recorded for the three presented fur quality traits. For the QTL-analyses a regression analysis implemented in QTL Express software was used. Evidence was found for the existence of QTL for guard hair length, guard hair thickness and density of wool...

  1. Coeficientes de repetibilidade genética de caracteres em pupunheira Genetic repeatability coeficient of caracters in peach palm

    Directory of Open Access Journals (Sweden)

    João Tomé de Farias Neto

    2002-12-01

    Full Text Available No Brasil, a pupunheira é uma planta muito útil na alimentação, seja como fonte de frutos seja para palmito. O interesse pela pupunheira como produtora de palmito deve-se a características de precocidade de produção, rusticidade, perfilhamento, palatabilidade. Estimativas de parâmetros genéticos, como a repetibilidade em pupunheira, são importantes por constituir ferramentas fundamentais no direcionamento de um programa de melhoramento genético. O objetivo do trabalho foi estimar os coeficientes de repetibilidade dos caracteres altura da planta, diâmetro da planta à altura do colo e peso de palmito em três avaliações, em pupunheira, por meio dos seguintes procedimentos estatísticos: análise de variância, componentes principais e análise estrutural. Foram também determinados os números de repetições necessárias para proporcionar níveis de certeza da predição do valor real do indivíduo. Os coeficientes de repetibilidade dos caracteres diâmetro à altura do colo e peso de palmito líquido são de baixa magnitude (inferiores a 0,4, indicando irregularidade de comportamento de uma avaliação para outra. Para o caráter altura da planta, três avaliações são necessárias para ter-se predições com confiabilidade de 80% .Para o mesmo percentual de confiabilidade, são necessárias seis avaliações para os caracteres diâmetro à altura do colo e peso de palmito líquido.In Brazil, the Bactris gasipaes palm is a very useful plant for food as a source of fruits or heart palm. The interest for this species is due to the precocity of the heart palm production, rusticity, straightening up, and palatability of the heart palm. Estimates of genetic parameters, such as repeatability, are very important and fundamental for breeding program. The objective of this research was to estimate the repeatability coefficients of the characters: plant height, plant diameter and heart palm weight, using variance analysis, principal

  2. Tipos de herencia en capsaicinoides, antioxidantes, azúcares solubles y caracteres morfológicos del fruto en chile manzano

    OpenAIRE

    Sánchez Sánchez, Hermilo

    2012-01-01

    En frutos de los híbridos posibles formados con cinco progenitores de chile manzano (Capsicum pubescens R. y P.) provenientes de Huatusco, Perú, Puebla, Tacámbaro y Zongolica, se analizaron las concentraciones de capsaicinoides (capsaicina, nordihidrocapsaicina y dihidrocapsaicina), clorofilas (a y b), vitamina C (ácido ascórbico y dehidroascórbico) y azúcares solubles (estaquiosa, rafinosa, sacarosa, glucosa, galactosa, fructosa y sorbitol), y se registraron los caractere...

  3. An interval of the obesity QTL Nob3.38 within a QTL hotspot on chromosome 1 modulates behavioral phenotypes.

    Directory of Open Access Journals (Sweden)

    Heike Vogel

    Full Text Available A region on mouse distal chromosome 1 (Chr. 1 that is highly enriched in quantitative trait loci (QTLs controlling neural and behavioral phenotypes overlaps with the peak region of a major obesity QTL (Nob3.38, which we identified in an intercross of New Zealand Obese (NZO mice with C57BL/6J (B6. By positional cloning we recently identified a microdeletion within this locus causing the disruption of Ifi202b that protects from adiposity by suppressing expression of 11β-Hsd1. Here we show that the Nob3.38 segment also corresponds with the QTL rich region (Qrr1 on Chr. 1 and associates with increased voluntary running wheel activity, Rota-rod performance, decreased grip strength, and anxiety-related traits. The characterization of a subcongenic line carrying 14.2 Mbp of Nob3.38 with a polymorphic region of 4.4 Mbp indicates that the microdeletion and/or other polymorphisms in its proximity alter body weight, voluntary activity, and exploration. Since 27 out of 32 QTL were identified in crosses with B6, we hypothesized that the microdeletion and or adjacent SNPs are unique for B6 mice and responsible for some of the complex Qrr1-mediated effects. Indeed, a phylogenic study of 28 mouse strains revealed a NZO-like genotype for 22 and a B6-like genotype for NZW/LacJ and 4 other C57BL strains. Thus, we suggest that a Nob3.38 interval (173.0-177.4 Mbp does not only modify adiposity but also neurobehavioral traits by a haplotype segregating with C57BL strains.

  4. An Interval of the Obesity QTL Nob3.38 within a QTL Hotspot on Chromosome 1 Modulates Behavioral Phenotypes

    Science.gov (United States)

    Vogel, Heike; Montag, Dirk; Kanzleiter, Timo; Jonas, Wenke; Matzke, Daniela; Scherneck, Stephan; Chadt, Alexandra; Töle, Jonas; Kluge, Reinhart; Joost, Hans-Georg; Schürmann, Annette

    2013-01-01

    A region on mouse distal chromosome 1 (Chr. 1) that is highly enriched in quantitative trait loci (QTLs) controlling neural and behavioral phenotypes overlaps with the peak region of a major obesity QTL (Nob3.38), which we identified in an intercross of New Zealand Obese (NZO) mice with C57BL/6J (B6). By positional cloning we recently identified a microdeletion within this locus causing the disruption of Ifi202b that protects from adiposity by suppressing expression of 11β-Hsd1. Here we show that the Nob3.38 segment also corresponds with the QTL rich region (Qrr1) on Chr. 1 and associates with increased voluntary running wheel activity, Rota-rod performance, decreased grip strength, and anxiety-related traits. The characterization of a subcongenic line carrying 14.2 Mbp of Nob3.38 with a polymorphic region of 4.4 Mbp indicates that the microdeletion and/or other polymorphisms in its proximity alter body weight, voluntary activity, and exploration. Since 27 out of 32 QTL were identified in crosses with B6, we hypothesized that the microdeletion and or adjacent SNPs are unique for B6 mice and responsible for some of the complex Qrr1-mediated effects. Indeed, a phylogenic study of 28 mouse strains revealed a NZO-like genotype for 22 and a B6-like genotype for NZW/LacJ and 4 other C57BL strains. Thus, we suggest that a Nob3.38 interval (173.0–177.4 Mbp) does not only modify adiposity but also neurobehavioral traits by a haplotype segregating with C57BL strains. PMID:23308133

  5. QTL map meets population genomics: an application to rice.

    Directory of Open Access Journals (Sweden)

    Jeffrey A Fawcett

    Full Text Available Genes involved in the transition from wild to cultivated crop species should be of great agronomic importance. Population genomic approaches utilizing genome resequencing data have been recently applied for this purpose, although it only reports a large list of candidate genes with no biological information. Here, by resequencing more than 30 genomes altogether of wild rice Oryza rufipogon and cultivated rice O. sativa, we identified a number of regions with clear footprints of selection during the domestication process. We then focused on identifying candidate domestication genes in these regions by utilizing the wealth of QTL information in rice. We were able to identify a number of interesting candidates such as transcription factors that should control key domestication traits such as shattering, awn length, and seed dormancy. Other candidates include those that might have been related to the improvement of grain quality and those that might have been involved in the local adaptation to dry conditions and colder environments. Our study shows that population genomic approaches and QTL mapping information can be used together to identify genes that might be of agronomic importance.

  6. The evolution of gene expression QTL in Saccharomyces cerevisiae.

    Directory of Open Access Journals (Sweden)

    James Ronald

    Full Text Available Understanding the evolutionary forces that influence patterns of gene expression variation will provide insights into the mechanisms of evolutionary change and the molecular basis of phenotypic diversity. To date, studies of gene expression evolution have primarily been made by analyzing how gene expression levels vary within and between species. However, the fundamental unit of heritable variation in transcript abundance is the underlying regulatory allele, and as a result it is necessary to understand gene expression evolution at the level of DNA sequence variation. Here we describe the evolutionary forces shaping patterns of genetic variation for 1206 cis-regulatory QTL identified in a cross between two divergent strains of Saccharomyces cerevisiae. We demonstrate that purifying selection against mildly deleterious alleles is the dominant force governing cis-regulatory evolution in S. cerevisiae and estimate the strength of selection. We also find that essential genes and genes with larger codon bias are subject to slightly stronger cis-regulatory constraint and that positive selection has played a role in the evolution of major trans-acting QTL.

  7. Analysis of rice blast resistance genes by QTL mapping

    Institute of Scientific and Technical Information of China (English)

    XU Jichen; WANG Jiulin; LING Zhongzhuan; ZHU Lihuang

    2004-01-01

    Resistance to rice blast pathogen mostly shows a quantitative trait controlled by several minor genes. Its complexity and the mutable characteristic of rice blast isolates both hinder the development of the blast resistance research. The article here tried to explore the resistance gene distribution on rice chromosomes and the way of function. Totally 124 QTLs have been identified against 20 isolates using Cartographer software with a ZYQ8/JX17 DH population, which separately are at 100 loci of 72 marker intervals on 12 rice chromosomes. Of them, 16 QTLs were determined by the isolate HB-97-36-1. 82 QTLs (66.13%) are from the resistant parent alleles, ZYQ8, while 42 QTLs (33.87%) are from the susceptible parent alleles, JX17. In comparison of their positions on chromosome, most QTLs are clustered together and distributed nearby the major genes especially the regions on chromosomes 1, 2, 8, 10 and 12. Each QTL could account for the resistance variation between 3.52%-68.64%. And, a positional QTL might display the resistance to several different isolates with different contributions.

  8. Mapping Quantitative Trait Loci (QTL in sheep. III. QTL for carcass composition traits derived from CT scans and aligned with a meta-assembly for sheep and cattle carcass QTL

    Directory of Open Access Journals (Sweden)

    Thomson Peter C

    2010-09-01

    Full Text Available Abstract An (Awassi × Merino × Merino single-sire backcross family with 165 male offspring was used to map quantitative trait loci (QTL for body composition traits on a framework map of 189 microsatellite loci across all autosomes. Two cohorts were created from the experimental progeny to represent alternative maturity classes for body composition assessment. Animals were raised under paddock conditions prior to entering the feedlot for a 90-day fattening phase. Body composition traits were derived in vivo at the end of the experiment prior to slaughter at 2 (cohort 1 and 3.5 (cohort 2 years of age, using computed tomography. Image analysis was used to gain accurate predictions for 13 traits describing major fat depots, lean muscle, bone, body proportions and body weight which were used for single- and two-QTL mapping analysis. Using a maximum-likelihood approach, three highly significant (LOD ≥ 3, 15 significant (LOD ≥ 2, and 11 suggestive QTL (1.7 ≤ LOD P P A meta-assembly of ovine QTL for carcass traits from this study and public domain sources was performed and compared with a corresponding bovine meta-assembly. The assembly demonstrated QTL with effects on carcass composition in homologous regions on OAR1, 2, 6 and 21.

  9. Parámetros genéticos de caracteres biométricos en caballos Mangalarga

    Directory of Open Access Journals (Sweden)

    Raul Sampaio de Almeida Prado and Marcilio Dias Silveira da Mota

    2008-12-01

    Full Text Available El objetivo del presente estudio fue estimar los parámetros genéticos de caracteres biométricos en caballos de la raza Mangalarga. Los datos fueron proporcionados por el Studbook de la Asociación Brasileña de Criadores de Caballos Mangalarga (ABCCRM y compuesto por 36.036 registros de alzada a la cruz, 6.906 de la circunferencia del tórax y 6.916 de la circunferencia del hueso frontal de la caña, realizado en caballos nacidos entre enero de1980 y diciembre de 2003, y comprende 169.228 caballos en la matriz de parentesco. El modelo utilizado para estimar los componentes de lacovarianza necesarios para obtener la heredabilidades y las correlaciones incluyen: el efecto aleatorio de los caballos y los efectos fijos de edad, creador y el grupo de contemporáneos, utilizando el programa MTGSAM para las análisis. La media de heredabilidad encontradas oscilaron entre 0,41 (circunferencia del hueso de la caña a 0,7 (circunferencia torácica y elcorrelaciones genéticas y fenotípicas, fueron todos positivos, desde 0,28 a 0,47 y de 0,19 a 0,35, respectivamente.

  10. Divergência genética em trigo de sequeiro por meio de caracteres morfoagronômicos

    Directory of Open Access Journals (Sweden)

    Aurinelza Batista Teixeira Condé

    2010-12-01

    Full Text Available O cultivo de trigo de sequeiro constitui ótima opção para o Estado de Minas Gerais em regiões com altitude superior a 800 m. Neste estudo objetivou-se estimar a divergência genética entre genótipos de trigo com o auxílio de métodos de análise multivariada, objetivando identificar potenciais genótipos para obtenção de combinações híbridas promissoras. Foi utilizado o delineamento experimental em blocos ao acaso, com quatro repetições. Avaliaram-se seis caracteres morfoagronômicos em 11 genótipos de trigo cultivados em condições de sequeiro no município de Patos de Minas-MG, nos anos de 2007 e 2008. Houve grande variabilidade fenotípica entre os genótipos de trigo avaliados em cultivo de sequeiro. Os genótipos IAC 289-L22 e IAC 289-L4 foram os mais similares, enquanto os CD 113 e EP 011106, os maisdivergentes, promissores nos cruzamentos para obtenção de materiais adaptados e com bons atributos fenotípicos em cultivo de sequeiro.

  11. Optimizing purebred selection for crossbred performance using QTL with different degrees of dominance

    Directory of Open Access Journals (Sweden)

    Chakraborty Reena

    2004-05-01

    Full Text Available Abstract A method was developed to optimize simultaneous selection for a quantitative trait with a known QTL within a male and a female line to maximize crossbred performance from a two-way cross. Strategies to maximize cumulative discounted response in crossbred performance over ten generations were derived by optimizing weights in an index of a QTL and phenotype. Strategies were compared to selection on purebred phenotype. Extra responses were limited for QTL with additive and partial dominance effects, but substantial for QTL with over-dominance, for which optimal QTL selection resulted in differential selection in male and female lines to increase the frequency of heterozygotes and polygenic responses. For over-dominant QTL, maximization of crossbred performance one generation at a time resulted in similar responses as optimization across all generations and simultaneous optimal selection in a male and female line resulted in greater response than optimal selection within a single line without crossbreeding. Results show that strategic use of information on over-dominant QTL can enhance crossbred performance without crossbred testing.

  12. Quantitative trait loci (QTL mapping for growth traits on bovine chromosome 14

    Directory of Open Access Journals (Sweden)

    Marcelo Miyata

    2007-03-01

    Full Text Available Quantitative trait loci (QTL mapping in livestock allows the identification of genes that determine the genetic variation affecting traits of economic interest. We analyzed the birth weight and weight at 60 days QTL segregating on bovine chromosome BTA14 in a F2 resource population using genotypes produced from seven microsatellite markers. Phenotypes were derived from 346 F2 progeny produced from crossing Bos indicus Gyr x Holstein Bos taurus F1 parents. Interval analysis to detect QTL for birth weight revealed the presence of a QTL (p < 0.05 at 1 centimorgan (cM from the centromere with an additive effect of 1.210 ± 0.438 kg. Interval analysis for weight at 60 days revealed the presence of a QTL (p < 0.05 at 0 cM from the centromere with an additive effect of 2.122 ± 0.735 kg. The region to which the QTL were assigned is described in the literature as responsible for some growth traits, milk yield, milk composition, fat deposition and has also been related to reproductive traits such as daughter pregnancy rate and ovulation rate. The effects of the QTL described on other traits were not investigated.

  13. A high-density genetic map and growth related QTL mapping in bighead carp (Hypophthalmichthys nobilis).

    Science.gov (United States)

    Fu, Beide; Liu, Haiyang; Yu, Xiaomu; Tong, Jingou

    2016-01-01

    Growth related traits in fish are controlled by quantitative trait loci (QTL), but no QTL for growth have been detected in bighead carp (Hypophthalmichthys nobilis) due to the lack of high-density genetic map. In this study, an ultra-high density genetic map was constructed with 3,121 SNP markers by sequencing 117 individuals in a F1 family using 2b-RAD technology. The total length of the map was 2341.27 cM, with an average marker interval of 0.75 cM. A high level of genomic synteny between our map and zebrafish was detected. Based on this genetic map, one genome-wide significant and 37 suggestive QTL for five growth-related traits were identified in 6 linkage groups (i.e. LG3, LG11, LG15, LG18, LG19, LG22). The phenotypic variance explained (PVE) by these QTL varied from 15.4% to 38.2%. Marker within the significant QTL region was surrounded by CRP1 and CRP2, which played an important role in muscle cell division. These high-density map and QTL information provided a solid base for QTL fine mapping and comparative genomics in bighead carp. PMID:27345016

  14. Mapping of quantitative trait loci (QTL) for production, resistance and tolerance traits in Salix. Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Roennberg-Waestljung, Ann Christin; Bertholdsson, Nils-Ove; Glynn, Carolyn; Weih, Martin; Aahman, Inger [SLU, Uppsala (Sweden). Dept. of Plant Biology and Forest Genetics

    2004-05-01

    Quantitative trait loci (QTL) for growth traits, water use efficiency and tolerance/resistance against metals and herbivores have been identified. A hybrid F2 population originating from a cross between a Salix dasyclados-clone (SW901290) and a S. viminalis-clone ('Jorunn') was used for the different studies in this project. The growth response was analyzed in a greenhouse experiment with two water treatments, normal and drought. In addition, three field experiments with contrasting soils and climates were established. QTL specific for each treatment or field environment but also QTL stable over the treatments or field environments were detected. Each QTL explained from 8 to 29 % of the phenotypic variation depending on trait, treatment or field environment. Clusters of QTL for different traits were mapped indicating a common genetic base or tightly-linked QTL. Stable QTL identified for dryweight can be useful tools for early selection in Salix. In a separate greenhouse experiment, with a subset of ten genotypes from the F2 population, we show that genotype is more important than irrigation treatment for production of phenolic substances as well as for resistance to herbivory by P vulgatissima.

  15. EL ÍNDICE CUANTITATIVO DE CALIDAD WEB COMO INSTRUMENTO OBJETIVO DE MEDICIÓN DE LA CALIDAD DE SITIOS WEB CORPORATIVOS

    Directory of Open Access Journals (Sweden)

    González López, Óscar R.

    2013-01-01

    Full Text Available El nuevo entorno marcado por la crisis económica hace imprescindible conocer la eficiencia de las acciones online llevadas a cabo por la empresa. Este trabajo propone una serie de indicadores para evaluar los sitios web de las compañías de todo el mundo. Para ello se ha diseñado la investigación del problema a tratar, basada en la evaluación manual y automática de una serie de variables objetivas, con la posterior aplicación de un análisis factorial para la elaboración de indicadores. El índice cuantitativo de calidad web (ICCW es una herramienta versátil que nos permite comparar cualquier tipo de organización y detectar los puntos fuertes y débiles del sitio web de la compañía.

  16. Complex trait subtypes identification using transcriptome profiling reveals an interaction between two QTL affecting adiposity in chicken

    Directory of Open Access Journals (Sweden)

    Blum Yuna

    2011-11-01

    Full Text Available Abstract Background Integrative genomics approaches that combine genotyping and transcriptome profiling in segregating populations have been developed to dissect complex traits. The most common approach is to identify genes whose eQTL colocalize with QTL of interest, providing new functional hypothesis about the causative mutation. Another approach includes defining subtypes for a complex trait using transcriptome profiles and then performing QTL mapping using some of these subtypes. This approach can refine some QTL and reveal new ones. In this paper we introduce Factor Analysis for Multiple Testing (FAMT to define subtypes more accurately and reveal interaction between QTL affecting the same trait. The data used concern hepatic transcriptome profiles for 45 half sib male chicken of a sire known to be heterozygous for a QTL affecting abdominal fatness (AF on chromosome 5 distal region around 168 cM. Results Using this methodology which accounts for hidden dependence structure among phenotypes, we identified 688 genes that are significantly correlated to the AF trait and we distinguished 5 subtypes for AF trait, which are not observed with gene lists obtained by classical approaches. After exclusion of one of the two lean bird subtypes, linkage analysis revealed a previously undetected QTL on chromosome 5 around 100 cM. Interestingly, the animals of this subtype presented the same q paternal haplotype at the 168 cM QTL. This result strongly suggests that the two QTL are in interaction. In other words, the "q configuration" at the 168 cM QTL could hide the QTL existence in the proximal region at 100 cM. We further show that the proximal QTL interacts with the previous one detected on the chromosome 5 distal region. Conclusion Our results demonstrate that stratifying genetic population by molecular phenotypes followed by QTL analysis on various subtypes can lead to identification of novel and interacting QTL.

  17. Mapping QTL for Resistance Against Viral Nervous Necrosis Disease in Asian Seabass.

    Science.gov (United States)

    Liu, Peng; Wang, Le; Wan, Zi Yi; Ye, Bao Qing; Huang, Shuqing; Wong, Sek-Man; Yue, Gen Hua

    2016-02-01

    Viral nervous necrosis disease (VNN), caused by nervous necrosis virus (NNV), leads to mass mortality in mariculture. However, phenotypic selection for resistance against VNN is very difficult. To facilitate marker-assisted selection (MAS) for resistance against VNN and understanding of the genetic architecture underlying the resistance against this disease, we mapped quantitative trait loci (QTL) for resistance against VNN in Asian seabass. We challenged fingerlings at 37 days post-hatching (dph), from a single back-cross family, with NNV at a concentration of 9 × 10(6) TCID50/ml for 2 h. Daily mortalities were recorded and collected. A panel of 330 mortalities and 190 surviving fingerlings was genotyped using 149 microsatellites with 145 successfully mapped markers covering 24 linkage groups (LGs). Analysis of QTL for both resistance against VNN and survival time was conducted using interval mapping. Five significant QTL located in four LGs and eight suggestive QTL in seven LGs were identified for resistance. Another five significant QTL in three LGs and five suggestive QTL in three LGs were detected for survival time. One significant QTL, spanning 3 cM in LG20, was identified for both resistance and survival time. These QTL explained 2.2-4.1% of the phenotypic variance for resistance and 2.2-3.3% of the phenotypic variance for survival time, respectively. Our results suggest that VNN resistance in Asian seabass is controlled by many loci with small effects. Our data provide information for fine mapping of QTL and identification of candidate genes for a better understanding of the mechanism of disease resistance.

  18. Joint QTL analysis of three connected F2-crosses in pigs

    Directory of Open Access Journals (Sweden)

    Bennewitz Jörn

    2010-11-01

    Full Text Available Abstract Background Numerous QTL mapping resource populations are available in livestock species. Usually they are analysed separately, although the same founder breeds are often used. The aim of the present study was to show the strength of analysing F2-crosses jointly in pig breeding when the founder breeds of several F2-crosses are the same. Methods Three porcine F2-crosses were generated from three founder breeds (i.e. Meishan, Pietrain and wild boar. The crosses were analysed jointly, using a flexible genetic model that estimated an additive QTL effect for each founder breed allele and a dominant QTL effect for each combination of alleles derived from different founder breeds. The following traits were analysed: daily gain, back fat and carcass weight. Substantial phenotypic variation was observed within and between crosses. Multiple QTL, multiple QTL alleles and imprinting effects were considered. The results were compared to those obtained when each cross was analysed separately. Results For daily gain, back fat and carcass weight, 13, 15 and 16 QTL were found, respectively. For back fat, daily gain and carcass weight, respectively three, four, and five loci showed significant imprinting effects. The number of QTL mapped was much higher than when each design was analysed individually. Additionally, the test statistic plot along the chromosomes was much sharper leading to smaller QTL confidence intervals. In many cases, three QTL alleles were observed. Conclusions The present study showed the strength of analysing three connected F2-crosses jointly. In this experiment, statistical power was high because of the reduced number of estimated parameters and the large number of individuals. The applied model was flexible and was computationally fast.

  19. Dynamic QTL analysis and candidate gene mapping for waterlogging tolerance at maize seedling stage.

    Directory of Open Access Journals (Sweden)

    Khalid A Osman

    Full Text Available Soil waterlogging is one of the major abiotic stresses adversely affecting maize growth and yield. To identify dynamic expression of genes or quantitative trait loci (QTL, QTL associated with plant height, root length, root dry weight, shoot dry weight and total dry weight were identified via conditional analysis in a mixed linear model and inclusive composite interval mapping method at three respective periods under waterlogging and control conditions. A total of 13, 19 and 23 QTL were detected at stages 3D|0D (the period during 0-3 d of waterlogging, 6D|3D and 9D|6D, respectively. The effects of each QTL were moderate and distributed over nine chromosomes, singly explaining 4.14-18.88% of the phenotypic variation. Six QTL (ph6-1, rl1-2, sdw4-1, sdw7-1, tdw4-1 and tdw7-1 were identified at two consistent stages of seedling development, which could reflect a continuous expression of genes; the remaining QTL were detected at only one stage. Thus, expression of most QTL was influenced by the developmental status. In order to provide additional evidence regarding the role of corresponding genes in waterlogging tolerance, mapping of Expressed Sequence Tags markers and microRNAs were conducted. Seven candidate genes were observed to co-localize with the identified QTL on chromosomes 1, 4, 6, 7 and 9, and may be important candidate genes for waterlogging tolerance. These results are a good starting point for understanding the genetic basis for selectively expressing of QTL in different stress periods and the common genetic control mechanism of the co-localized traits.

  20. Detection of nitrogen deficiency QTL in juvenile wild barley introgression lines growing in a hydroponic system

    Directory of Open Access Journals (Sweden)

    Hoffmann Astrid

    2012-10-01

    Full Text Available Abstract Background In this report we studied the genetic regulation of juvenile development of wild barley introgression lines (S42ILs under two contrasting hydroponic nitrogen (N supplies. Ten shoot and root related traits were examined among 42 S42ILs and the recurrent parent ‘Scarlett’. The traits included tiller number, leaf number, plant height, leaf and root length, leaf to root length ratio, shoots and root dry weight, shoot to root weight ratio, and chlorophyll content. Our aims were (1 to test the suitability of a hydroponic system for early detection of favourable S42ILs, (2 to locate quantitative trait loci (QTL that control the examined traits, (3 to identify favourable wild barley alleles that improve trait performances in regard to N treatment and, finally, (4 to validate the identified QTL through comparison with previously reported QTL originating from the same parental cross. Results The phenotypic data were analysed in a mixed model association study to detect QTL. The post-hoc Dunnett test identified 28 S42ILs that revealed significant (P Hsp effects for tiller number, leaf number, leaf length, plant height and leaf to root ratio on the long arm of chromosome 7H. These QTL correspond to QTL for ears per plant and plant height that were previously detected in field trials conducted with the same S42ILs or with the S42 population. Conclusion Our results suggest that the QTL we identified under hydroponic N cultivation partly correspond to QTL detected in field experiments. Due to this finding, screening of plants in early developmental stages grown in a hydroponic system may be a fast and cost effective method for early QTL detection and marker-assisted allelic selection, potentially speeding up elite barley breeding programs.

  1. Refining QTL with high-density SNP genotyping and whole genome sequence in three cattle breeds

    DEFF Research Database (Denmark)

    Sahana, Goutam; Guldbrandtsen, Bernt; Lund, Mogens Sandø

    2012-01-01

    method. Principal components were used to account for population structure. The QTL segregating in all three breeds were selected and a few of the most significant ones were followed in further analyses. The polymorphisms in the identified QTL regions were imputed using 90 whole genome sequences...... available from these three breeds. Imputations were done using IMPUTE v2.2. Association analyses with imputed polymorphisms were repeated for the targeted regions. The QTL genotypes of the sires with more than 20 sons were determined by an a posteriori granddaughter design. The concordance of sires...

  2. Genome scan for parent-of-origin QTL effects on bovine growth and carcass traits

    OpenAIRE

    Ikhide G. Imumorin; Eun-Hee eKim; Yun-Mi eLee; Dirk-Jan eDe Koning; Johan eVan Arendonk; Marcos eDe Donato; Jeremy Francis Taylor; Jong-Joo eKim

    2011-01-01

    Parent-of-origin effects (POE) such as genomic imprinting influence growth and body composition in livestock, rodents and humans. Here, we report the results of a genome scan to detect quantitative trait loci (QTL) with POE on growth and carcass traits in Angus x Brahman cattle crossbreds. We identified 24 POE-QTL on 15 Bos taurus autosomes (BTAs) of which 6 were significant at 5% genome-wide level and 18 at the 5% chromosome-wide significance level. Six QTL were paternally expressed while 15...

  3. QTL Mapping for Parthenocarpy in Cucumber%黄瓜单性结实性状的 QTL 定位

    Institute of Scientific and Technical Information of China (English)

    武喆; 李蕾; 张婷; 张停林; 李季; 娄群峰; 陈劲枫

    2015-01-01

    [Objective]Cucumber is one of the ten vegetables in the world and parhenocarpy is an important trait closely related to production and quality of cucumber. To explore the inheritance and QTL mapping for parthenocarpy in cucumber could provide a preliminary basis for further study on mechanism of parthenocarpy and molecular assistant selection breeding, and lay a theoretical foundation for breeding of parthenocarpy.[Method]In this study, The authers clipped eight female flowers on main stem and branches, respectively, for every individual plant and investigated parthenocarpic fruit once when all plants treament finished 8-10 days later to calculate the parthenocarpy percentage (numbers of parthenocarpis fruit/numbers of clipped female flower) in order to evaluate parthenocarpy ability. Two F2 progenies derived from two crosses between EC1, a gynoecious parthenocarpic line, and two monoecious non-parthenocarpic lines 8419 and 14519 were constructed to determine the inheritance of parthenocarpy in cucumber. A linkage map from part of F2 plants from the cross of EC1×8419 was constructed with JoinMap4.0 software by screening 1 335 SSR from 9930 and gy14 cucumber genome sequencing and 143 Indel primers from two parents resequencing and QTL detection for parthenocarpy was conducted with WinQTLcart2.5 software using F2:3 families from the same cross. The candidate genes in major QTL region were predicted using bioinformatic analysis method.[Result]Parthenocarpy in EC1 was inherited quantitatively but segregated towards different parents in two F2 progenies. A linkage map containing 7 chromosomes, 116 SSR and 9 Indel markers was constructed, which total length was 802.9 cM and average distance between two markers was 6.3 cM. QTL analysis identified 7 QTLs, Parth1, Parth2-1, Parth2-2, Parth3-1, Parth3-2, Parth5, and Parth7,distributing on chromosomes 1, 2, 3, 5, and 7. The major QTL Parth2-1 locating between SSR00684-SSR22083 was the only locus detected in two seasons

  4. Analysis of QTL for resistance to radiation in rice

    International Nuclear Information System (INIS)

    The recombinant inbred line (RIL) population derived from rice variates Zhenshan 97B/Miyang 46 and their genetic linkage maps were used to map QTLs controlling resistant to radiation. The trait was measured by the relative germination rate (RGR) and the relative surviving plant rate (RSPR) after the seeds of each line treated with γ-rays irradiation at two 350 and 550 Gy. The results indicated that the lines treated with γ-irradiation showed different performance in resistance to radiation. Under the treatment of 350 Gy, two QTLs with additive effects were detected, of which qRR (g) 81 was only significant for relative germination rate, and it had the positive additive effects from the male parent, explaining 6.53% of the total phenotypic variations. The qRR(s)2-2 was another significant one for relative surviving plant rate, whose positive effects came from the female parent,explaining 12.81% of the total phenotypic variations. Similarly, 4 QTLs were detected under irradiation dose of 550 Gy, and qRR(g)1-2 and qRR(g)8-2 were detected for relative germination rate, with positive effects coming from female and male parent,respectively,explaining 14.38% of the total variations. qRR(s)5-2 and qRR(s)10 were detected for relative surviving plant rate, with positive effects coming from the male parent, explaining 19.65% of total variations. Under different irradiation dose, 9 pairs of double QTL epistasis effects could be identified in this population. The results suggested that the expression of QTL with resistance to radiation might have relation with the irradiation dose. (authors)

  5. Caracteres diagnósticos foliares en táxones ibéricos de Isoetes L. (Isoetaceae, Pteridophyta

    Directory of Open Access Journals (Sweden)

    Rolleri, Cristina H.

    2003-12-01

    . echinosporum, I. x hickeyi, I. lacustre, I. longissimum e /. velatum subsp. Asturicense (acuáticos. Se incluye también en la comparación un taxon anfibio tetraploide no descrito, relacionado morfológicamente con /. velatum, que hasta su descripción se designa provisionalmente como Isoetes sp. Se estudiaron varias colecciones ibéricas y, en el caso de algunos táxones, se incluyeron ejemplares procedentes de otras localidades de Europa y América, con el fin de contrastar los rasgos analizados. Los caracteres estudiados fueron: ornamentaciones cuticulares, modelos epidérmicos y estomas (morfología, distribución y dimensiones, contorno de las secciones transversales foliares, epidermis en corte (membrana cuticular, cutícula, ornamentaciones cuticulares, desarrollo relativo del mesofilo, presencia o ausencia y distribución del colénquima, diafragmas foliares y presencia o ausencia de protuberancias intercelulares pécticas de las células de los diafragmas (de tipo filamento. Todos los caracteres son independientes de la edad de los microfilos, de la madurez de las plantas y, en general, del hábitat, y se observan por igual en material fresco o restaurado mediante una técnica que se propone en este trabajo.

  6. Observaciones sobre algunos caracteres de valor taxonómico en el grupo de los carófitos

    Directory of Open Access Journals (Sweden)

    Pedrola, J.

    1990-05-01

    Full Text Available The variability of the microstructurals characters and mineralogical composition of the oogonia of some charophytes extant and fossils is described. Two types of microstructures (W & V are find. These are conservative into populations and are not able to change by the environmental factors. Moreover, these structures are quite constant in some of the phylogenetics groups studied. Consequently it is proposed its utilization in taxonomy. The apparition of original compounds in the Charophyta (vaterite. whewelite, aragonite, etc. is important because it supports an old idea that considerates the Charophyta as an autonomous class between the Clorophyta and the Traqueophyta.

    Se describe la variabilidad de los caracteres microestructurales y la composición mineralógica de las células espirales del oogonio en diversas especies actuales y fósiles del grupo de los carófitos. Se encuentran así, dos tipos de microestructuras diferentes (W y V que se muestran conservativas en el seno de las poblaciones, no moldeables por el ambiente y relativamente constantes dentro de los distintos grupos filogenéticos. En consecuencia, se propone su utilización con fines taxonómicos. La aparición de ciertos elementos mineralógicos (vaterita, whewelita, aragonito etc. resulta remarcable por su originalidad y su apoyo al viejo criterio que consideraba los carófitos como una clase autónoma y quizás de "enlace" entre clorófitos y traqueófitos.

  7. Dissimilaridade genética de girassol por meio de caracteres quantitativos Agronomic performance and genetic dissimilarity sunflower

    Directory of Open Access Journals (Sweden)

    João Paulo Gonsiorkiewicz Rigon

    2012-11-01

    Full Text Available Objetivou-se com este estudo avaliar, por meio de caracteres quantitativos, a dissimilaridade genética entre cultivares de girassol em diferentes localidades, além da concordância entre os métodos, visando à extração de linhagens para possíveis cruzamentos. Foram cultivados oito híbridos de girassol em duas localidades no noroeste do Rio Grande do Sul, com solo predominantemente do tipo Latossolo Vermelho distrófico. Foram utilizados métodos multivariados para determinar a divergência genética, utilizando a distância generalizada de Mahalanobis. Apesar dos rendimentos distintos entre locais e cultivares, os métodos de agrupamento tiveram concordância entre si. Para obtenção de populações segregantes, a cultivar 'Olisun 5', independente da localidade, demonstrou-se com maior potencial de hibridação, tendo as maiores contribuições por meio do número de aquênios por capítulo e altura de inserção do capítulo.The aim of this study to evaluate by means of quantitative traits, the genetic dissimilarity among sunflower cultivars in different locations, in addition to the agreement between the methods in order to extract lines for future crosses. There were eight sunflower hybrids grown in two locations in northwestern Rio Grande do Sul, mainly with soil type Oxisol. Multivariate methods were used to determine the genetic diversity, using the Mahalanobis distance. Although the different yield between locations and cultivars, methods of grouping agreed among them selves. To obtain segregating populations, regardless of location, the cultivate 'Olisun 5', demonstrated greater potential for hybridization, with major contributions through number of achenes per chapter and height of the insertion section.

  8. Power of QTL detection by either fixed or random models in half-sib designs

    Directory of Open Access Journals (Sweden)

    Schaeffer Lawrence R

    2005-11-01

    Full Text Available Abstract The aim of this study was to compare the variance component approach for QTL linkage mapping in half-sib designs to the simple regression method. Empirical power was determined by Monte Carlo simulation in granddaughter designs. The factors studied (base values in parentheses included the number of sires (5 and sons per sire (80, ratio of QTL variance to total genetic variance (λ = 0.1, marker spacing (10 cM, and QTL allele frequency (0.5. A single bi-allelic QTL and six equally spaced markers with six alleles each were simulated. Empirical power using the regression method was 0.80, 0.92 and 0.98 for 5, 10, and 20 sires, respectively, versus 0.88, 0.98 and 0.99 using the variance component method. Power was 0.74, 0.80, 0.93, and 0.95 using regression versus 0.77, 0.88, 0.94, and 0.97 using the variance component method for QTL variance ratios (λ of 0.05, 0.1, 0.2, and 0.3, respectively. Power was 0.79, 0.85, 0.80 and 0.87 using regression versus 0.80, 0.86, 0.88, and 0.85 using the variance component method for QTL allele frequencies of 0.1, 0.3, 0.5, and 0.8, respectively. The log10 of type I error profiles were quite flat at close marker spacing (1 cM, confirming the inability to fine-map QTL by linkage analysis in half-sib designs. The variance component method showed slightly more potential than the regression method in QTL mapping.

  9. Strategy for Mapping Quantitative Trait Loci (QTL) by Using Human Metapopulations

    OpenAIRE

    Rudan, I; Campbell, H.; Biloglav, Z.; Carothers, A D; Wright, A F

    2006-01-01

    AIM:To present a novel strategy for mapping quantitative trait loci (QTL), using human metapopulations. The strategy is based on the expectation that in geographic clusters of small and distinct human isolates, a combination of founder effect and genetic drift can dramatically increase population frequency of rare QTL variants with large effect. In such cases, the distribution of QT measurements in an (affected) isolate is expected to deviate from that observed in neighboring isolates.METHODS...

  10. Identification of environmentally stable QTL for resistance against Leptosphaeria maculans in oilseed rape (Brassica napus)

    OpenAIRE

    Huang, Y J; Jestin, C.; Welham, S. J.; King, G. J.; Manzanares-Dauleux, M. J.; Fitt, B. D. L.; Delourme, R

    2015-01-01

    Key message Six stable QTL for resistance against L. maculans (phoma stem canker) have been identified by QTL × environment interaction analysis using data from five winter oilseed rape field experiments. Abstract Phoma stem canker, caused by Leptosphaeria maculans, is a disease of worldwide importance on oilseed rape (Brassica napus). Quantitative trait loci (QTL)-mediated resistance against L. maculans in B. napus is considered to be race non-specific and potentially durable. Identification...

  11. QTL Mapping of Low-Temperature Germination Ability in the Maize IBM Syn4 RIL Population

    OpenAIRE

    Hu, Shuaidong; Lübberstedt, Thomas; Zhao, Guangwu; Lee, Michael

    2016-01-01

    Low temperature is the primary factor to affect maize sowing in early spring. It is, therefore, vital for maize breeding programs to improve tolerance to low temperatures at seed germination stage. However, little is known about maize QTL involved in low-temperature germination ability. 243 lines of the intermated B73×Mo17 (IBM) Syn4 recombinant inbred line (RIL) population was used for QTL analysis of low-temperature germination ability. There were significant differences in germination-rela...

  12. Genetic background effects on QTL and QTL × environment interaction for yield and its component traits as revealed by reciprocal introgression lines in rice

    Institute of Scientific and Technical Information of China (English)

    Xiaoqian; Wang; Yunlong; Pang; Jian; Zhang; Qiang; Zhang; Yonghong; Tao; Bo; Feng; Tianqing; Zheng; Jianlong; Xu; Zhikang; Li

    2014-01-01

    QTLs for quantitative traits are influenced by genetic background(GB) and environment.Identification of QTL with GB independency and environmental stability is prerequisite for effective marker-assisted selection(MAS). In this study, QTLs and QTL × environment interactions affecting grain yield per plant(GY) and its component traits, filled grain number per panicle(FGN), panicle number per plant(PN) and 1000-grain weight(TGW) across six environments were dissected using two sets of reciprocal introgression lines(ILs) derived from the cross Lemont × Teqing and SNP genotypic data. ANOVA indicated that the differences among genotypes and environments within each set of ILs were highly significant for all traits. A total of 72 distinct QTLs for GY and its component traits including 15 for GY, 25 for FGN, 18 for PN, and 29 for TGW were detected over the six environments. Most QTLs(87.4%) showed significant QTL × environment interactions(QEIs) and appeared to be more or less environment-specific. Among 72 QTLs, 15(20.8%) QTLs and 12(16.7%) QEIs were commonly identified in both backgrounds, indicating QTL especially QEI for yield and its component traits had strong GB effects. Four QTL regions affecting GY and its component traits, including S1269707–S4288071, S16661497–S17511092, and S35861863–S36341768 on chromosome 3, and S4134205–S7643153 on chromosome 5, were detected in both backgrounds and coincided with cloned genes for yield-related traits. These regions can be the targeted in rice breeding for high yield potential through MAS. Application of QTL main effects and their environmental interaction effects in MAS was discussed in detail.

  13. Comparative QTL mapping of resistance to sugarcane mosaic virus in maize based on bioinformatics

    Institute of Scientific and Technical Information of China (English)

    Xiangling L(U); Xinhai LI; Chuanxiao XIE; Zhuanfang HAO; Hailian JI; Liyu SHI; Shihuang ZHANG

    2008-01-01

    The development of genomics and bioinfor-matics offers new tools for comparative gene mapping. In this paper, an integrated QTL map for sugarcane mosaic virus (SCMV) resistance in maize was constructed by compiling a total of 81 QTL loci available, using the Genetic Map IBM2 2005 Neighbors as reference. These 81 QTL loci were scattered on 7 chromosomes of maize, and most of them were clustered on chromosomes 3 and 6. By using the method of meta-analysis, we identified one "consensus QTL" on chromosome 3 covering a genetic distance of 6.44 cM, and two on chromosome 6 covering genetic distances of 16 cM and 27.48 cM, respectively. Four positional candidate resistant genes were identified within the "consensus QTL" on chromosome 3 via the strategy of comparative genomics. These results suggest that application of a combination of meta-analysis within a species with sequence homology comparison in a related model plant is an efficient approach to identify the major QTL and its candidate gene(s) for the target traits. The results of this study provide useful information for iden-tifying and cloning the major gene(s) conferring resistance to SCMV in maize.

  14. Detection on OAR7 of QTL affecting fat and protein yields in dairy sheep

    Directory of Open Access Journals (Sweden)

    Antonello Carta

    2010-01-01

    Full Text Available The objective of this paper was identifying QTL that affect fat and protein yields in dairy sheep independently of milk yield. Data were collected in an experimental flock of 887 ewes organized in a daughter design. QTL detection focused on OAR7 where 13 microsatellites were available. The genetic abilities to produce fat and protein independently from the ability to produce milk were estimated as the residuals of the regression of EBV for fat and protein yields on EBV for milk yield. One QTL affecting fat yield (CWP=0.00009 and one QTL affecting protein yield (CWP=0.006 were detected. The most probable QTL location was 115.3 cM in the Sheep Best Position Linkage Map Version 4.7 for both traits. No QTL affecting milk yield was detected. The analysis of fat and protein yields independently of milk yield is an effective strategy to identify chromosomal regions affecting milk composition with no detrimental effect on milk yield.

  15. eQTL Regulating Transcript Levels Associated with Diverse Biological Processes in Tomato.

    Science.gov (United States)

    Ranjan, Aashish; Budke, Jessica M; Rowland, Steven D; Chitwood, Daniel H; Kumar, Ravi; Carriedo, Leonela; Ichihashi, Yasunori; Zumstein, Kristina; Maloof, Julin N; Sinha, Neelima R

    2016-09-01

    Variation in gene expression, in addition to sequence polymorphisms, is known to influence developmental, physiological, and metabolic traits in plants. Genetic mapping populations have facilitated identification of expression quantitative trait loci (eQTL), the genetic determinants of variation in gene expression patterns. We used an introgression population developed from the wild desert-adapted Solanum pennellii and domesticated tomato (Solanum lycopersicum) to identify the genetic basis of transcript level variation. We established the effect of each introgression on the transcriptome and identified approximately 7,200 eQTL regulating the steady-state transcript levels of 5,300 genes. Barnes-Hut t-distributed stochastic neighbor embedding clustering identified 42 modules revealing novel associations between transcript level patterns and biological processes. The results showed a complex genetic architecture of global transcript abundance pattern in tomato. Several genetic hot spots regulating a large number of transcript level patterns relating to diverse biological processes such as plant defense and photosynthesis were identified. Important eQTL regulating transcript level patterns were related to leaf number and complexity as well as hypocotyl length. Genes associated with leaf development showed an inverse correlation with photosynthetic gene expression, but eQTL regulating genes associated with leaf development and photosynthesis were dispersed across the genome. This comprehensive eQTL analysis details the influence of these loci on plant phenotypes and will be a valuable community resource for investigations on the genetic effects of eQTL on phenotypic traits in tomato. PMID:27418589

  16. QTL Detection on Chromosome 6 in Landrace×Lantang Pig Resource Population

    Institute of Scientific and Technical Information of China (English)

    LI Jia-qi; ZHANG Hao; LIU Xiao-hong; GAO Ping; WANG Chong; WU Qiu-hao; ZHANG Xi-quan; CHEN Yao-sheng

    2004-01-01

    A resource population constructed by F2 design with Landrace and Chinese indigenous Lantang pigs was used in this study. Seven microsatellite DNA markers on chromosome 6 and USDA2.6 pig genetic linkage map were used for interval QTL mapping, The results revealed that at the position of 38- 41 cM there was a chromosome-wide highly significant QTL affecting carcass backfat A thickness (P<0.01), which was closely linked with MN007 and the ratio of QTL additive variance to F2 phenotypic variance was 5.90%. At the position of 60-70 cM there were two chromosome-wide significant QTLs affecting carcass lean percentage (P<0.01) and skin and fat percentage (P<0.05), which were closely linked with MN003 and the ratio of QTL additive variance to F2 phenotypic variance were 18.44 and 3.75%, respectively. At the same position, there was a single-point QTL also closely linked with MN003 and highly significantly (P<0.01) affecting carcass lean. In addition, there were two chromosome-wide highly significant (P<0.01) QTLs affecting meat color and marbling, which were closely linked with MN13 at the position of 70-75 cM and the ratio of QTL additive variance to F2 phenotypic variance were 14.05 and 1.77%, respectively.

  17. Feasibility of the grandprogeny design for quantitative trait loci (QTL) detection in purebred beef cattle.

    Science.gov (United States)

    Moody, D E; Pomp, D; Buchanan, D S

    1997-04-01

    The grandprogeny design (GPD) was developed for dairy cattle to use existing pedigreed populations for quantitative trait locus (QTL) detection. Marker genotypes of grandsires and sons are determined, and trait phenotypic data from grandprogeny are analyzed. The objective of this study was to investigate the potential application of GPD in purebred beef cattle populations. Pedigree structures of Angus (n = 123,319), Hereford (n = 107,778), Brangus (n = 14,449), and Gelbvieh (n = 8,114) sire evaluation reports were analyzed to identify potentially useful families. Power of QTL detection was calculated for a range of QTL effects (.1 to .5 SD) and two Type I error rates (.01 and .001). Reasonable power (> .75) could be achieved using GPD in Angus and Hereford for QTL having moderate effects (.3 SD) on weaning weight and large effects (.4 to .5 SD) on birth, yearling, and maternal weaning weights by genotyping 500 animals. Existing Gelbvieh and Brangus families useful for GPD were limited, and reasonable power could be expected only for QTL having large effects on weaning or birth weights. Although family structures suitable for GPD exist in purebred beef populations, large amounts of genotyping would be required to achieve reasonable power, and only QTL having moderate to large effects could be expected to be identified. PMID:9110205

  18. QTL mapping for test weight by using F2:3 population in maize

    Indian Academy of Sciences (India)

    Jun-Qiang Ding; Jin-Liang Ma; Chun-Rong Zhang; Hua-Fang Dong; Zhang-Ying Xi; Zong-Liang Xia; Jian-Yu Wu

    2011-04-01

    Test weight is an important trait in maize breeding. Understanding the genetic mechanism of test weight is important for effective selection of maize test weight improvement. In this study, quantitative trait loci (QTL) for maize test weight were identified. In the years 2007 and 2008, a F2:3 population along with the parents Chang7-2 and Zheng58 were planted in Zhengzhou, People’s Republic of China. Significant genotypic variation for maize test weight was observed in both years. Based on the genetic map containing 180 polymorphic SSR markers with an average linkage distance of 11.0 cM, QTL for maize test weight were analysed by mixed-model composite interval mapping. Five QTL, including four QTL with only additive effects, were identified on chromosomes 1, 2, 3, 4 and 5, and together explained 25.2% of the phenotypic variation. Seven pairs of epistatic interactions were also detected, involving 11 loci distributed on chromosomes 1, 2, 3, 4, 5 and 7, respectively, which totally contributed 18.2% of the phenotypic variation. However, no significant QTL × environment (Q×E) interaction and epistasis × environment interaction effects were detected. The results showed that besides the additive QTL, epistatic interactions also formed an important genetic basis for test weight in maize.

  19. Número de repetições para avaliação de caracteres em genótipos de feijão-caupi

    Directory of Open Access Journals (Sweden)

    Francisco Eduardo Torres

    2015-06-01

    Full Text Available O objetivo deste trabalho foi determinar o número de medições (repetições necessário para avaliar caracteres de genótipos de feijão-caupi (Vigna unguiculata. Vinte genótipos de feijão-caupi de porte ereto e vinte de porte semiprostrado foram avaliados no Estado do Mato Grosso do Sul, em seis e quatro ensaios, respectivamente. Os dez ensaios foram conduzidos no delineamento blocos ao acaso, com quatro repetições. Foram mensurados os caracteres comprimento de vagem, massa de vagem, massa de grãos por vagem, número de grãos por vagem, massa de cem grãos e produtividade de grãos. Foram verificados os pressupostos do modelo matemático, realizada a análise de variância, estimado o coeficiente de repetibilidade e calculado o número de repetições. Ensaios com quatro repetições identificam genótipos superiores de feijão-caupi em relação aos caracteres comprimento de vagem, massa de vagem, massa de grãos por vagem, número de grãos por vagem, massa de cem grãos e produtividade de grãos, com, respectivamente, 84,57, 75,62, 73,14, 75,25, 81,53 e 79,19% de exatidão no prognóstico de seu valor real.

  20. Dissimilaridade genética em variedades de Artemisia annua L. embasada em caracteres agronômicos, fisiológicos e fitoquímicos

    Directory of Open Access Journals (Sweden)

    C.O. Bolina

    2014-01-01

    Full Text Available O presente estudo objetivou estimar a variabilidade genética existente entre caracteres agronômicos, fisiológicos e fitoquímicos em variedades de A. annua. O delineamento experimental foi inteiramente casualizado e os tratamentos foram as variedades Artemis, 2/39x5x3M, e 2/39x1V de A. annua, submetidas a avaliações agronômicas, fisiológicas e fitoquímicas. Para a realização das estimativas de distância genética foram geradas matrizes de dissimilaridade utilizando a distância Euclidiana e os métodos de agrupamento de Tocher e UPGMA. Além disso, avaliou-se a importância relativa dos caracteres para divergência genética pelo método de Singh. As análises foram realizadas pelo software Genes e os dendrogramas obtidos pelo NTSYS. A presença de variabilidade genética dentro das variedades permitiu a identificação de acessos dissimilares e com média elevada para as características estudadas. O número de ramificações, concentração intracelular de CO2, e o rendimento de óleo essencial foram os caracteres que mais contribuíram para a dissimilaridade genética de A. annua. Os acessos B24, C5 e C32 foram os mais promissores dentro das variedades e devem ser conservados para futuras hibridações, sendo que as hibridações mais promissoras na obtenção de populações segregantes desejadas são B24 x C5, B24 x C32 e C5 x C32.

  1. Variación morfológica en el esqueleto de Liolaemus (Iguania: Liolaemidae. Búsqueda y descripción de caracteres

    Directory of Open Access Journals (Sweden)

    Lobo, Fernando

    2001-12-01

    Full Text Available Estudiamos los esqueletos teñidos y transparentados como también secos de veinticuatro especies pertenecientes a los principales clados de Liolaemus (grupos L. kingii - L. archeforus, L. lineomaculatus, L. chiliensis, L. signifer, L. boulengeri y L. wiegmannii de acuerdo con la taxonomía de Etheridge, 1995. Pudimos describir variación en la morfología, proporciones y otras carácterísticas que pueden definirse como caracteres. Los caracteres descriptos en este estudio incluyen variación en los cartílagos de las costillas preesternales, procesos de la cintura pélvica, laringe, anillos traqueales y aparato hioideo, variación en la morfología de huesos craneales y poscraneales. Se describe un total de 35 caracteres (uno autoapomórfico que representan diecisiete continuos (morfométricos o no, nueve binarios polimórficos, seis binarios no polimórficos, dos multiestado polimórficos y un multiestado no polimórfico. Se encontró un alto grado de congruencia de la información brindada por los caracteres encontrados en el esqueleto con los principales grupos de especies aceptados actualmente en la literatura. We studied claired and stained and dry skeletons of twenty four species belonging to the main clades of Liolaemus (L. kingii- L. archeforus, L. lineomaculatus, L. chiliensis, L. signifer, L. boulengeri and L. wiegmannii groups, according to the taxonomy of Etheridge, 1995. We were able to describe variation in the morphology, measurement ratios and other features that could be defined as characters. Characters described in this study include variation on cartilages of presternal ribs, pelvic processes, larynx, tracheal rings and hyoid apparatus, variation on the morphology of cranial and postcranial bones. The total number of characters described here is thirty five (one autapomorphic that represent seventeen continuos (morphometric or not, nine binary polymorphic, six binary not polymorphic, two multistate polymorphic and one

  2. Relação entre os caracteres determinantes das eficiências no uso de nitrogênio e fósforo em milho

    Directory of Open Access Journals (Sweden)

    Felipe Bermudez Pereira

    2013-10-01

    Full Text Available O melhoramento genético das eficiências no uso de N (EUN e P (EUP é um dos meios para se obterem produtividades de grãos satisfatórias, com menores custos e de modo sustentável. Todavia, pouco se sabe a respeito da relação entre os caracteres determinantes dessas eficiências, o que tem dificultado o uso da seleção precoce e indireta. Portanto, objetivou-se, com este trabalho, identificar a relação entre os caracteres determinantes das eficiências no uso de nitrogênio e fósforo, em milho. Para isso, avaliaram-se 14 linhagens e 39 híbridos simples, em dois experimentos, em baixa e alta disponibilidade de N e P, em delineamento inteiramente ao acaso, com duas repetições, em esquema fatorial simples. Os experimentos foram conduzidos em telado. Foram utilizados tubos cilíndricos de PVC, com 4 dm³ de capacidade, preenchidos com dois tipos de substrato, de acordo com o experimento. As soluções nutritivas foram fornecidas a partir do sétimo dia após o transplantio, aplicando-se 250 ml tubo-1, a cada dois dias. As plantas foram colhidas em estádio de seis folhas completamente expandidas (V6 e os caracteres avaliados foram: massa da parte aérea seca (MPS, área de raiz específica (ARE, comprimento de raízes laterais (CRLat e axiais (CRAxi e os dois componentes da EUN e EUP, as eficiências de utilização (EUt e a de absorção (EAb. Foram realizadas análises de variância e de trilha dos dados coletados. Os caracteres de raiz não apresentaram efeitos significativos sobre as EUN e EUP. A MPS é o principal determinante das EUN e EUP, independentemente da disponibilidade nutricional.

  3. Inter-relação entre caracteres de caupi de porte ereto e crescimento determinado Interrelation among characters of upright cowpea plants with determined growth

    OpenAIRE

    Antonio Aécio de Carvalho Bezerra; Clodoaldo José da Anunciação Filho; Francisco Rodrigues Freire Filho; Valdenir Queiroz Ribeiro

    2001-01-01

    Foram estudados dez caracteres em 32 genótipos de caupi [Vigna unguiculata (L.)Walp.], com o objetivo de avaliar o grau de associação existente entre o rendimento de grãos e seus componentes. Oensaio foi conduzido no Campo Experimental da Embrapa-Centro de Pesquisa Agropecuária do Meio-Norte, em Teresina, PI. Utilizou-se o delineamento experimental de blocos casualizados, com seis repetições. Os dados foram coletados nas duas fileiras centrais, subtraídas das duas primeiras covas em cada extr...

  4. Caracteres morfoanatómicos de diferentes cortezas de la medicina folklórica argentina : II. Punica granatum L. (Punicaceae) y su adulterante Buxus sempervirens L. (Buxaceae)

    OpenAIRE

    Di Sapio Osvaldo Antonio; Gattuso, Martha

    1994-01-01

    Se presenta un estudio comparativo, morfoanatómico e histoquímico, de la corteza de raíz y tailo de Punica granatum L. (Punicaceae), "corteza de granado" -utilizada en medicina popular por sus propiedades tenífugas y antiheimínticas- y de su adulterante, Buxus sempervirens L. (Buxaceae), "boj". El análisis efectuado posibilita la confección de un cuadro de caracteres con valor diagnóstico. Estos permiten la identificación de las citadas especies al estado de droga entera o fragmentada.

  5. QTL for the thermotolerance effect of heat hardening, knowckdown resistance to heat and chill-coma recovery in an intercontinental set of recombinant inbred lines of Drosophila melanogaster

    DEFF Research Database (Denmark)

    Norry, Fabian M.; Scannapieco, Alejandra C.; Sambucetti, Pablo;

    2008-01-01

    The thermotolerance effect of heat hardening (also called short-term acclimation), knockdown resistance to high temperature (KRHT) with and without heat hardening and chill-coma recovery (CCR) are important phenotypes of thermal adaptation in insects and other organisms. Drosophila melanogaster...... decreased by heat hardening. We discuss candidate loci for each QTL. One HHE-QTL was found in the region of small heat-shock protein genes. However, HHE-QTL explained only a small fraction of the phenotypic variance. Most heat-resistance QTL did not colocalize with CCR-QTL. Large-effect QTL for CCR and KRHT...

  6. Fine mapping and replication of QTL in outbred chicken advanced intercross lines

    Directory of Open Access Journals (Sweden)

    Andersson Leif

    2011-01-01

    Full Text Available Abstract Background Linkage mapping is used to identify genomic regions affecting the expression of complex traits. However, when experimental crosses such as F2 populations or backcrosses are used to map regions containing a Quantitative Trait Locus (QTL, the size of the regions identified remains quite large, i.e. 10 or more Mb. Thus, other experimental strategies are needed to refine the QTL locations. Advanced Intercross Lines (AIL are produced by repeated intercrossing of F2 animals and successive generations, which decrease linkage disequilibrium in a controlled manner. Although this approach is seen as promising, both to replicate QTL analyses and fine-map QTL, only a few AIL datasets, all originating from inbred founders, have been reported in the literature. Methods We have produced a nine-generation AIL pedigree (n = 1529 from two outbred chicken lines divergently selected for body weight at eight weeks of age. All animals were weighed at eight weeks of age and genotyped for SNP located in nine genomic regions where significant or suggestive QTL had previously been detected in the F2 population. In parallel, we have developed a novel strategy to analyse the data that uses both genotype and pedigree information of all AIL individuals to replicate the detection of and fine-map QTL affecting juvenile body weight. Results Five of the nine QTL detected with the original F2 population were confirmed and fine-mapped with the AIL, while for the remaining four, only suggestive evidence of their existence was obtained. All original QTL were confirmed as a single locus, except for one, which split into two linked QTL. Conclusions Our results indicate that many of the QTL, which are genome-wide significant or suggestive in the analyses of large intercross populations, are true effects that can be replicated and fine-mapped using AIL. Key factors for success are the use of large populations and powerful statistical tools. Moreover, we believe that

  7. Controversias epistemológicas y metodológicas entre el paradigma cualitativo y cuantitativo en psicología

    Directory of Open Access Journals (Sweden)

    Lucas Cuenya

    2010-01-01

    Full Text Available La distinción entre metodología cuantitativa y cualitativa define dos campos de investigación que profesan postulados paradigmáticos encontrados. El conocimiento científico se caracteriza por ser racional y objetivo, fáctico y verificable, caracterización que sintoniza, en buena medida, con los atributos del método cuantitativo. Por el contrario, el estudio cualitativo busca comprender los fenómenos dentro de su ambiente usual, utilizando como datos descripciones de situaciones, eventos, personas, interacciones, documentos, etc. Este enfoque se utiliza para descubrir y refinar preguntas de investigación, pero solo a veces se ponen a prueba las hipótesis. En este trabajo se analizan las principales características de las metodologías cuantitativa y cualitativa, y se discute la importancia de asegurar el control y la rigurosidad científica al analizar los fenómenos complejos del comportamiento.

  8. Herencia del vigor de plántula y su relación con caracteres de planta adulta en líneas endogámicas de maíz tropical

    OpenAIRE

    Francisco Cervantes Ortiz; Gabino García de los Santos; Aquiles Carballo Carballo; David Bergvinson; J. Luis Crossa; Mariano Mendoza Elos; Ernesto Moreno Martínez

    2007-01-01

    En los programas de fitomejoramiento es importante el vigor de la semilla y de la plántula para asegurar la germinación, emergencia, y desarrollo inicial de la planta. El objetivo de este estudio fue determinar el tipo de herencia de caracteres relacionados con el vigor de la plántula de maíz y de la planta adulta, así como correlacionar el vigor inicial de plántula con los caracteres de la planta adulta. Con este fin se usaron los efectos de aptitud combinatoria general (ACG), aptitud combin...

  9. Tamanho de amostra para estimação do coeficiente de correlação de Pearson entre caracteres de Crambe abyssinica Sample size to estimate the Pearson correlation coefficient among characters of Crambe abyssinica

    OpenAIRE

    Alberto Cargnelutti Filho; Sidinei José Lopes; Marcos Toebe; Tatiani Reis da Silveira; Ismael Albino Schwantes

    2011-01-01

    É importante dimensionar adequadamente o tamanho de amostra, para estimação, com confiabilidade aceitável, do coeficiente de correlação linear de Pearson entre pares de caracteres. O objetivo deste experimento foi determinar o tamanho de amostra (número de plantas) para estimação do coeficiente de correlação linear de Pearson, entre 21 caracteres de crambe (Crambe abyssinica Hochst). Um experimento em campo foi conduzido no ano de 2008. Na colheita foram selecionadas, aleatoriamente, 75 plant...

  10. Estimación bayesiana de componentes de (co)varianza en Brangus argentino para caracteres de res mediante el algoritmo FCG Bayesian estimation of (co) variance components in Argentinian Brangus for carcass traits using the FCG algorithm

    OpenAIRE

    Cantet, R. J. C.; A. N. Birchmeier

    2010-01-01

    Se emplearon los datos de 2273 toritos y vaquillonas Brangus para estimar las heredabilidades (h²) y las correlaciones aditivas y ambientales de caracteres de calidad de carne medidos por ultrasonido. Los registros provenían del programa de evaluación genética de la Asociación Argentina de Brangus. Los caracteres medidos fueron el área del ojo del bife (AOB), el marmoreado (MB), la grasa dorsal (GD) y la grasa de cadera (GC). La edad media de los animales al momento de la medición fue 641 día...

  11. QTL Mapping of Sex Determination Loci Supports an Ancient Pathway in Ants and Honey Bees.

    Directory of Open Access Journals (Sweden)

    Misato O Miyakawa

    2015-11-01

    Full Text Available Sex determination mechanisms play a central role in life-history characteristics, affecting mating systems, sex ratios, inbreeding tolerance, etc. Downstream components of sex determination pathways are highly conserved, but upstream components evolve rapidly. Evolutionary dynamics of sex determination remain poorly understood, particularly because mechanisms appear so diverse. Here we investigate the origins and evolution of complementary sex determination (CSD in ants and bees. The honey bee has a well-characterized CSD locus, containing tandemly arranged homologs of the transformer gene [complementary sex determiner (csd and feminizer (fem]. Such tandem paralogs appear frequently in aculeate hymenopteran genomes. However, only comparative genomic, but not functional, data support a broader role for csd/fem in sex determination, and whether species other than the honey bee use this pathway remains controversial. Here we used a backcross to test whether csd/fem acts as a CSD locus in an ant (Vollenhovia emeryi. After sequencing and assembling the genome, we computed a linkage map, and conducted a quantitative trait locus (QTL analysis of diploid male production using 68 diploid males and 171 workers. We found two QTLs on separate linkage groups (CsdQTL1 and CsdQTL2 that jointly explained 98.0% of the phenotypic variance. CsdQTL1 included two tandem transformer homologs. These data support the prediction that the same CSD mechanism has indeed been conserved for over 100 million years. CsdQTL2 had no similarity to CsdQTL1 and included a 236-kb region with no obvious CSD gene candidates, making it impossible to conclusively characterize it using our data. The sequence of this locus was conserved in at least one other ant genome that diverged >75 million years ago. By applying QTL analysis to ants for the first time, we support the hypothesis that elements of hymenopteran CSD are ancient, but also show that more remains to be learned about the

  12. Identification of Polymorphisms Associated with Drought Adaptation QTL in Brassica napus by Resequencing

    Directory of Open Access Journals (Sweden)

    Richard S. Fletcher

    2016-04-01

    Full Text Available Brassica napus is a globally important oilseed for which little is known about the genetics of drought adaptation. We previously mapped twelve quantitative trait loci (QTL underlying drought-related traits in a biparental mapping population created from a cross between winter and spring B. napus cultivars. Here we resequence the genomes of the mapping population parents to identify genetic diversity across the genome and within QTL regions. We sequenced each parental cultivar on the Illumina HiSeq platform to a minimum depth of 23 × and performed a reference based assembly in order to describe the molecular variation differentiating them at the scale of the genome, QTL and gene. Genome-wide patterns of variation were characterized by an overall higher single nucleotide polymorphism (SNP density in the A genome and a higher ratio of nonsynonymous to synonymous substitutions in the C genome. Nonsynonymous substitutions were used to categorize gene ontology terms differentiating the parent genomes along with a list of putative functional variants contained within each QTL. Marker assays were developed for several of the discovered polymorphisms within a pleiotropic QTL on chromosome A10. QTL analysis with the new, denser map showed the most associated marker to be that developed from an insertion/deletion polymorphism located in the candidate gene Bna.FLC.A10, and it was the only candidate within the QTL interval with observed polymorphism. Together, these results provide a glimpse of genome-wide variation differentiating annual and biennial B. napus ecotypes as well as a better understanding of the genetic basis of root and drought phenotypes.

  13. Quantitative trait locus (QTL mapping reveals a role for unstudied genes in Aspergillus virulence.

    Directory of Open Access Journals (Sweden)

    Julian K Christians

    Full Text Available Infections caused by the fungus Aspergillus are a major cause of morbidity and mortality in immunocompromised populations. To identify genes required for virulence that could be used as targets for novel treatments, we mapped quantitative trait loci (QTL affecting virulence in the progeny of a cross between two strains of A. nidulans (FGSC strains A4 and A91. We genotyped 61 progeny at 739 single nucleotide polymorphisms (SNP spread throughout the genome, and constructed a linkage map that was largely consistent with the genomic sequence, with the exception of one potential inversion of ∼527 kb on Chromosome V. The estimated genome size was 3705 cM and the average intermarker spacing was 5.0 cM. The average ratio of physical distance to genetic distance was 8.1 kb/cM, which is similar to previous estimates, and variation in recombination rate was significantly positively correlated with GC content, a pattern seen in other taxa. To map QTL affecting virulence, we measured the ability of each progeny strain to kill model hosts, larvae of the wax moth Galleria mellonella. We detected three QTL affecting in vivo virulence that were distinct from QTL affecting in vitro growth, and mapped the virulence QTL to regions containing 7-24 genes, excluding genes with no sequence variation between the parental strains and genes with only synonymous SNPs. None of the genes in our QTL target regions have been previously associated with virulence in Aspergillus, and almost half of these genes are currently annotated as "hypothetical". This study is the first to map QTL affecting the virulence of a fungal pathogen in an animal host, and our results illustrate the power of this approach to identify a short list of unknown genes for further investigation.

  14. A mixed model QTL analysis for sugarcane multiple-harvest-location trial data.

    Science.gov (United States)

    Pastina, M M; Malosetti, M; Gazaffi, R; Mollinari, M; Margarido, G R A; Oliveira, K M; Pinto, L R; Souza, A P; van Eeuwijk, F A; Garcia, A A F

    2012-03-01

    Sugarcane-breeding programs take at least 12 years to develop new commercial cultivars. Molecular markers offer a possibility to study the genetic architecture of quantitative traits in sugarcane, and they may be used in marker-assisted selection to speed up artificial selection. Although the performance of sugarcane progenies in breeding programs are commonly evaluated across a range of locations and harvest years, many of the QTL detection methods ignore two- and three-way interactions between QTL, harvest, and location. In this work, a strategy for QTL detection in multi-harvest-location trial data, based on interval mapping and mixed models, is proposed and applied to map QTL effects on a segregating progeny from a biparental cross of pre-commercial Brazilian cultivars, evaluated at two locations and three consecutive harvest years for cane yield (tonnes per hectare), sugar yield (tonnes per hectare), fiber percent, and sucrose content. In the mixed model, we have included appropriate (co)variance structures for modeling heterogeneity and correlation of genetic effects and non-genetic residual effects. Forty-six QTLs were found: 13 QTLs for cane yield, 14 for sugar yield, 11 for fiber percent, and 8 for sucrose content. In addition, QTL by harvest, QTL by location, and QTL by harvest by location interaction effects were significant for all evaluated traits (30 QTLs showed some interaction, and 16 none). Our results contribute to a better understanding of the genetic architecture of complex traits related to biomass production and sucrose content in sugarcane. PMID:22159754

  15. Identification of Polymorphisms Associated with Drought Adaptation QTL in Brassica napus by Resequencing.

    Science.gov (United States)

    Fletcher, Richard S; Herrmann, David; Mullen, Jack L; Li, Qinfei; Schrider, Daniel R; Price, Nicholas; Lin, Junjiang; Grogan, Kelsi; Kern, Andrew; McKay, John K

    2016-01-01

    Brassica napus is a globally important oilseed for which little is known about the genetics of drought adaptation. We previously mapped twelve quantitative trait loci (QTL) underlying drought-related traits in a biparental mapping population created from a cross between winter and spring B. napus cultivars. Here we resequence the genomes of the mapping population parents to identify genetic diversity across the genome and within QTL regions. We sequenced each parental cultivar on the Illumina HiSeq platform to a minimum depth of 23 × and performed a reference based assembly in order to describe the molecular variation differentiating them at the scale of the genome, QTL and gene. Genome-wide patterns of variation were characterized by an overall higher single nucleotide polymorphism (SNP) density in the A genome and a higher ratio of nonsynonymous to synonymous substitutions in the C genome. Nonsynonymous substitutions were used to categorize gene ontology terms differentiating the parent genomes along with a list of putative functional variants contained within each QTL. Marker assays were developed for several of the discovered polymorphisms within a pleiotropic QTL on chromosome A10. QTL analysis with the new, denser map showed the most associated marker to be that developed from an insertion/deletion polymorphism located in the candidate gene Bna.FLC.A10, and it was the only candidate within the QTL interval with observed polymorphism. Together, these results provide a glimpse of genome-wide variation differentiating annual and biennial B. napus ecotypes as well as a better understanding of the genetic basis of root and drought phenotypes. PMID:26801646

  16. Application of non-parametric bootstrap methods to estimate confidence intervals for QTL location in a beef cattle QTL experimental population.

    Science.gov (United States)

    Jongjoo, Kim; Davis, Scott K; Taylor, Jeremy F

    2002-06-01

    Empirical confidence intervals (CIs) for the estimated quantitative trait locus (QTL) location from selective and non-selective non-parametric bootstrap resampling methods were compared for a genome scan involving an Angus x Brahman reciprocal fullsib backcross population. Genetic maps, based on 357 microsatellite markers, were constructed for 29 chromosomes using CRI-MAP V2.4. Twelve growth, carcass composition and beef quality traits (n = 527-602) were analysed to detect QTLs utilizing (composite) interval mapping approaches. CIs were investigated for 28 likelihood ratio test statistic (LRT) profiles for the one QTL per chromosome model. The CIs from the non-selective bootstrap method were largest (87 7 cM average or 79-2% coverage of test chromosomes). The Selective II procedure produced the smallest CI size (42.3 cM average). However, CI sizes from the Selective II procedure were more variable than those produced by the two LOD drop method. CI ranges from the Selective II procedure were also asymmetrical (relative to the most likely QTL position) due to the bias caused by the tendency for the estimated QTL position to be at a marker position in the bootstrap samples and due to monotonicity and asymmetry of the LRT curve in the original sample.

  17. Application of non-parametric bootstrap methods to estimate confidence intervals for QTL location in a beef cattle QTL experimental population.

    Science.gov (United States)

    Jongjoo, Kim; Davis, Scott K; Taylor, Jeremy F

    2002-06-01

    Empirical confidence intervals (CIs) for the estimated quantitative trait locus (QTL) location from selective and non-selective non-parametric bootstrap resampling methods were compared for a genome scan involving an Angus x Brahman reciprocal fullsib backcross population. Genetic maps, based on 357 microsatellite markers, were constructed for 29 chromosomes using CRI-MAP V2.4. Twelve growth, carcass composition and beef quality traits (n = 527-602) were analysed to detect QTLs utilizing (composite) interval mapping approaches. CIs were investigated for 28 likelihood ratio test statistic (LRT) profiles for the one QTL per chromosome model. The CIs from the non-selective bootstrap method were largest (87 7 cM average or 79-2% coverage of test chromosomes). The Selective II procedure produced the smallest CI size (42.3 cM average). However, CI sizes from the Selective II procedure were more variable than those produced by the two LOD drop method. CI ranges from the Selective II procedure were also asymmetrical (relative to the most likely QTL position) due to the bias caused by the tendency for the estimated QTL position to be at a marker position in the bootstrap samples and due to monotonicity and asymmetry of the LRT curve in the original sample. PMID:12220133

  18. Herdabilidades e correlações entre caracteres de linhagens de feijão obtidas em monocultivo e em consórcio com o milho

    Directory of Open Access Journals (Sweden)

    Lana Ângela Maria Quintão

    2003-01-01

    Full Text Available Foram realizados os cruzamentos entre 'Ouro 1919' x 'Ouro Negro 1992', 'Ouro 1919' x Raça D e 'Ouro 1919' x Phaseolus aborigineus 283, com o objetivo de estimar as herdabilidades, no sentido amplo e as correlações fenotípica e genotípica da produtividade de grãos e seus componentes de rendimento, nos sistemas de monocultivo e de consórcio com a cultura do milho nas épocas de semeadura das "águas" e da "seca'. Para obtenção dessas estimativas, utilizaram-se, no ensaio de campo, as populações, F1, F2 e F3 e seus genitores. As populações segregantes foram conduzidas pelo método de melhoramento "Single Seed Descent" (SSD. De modo geral, os coeficientes de herdabilidade foram maiores no sistema de consórcio do que no monocultivo. Entre os caracteres estudados, as maiores herdabilidades foram, de modo geral, obtidas para o número de vagens por planta. Os coeficientes de correlação entre os caracteres avaliados, em cada sistema de cultivo, mostraram que, no caso de seleção no monocultivo visando semeadura no consórcio, o número de vagens por planta é o caráter com maior potencial a ser utilizado no processo seletivo.

  19. Inheritance and QTL Mapping of Salt Tolerance in Rice

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    An F2 population derived from the cross between Jiucaiqing (japonica) and IR36 (indica) was used to analyze the inheritance of salt tolerance in rice by genetic model of major-genes plus polygenes, and to map the corresponding QTLs by SSR molecular markers. Rice plants of P1, P2, F1 and F2 at 5- to 6- leaf stage were treated under 140 mmol/L NaCl for 10 days. Three indices representing the ability of salt tolerance of rice seedlings were measured, including salt tolerance rating (STR), Na+/K+ ratio in roots and dry matter weight of shoots (DWS). STR, Na+/K+ and DWS were all controlled by two major genes with modification by polygenes. Heritability of these traits from major genes was 17.8, 53.3 and 52.3%, respectively. The linkage map constructed by 62 SSR molecular markers covered a total length of about 1 142 cM. There were three QTLs detected for STR located on chromosome 1, 5 and 9, two QTLs for DWS on chromosomes 8 and 9, and two QTLs for Na+/K+ on chromosomes 2 and 6, one on each chromosome respectively. Single QTL accounted for 6.7 to 19.3% of phenotypic variation. Identification method of salt tolerance in rice and breeding of rice varieties with salt tolerance based on molecular markers assisted selection had been discussed.

  20. QTL Mapping of Low Temperature on Germination rate of Rice

    Institute of Scientific and Technical Information of China (English)

    CHEN Liang; LOU Qiao-jun; SUN Zong-xiu; XING Yong-zhong; YU Xin-qiao; LUO Li-jun

    2006-01-01

    To investigate the low temperature on germination capacity (LTG) a double haploid rice (DH) population with 198 lines derived from anther culture of F1 hybrid with indica line Zhenshan 97B and a perennial japonica line AAV002863 was used to construct a linkage map with 140 SSR markers. The germination rate in Zhenshan 97B and AAV002863 was 79.7% and 30.1%, while in DH population it ranged from 0 to 100% at 15℃ after 6 days. Quantitative trait loci (QTLs) controlling low temperature germinability were identified on chromosomes 3 and 10. The percentage of observed phenotypic variance attributed to qLTG-3 and qLTG-10 was 12.6% and 12.9%, respectively. Allele from Zhenshan 97B increased the LTG at qLTG-3 region, while allele from AAV002863 increased the LTG at qLTG-10 region. One pair of epistatic interaction was detected between loci on chromosomes 3 and 10. The main-effect of QTL on chromosome 10 was also involved in epistatic interaction.

  1. AGRONOMIC AND QUALITY QTL MAPPING IN SPRING WHEAT

    Directory of Open Access Journals (Sweden)

    Mohamed Mergoum

    2013-04-01

    Full Text Available Wheat (Triticum aestivum L. flour represents one of the primary sources of calories and proteins for the human diet. The increase in the wheat yield without losing its baking and milling quality is an important breeding objective. The use of QTL analysis is an expedient methodology to help breeders to face this multifaceted challenge. Here, a population of 129 recombinant inbred lines (RILs developed from a cross between ‘Steele-ND’ cultivar and ‘ND 735’ advanced line was used to evaluate several yield and quality traits and map the genomic regions controlling these traits. The phenotypic data were collected from field experiments conducted at four North Dakota (ND, USA environments. Transgressive segregation was observed for all traits, with RILs outperforming the most adapted parent and commercial cultivars. Using a linkage map of 392 markers, composite interval mapping identified a total of 13 environment-specific QTLs, all explaining large phenotypic variations (R2=16-44%. The genotypic values of these “reserve” alleles were directly used as criteria of selection in breeding programs.

  2. QTL Analysis of Major Agronomic Traits in Soybean

    Institute of Scientific and Technical Information of China (English)

    CHEN Qing-shan; ZHANG Zhong-chen; LIU Chun-yan; XIN Da-wei; QIU Hong-mei; SHAN Da-peng; SHAN Cai-yun; HU Guo-hua

    2007-01-01

    Soybean is a main crop, and most agronomic traits of soybean are quantitative; therefore, there is very important studying and applying value to locating these traits. A F2:10 RIL population containing 154 lines, derived from the cross between Charleston as female and Dongnong 594 as male parent, were used in this experiment. A genetic linkage map was constructed with 164 SSR primers, which were screened with the two parents and amplified on the 154 lines. 12 agronomic traits different between the two parents were investigated, and QTLs of all the traits were analyzed using the software Windows QTL Cartographer V2.0. The agronomic traits included quality traits: protein content, oil content, and content of protein and oil; yield traits: pods per plant, seed weight per plant, arnd 100 seeds weight; and other agronomic traits: plant height, days to maturity, branches, nod number in main stem, average leaf length, and average leaf width. The results showed that 68 QTLs in total were found for the 12 agronomic traits. The number of QTLs per trait varied from 3 for the average leaf width to 11 for 100 seeds weight and plant height, and was 5.8 on average. Good accordance was seen in many QTLs between the results of this study and the results obtained by other similar studies; therefore, these QTLs may be valuable for molecular marker assistant selection in soybean. In this study, 68 major QTLs of 12 important traits of soybean were analyzed.

  3. QTL Mapping of Low-Temperature Germination Ability in the Maize IBM Syn4 RIL Population.

    Science.gov (United States)

    Hu, Shuaidong; Lübberstedt, Thomas; Zhao, Guangwu; Lee, Michael

    2016-01-01

    Low temperature is the primary factor to affect maize sowing in early spring. It is, therefore, vital for maize breeding programs to improve tolerance to low temperatures at seed germination stage. However, little is known about maize QTL involved in low-temperature germination ability. 243 lines of the intermated B73×Mo17 (IBM) Syn4 recombinant inbred line (RIL) population was used for QTL analysis of low-temperature germination ability. There were significant differences in germination-related traits under both conditions of low temperature (12°C/16 h, 18°C/8 h) and optimum temperature (28°C/24 h) between the parental lines. Only three QTL were identified for controlling optimum-temperature germination rate. Six QTL controlling low-temperature germination rate were detected on chromosome 4, 5, 6, 7 and 9, and contribution rate of single QTL explained between 3.39%~11.29%. In addition, six QTL controlling low-temperature primary root length were detected in chromosome 4, 5, 6, and 9, and the contribution rate of single QTL explained between 3.96%~8.41%. Four pairs of QTL were located at the same chromosome position and together controlled germination rate and primary root length under low temperature condition. The nearest markers apart from the corresponding QTL (only 0.01 cM) were umc1303 (265.1 cM) on chromosome 4, umc1 (246.4 cM) on chromosome 5, umc62 (459.1 cM) on chromosome 6, bnl14.28a (477.4 cM) on chromosome 9, respectively. A total of 3155 candidate genes were extracted from nine separate intervals based on the Maize Genetics and Genomics Database (http://www.maizegdb.org). Five candidate genes were selected for analysis as candidates putatively affecting seed germination and seedling growth at low temperature. The results provided a basis for further fine mapping, molecular marker assisted breeding and functional study of cold-tolerance at the stage of seed germination in maize. PMID:27031623

  4. QTL Mapping of Low-Temperature Germination Ability in the Maize IBM Syn4 RIL Population.

    Directory of Open Access Journals (Sweden)

    Shuaidong Hu

    Full Text Available Low temperature is the primary factor to affect maize sowing in early spring. It is, therefore, vital for maize breeding programs to improve tolerance to low temperatures at seed germination stage. However, little is known about maize QTL involved in low-temperature germination ability. 243 lines of the intermated B73×Mo17 (IBM Syn4 recombinant inbred line (RIL population was used for QTL analysis of low-temperature germination ability. There were significant differences in germination-related traits under both conditions of low temperature (12°C/16h, 18°C/8h and optimum temperature (28°C/24h between the parental lines. Only three QTL were identified for controlling optimum-temperature germination rate. Six QTL controlling low-temperature germination rate were detected on chromosome 4, 5, 6, 7 and 9, and contribution rate of single QTL explained between 3.39%~11.29%. In addition, six QTL controlling low-temperature primary root length were detected in chromosome 4, 5, 6, and 9, and the contribution rate of single QTL explained between 3.96%~8.41%. Four pairs of QTL were located at the same chromosome position and together controlled germination rate and primary root length under low temperature condition. The nearest markers apart from the corresponding QTL (only 0.01 cM were umc1303 (265.1 cM on chromosome 4, umc1 (246.4 cM on chromosome 5, umc62 (459.1 cM on chromosome 6, bnl14.28a (477.4 cM on chromosome 9, respectively. A total of 3155 candidate genes were extracted from nine separate intervals based on the Maize Genetics and Genomics Database (http://www.maizegdb.org. Five candidate genes were selected for analysis as candidates putatively affecting seed germination and seedling growth at low temperature. The results provided a basis for further fine mapping, molecular marker assisted breeding and functional study of cold-tolerance at the stage of seed germination in maize.

  5. QTL mapping for two commercial traits in farmed saltwater crocodiles (Crocodylus porosus).

    Science.gov (United States)

    Miles, L G; Isberg, S R; Thomson, P C; Glenn, T C; Lance, S L; Dalzell, P; Moran, C

    2010-04-01

    The recent generation of a genetic linkage map for the saltwater crocodile (Crocodylus porosus) has now made it possible to carry out the systematic searches necessary for the identification of quantitative trait loci (QTL) affecting traits of economic, as well as evolutionary, importance in crocodilians. In this study, we conducted genome-wide scans for two commercially important traits, inventory head length (which is highly correlated with growth rate) and number of scale rows (SR, a skin quality trait), for the existence of QTL in a commercial population of saltwater crocodiles at Darwin Crocodile Farm, Northern Territory, Australia. To account for the uncommonly large difference in sex-specific recombination rates apparent in the saltwater crocodile, a duel mapping strategy was employed. This strategy employed a sib-pair analysis to take advantage of our full-sib pedigree structure, together with a half-sib analysis to account for, and take advantage of, the large difference in sex-specific recombination frequencies. Using these approaches, two putative QTL regions were identified for SR on linkage group 1 (LG1) at 36 cM, and on LG12 at 0 cM. The QTL identified in this investigation represent the first for a crocodilian and indeed for any non-avian member of the Class Reptilia. Mapping of QTL is an important first step towards the identification of genes and causal mutations for commercially important traits and the development of selection tools for implementation in crocodile breeding programmes for the industry. PMID:19917044

  6. QTL linkage analysis of connected populations using ancestral marker and pedigree information.

    Science.gov (United States)

    Bink, Marco C A M; Totir, L Radu; ter Braak, Cajo J F; Winkler, Christopher R; Boer, Martin P; Smith, Oscar S

    2012-04-01

    The common assumption in quantitative trait locus (QTL) linkage mapping studies that parents of multiple connected populations are unrelated is unrealistic for many plant breeding programs. We remove this assumption and propose a Bayesian approach that clusters the alleles of the parents of the current mapping populations from locus-specific identity by descent (IBD) matrices that capture ancestral marker and pedigree information. Moreover, we demonstrate how the parental IBD data can be incorporated into a QTL linkage analysis framework by using two approaches: a Threshold IBD model (TIBD) and a Latent Ancestral Allele Model (LAAM). The TIBD and LAAM models are empirically tested via numerical simulation based on the structure of a commercial maize breeding program. The simulations included a pilot dataset with closely linked QTL on a single linkage group and 100 replicated datasets with five linkage groups harboring four unlinked QTL. The simulation results show that including parental IBD data (similarly for TIBD and LAAM) significantly improves the power and particularly accuracy of QTL mapping, e.g., position, effect size and individuals' genotype probability without significantly increasing computational demand.

  7. pain2: A neuropathic pain QTL identified on rat chromosome 2.

    Science.gov (United States)

    Nissenbaum, Jonathan; Shpigler, Hagai; Pisanté, Anne; DelCanho, Sonia; Minert, Anne; Seltzer, Ze'ev; Devor, Marshall; Darvasi, Ariel

    2008-03-01

    We aimed to locate a chronic pain-associated QTL in the rat (Rattus norvegicus) based on previous findings of a QTL (pain1) on chromosome 15 of the mouse (Mus musculus). The work was based on rat selection lines HA (high autotomy) and LA (low autotomy) which show a contrasting pain phenotype in response to nerve injury in the neuroma model of neuropathic pain. An F(2) segregating population was generated from HA and LA animals. Phenotyped F(2) rats were genotyped on chromosome 7 and chromosome 2, regions that share a partial homology with mouse chromosome 15. Our interval mapping analysis revealed a LOD score value of 3.63 (corresponding to p=0.005 after correcting for multiple testing using permutations) on rat chromosome 2, which is suggestive of the presence of a QTL affecting the predisposition to neuropathic pain. This QTL was mapped to the 14-26cM interval of chromosome 2. Interestingly, this region is syntenic to mouse chromosome 13, rather than to the region of mouse chromosome 15 that contains pain1. This chromosomal position indicates that it is possibly a new QTL, and hence we name it pain2. Further work is needed to replicate and to uncover the underlying gene(s) in both species.

  8. Ancestral QTL alleles from wild emmer wheat improve drought resistance and productivity in modern wheat cultivars

    Directory of Open Access Journals (Sweden)

    Lianne eMerchuk-Ovnat

    2016-04-01

    Full Text Available Wild emmer wheat (Triticum turgidum ssp. dicoccoides is considered a promising source for improving stress resistances in domesticated wheat. Here we explored the potential of selected quantitative trait loci (QTLs from wild emmer wheat, introgressed via marker-assisted selection, to enhance drought resistance in elite durum (T. turgidum ssp. durum and bread (T. aestivum wheat cultivars. The resultant near-isogenic lines (BC3F3 and BC3F4 were genotyped using SNP array to confirm the introgressed genomic regions and evaluated in two consecutive years under well-watered (690–710 mm and water-limited (290–320 mm conditions. Three of the introgressed QTLs were successfully validated, two in the background of durum wheat cv. Uzan (on chromosomes 1BL and 2BS, and one in the background of bread wheat cvs. Bar Nir and Zahir (chromosome 7AS. In most cases, the QTL x environment interaction was validated in terms of improved grain yield and biomass - specifically under drought (7AS QTL in cv. Bar Nir background, under both treatments (2BS QTL, and a greater stability across treatments (1BL QTL. The results provide a first demonstration that introgression of wild emmer QTL alleles can enhance productivity and yield stability across environments in domesticated wheat, thereby enriching the modern gene pool with essential diversity for the improvement of drought resistance.

  9. Comparative QTL analysis of maize seed artificial aging between an immortalized F2 population and its corresponding RILs

    Institute of Scientific and Technical Information of China (English)

    Bin Wang; Zhanhui Zhang; Zhiyuan Fu; Zonghua Liu; Yanmin Hu; Jihua Tang

    2016-01-01

    Seed aging decreases the quality and vigor of crop seeds, thereby causing substantial agricultural and economic losses in crops. To identify genetic differences in seed aging between homozygotes and heterozygotes in maize, the seeds of a set of recombinant inbred lines (RILs) and an immortalized F2 (IF2) population were subjected to artificial aging treatments for 0, 2, 3, and 4 days under 45 ºC and 85%relative humidity and seed vigor was then evaluated in a field experiment. Seed vigor of all entries tested decreased sharply with longer aging treatment and seed vigor decreased more slowly in heterozygotes than in homozygotes. Forty-nine QTL were detected for four measured seed vigor traits in the RIL (28 QTL) and IF2 (21 QTL) populations. Only one QTL, qGP5, was detected in both populations, indicating that the genes involved in anti-aging mechanisms differed between inbred lines and hybrids. Several QTL were identified to be responsible for multiple seed vigor traits simultaneously in the RIL and IF2 populations under artificial aging conditions. These QTL may include major genes for seed vigor or seed aging. QTL qVI4b and qGE3a detected in the RIL population coincided with genes ZmLOX1 and ZmPLD1 in the same respective chromosomal regions. These QTL would be useful for screening for anti-aging genes in maize breeding.

  10. QTL mapping and correlation analysis for 1000-grain weight and percentage of grains with chalkiness in rice

    Indian Academy of Sciences (India)

    Jian-Min Bian; Huan Shi; Cui-Juan Li; Chang-Lan Zhu; Qiu-Ying Yu; Xiao-Song Peng; Jun-Ru Fu; Xiao-Peng He; Xiao-Rong Chen; Li-Fang Hu; Lin-Juan Ouyang; Hao-Hua He

    2013-08-01

    The study of 1000-grain weight (TGW) and percentage of grains with chalkiness (PGWC) is very important in rice. In this study, a set of introgression lines (ILs), derived from Sasanishiki/Habataki with Sasanishiki as the recurrent parent, were used to detect correlations and quantitative trait loci (QTL) on TGW and PGWC in two different environments. Phenotypic correlation analysis showed that there was no significant correlation between TGW and PGWC in both environments, which indicated that the linkage of TGW and PGWC traits could be broken via suitable population. A total of 20 QTL were detected in both environments, nine QTL for 1000-paddy-grain weight (PTGW), five QTL for 1000-brown-grain weight (BTGW) and six QTL for percentage of grains with chalkiness (PGWC). Moreover, five QTL, qPTGW3, qPTGW8.2, qPTGW11.1 for PTGW and qPGWC1.1, qPGWC1.2 for PGWC, were stably expressed in both environments. Phenotypic values were significantly different ($P \\lt 0.01$) between the introgression lines carrying these five QTL alleles and the genetic background parent, Sasanishiki. The introgression lines carrying these QTL also represent a useful genetic resource in the context of rice yield and quality improvement via a design-breeding approach.

  11. Application of the BovineSNP50 assay for QTL mapping and prediction of genetic merit in Holstein cattle

    Science.gov (United States)

    The previous fifteen years have produced numerous QTL mapping experiments aimed at the identification of causal or linked polymorphisms for use in marker assisted selection programs to increase the rate of genetic gain in livestock species. To date, very few causal mutations for QTL have been ident...

  12. Replication of long-bone length QTL in the F9-F10 LG,SM advanced intercross.

    Science.gov (United States)

    Norgard, Elizabeth A; Jarvis, Joseph P; Roseman, Charles C; Maxwell, Taylor J; Kenney-Hunt, Jane P; Samocha, Kaitlin E; Pletscher, L Susan; Wang, Bing; Fawcett, Gloria L; Leatherwood, Christopher J; Wolf, Jason B; Cheverud, James M

    2009-04-01

    Quantitative trait locus (QTL) mapping techniques are frequently used to identify genomic regions associated with variation in phenotypes of interest. However, the F(2) intercross and congenic strain populations usually employed have limited genetic resolution resulting in relatively large confidence intervals that greatly inhibit functional confirmation of statistical results. Here we use the increased resolution of the combined F(9) and F(10) generations (n = 1455) of the LG,SM advanced intercross to fine-map previously identified QTL associated with the lengths of the humerus, ulna, femur, and tibia. We detected 81 QTL affecting long-bone lengths. Of these, 49 were previously identified in the combined F(2)-F(3) population of this intercross, while 32 represent novel contributors to trait variance. Pleiotropy analysis suggests that most QTL affect three to four long bones or serially homologous limb segments. We also identified 72 epistatic interactions involving 38 QTL and 88 novel regions. This analysis shows that using later generations of an advanced intercross greatly facilitates fine-mapping of confidence intervals, resolving three F(2)-F(3) QTL into multiple linked loci and narrowing confidence intervals of other loci, as well as allowing identification of additional QTL. Further characterization of the biological bases of these QTL will help provide a better understanding of the genetics of small variations in long-bone length.

  13. License - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods License License ...stered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods © Satoshi Tabata (Kazusa D...Update History of This Database Site Policy | Contact Us License - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive ...

  14. A multi-trait multi-environment QTL mixed model with an application to drought and nitrogen stress trials in maize (Zea mays L.)

    NARCIS (Netherlands)

    Malosetti, M.; Ribaut, J.M.; Vargas, M.; Crossa, J.; Eeuwijk, van F.A.

    2008-01-01

    Despite QTL mapping being a routine procedure in plant breeding, approaches that fully exploit data from multi-trait multi-environment (MTME) trials are limited. Mixed models have been proposed both for multi-trait QTL analysis and multi-environment QTL analysis, but these approaches break down when

  15. Simultaneous estimation of QTL effects and positions when using genotype data with errors

    Indian Academy of Sciences (India)

    Liang Tong; Weijun Ma; Haidong Liu; Chaofeng Yuan; Ying Zhou

    2015-03-01

    Accurate genetic data are important prerequisite of performing genetic linkage test or association test. Currently, most analytical methods assume that the observed genotypes are correct. However, due to the constraint at the technical level, most of the genetic data that people used so far contain errors. In this paper, we considered the problem of QTL mapping based on biological data with genotyping errors. By analysing all possible genotypes of each individual in framework of multiple-interval mapping, we proposed an algorithm of inferring all model parameters through the expectation-maximization (EM) algorithm and discussed the hypothesis testing of the existence of QTL. We carried out extensive simulation studies to assess the proposed method. Simulation results showed that the new method outperforms the method that does not take the genotyping errors into account, and therefore it can decrease the impact of genotyping errors on QTL mapping. The proposed method was also applied to analyse a real barley dataset.

  16. The phenotypic difference discards sib-pair QTL linkage information

    Energy Technology Data Exchange (ETDEWEB)

    Wright, F.A. [Univ. of California, San Diego, CA (United States)]|[Univ. of Texas, El Paso, TX (United States)

    1997-03-01

    Kruglyak and Lander provide an important synthesis of methods for (IBD) sib-pair linkage mapping, with an emphasis on the use of complete multipoint inheritance information for each sib pair. These procedures are implemented in the computer program MAPMAKER/SIBS, which performs interval mapping for dichotomous and quantitative traits. The authors present three methods for mapping quantitative trait loci (QTLs): a variant of the commonly used Haseman-Elston regression approach, a maximum-likelihood procedure involving variance components, and a rank-based nonparametric procedure. These approaches and related work use the magnitude of the difference in the sibling phenotype values for each sib pair as the observation for analysis. Linkage is detected if siblings sharing more alleles IBD have similar phenotypes (i.e., a small difference in the phenotype values), while siblings sharing fewer alleles IBD have less similar phenotypes. Such techniques have been used to detect linkage for a number of quantitative traits. However, the exclusive reliance on the phenotypic differences may be due in large part to historical inertia. A likelihood argument is presented here to show that, under certain classical assumptions, the phenotypic differences do not contain the full likelihood information for QTL mapping. Furthermore, considerable gains in power to detect linkage can be achieved with an expanded likelihood model. The development here is related to previous work, which incorporates the full set of phenotypic data using likelihood and robust quasi-likelihood methods. The purpose of this letter is not to endorse a particular approach but to spur research in alternative and perhaps more powerful linkage tests. 17 refs.

  17. Genética de coffea VII: hereditariedade dos caracteres de coffea arabica L. var. maragogipe hort ex froehner

    Directory of Open Access Journals (Sweden)

    C. A. Krug

    1942-01-01

    Full Text Available A variedade maragogipe do Coffea arabica L. foi encontrada pela primeira vez por Crisógono José Fernandes, em 1870, no município baiano de Maragogipe onde, provavelmente, se originou por mutação. Desde 1933 esta variedade vem sendo estudada pela Secção de Genética do Instituto Agronômico do Estado de São Paulo, em Campinas, com o fim de se determinar a sua constituição genética. Muitas autofecundações, cruzamentos e back-crosses foram, então, realizados. Grande parte das plantas obtidas só puderam ser classificadas após a colheita do ano de 1940. Todas foram examinadas quanto à forma e dimensões das folhas e um grande número ainda quanto à forma e dimensões das flores, frutos e sementes. Verificou-se que o caráter maragogipe mostra dominância quase completa em F1, não sendo possivel uma separação das ciasses maragogipe puro e híbrido. Em F2, e nos back-crosses com as formas normais, obtiveram-se, respectivamente, relações de 3:1 e 1:1 entre plantas maragogipe e plantas normais, relações essas que demonstram que os caracteres do maragogipe são controlados por um único par de fatores genéticos dominantes, para os quais se propõe o símbolo Mg-Mg, derivado do próprio nome desta variedade.In the present article the results of the genetical analysis of the characters of the maragogipe variety of Coffea arabica L are presented. This variety which originated as a mutation from C. arabica L. var. typica Cramer, in 1870, in the State of Baía in North Brazil, represents a gigas form of that variety, having larger leaves, flowers and fruits, its plants being also taller; it is also known for its low productivity. Since 1933 a genetical analysis of this variety was undertaken, many of its plants being selfed and crossed with other maragogipe plants and also with individuals of the typica and bourbon varieties of C. arabica; two generations have been studied, including F2's and several back-crosses. It was concluded

  18. Estimativas de repetibilidade para caracteres forrageiros em Panicum maximum Repeatability estimates for forage characters in Panicum maximum

    Directory of Open Access Journals (Sweden)

    Francisco José da Silva Lédo

    2008-08-01

    Full Text Available Objetiva-se com este trabalho estimar a repetibilidade para caracteres forrageiros de Panicum, e determinar o número de cortes de avaliação necessários para a seleção de genótipos de Panicum, com confiabilidade. Utilizaram-se os dados de um ensaio conduzido no período de 21/11/2002 a 08/04/2005, no Campo Experimental da Embrapa Gado de Leite, localizado em Valença-RJ, onde foram realizados 15 cortes de avaliação. No ensaio, foram avaliados 23 genótipos de Panicum maximum, em parcelas experimentais, dispostas no delineamento de blocos casualizados, com três repetições. Foram estimados os coeficientes de repetibilidade para as características produção de matéria verde de forragem (PMV; produção de matéria seca de forragem (PMS e de folhas (PMSF; porcentagem de folhas na PMS (%FOL e altura da planta (AP, utilizando os métodos da análise de variância, componentes principais e análise estrutural. Para todas as características avaliadas os efeitos de genótipos, cortes e interação genótipos x cortes foram significativos (PThe objective of this work was to estimate the repeatability for forage characters of Panicum and to determinate the necessary number of evaluation cuts to select Panicum genotypes with confidence. Data of a trial with 15 cuts, carried out between 21/11/2002 and 08/04/2005 in the experimental station of Embrapa Gado de Leite located in Valença, RJ, Brazil, were used. In this study. 23 genotypes of " Panicum maximum" were evaluated, in a complete randomized block, with three replications. The coefficient of repeatability for fresh forage production (PMV, total plant dry matter production (PMS and leaves dry matter production (PMSF were recorded along with leaves percentage in PMS (%FOL and plant hight (AP, using the variance analysis, main components and structural analysis methods. For all evaluated parameters the effects of genotype, cut and genotype x cut interaction were significant (P<0.01. When

  19. Phenotypic correlations between quantitative characteristics in soybean/ Correlações fenotípicas entre caracteres quantitativos em soja

    Directory of Open Access Journals (Sweden)

    Antonio Eduardo Pipolo

    2005-05-01

    Full Text Available The association between yield and other characteristics of the plant identifies characters to be used in the indirect selection for high yield. With the objective of identifying parentals to be included in an breeding program, thirty and four soybean lines for twelve characteristics (weight of the seeds per plot, height of the plant, height of the first pod, number of pods per plant, number of pods with one seeds, number of pods with two seeds, number of pods with three seeds, diameter of the stalk, weight of the stem, weight of one hundred seeds, number of days of flourishing and number of days for maturation were evaluated. This research quantified these relations and identified possible criteria of indirect selection in relation to yield. The correlations between weight of stem with the diameter of the stalk and weight of the stem with the weight of the seeds per plot were significant and positive. Values of interest to make selection easier were obtained in the correlations between number of pods per plant and number of pods with 1, 2, and 3 seeds, which were significant and positive, indicating that it is possible to use in the selection the character with higher genetic gain or the one which allows easier visual selection.A associação entre a produtividade e outras características da planta identifica caracteres para uso na seleção indireta para produtividade. Com objetivo de identificar parentais a serem incluídos em um programa de melhoramento, foram avaliadas trinta e quatro linhagens de soja para doze características (peso de sementes por parcela, altura de planta, altura da primeira vagem, número de vagens por planta, número de vagens com um grão, número de vagens com dois grãos, número de vagens com três grãos, diâmetro do caule, peso da haste mais a casca, peso de cem sementes, número de dias de florescimento e número de dias para maturação. Esta pesquisa procurou quantificar estas relações e identificar poss

  20. High-throughput phenotyping to detect drought tolerance QTL in wild barley introgression lines.

    Directory of Open Access Journals (Sweden)

    Nora Honsdorf

    Full Text Available Drought is one of the most severe stresses, endangering crop yields worldwide. In order to select drought tolerant genotypes, access to exotic germplasm and efficient phenotyping protocols are needed. In this study the high-throughput phenotyping platform "The Plant Accelerator", Adelaide, Australia, was used to screen a set of 47 juvenile (six week old wild barley introgression lines (S42ILs for drought stress responses. The kinetics of growth development was evaluated under early drought stress and well watered treatments. High correlation (r=0.98 between image based biomass estimates and actual biomass was demonstrated, and the suitability of the system to accurately and non-destructively estimate biomass was validated. Subsequently, quantitative trait loci (QTL were located, which contributed to the genetic control of growth under drought stress. In total, 44 QTL for eleven out of 14 investigated traits were mapped, which for example controlled growth rate and water use efficiency. The correspondence of those QTL with QTL previously identified in field trials is shown. For instance, six out of eight QTL controlling plant height were also found in previous field and glasshouse studies with the same introgression lines. This indicates that phenotyping juvenile plants may assist in predicting adult plant performance. In addition, favorable wild barley alleles for growth and biomass parameters were detected, for instance, a QTL that increased biomass by approximately 36%. In particular, introgression line S42IL-121 revealed improved growth under drought stress compared to the control Scarlett. The introgression line showed a similar behavior in previous field experiments, indicating that S42IL-121 may be an attractive donor for breeding of drought tolerant barley cultivars.

  1. High-throughput phenotyping to detect drought tolerance QTL in wild barley introgression lines

    KAUST Repository

    Honsdorf, Nora

    2014-05-13

    Drought is one of the most severe stresses, endangering crop yields worldwide. In order to select drought tolerant genotypes, access to exotic germplasm and efficient phenotyping protocols are needed. In this study the high-throughput phenotyping platform "The Plant Accelerator", Adelaide, Australia, was used to screen a set of 47 juvenile (six week old) wild barley introgression lines (S42ILs) for drought stress responses. The kinetics of growth development was evaluated under early drought stress and well watered treatments. High correlation (r = 0.98) between image based biomass estimates and actual biomass was demonstrated, and the suitability of the system to accurately and non-destructively estimate biomass was validated. Subsequently, quantitative trait loci (QTL) were located, which contributed to the genetic control of growth under drought stress. In total, 44 QTL for eleven out of 14 investigated traits were mapped, which for example controlled growth rate and water use efficiency. The correspondence of those QTL with QTL previously identified in field trials is shown. For instance, six out of eight QTL controlling plant height were also found in previous field and glasshouse studies with the same introgression lines. This indicates that phenotyping juvenile plants may assist in predicting adult plant performance. In addition, favorable wild barley alleles for growth and biomass parameters were detected, for instance, a QTL that increased biomass by approximately 36%. In particular, introgression line S42IL-121 revealed improved growth under drought stress compared to the control Scarlett. The introgression line showed a similar behavior in previous field experiments, indicating that S42IL-121 may be an attractive donor for breeding of drought tolerant barley cultivars. © 2014 Honsdorf et al.

  2. Genome Scan for Parent-of-Origin QTL Effects on Bovine Growth and Carcass Traits.

    Science.gov (United States)

    Imumorin, Ikhide G; Kim, Eun-Hee; Lee, Yun-Mi; De Koning, Dirk-Jan; van Arendonk, Johan A; De Donato, Marcos; Taylor, Jeremy F; Kim, Jong-Joo

    2011-01-01

    Parent-of-origin effects (POE) such as genomic imprinting influence growth and body composition in livestock, rodents, and humans. Here, we report the results of a genome scan to detect quantitative trait loci (QTL) with POE on growth and carcass traits in Angus × Brahman cattle crossbreds. We identified 24 POE-QTL on 15 Bos taurus autosomes (BTAs) of which six were significant at 5% genome-wide (GW) level and 18 at the 5% chromosome-wide (CW) significance level. Six QTL were paternally expressed while 15 were maternally expressed. Three QTL influencing post-weaning growth map to the proximal end of BTA2 (linkage region of 0-9 cM; genomic region of 5.0-10.8 Mb), for which only one imprinted ortholog is known so far in the human and mouse genomes, and therefore may potentially represent a novel imprinted region. The detected QTL individually explained 1.4 ∼ 5.1% of each trait's phenotypic variance. Comparative in silico analysis of bovine genomic locations show that 32 out of 1,442 known mammalian imprinted genes from human and mouse homologs map to the identified QTL regions. Although several of the 32 genes have been associated with quantitative traits in cattle, only two (GNAS and PEG3) have experimental proof of being imprinted in cattle. These results lend additional support to recent reports that POE on quantitative traits in mammals may be more common than previously thought, and strengthen the need to identify and experimentally validate cattle orthologs of imprinted genes so as to investigate their effects on quantitative traits.

  3. Genome scan for parent-of-origin QTL effects on bovine growth and carcass traits

    Directory of Open Access Journals (Sweden)

    Ikhide G. Imumorin

    2011-07-01

    Full Text Available Parent-of-origin effects (POE such as genomic imprinting influence growth and body composition in livestock, rodents and humans. Here, we report the results of a genome scan to detect quantitative trait loci (QTL with POE on growth and carcass traits in Angus x Brahman cattle crossbreds. We identified 24 POE-QTL on 15 Bos taurus autosomes (BTAs of which 6 were significant at 5% genome-wide level and 18 at the 5% chromosome-wide significance level. Six QTL were paternally expressed while 15 were maternally expressed. Three QTL influencing post-weaning growth map to the proximal end of BTA2 [linkage region of 0 – 9 cM; genomic region of 5.0 – 10.8 Mb], for which only one imprinted orthologue is known so far in the human and mouse genomes, and therefore may potentially represent a novel imprinted region. The detected QTL individually explained 1.4% ~ 5.1% of each trait’s phenotypic variance. Comparative in-silico analysis of bovine genomic locations show that 32 out of 1,442 known mammalian imprinted genes from human and mouse homologues map to the identified QTL regions. Although several of the 32 genes have been associated with quantitative traits in cattle, only 2 (GNAS and PEG3 have experimental proof of being imprinted in cattle. These results lend additional support to recent reports that POE on quantitative traits in mammals may be more common than previously thought, and strengthen the need to identify and experimentally validate cattle orthologues of imprinted genes so as to investigate their effects on quantitative traits.

  4. Genome Scan for Parent-of-Origin QTL Effects on Bovine Growth and Carcass Traits.

    Science.gov (United States)

    Imumorin, Ikhide G; Kim, Eun-Hee; Lee, Yun-Mi; De Koning, Dirk-Jan; van Arendonk, Johan A; De Donato, Marcos; Taylor, Jeremy F; Kim, Jong-Joo

    2011-01-01

    Parent-of-origin effects (POE) such as genomic imprinting influence growth and body composition in livestock, rodents, and humans. Here, we report the results of a genome scan to detect quantitative trait loci (QTL) with POE on growth and carcass traits in Angus × Brahman cattle crossbreds. We identified 24 POE-QTL on 15 Bos taurus autosomes (BTAs) of which six were significant at 5% genome-wide (GW) level and 18 at the 5% chromosome-wide (CW) significance level. Six QTL were paternally expressed while 15 were maternally expressed. Three QTL influencing post-weaning growth map to the proximal end of BTA2 (linkage region of 0-9 cM; genomic region of 5.0-10.8 Mb), for which only one imprinted ortholog is known so far in the human and mouse genomes, and therefore may potentially represent a novel imprinted region. The detected QTL individually explained 1.4 ∼ 5.1% of each trait's phenotypic variance. Comparative in silico analysis of bovine genomic locations show that 32 out of 1,442 known mammalian imprinted genes from human and mouse homologs map to the identified QTL regions. Although several of the 32 genes have been associated with quantitative traits in cattle, only two (GNAS and PEG3) have experimental proof of being imprinted in cattle. These results lend additional support to recent reports that POE on quantitative traits in mammals may be more common than previously thought, and strengthen the need to identify and experimentally validate cattle orthologs of imprinted genes so as to investigate their effects on quantitative traits. PMID:22303340

  5. Application of alternative models to identify QTL for growth traits in an F2 Duroc x Pietrain pig resource population

    Directory of Open Access Journals (Sweden)

    Rumph Janice M

    2010-11-01

    Full Text Available Abstract Background A variety of analysis approaches have been applied to detect quantitative trait loci (QTL in experimental populations. The initial genome scan of our Duroc x Pietrain F2 resource population included 510 F2 animals genotyped with 124 microsatellite markers and analyzed using a line-cross model. For the second scan, 20 additional markers on 9 chromosomes were genotyped for 954 F2 animals and 20 markers used in the first scan were genotyped for 444 additional F2 animals. Three least-squares Mendelian models for QTL analysis were applied for the second scan: a line-cross model, a half-sib model, and a combined line-cross and half-sib model. Results In total, 26 QTL using the line-cross model, 12 QTL using the half-sib model and 3 additional QTL using the combined line-cross and half-sib model were detected for growth traits with a 5% false discovery rate (FDR significance level. In the line-cross analysis, highly significant QTL for fat deposition at 10-, 13-, 16-, 19-, and 22-wk of age were detected on SSC6. In the half-sib analysis, a QTL for loin muscle area at 19-wk of age was detected on SSC7 and QTL for 10th-rib backfat at 19- and 22-wk of age were detected on SSC15. Conclusions Additional markers and animals contributed to reduce the confidence intervals and increase the test statistics for QTL detection. Different models allowed detection of new QTL which indicated differing frequencies for alternative alleles in parental breeds.

  6. Identification of QTL genes for BMD variation using both linkage and gene-based association approaches

    OpenAIRE

    Li, Gloria Hoi-Yee; Cheung, Ching-Lung; Xiao, Su-Mei; Lau, Kam-Shing; Gao, Yi; Bow, Cora H.; Huang, Qing-Yang; Sham, Pak-Chung; Kung, Annie Wai-Chee

    2011-01-01

    Low bone mineral density (BMD) is a risk factor for osteoporotic fracture with a high heritability. Previous large scale linkage study in Northern Chinese has identified four significant quantitative trait loci (QTL) for BMD variation on chromosome 2q24, 5q21, 7p21 and 13q21. We performed a replication study of these four QTL in 1,459 Southern Chinese from 306 pedigrees. Successful replication was observed on chromosome 5q21 for femoral neck BMD with a LOD score of 1.38 (nominal p value = 0.0...

  7. [download] (969dlmap: An R Package for Mixed Model QTL and Association Analysis

    Directory of Open Access Journals (Sweden)

    B. Emma Huang

    2012-08-01

    Full Text Available dlmap is a software package capable of mapping quantitative trait loci (QTL in a variety of genetic studies. Unlike most other QTL mapping packages, dlmap is built on a linear mixed model platform, and thus can simultaneously handle multiple sources of genetic and environmental variation. Furthermore, it can accommodate both experimental crosses and association mapping populations within a versatile modeling framework. The software implements a mapping algorithm with separate detection and localization stages in a user-friendly manner. It accepts data in various common formats, has a flexible modeling environment, and summarizes results both graphically and numerically.

  8. Repetibilidade de caracteres de fruto em araçazeiro e pitangueira Repeatability traits of strawberry guava and surinam cherry fruits

    Directory of Open Access Journals (Sweden)

    Moeses Andrigo Danner

    2010-10-01

    Full Text Available O objetivo deste trabalho foi estimar a repetibilidade de carateres de fruto em araçazeiro e pitangueira. Foram avaliados, em quatro ciclos produtivos, os caracteres peso, diâmetro, sólidos solúveis totais e produção de frutos em 10 seleções de araçazeiro e peso, diâmetro e sólidos solúveis totais em nove seleções de pitangueira, do Banco de Germoplasma da Embrapa Clima Temperado, em Pelotas-RS. O coeficiente de repetibilidade, o número de medições necessárias e o coeficiente de determinação foram estimados pelos métodos de análise de variância, componentes principais e análise estrutural. O coeficiente de repetibilidade foi mais eficientemente estimado pelo método dos componentes principais, com base na matriz de covariâncias. O caractere peso de fruto é mais adequado para ser utilizado na seleção fenotípica em araçazeiro e pitangueira. É necessária apenas uma medição para predizer o valor de peso de fruto de genótipos de araçazeiro, com 90% de acurácia. Com quatro anos de avaliação, é possível inferir o valor real com confiabilidade acima de 80% para todos os caracteres. Isso facilita a seleção fenotípica para esses caracteres em programas de melhoramento de araçazeiro e pitangueira.The aim of this research was to estimate the repeatability traits of strawberry guava and surinam cherry fruits. It was evaluated in four productive cycles, the traits weight, diameter, total soluble solids and fruit production in ten selection of strawberry guava and weight, diameter and total soluble solids in nine selection of surinam cherry from the Germplasm Bank of the Embrapa Clima Temperado, in Pelotas-RS, Brazil. The repeatability coefficient, minimum observations number and determination coefficient were estimated by analysis of variance, principal components analysis and structural analysis. The repeatability coefficient was better estimated by the method of principal components analysis, based on covariance

  9. Evaluación de poblaciones de zapallo (Cucurbita moschata por caracteres de importancia agroindustrial Evaluation of squash (Cucurbita moschata populations for significant agribusiness traits

    Directory of Open Access Journals (Sweden)

    Magda Piedad Valdés Restrepo

    2010-01-01

    Full Text Available Se evaluó el potencial agroindustrial de siete poblaciones de zapallo (Cucurbita moschata derivadas de la recombinación de genotipos de alto desempeño en caracteres asociados con rendimiento y calidad de fruto. Los análisis de varianza para los resultados obtenidos en los semestres 2008-A y 2008-B permitieron detectar diferencias altamente significativas (P The agribusiness potential of seven squash (Cucurbita moschata populations derived of the recombination of genotypes of high performing in characters associated with yield and quality of the fruit was evaluated. The Anova analyses for semesters 2008-A and 2008-B allowed to detect highly significant differences (P < 0.01 among populations, for all the variables, except for color flesh fruit in 2008-A. The populations 1 and 5 showed a relative permanence in dry matter content in two cycles of genetic recombination.

  10. La inscripción en caracteres ibéricos de Los Maíllos (Belvís de la Jara, Toledo

    Directory of Open Access Journals (Sweden)

    Luján Martínez, Eugenio Ramón

    1997-12-01

    Full Text Available We study in this paper an inscription written in Iberian script found in Belvís de la Jara (province of Toledo, central Spain. Its importance lies in the fact that no other inscription of this kind has been found so far this West of the territory usually ascribed to the Levantine semisillabary.Se estudia una inscripción en caracteres ibéricos aparecida en el término municipal de Belvís de la Jara (Toledo. Su gran interés radica en el lugar de hallazgo, que hace variar significativamente hacia Occidente los límites de distribución del semisilabario levantino.

  11. Mapping and introgression of QTL for yield and related traits in two backcross populations derived from Oryza sativa cv. Swarna and two accessions of O. nivara

    Indian Academy of Sciences (India)

    B. P. Mallikarjuna Swamy; K. Kaladhar; G. Ashok Reddy; B. C. Viraktamath; N. Sarla

    2014-12-01

    Advanced backcross QTL (AB-QTL) analysis was carried out in two Oryza nivara-derived BC2F2 populations. For nine traits, we identified 28 QTL in population 1 and 26 QTL in population 2. The two most significant yield-enhancing QTL, yldp9.1 and yldp2.1 showed an additive effect of 16 and 7 g per plant in population 1, while yld2.1 and yld11.1 showed an additive effect of 11 and 10 g per plant in population 2. At least one O. nivara-derived QTL with a phenotypic variance of >15% was detected for seven traits in population 1 and three traits in population 2. The O. nivara-derived QTL ph1.1, nt12.1, nsp1.1, nfg1.1, bm11.1, yld2.1 and yld11.1 were conserved at the same chromosomal locations in both populations. Two major QTL clusters were detected at the marker intervals RM488–RM431 and RM6–RM535 on chromosomes 1 and 2, respectively. The colocation of O. nivara-derived yield QTL with yield meta-QTL on chromosomes 1, 2 and 9 indicates their accuracy and consistency. The major-effect QTL reported in this study are useful for marker-assisted breeding and are also suitable for further fine mapping and candidate gene identification.

  12. QTL identification of grain protein concentration and its genetic correlation with starch concentration and grain weight using two populations in maize (Zea mays L.)

    Indian Academy of Sciences (India)

    Yuling Li; Yanzhao Wang; Mengguan Wei; Xuehui Li; Jiafeng Fu

    2009-04-01

    Protein is one of the three main storage chemical components in maize grains, and is negatively correlated with starch concentration (SC). Our objective was to analyse the influence of genetic backgrounds on QTL detection for protein concentration (PC) and to reveal the molecular genetic associations between PC and both SC and grain weight (GWP). Two hundred and eighty-four (Pop1) and 265 (Pop2) F2:3 families were developed from two crosses between one high-oil maize inbred GY220 and two normal maize inbreds 8984 and 8622 respectively, and were genotyped with 185 and 173 pairs of SSR markers. PC, SC and GWP were evaluated under two environments. Composite interval mapping (CIM) and multiple interval mapping (MIM) methods were used to detect single-trait QTL for PC, and multiple-trait QTL for PC with both SC and GWP. No common QTL were shared between the two populations for their four and one PC QTL. Common QTL with opposite signs of effects for PC and SC/GWP were detected on three marker intervals at bins 6.07–6.08, 8.03 and 8.03–8.04. Multiple-traits QTL mapping showed that tightly-linked QTL, pleiotropic QTL and QTL having effects with opposite directions for PC and SC/GWP were all observed in Pop1, while all QTL reflected opposite effects in Pop2.

  13. Behavioural research on human working memory: mixing qualitative and quantitative methods (Investigación conductual sobre memoria de trabajo: Integrando métodos cualitativos y cuantitativos

    Directory of Open Access Journals (Sweden)

    María de los Angeles Bacigalupe

    2013-12-01

    Full Text Available ABSTRACT: The long lasting opposition between qualitative and quantitative methods for studying behaviour has been overridden by interdisciplinary work in which methods can be combined to approach animal and human behaviour, thus contributing to drawing rigorous and useful conclusions. We show an example of this by combining a quasi-experimental design and descriptive methods to study working memory for the resolution of a spatial problem task (the Tower of Hanoi in a neuropsychiatric hospital inpatient with amnesia and executive deficits. Results from the quasi-experiment showed that the patient acquired strategies to solve the task with a high level of efficiency (F3/35 = 7, 19, p < .01. Qualitatively speaking, the patient developed more than one strategy to solve the problem, which indicates the presence of learning based on working memory. In the light of these findings, we discuss issues of mixed methods research and suggest the importance of developing mixed methods to study behaviour. RESUMEN: La oposición duradera entre métodos cualitativos y cuantitativos para estudiar el comportamiento ha sido anulada por el trabajo interdisciplinario en que los métodos pueden combinarse para enfocar el comportamiento humano y animal, contribuyendo así a obtener conclusiones útiles y rigurosas. Se presenta una muestra, combinando métodos descriptivos y un diseño cuasiexperimental para estudiar la memoria de trabajo en la resolución de una tarea de problema espacial (la Torre de Hanoi, en un paciente internado en un hospital neuropsiquiátrico con amnesia y déficit ejecutivo. Resultados del cuasiexperimento demostraron que el paciente adquirió estrategias para resolver la tarea con un alto nivel de eficiencia (F3/35 = 7, 19, p < .01. Cualitativamente el paciente desarrolló más de una estrategia para resolver el problema, lo cual indica la presencia de aprendizaje basado en memoria de trabajo. A la luz de estos resultados, se discuten m

  14. Quantitative physic behavior of fine soils: collapsible aeolian and expansive residual; Comportamiento fisico cuantitativo de los suelos finos: eolicos colapsibles y residuales expansivos

    Energy Technology Data Exchange (ETDEWEB)

    Zeevaert-Wiechers, L. [Universidad Nacional Autonoma de Mexico, Mexico, D.F. (Mexico)

    2000-06-01

    apoyan sobre ellos. De ahi la necesidad de conocer los parametros cuantitativos que rigen el comportamiento estatico y dinamico de este tipo de suelos en relacion con los cambios ambientales de humedad. La investigacion basica es importante y necesaria en mecanica de suelos e ingenieria de cimentaciones, y debera efectuarse en los diferentes tipos de suelos que se encuentran en la naturaleza. Se muestran las curvas de compresibilidad de sedimentos eolicos finos, asi como curva de colapsos por hidratacion de suelo tipo loessial. Se presenta una figura de la relacion de colapsos, de esfuerzos y finalmente se da una tabla de los elementos.

  15. Genetic Analysis and QTL Detection on Fiber Traits Using Two Recombinant Inbred Lines and Their Backcross Populations in Upland Cotton.

    Science.gov (United States)

    Shang, Lianguang; Wang, Yumei; Wang, Xiaocui; Liu, Fang; Abduweli, Abdugheni; Cai, Shihu; Li, Yuhua; Ma, Lingling; Wang, Kunbo; Hua, Jinping

    2016-01-01

    Cotton fiber, a raw natural fiber material, is widely used in the textile industry. Understanding the genetic mechanism of fiber traits is helpful for fiber quality improvement. In the present study, the genetic basis of fiber quality traits was explored using two recombinant inbred lines (RILs) and corresponding backcross (BC) populations under multiple environments in Upland cotton based on marker analysis. In backcross populations, no significant correlation was observed between marker heterozygosity and fiber quality performance and it suggested that heterozygosity was not always necessarily advantageous for the high fiber quality. In two hybrids, 111 quantitative trait loci (QTL) for fiber quality were detected using composite interval mapping, in which 62 new stable QTL were simultaneously identified in more than one environment or population. QTL detected at the single-locus level mainly showed additive effect. In addition, a total of 286 digenic interactions (E-QTL) and their environmental interactions [QTL × environment interactions (QEs)] were detected for fiber quality traits by inclusive composite interval mapping. QE effects should be considered in molecular marker-assisted selection breeding. On average, the E-QTL explained a larger proportion of the phenotypic variation than the main-effect QTL did. It is concluded that the additive effect of single-locus and epistasis with few detectable main effects play an important role in controlling fiber quality traits in Upland cotton. PMID:27342735

  16. Quantitative Trait Loci (QTL Analysis for Production Traits of Birth Weight and Weight 360 days in Backcross Sheep

    Directory of Open Access Journals (Sweden)

    ENDANG TRI MARGAWATI

    2006-03-01

    Full Text Available Four half-sib families (n = 382 consisting predominantly of ITT x Merino x Merino backcross progeny, including some F2 progeny were used to analyze QTL for two production traits (Birth weight = BW1 and Body weight at 360 days = BW360. The study exploited differences in weight performance between the Merino and ITT sheep. A total of 141 informative microsatellite markers were used in a genome-wide scan covering the 26 autosomal sheep chromosomes. QTL analysis was conducted online using QTL Express. This study reports the effect of QTL for birth weight on Chromosomes 5 (p < 0.05 at 112cM (0cM-128cM. Location of candidate genes for birth weight was predicted at the region of flanking markers MCM527-BMS1247. A QTL for BW360 days existed on Chromosome 18 (p < 0.01 at 104cM (25.0-125cM. Location of candidate genes related to production traits for body weight 360 days was predicted at the segment of flanking markers of CSSM018-TMR1. Only the QTL on Chromosome 18 retained significance (p < 0.01 under experiment-wide significance testing. This QTL region is being examined for candidate genes by investigating to the homologous human chromosomal segments.

  17. Multiple QTL Determine Dorsal Abdominal Scale Patterns in the Mosquito Aedes aegypti.

    Science.gov (United States)

    Mori, Akio; Tsuda, Yoshio; Takagi, Masahiro; Higa, Yukiko; Severson, David W

    2016-09-01

    The mosquito, Aedes aegypti (L.) originated in Sub-Saharan Africa as a dark form sylvan species (A. aegypti formosus). Evolution of A. aegypti aegypti type form as a human commensal facilitated its colonization of most semitropical and tropical areas. We investigated the genetic basis for abdominal white scale presence that represents the diagnostic for sylvan A. aegypti formosus (scales absent), from type form (scales present) and A. aegypti queenslandensis form (dense scaling). We performed quantitative trait locus (QTL) mapping using 3 criteria for scale patterns among 192 F1 intercross progeny from matings between a queenslandensis type and an aegypti type form. Results identified 3 QTL determining scale patterns and indicated that classification criteria impact robustness of QTL LOD support. Dark- and light-colored forms exist in sympatry, but vary in multiple phenotypic characteristics, including preferences for vertebrate host, oviposition container, house-entering behavior, and dengue vector competence. Markers associated with 2 QTL regions reflected major reductions in recombination frequencies compared with the standard type form linkage map, suggestive of inversion polymorphisms associated with observed linkage disequilibrium between type-specific characteristics. Understanding the genic basis for differences in A. aegypti forms could inform efforts to develop new mosquito and arboviral disease control strategies. PMID:27130203

  18. QTL linkage analysis of connected populations using ancestral marker and pedigree information

    NARCIS (Netherlands)

    Bink, M.C.A.M.; Radu Totir, L.; Braak, ter C.J.F.; Winkler, C.R.; Boer, M.P.; Smith, O.S.

    2012-01-01

    The common assumption in quantitative trait locus (QTL) linkage mapping studies that parents of multiple connected populations are unrelated is unrealistic for many plant breeding programs. We remove this assumption and propose a Bayesian approach that clusters the alleles of the parents of the curr

  19. Detection of QTL for immune response to Sheep Red Blood Cells in laying hens

    NARCIS (Netherlands)

    Siwek-Gapinska, M.Z.; Cornelissen, S.J.B.; Nieuwland, M.G.B.; Buitenhuis, A.J.; Bovenhuis, H.; Crooijmans, R.P.M.A.; Groenen, M.A.M.; Vries Reilingh, de G.; Parmentier, H.K.; Poel, van der J.J.

    2003-01-01

    The aim of this study is to detect quantitative trait loci (QTL) involved in the regulation of the primary and the secondary immune response to sheep red blood cells (SRBC) in a resource population using microsatellite DNA markers. The F2 resource population originates from a cross of two divergentl

  20. QTL mapping of genome regions controlling temephos resistance in larvae of the mosquito Aedes aegypti.

    Directory of Open Access Journals (Sweden)

    Guadalupe Del Carmen Reyes-Solis

    2014-10-01

    Full Text Available The mosquito Aedes aegypti is the principal vector of dengue and yellow fever flaviviruses. Temephos is an organophosphate insecticide used globally to suppress Ae. aegypti larval populations but resistance has evolved in many locations.Quantitative Trait Loci (QTL controlling temephos survival in Ae. aegypti larvae were mapped in a pair of F3 advanced intercross lines arising from temephos resistant parents from Solidaridad, México and temephos susceptible parents from Iquitos, Peru. Two sets of 200 F3 larvae were exposed to a discriminating dose of temephos and then dead larvae were collected and preserved for DNA isolation every two hours up to 16 hours. Larvae surviving longer than 16 hours were considered resistant. For QTL mapping, single nucleotide polymorphisms (SNPs were identified at 23 single copy genes and 26 microsatellite loci of known physical positions in the Ae. aegypti genome. In both reciprocal crosses, Multiple Interval Mapping identified eleven QTL associated with time until death. In the Solidaridad×Iquitos (SLD×Iq cross twelve were associated with survival but in the reciprocal IqxSLD cross, only six QTL were survival associated. Polymorphisms at acetylcholine esterase (AchE loci 1 and 2 were not associated with either resistance phenotype suggesting that target site insensitivity is not an organophosphate resistance mechanism in this region of México.Temephos resistance is under the control of many metabolic genes of small effect and dispersed throughout the Ae. aegypti genome.

  1. An Empirical Method for Establishing Positional Confidence Intervals Tailored for Composite Interval Mapping of QTL

    Science.gov (United States)

    Improved genetic resolution and availability of sequenced genomes have made positional cloning of moderate-effect QTL (quantitative trait loci) realistic in several systems, emphasizing the need for precise and accurate derivation of positional confidence intervals (CIs). Support interval (SI) meth...

  2. QTL with dominance effect affecting residual feed intake on BTA6

    Science.gov (United States)

    Residual feed intake (RFI) is a measure of feed efficiency and therefore an economically relevant trait. A genome-wide scan for quantitative trait loci (QTL) affecting RFI in beef cattle was conducted. Approximately equally spaced microsatellite markers (n = 229) spanned the 29 bovine autosomes. Tw...

  3. A new method to infer causal phenotype networks using QTL and phenotypic information.

    Directory of Open Access Journals (Sweden)

    Huange Wang

    Full Text Available In the context of genetics and breeding research on multiple phenotypic traits, reconstructing the directional or causal structure between phenotypic traits is a prerequisite for quantifying the effects of genetic interventions on the traits. Current approaches mainly exploit the genetic effects at quantitative trait loci (QTLs to learn about causal relationships among phenotypic traits. A requirement for using these approaches is that at least one unique QTL has been identified for each trait studied. However, in practice, especially for molecular phenotypes such as metabolites, this prerequisite is often not met due to limited sample sizes, high noise levels and small QTL effects. Here, we present a novel heuristic search algorithm called the QTL+phenotype supervised orientation (QPSO algorithm to infer causal directions for edges in undirected phenotype networks. The two main advantages of this algorithm are: first, it does not require QTLs for each and every trait; second, it takes into account associated phenotypic interactions in addition to detected QTLs when orienting undirected edges between traits. We evaluate and compare the performance of QPSO with another state-of-the-art approach, the QTL-directed dependency graph (QDG algorithm. Simulation results show that our method has broader applicability and leads to more accurate overall orientations. We also illustrate our method with a real-life example involving 24 metabolites and a few major QTLs measured on an association panel of 93 tomato cultivars. Matlab source code implementing the proposed algorithm is freely available upon request.

  4. Identification of nutrient and physical seed trait QTL in the model legume Lotus japonicus.

    Science.gov (United States)

    Klein, Melinda A; Grusak, Michael A

    2009-08-01

    Legume seeds have the potential to provide a significant portion of essential micronutrients to the human diet. To identify the genetic basis for seed nutrient density, quantitative trait locus (QTL) analysis was conducted with the Miyakojima MG-20 x Gifu B-129 recombinant inbred population from the model legume Lotus japonicus. This population was grown to seed under greenhouse conditions in 2006 and 2007. Phenotypic data were collected for seed calcium (Ca), copper (Cu), iron (Fe), potassium (K), magnesium (Mg), manganese (Mn), phosphorus (P), sulfur (S), and zinc (Zn) concentrations and content. Data for physical seed traits (average seed mass and seed-pod allocation values) were also collected. Based on these phenotypic data, QTL analyses identified 103 QTL linked to 55 different molecular markers. Transgressive segregation, identified within this recombinant inbred population for both seed nutrient and physical traits, suggests new allelic combinations are available for agronomic trait improvement. QTL co-localization was also seen, suggesting that common transport processes might contribute to seed nutrient loading. Identification of loci involved in seed mineral density can be an important first step in identifying the genetic factors and, consequently, the physiological processes involved in mineral distribution to developing seeds. Longer term research efforts will focus on facilitating agronomic breeding efforts through ortholog identification in related crop legumes.

  5. Fine Mapping and Evolution of a QTL Region on Cattle Chromosome 3

    Science.gov (United States)

    Donthu, Ravikiran

    2009-01-01

    The goal of my dissertation was to fine map the milk yield and composition quantitative trait loci (QTL) mapped to cattle chromosome 3 (BTA3) by Heyen et al. (1999) and to identify candidate genes affecting these traits. To accomplish this, the region between "BL41" and "TGLA263" was mapped to the cattle genome sequence assembly Btau 3.1 and a…

  6. Genome scan for parent-of-origin QTL effects on bovine growth and carcass traits

    NARCIS (Netherlands)

    Imumorin, I.G.; Kim, B.; Li, Y.; Koning, de D.J.; Arendonk, van J.A.M.; Donato, S.

    2011-01-01

    Parent-of-origin effects (POE) such as genomic imprinting influence growth and body composition in livestock, rodents, and humans. Here, we report the results of a genome scan to detect quantitative trait loci (QTL) with POE on growth and carcass traits in Angus × Brahman cattle crossbreds. We ident

  7. Identification of novel QTL governing root architectural traits in an interspecific soybean population.

    Directory of Open Access Journals (Sweden)

    Lakshmi P Manavalan

    Full Text Available Cultivated soybean (Glycine max L. cv. Dunbar (PI 552538 and wild G. soja (PI 326582A exhibited significant differences in root architecture and root-related traits. In this study, phenotypic variability for root traits among 251 BC2F5 backcross inbred lines (BILs developed from the cross Dunbar/PI 326582A were identified. The root systems of the parents and BILs were evaluated in controlled environmental conditions using a cone system at seedling stage. The G. max parent Dunbar contributed phenotypically favorable alleles at a major quantitative trait locus on chromosome 8 (Satt315-I locus that governed root traits (tap root length and lateral root number and shoot length. This QTL accounted for >10% of the phenotypic variation of both tap root and shoot length. This QTL region was found to control various shoot- and root-related traits across soybean genetic backgrounds. Within the confidence interval of this region, eleven transcription factors (TFs were identified. Based on RNA sequencing and Affymetrix expression data, key TFs including MYB, AP2-EREBP and bZIP TFs were identified in this QTL interval with high expression in roots and nodules. The backcross inbred lines with different parental allelic combination showed different expression pattern for six transcription factors selected based on their expression pattern in root tissues. It appears that the marker interval Satt315-I locus on chromosome 8 contain an essential QTL contributing to early root and shoot growth in soybean.

  8. Identification of QTL for maize grain yield and kernel-related traits.

    Science.gov (United States)

    Yang, Cong; Zhang, Lei; Jia, Aimin; Rong, Tingzhao

    2016-06-01

    Grain yield (GY) is one of the most important and complex quantitative traits in maize (Zea mays L.) breeding practice. Quantitative trait loci (QTLs) for GY and three kernel-related traits were detected in a set of recombinant inbred lines (RILs). One hundred and seven simple sequence repeats (SSRs) and 168 insertion/deletion polymorphism markers (Indels) were used to genotype RILs. Eight QTLs were found to be associated with four yield-related traits: GY, 100-kernel weight (HKW), 10-kernel length (KL), and 10-kernel length width (KW). Each QTL explained between 5.96 (qKL2-1) and 13.05 (qKL1-1) per cent of the phenotypic variance. Notably, one common QTL, located at the marker interval between bnlg1893 and chr2- 236477 (chromosomal bin 2.09) simultaneously controlled GY and HKW; another common QTL, at bin 2.03 was simultaneously responsible for HKW and KW. Of the QTLs identified, only one pair of significant epistatic interaction involved in chromosomal region at bin 2.03 was detected for HKW; no significant QTL × environment interactions were observed. These results provide the common QTLs and for marker-assisted breeding. PMID:27350665

  9. Mapping the quantitative trait loci (QTL) controlling seed morphology in sunflower (Helianthus annuus L.)

    Science.gov (United States)

    This paper reports the results of analyzing the quantitative trait loci (QTL) underlying sunflower seed morphological traits in a segregating population derived from an oilseed by confection cross. A linkage map containing 165 target region amplification polymorphism (TRAP) and 44 simple sequence re...

  10. Regulatory variation at glypican-3 underlies a major growth QTL in mice.

    Directory of Open Access Journals (Sweden)

    Fiona Oliver

    2005-05-01

    Full Text Available The genetic basis of variation in complex traits remains poorly understood, and few genes underlying variation have been identified. Previous work identified a quantitative trait locus (QTL responsible for much of the response to selection on growth in mice, effecting a change in body mass of approximately 20%. By fine-mapping, we have resolved the location of this QTL to a 660-kb region containing only two genes of known function, Gpc3 and Gpc4, and two other putative genes of unknown function. There are no non-synonymous polymorphisms in any of these genes, indicating that the QTL affects gene regulation. Mice carrying the high-growth QTL allele have approximately 15% lower Gpc3 mRNA expression in kidney and liver, whereas expression differences at Gpc4 are non-significant. Expression profiles of the two other genes within the region are inconsistent with a factor responsible for a general effect on growth. Polymorphisms in the 3' untranslated region of Gpc3 are strong candidates for the causal sequence variation. Gpc3 loss-of-function mutations in humans and mice cause overgrowth and developmental abnormalities. However, no deleterious side-effects were detected in our mice, indicating that genes involved in Mendelian diseases also contribute to complex trait variation. Furthermore, these findings show that small changes in gene expression can have substantial phenotypic effects.

  11. Identification of QTL for maize grain yield and kernel-related traits

    Indian Academy of Sciences (India)

    CONG YANG; LEI ZHANG; AIMIN JIA; TINGZHAO RONG

    2016-06-01

    Grain yield (GY) is one of the most important and complex quantitative traits in maize (Zea maysL.) breeding practice.Quantitative trait loci (QTLs) for GY and three kernel-related traits were detected in a set of recombinant inbred lines (RILs).One hundred and seven simple sequence repeats (SSRs) and 168 insertion/deletion polymorphism markers (Indels) were usedto genotype RILs. Eight QTLs were found to be associated with four yield-related traits: GY, 100-kernel weight (HKW),10-kernel length (KL), and 10-kernel length width (KW). Each QTL explained between 5.96 (qKL2-1) and 13.05 (qKL1-1)per cent of the phenotypic variance. Notably, one common QTL, located at the marker interval betweenbnlg1893andchr2-236477(chromosomal bin 2.09) simultaneously controlled GY and HKW; another common QTL, at bin 2.03 was simulta-neously responsible for HKW and KW. Of the QTLs identified, only one pair of significant epistatic interaction involved inchromosomal region at bin 2.03 was detected for HKW; no significant QTL ×environment interactions were observed. Theseresults provide the common QTLs and for marker-assisted breeding

  12. Vacuolar invertase regulates elongation of Arabidopsis thaliana roots as revealed by QTL and mutant analysis.

    NARCIS (Netherlands)

    Sergeeva, L.I.; Keurentjes, J.J.B.; Bentsink, L.; Vonk, J.; Plas, van der L.H.W.; Koornneef, M.; Vreugdenhil, D.

    2006-01-01

    The possible role of the sucrose-splitting enzymes sucrose synthase and invertase in elongating roots and hypocotyls of Arabidopsis was tested by using a combination of histochemical methods and quantitative trait locus (QTL) analysis. Lengths of roots and hypocotyls correlated better with invertase

  13. Epistatic QTL pairs associated with meat quality and carcass composition traits in a porcine Duroc × Pietrain population

    Directory of Open Access Journals (Sweden)

    Jüngst Heinz

    2010-10-01

    Full Text Available Abstract Background Quantitative trait loci (QTL analyses in pig have revealed numerous individual QTL affecting growth, carcass composition, reproduction and meat quality, indicating a complex genetic architecture. In general, statistical QTL models consider only additive and dominance effects and identification of epistatic effects in livestock is not yet widespread. The aim of this study was to identify and characterize epistatic effects between common and novel QTL regions for carcass composition and meat quality traits in pig. Methods Five hundred and eighty five F2 pigs from a Duroc × Pietrain resource population were genotyped using 131 genetic markers (microsatellites and SNP spread over the 18 pig autosomes. Phenotypic information for 26 carcass composition and meat quality traits was available for all F2 animals. Linkage analysis was performed in a two-step procedure using a maximum likelihood approach implemented in the QxPak program. Results A number of interacting QTL was observed for different traits, leading to the identification of a variety of networks among chromosomal regions throughout the porcine genome. We distinguished 17 epistatic QTL pairs for carcass composition and 39 for meat quality traits. These interacting QTL pairs explained up to 8% of the phenotypic variance. Conclusions Our findings demonstrate the significance of epistasis in pigs. We have revealed evidence for epistatic relationships between different chromosomal regions, confirmed known QTL loci and connected regions reported in other studies. Considering interactions between loci allowed us to identify several novel QTL and trait-specific relationships of loci within and across chromosomes.

  14. QTL detection for Aeromonas salmonicida resistance related traits in turbot (Scophthalmus maximus

    Directory of Open Access Journals (Sweden)

    Martínez Paulino

    2011-11-01

    Full Text Available Abstract Background Interactions between fish and pathogens, that may be harmless under natural conditions, often result in serious diseases in aquaculture systems. This is especially important due to the fact that the strains used in aquaculture are derived from wild strains that may not have had enough time to adapt to new disease pressures. The turbot is one of the most promising European aquaculture species. Furunculosis, caused by the bacterium Aeromonas salmonicida, produces important losses to turbot industry. An appealing solution is to achieve more robust broodstock, which can prevent or diminish the devastating effects of epizooties. Genomics strategies have been developed in turbot to look for candidate genes for resistance to furunculosis and a genetic map with appropriate density to screen for genomic associations has been also constructed. In the present study, a genome scan for QTL affecting resistance and survival to A. salmonicida in four turbot families was carried out. The objectives were to identify consistent QTL using different statistical approaches (linear regression and maximum likelihood and to locate the tightest associated markers for their application in genetic breeding strategies. Results Significant QTL for resistance were identified by the linear regression method in three linkage groups (LGs 4, 6 and 9 and for survival in two LGs (6 and 9. The maximum likelihood methodology identified QTL in three LGs (5, 6 and 9 for both traits. Significant association between disease traits and genotypes was detected for several markers, some of them explaining up to 17% of the phenotypic variance. We also identified candidate genes located in the detected QTL using data from previously mapped markers. Conclusions Several regions controlling resistance to A. salmonicida in turbot have been detected. The observed concordance between different statistical methods at particular linkage groups gives consistency to our results. The

  15. Phenotypic plasticity, QTL mapping and genomic characterization of bud set in black poplar

    Directory of Open Access Journals (Sweden)

    Fabbrini Francesco

    2012-04-01

    Full Text Available Abstract Background The genetic control of important adaptive traits, such as bud set, is still poorly understood in most forest trees species. Poplar is an ideal model tree to study bud set because of its indeterminate shoot growth. Thus, a full-sib family derived from an intraspecific cross of P. nigra with 162 clonally replicated progeny was used to assess the phenotypic plasticity and genetic variation of bud set in two sites of contrasting environmental conditions. Results Six crucial phenological stages of bud set were scored. Night length appeared to be the most important signal triggering the onset of growth cessation. Nevertheless, the effect of other environmental factors, such as temperature, increased during the process. Moreover, a considerable role of genotype × environment (G × E interaction was found in all phenological stages with the lowest temperature appearing to influence the sensitivity of the most plastic genotypes. Descriptors of growth cessation and bud onset explained the largest part of phenotypic variation of the entire process. Quantitative trait loci (QTL for these traits were detected. For the four selected traits (the onset of growth cessation (date2.5, the transition from shoot to bud (date1.5, the duration of bud formation (subproc1 and bud maturation (subproc2 eight and sixteen QTL were mapped on the maternal and paternal map, respectively. The identified QTL, each one characterized by small or modest effect, highlighted the complex nature of traits involved in bud set process. Comparison between map location of QTL and P. trichocarpa genome sequence allowed the identification of 13 gene models, 67 bud set-related expressional and six functional candidate genes (CGs. These CGs are functionally related to relevant biological processes, environmental sensing, signaling, and cell growth and development. Some strong QTL had no obvious CGs, and hold great promise to identify unknown genes that affect bud set

  16. New Insights on Eggplant/Tomato/Pepper Synteny and Identification of Eggplant and Pepper Orthologous QTL.

    Science.gov (United States)

    Rinaldi, Riccardo; Van Deynze, Allen; Portis, Ezio; Rotino, Giuseppe L; Toppino, Laura; Hill, Theresa; Ashrafi, Hamid; Barchi, Lorenzo; Lanteri, Sergio

    2016-01-01

    Eggplant, pepper, and tomato are the most exploited berry-producing vegetables within the Solanaceae family. Their genomes differ in size, but each has 12 chromosomes which have undergone rearrangements causing a redistribution of loci. The genome sequences of all three species are available but differ in coverage, assembly quality and percentage of anchorage. Determining their syntenic relationship and QTL orthology will contribute to exploit genomic resources and genetic data for key agronomic traits. The syntenic analysis between tomato and pepper based on the alignment of 34,727 tomato CDS to the pepper genome sequence, identified 19,734 unique hits. The resulting synteny map confirmed the 14 inversions and 10 translocations previously documented, but also highlighted 3 new translocations and 4 major new inversions. Furthermore, each of the 12 chromosomes exhibited a number of rearrangements involving small regions of 0.5-0.7 Mbp. Due to high fragmentation of the publicly available eggplant genome sequence, physical localization of most eggplant QTL was not possible, thus, we compared the organization of the eggplant genetic map with the genome sequence of both tomato and pepper. The eggplant/tomato syntenic map confirmed all the 10 translocations but only 9 of the 14 known inversions; on the other hand, a newly detected inversion was recognized while another one was not confirmed. The eggplant/pepper syntenic map confirmed 10 translocations and 8 inversions already detected and suggested a putative new translocation. In order to perform the assessment of eggplant and pepper QTL orthology, the eggplant and pepper sequence-based markers located in their respective genetic map were aligned onto the pepper genome. GBrowse in pepper was used as reference platform for QTL positioning. A set of 151 pepper QTL were located as well as 212 eggplant QTL, including 76 major QTL (PVE ≥ 10%) affecting key agronomic traits. Most were confirmed to cluster in orthologous

  17. New Insights on Eggplant/Tomato/Pepper Synteny and Identification of Eggplant and Pepper Orthologous QTL

    Directory of Open Access Journals (Sweden)

    Riccardo Rinaldi

    2016-07-01

    Full Text Available Eggplant, pepper and tomato are the most exploited berry-producing vegetables within the Solanaceae family. Their genomes differ in size, but each has 12 chromosomes which have undergone rearrangements causing a redistribution of loci. The genome sequences of all three species are available but differ in coverage, assembly quality and percentage of anchorage.Determining their syntenic relationship and QTL orthology will contribute to exploit genomic resources and genetic data for key agronomic traits.The syntenic analysis between tomato and pepper based on the alignment of 34,727 tomato CDS to the pepper genome sequence, identified 19,734 unique hits. The resulting synteny map confirmed the 14 inversions and 10 translocations previously documented, but also highlighted 3 new translocations and 4 major new inversions. Furthermore, each of the 12 chromosomes exhibited a number of rearrangements involving small regions of 0.5-0.7 Mbp.Due to high fragmentation of the publicly available eggplant genome sequence, physical localization of most eggplant QTL was not possible, thus, we compared the organization of the eggplant genetic map with the genome sequence of both tomato and pepper. The eggplant/tomato syntenic map confirmed all the 10 translocations but only 9 of the 14 known inversions; on the other hand, a newly detected inversion was recognized while another one was not confirmed. The eggplant/pepper syntenic map confirmed 10 translocations and 8 inversions already detected and suggested a putative new translocation.In order to perform the assessment of eggplant and pepper QTL orthology, the eggplant and pepper sequence-based markers located in their respective genetic map were aligned onto the pepper genome. GBrowse in pepper was used as reference platform for QTL positioning. A set of 151 pepper QTL were located as well as 212 eggplant QTL, including 76 major QTL (PVE ≥ 10% affecting key agronomic traits. Most were confirmed to cluster in

  18. 茶树炭疽病抗性的 QTL 分析%QTL Analysis for Anthracnose Resistance in Tea Plant (Camellia sinensis)

    Institute of Scientific and Technical Information of China (English)

    徐礼羿; 谭礼强; 王丽鸳; 齐桂年; 成浩; 韦康

    2016-01-01

    In order to provide a basis for breeding tea plants with anthracnose resistance, 170 F1 plants, derived from LJ43♀×BHZ♂, were used to constructed a linkage map by SSR markers. Field observation and indoor test were carried out in 2014. The data of phenotypic characters were used for QTL mapping and analysis by the method of MQM mapping. A pathogen was isolated from a diseased leaf of the F1 plants, and its gene sequence of ITS had 99%similarity with Colletotrichum sp. based on NCBI BLAST. The plants grown in open field were more easy to be infected by the pathogen than those grown in rooms. Eight QTLs were detected in six different linkage groups by QTL analysis. The LOD and PVE of individual QTLs ranged from 2.53 to 6.80 and 5.6% to 13.8%, respectively. A main QTL with LOD 6.80 and PVE 13.8% was detected in LG10.%以茶树 SSR 遗传连锁图谱为基础,选取龙井43为母本,白毫早为父本的170株 F1遗传群体为试验材料,于2014年对该群体分别进行了茶树炭疽病抗性性状的田间观测和室内侵染试验,并采用复合区间作图法对该性状进行 QTL 定位与分析。结果显示:从 F1群体病叶上分离纯化出一种茶树炭疽病病菌 HZ-1,经NCBI BLAST 比对,其 ITS 基因序列与炭疽菌(Colletotrichum sp.)的亲缘关系最近,序列相似度为99%。对F1群体的炭疽病抗性表型分析发现,田间环境下的感病单株的占比(41%)高于室内环境(24%)。QTL 分析显示,在6个不同的遗传连锁群(Linkage group,LG)上共检测到8个 QTLs,单个 QTL 的 LOD 阈值变幅为2.53~6.80,单个 QTL 的表型变异贡献率的变幅为5.6%~13.8%。LG10存在1个控制茶树炭疽病抗性性状的主效 QTL,LOD 值6.80,表型变异贡献率13.8%。

  19. Using microarrays to identify positional candidate genes for QTL: the case study of ACTH response in pigs

    DEFF Research Database (Denmark)

    Jouffe, Vincent; Rowe, Suzanne; Liaubet, Laurence;

    2009-01-01

    of 237 differentially expressed cDNA clones in adrenal tissue from two pig breeds, before and after treatment with adrenocorticotropic hormone (ACTH) Microarray studies can supplement QTL studies by suggesting potential candidate genes in the QTL regions, which by themselves are too large to provide...... this with information on published QTL. The starting point is a set of 237 differentially expressed cDNA clones in adrenal tissue from two pig breeds, before and after treatment with adrenocorticotropic hormone (ACTH) Results: Different approaches to localize the differentially expressed (DE) genes to the pig genome...

  20. Mapping QTL Contributing to Variation in Posterior Lobe Morphology between Strains of Drosophila melanogaster.

    Science.gov (United States)

    Hackett, Jennifer L; Wang, Xiaofei; Smith, Brittny R; Macdonald, Stuart J

    2016-01-01

    Closely-related, and otherwise morphologically similar insect species frequently show striking divergence in the shape and/or size of male genital structures, a phenomenon thought to be driven by sexual selection. Comparative interspecific studies can help elucidate the evolutionary forces acting on genital structures to drive this rapid differentiation. However, genetic dissection of sexual trait divergence between species is frequently hampered by the difficulty generating interspecific recombinants. Intraspecific variation can be leveraged to investigate the genetics of rapidly-evolving sexual traits, and here we carry out a genetic analysis of variation in the posterior lobe within D. melanogaster. The lobe is a male-specific process emerging from the genital arch of D. melanogaster and three closely-related species, is essential for copulation, and shows radical divergence in form across species. There is also abundant variation within species in the shape and size of the lobe, and while this variation is considerably more subtle than that seen among species, it nonetheless provides the raw material for QTL mapping. We created an advanced intercross population from a pair of phenotypically-different inbred strains, and after phenotyping and genotyping-by-sequencing the recombinants, mapped several QTL contributing to various measures of lobe morphology. The additional generations of crossing over in our mapping population led to QTL intervals that are smaller than is typical for an F2 mapping design. The intervals we map overlap with a pair of lobe QTL we previously identified in an independent mapping cross, potentially suggesting a level of shared genetic control of trait variation. Our QTL additionally implicate a suite of genes that have been shown to contribute to the development of the posterior lobe. These loci are strong candidates to harbor naturally-segregating sites contributing to phenotypic variation within D. melanogaster, and may also be those

  1. Cell Wall Composition and Underlying QTL in an F1 Pseudo-Testcross Population of Switchgrass

    Energy Technology Data Exchange (ETDEWEB)

    Serba, Desalegn D.; Sykes, Robert W.; Gjersing, Erica L.; Decker, Stephen R.; Daverdin, Guillaume; Devos, Katrien M.; Brummer, E. Charles; Saha, Malay C.

    2016-09-01

    Natural genetic variation for reduced recalcitrance can be used to improve switchgrass for biofuel production. A full-sib switchgrass mapping population developed by crossing a lowland genotype, AP13, and upland genotype, VS16, was evaluated at three locations (Ardmore and Burneyville, OK and Watkinsville, GA). Biomass harvested after senescence in 2009 and 2010 was evaluated at the National Renewable Energy Laboratory (NREL) for sugar release using enzymatic hydrolysis and for lignin content and syringyl/guaiacyl lignin monomer (S/G) ratio using pyrolysis molecular beam mass spectrometry (py-MBMS). Glucose and xylose release ranged from 120 to 313 and 123 to 263 mg g-1, respectively, while lignin content ranged from 19 to 27% of the dry biomass. Statistically significant differences were observed among the genotypes and the environments for the cell wall composition traits. Regression analysis showed that a unit increase in lignin content reduced total sugar release by an average of 10 mg g-1. Quantitative trait loci (QTL) analysis detected 9 genomic regions underlying sugar release and 14 for lignin content. The phenotypic variation explained by the individual QTL identified for sugar release ranged from 4.5 to 9.4 and for lignin content from 3.8 to 11.1%. Mapping of the QTL regions to the switchgrass genome sequence (v1.1) found that some of the QTL colocalized with genes involved in carbohydrate processing and metabolism, plant development, defense systems, and transcription factors. The markers associated with QTL can be implemented in breeding programs to efficiently develop improved switchgrass cultivars for biofuel production.

  2. A genome scan for QTL affecting resistance to Haemonchus contortus in sheep.

    Science.gov (United States)

    Sallé, G; Jacquiet, P; Gruner, L; Cortet, J; Sauvé, C; Prévot, F; Grisez, C; Bergeaud, J P; Schibler, L; Tircazes, A; François, D; Pery, C; Bouvier, F; Thouly, J C; Brunel, J C; Legarra, A; Elsen, J M; Bouix, J; Rupp, R; Moreno, C R

    2012-12-01

    Gastrointestinal nematodes are one of the main health issues in sheep breeding. To identify loci affecting the resistance to Haemonchus contortus, a genome scan was carried out using 1,275 Romane × Martinik Black Belly backcross lambs. The entire population was challenged with Haemonchus contortus in 2 consecutive experimental infections, and fecal egg counts (FEC) and packed cell volumes were measured. A subgroup of 332 lambs with extreme FEC was necropsied to determine the total worm burden, length of female worms, sex ratio in the worm population, abomasal pH, and serum and mucosal G immunoglobulins (IgG) responses. Pepsinogen concentration was measured in another subset of 229 lambs. For QTL detection, 160 microsatellite markers were used as well as the Illumina OvineSNP50 BeadChip that provided 42,469 SNP markers after quality control. Linkage, association, and joint linkage and association analyses were performed with the QTLMAP software. Linkage disequilibrium (LD) was estimated within each pure breed, and association analyses were carried out either considering or not the breed origin of the haplotypes. Four QTL regions on sheep chromosomes (OAR)5, 12, 13, and 21 were identified as key players among many other QTL with small to moderate effects. A QTL on OAR21 affecting pepsinogen concentration exactly matched the pepsinogen (PGA5) locus. A 10-Mbp region affecting FEC after the 1st and 2nd infections was found on OAR12. The SNP markers outperformed microsatellites in the linkage analysis. Taking advantage of the LD helped to refine the locations of the QTL mapped on OAR5 and 13.

  3. Dynamic analysis of QTL for plant height at different developmental stages in maize (Zea mays L.)

    Institute of Scientific and Technical Information of China (English)

    YAN Jianbing; TANG Hua; HUANG Yiqin; SHI Yonggang; LI Jiansheng; ZHENG Yonglian

    2003-01-01

    Plant height in maize is not only one of important agronomic traits, but also one of model traits suitablefor study of developmental biology. Using data from fieldtests in two locations (Wuhan and Xiangfan) within the sameyear and a molecular linkage map covering all of 10 chro-mosomes, QTLs affecting plant height at five different de-velopmental stages were mapped and analyzed by the com-bination of composite interval mapping and the conditionalanalysis method. Eight QTLs for plant height at differentstages were located at different regions of five chromosomes(LOD≥2.5). The results showed that there were differenteffect values of QTL on plant height at different develop-mental stages. Three QTLs were detected at all of five stages.With different stages, contributory percentage of single QTL to plant height varied between 3.8% and 17.1%. It suggestedthat the expression of each QTL controlling plant height wasdifferent at different stages. With net growth, seven condi-tional QTLs for plant height were detected. Conditional QTLs were nearly detected at each stage, and QTLs of Ph1-1, Ph1-2, Ph3, Ph5-2 and Ph9 were detected at both locations (Wuhan and Xiangfan). The contributory percentage of single conditional QTL to plant height varied between 3.8% and 12.3%, indicating that QTLs for plant height are expressed in different time-space. Therefore, QTL expressed at different stages should be considered when marker assistant selection is conducted for quantitative traits.

  4. Correlation and QTL Analyses for Photosynthetic Traits in Maize%玉米光合性状的相关性及 QTL 分析

    Institute of Scientific and Technical Information of China (English)

    余婷婷; 刘朝显; 梅秀鹏; 王久光; 王国强; 蔡一林

    2015-01-01

    In order to explore the correlation and genetic mechanism of maize photosynthetic traits ,two F2 populations (Y and R) with different genetic backgrounds were used to identify correlation and QTLs for 10 photosynthetic traits ,which included chlorophyll‐a content ,chlorophyll‐b content ,total chlorophyll content ,net photosynthetic rate ,stomata conductance ,intercellular CO2 concentration ,transpiration rate and some others .The correlation between two of chlorophyll‐a content ,chlorophyll‐b content and total chlorophyll content in different periods was non‐significant in population Y ,and was highly significant in population R .The correlation between other traits of the two populations was highly consistent .In the same growth period of the plants ,total chlorophyll content was in highly significant correlation with chlo‐rophyll‐a content and chlorophyll‐b content ,highly significant correlation was also detected between net photosynthetic rate and stomata conductance ,between net photosynthetic rate and transpiration rate ,and between stomata conductance and transpiration rate ,stomata conductance was moderately correlated with intercellular CO2 concentration ,and chlorophyll content was weakly correlated with net photosynthetic rate ,stomata conductance ,intercellular CO2 concentration and transpiration rate .In population Y ,1 QTL was detected for chlorophyll‐a content (FCa) ,chlorophyll‐b content (FCb) and total chlorophyll content (FCt) each ,at the five‐leaf stage .All these QTLs were located in umc2391‐mmc0371 on chromosome 4 and each explained 8.65% to 9.87% of the phenotypic variance .And other three QTLs were detected at the milk stage ,one for chlorophyll‐a content ,one for chlorophyll‐b content and one for total chlorophyll content .They were located in mmc0501‐bnlg1451 on chromosome 10 and explained 6.77 to 6.93% of the phenotypic variance each .Six QTLs were detected at the pollination stage ,one for net photosynthetic

  5. Desarrollo de un Análisis Cuantitativo para Determinar la Composición de una Aleación mediante Fluorescencia de Rayos X y el Método de Monte Carlo

    OpenAIRE

    Querol Vives, Andrea; Ródenas Diago, José; Juste Vidal, Belen Jeanine; Gallardo Bermell, Sergio

    2011-01-01

    El análisis por fluorescencia de rayos X (XRFA) es una técnica que utiliza la interacción de rayos X con una muestra para determinar su composición. Analizando los espectros obtenidos resulta sencillo realizar un análisis cualitativo. No obstante, es más complicado realizar un análisis cuantitativo. Para desarrollar este análisis se ha llevado a cabo una combinación de métodos experimentales y de simulación por Monte Carlo. Para la parte experimental se utiliza un tubo de rayos...

  6. Controversias epistemológicas y metodológicas entre el paradigma cualitativo y cuantitativo en psicología/ epistemological and methodological controversies between the qualitative and quantitative paradigm in psychology

    OpenAIRE

    Cuenya, Lucas; Ruetti, Eliana

    2010-01-01

    La distinción entre metodología cuantitativa y cualitativa define dos campos de investigación que profesan postulados paradigmáticos encontrados. El conocimiento científico se caracteriza por ser racional y objetivo, fáctico y verificable, caracterización que sintoniza, en buena medida, con los atributos del método cuantitativo. Por el contrario, el estudio cualitativo busca comprender los fenómenos dentro de su ambiente usual, utilizando como datos descripciones de situaciones, eventos, pers...

  7. Estudio secuencial y cuantitativo del quimerismo hemopoyético en pacientes sometidos a un trasplante alogénico de progenitores hemopoyéticos con depleción linfoide T o con acondicionamiento sub-mieloablativo.

    OpenAIRE

    Fernández Avilés, Francesc

    2004-01-01

    [spa] El objetivo principal de esta Tesis Doctoral es analizar cual es la frecuencia y la relevancia clínica de la persistencia de células linfoides T y de células mieloides originarias del receptor (quimerismo mixto) tras un trasplante alogénico de progenitores hemopoyéticos. La hipótesis de trabajo es comprobar si el estudio secuencial y cuantitativo del patrón de quimerismo mixto en linfocitos T y en neutrófilos permite predecir el rechazo del injerto alogénico o la recidiva leucémica, res...

  8. Rapid identification of fruit length loci in cucumber (Cucumis sativus L.) using next-generation sequencing (NGS)-based QTL analysis.

    Science.gov (United States)

    Wei, Qing-Zhen; Fu, Wen-Yuan; Wang, Yun-Zhu; Qin, Xiao-Dong; Wang, Jing; Li, Ji; Lou, Qun-Feng; Chen, Jin-Feng

    2016-06-07

    The cucumber (Cucumis sativus L.) exhibits extensive variations in fruit size and shape. Fruit length is an important agronomic and domesticated trait controlled by quantitative trait loci (QTLs). Nonetheless, the underlying molecular and genetic mechanisms that determine cucumber fruit length remain unclear. QTL-seq is an efficient strategy for QTL identification that takes advantage of bulked-segregant analysis (BSA) and next-generation sequencing (NGS). In the present study, we conducted QTL mapping and QTL-seq of cucumber fruit length. QTL mapping identified 8 QTLs for immature and mature fruit length. A major-effect QTL fl3.2, which explained a maximum of 38.87% of the phenotypic variation, was detected. A genome-wide comparison of SNP profiles between two DNA bulks identified 6 QTLs for ovary length. QTLs ovl3.1 and ovl3.2 both had major effects on ovary length with a △ (SNP-index) of 0.80 (P < 0.01) and 0.74 (P < 0.01), respectively. Quantitative RT-PCR of fruit size-related homologous genes localized in the consensus QTL FL3.2 was conducted. Four candidate genes exhibited increased expression levels in long fruit genotypes. Our results demonstrated the power of the QTL-seq method in rapid QTL detection and provided reliable QTL regions for fine mapping of fruit length-related loci and for identifying candidate genes.

  9. Cis-eQTL analysis and functional validation of candidate susceptibility genes for high-grade serous ovarian cancer

    DEFF Research Database (Denmark)

    Lawrenson, Kate; Li, Qiyuan; Kar, Siddhartha;

    2015-01-01

    associated with HGSOC risk (P≤10−5). For three cis-eQTL associations (Pfunctional role of each candidate by perturbing expression of each gene in HGSOC precursor cells. Overexpression of HOXD9 increases anchorage...

  10. The comparative analysis based on maize integrated QTL map and meta-analysis of plant height QTLs

    Institute of Scientific and Technical Information of China (English)

    WANG Yi; YAO Ji; ZHANG Zhengfeng; ZHENG Yonglian

    2006-01-01

    1201 published maize QTLs conferring for 68 traits were collected and imported into local CMap software to construct an integrated QTL map, which can be used for marker-mining, QTL localization, gene cloning and marker-assisted selection. The maize integrated QTL map showed that maize QTLs for various traits usually clustered in all chromosomes. 22 plant height QTLs of maize were co-linear with 64 plant height QTLs of rice, 43 grain yield QTLs of maize were co-liner with 7 grain yield QTLs of rice. 127 plant height QTLs of maize were refined by means of "overview" analysis. At last, 40 "real" QTLs were identifed. A substantial number of candidate quantitative trait genes for plant height of maize were found. These results established an important bioinformatics platform for extracting most of maize QTL information.

  11. Molecular mapping of Verticillium wilt resistance QTL clustered on chromosomes D7 and D9 in upland cotton

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    Verticillium wilt is a destructive disease with international consequences for cotton production. Breeding broad-spectrum resistant cultivars is considered to be one of the most effective means for reducing crop losses. A resistant cotton cultivar,60182,was crossed with a susceptible cultivar,Jun-mian 1,to identify markers for Verticillium resistance genes and validate the mode of its inheritance. Genetic segregation analysis for Verticillium wilt resistance was evaluated based upon infected leaf percentage in the seedling stage using major gene-polygene mixed inheritance models and joint analysis of P1,P2,F1,B1,B2 and F2 populations obtained from the cultivar cross. We found that resistance of upland cotton cultivar 60182 to isolates BP2,VD8 and T9,and their isoconcentration mixture was controlled by two major genes with additive-dominance-epistatic effects,and the inheritance of the major gene was dominant. Furthermore,a genetic linkage map was constructed using F2 segregating population and resistance phenotypic data were obtained using F2:3 families inoculated with different isolates and detected in different developmental stages. The genetic linkage map with 139 loci was comprised of 31 linkage groups covering 1165 cM,with an average distance of 8.38 cM between two markers,or 25.89% of the cotton genome length. From 60182,we found 4 QTL on chromosome D7 and 4 QTL on D9 for BP2,5 QTL on D7 and 9 QTL on D9 for VD8,4 QTL on D7 and 5 QTL on D9 for T9 and 3 QTL on D7 and 7 QTL on D7 for mixed pathogens. The QTL mapping results revealed that QTL clusters with high contribution rates were screened simultaneously on chromosomes D9 and D7 by multiple interval mapping (CIM),whether from resistance phenotypic data from different developmental stages or for different isolates. The result is consistent with the genetic model of two major genes in 60182 and suggests broad-spectrum resistance to both defoliating isolates of V. dahliae and nondefoliating isolates. The markers

  12. Severidade da ferrugem-da-folha e seus efeitos sobre caracteres da panícula de aveia Crown rust severity and its effects on oat panicle characters

    Directory of Open Access Journals (Sweden)

    Renata Pereira da Cruz

    1999-04-01

    Full Text Available A ferrugem-da-folha (Puccinia coronata f.sp. avenae foi quantificada em quatro populações F3 de aveia (Avena sativa L. com o objetivo de estudar a severidade dessa moléstia e seus efeitos sobre seis caracteres da panícula. As populações utilizadas foram UFRGS 881920 x UFRGS 7, UFRGS 881920 x UFRGS 14, UFRGS 15 x UFRGS 7 e UFRGS 15 x UFRGS 14, sendo os genótipos UFRGS 881920 e UFRGS 15 resistentes à moléstia e os demais suscetíveis. A ferrugem-da-folha foi quantificada na época do florescimento, e próximo à maturação foram colhidas, em cada população, 10 plantas ao acaso por nota de ferrugem nas quais foram feitas as seguintes determinações: número de panículas, peso médio de panículas, número de grãos por planta e por panícula, peso de grãos e peso de mil grãos. A variabilidade em relação à severidade da ferrugem-da-folha foi analisada mediante a distribuição de freqüências das notas em cada população. A avaliação dos efeitos da moléstia sobre os caracteres da panícula foi feita pela análise de variância, análise de regressão polinomial e correlações fenotípicas. Os resultados obtidos demonstram haver ampla variação com respeito à severidade da moléstia nas populações estudadas, e os caracteres mais afetados foram o peso médio de panículas e o peso de mil grãos.Crown rust (Puccinia coronata f.sp. avenae was quantified in four F3 oat (Avena sativa L. populations with the objective of studying disease severity and its effects on six panicle characters. Populations used were UFRGS 881920 x UFRGS 7, UFRGS 881920 x UFRGS 14, UFRGS 15 x UFRGS 7 and UFRGS 15 x UFRGS 14, with genotypes UFRGS 881920 and UFRGS 15 being resistant and the others susceptible. Crown rust infection was quantified at flowering stage and near grain maturity 10 plants at random were harvested per crown rust score in each population, and the following determinations were made: number of panicles, mean panicle weight, number

  13. Saturation mapping of QTL regions and identification of putative candidate genes for drought tolerance in rice.

    Science.gov (United States)

    Nguyen, T T T; Klueva, N; Chamareck, V; Aarti, A; Magpantay, G; Millena, A C M; Pathan, M S; Nguyen, H T

    2004-08-01

    We have developed 85 new markers (50 RFLPs, 5 SSRs, 12 DD cDNAs, 9 ESTs, 8 HSP-encoding cDNAs and one BSA-derived AFLP marker) for saturation mapping of QTL regions for drought tolerance in rice, in our efforts to identify putative candidate genes. Thirteen of the markers were localized in the close vicinity of the targeted QTL regions. Fifteen of the additional markers mapped, respectively, inside one QTL region controlling osmotic adjustment on chromosome 3 ( oa3.1) and 14 regions that affect root traits on chromosomes 1, 2, 4, 5, 6, 7, 8, 9, 10 and 12. Differential display was used to identify more putative candidate genes and to saturate the QTL regions of the genetic map. Eleven of the isolated cDNA clones were found to be derived from drought-inducible genes. Two of them were unique and did not match any genes in the GenBank, while nine were highly similar to cDNAs encoding known proteins, including a DnaJ-related protein, a zinc-finger protein, a protease inhibitor, a glutathione-S-transferase, a DNA recombinase, and a protease. Twelve new cDNA fragments were mapped onto the genetic linkage map; seven of these mapped inside, or in close proximity to, the targeted QTL regions determining root thickness and osmotic adjustment capacity. The gene I12A1, which codes for a UDP-glucose 4-epimerase homolog, was identified as a putative target gene within the prt7.1/brt7.1 QTL region, as it is involved in the cell wall biogenesis pathway and hence may be implicated in modulating the ability of rice roots to penetrate further into the substratum when exposed to drought conditions. RNAs encoding elongation factor 1beta, a DnaJ-related protein, and a homolog of wheat zinc-finger protein were more prominently induced in the leaves of IR62266 (the lowland rice parent of the mapping materials used) than in those of CT9993 (the upland rice parent) under drought conditions. Homologs of 18S ribosomal RNA, and mRNAs for a multiple-stress induced zinc-finger protein, a protease

  14. A high-density SNP map for accurate mapping of seed fibre QTL in Brassica napus L.

    Directory of Open Access Journals (Sweden)

    Liezhao Liu

    Full Text Available A high density genetic linkage map for the complex allotetraploid crop species Brassica napus (oilseed rape was constructed in a late-generation recombinant inbred line (RIL population, using genome-wide single nucleotide polymorphism (SNP markers assayed by the Brassica 60 K Infinium BeadChip Array. The linkage map contains 9164 SNP markers covering 1832.9 cM. 1232 bins account for 7648 of the markers. A subset of 2795 SNP markers, with an average distance of 0.66 cM between adjacent markers, was applied for QTL mapping of seed colour and the cell wall fiber components acid detergent lignin (ADL, cellulose and hemicellulose. After phenotypic analyses across four different environments a total of 11 QTL were detected for seed colour and fiber traits. The high-density map considerably improved QTL resolution compared to the previous low-density maps. A previously identified major QTL with very high effects on seed colour and ADL was pinpointed to a narrow genome interval on chromosome A09, while a minor QTL explaining 8.1% to 14.1% of variation for ADL was detected on chromosome C05. Five and three QTL accounting for 4.7% to 21.9% and 7.3% to 16.9% of the phenotypic variation for cellulose and hemicellulose, respectively, were also detected. To our knowledge this is the first description of QTL for seed cellulose and hemicellulose in B. napus, representing interesting new targets for improving oil content. The high density SNP genetic map enables navigation from interesting B. napus QTL to Brassica genome sequences, giving useful new information for understanding the genetics of key seed quality traits in rapeseed.

  15. Mapping QTL for drought stress-induced premature senescence and maturity in cowpea [Vigna unguiculata (L.) Walp.].

    Science.gov (United States)

    Muchero, Wellington; Ehlers, Jeffrey D; Close, Timothy J; Roberts, Philip A

    2009-03-01

    Cowpea is an important crop for subsistence farmers in arid regions of Africa, Asia, and South America. Efforts to develop cultivars with improved productivity under drought conditions are constrained by lack of molecular markers associated with drought tolerance. Here, we report the mapping of 12 quantitative trait loci (QTL) associated with seedling drought tolerance and maturity in a cowpea recombinant inbred (RIL) population. One hundred and twenty-seven F(8) RILs developed from a cross between IT93K503-1 and CB46 were screened with 62 EcoR1 and Mse1 primer combinations to generate 306 amplified fragment length polymorphisms for use in genetic linkage mapping. The same population was phenotyped for maintenance of stem greenness (stg) and recovery dry weight (rdw) after drought stress in six greenhouse experiments. In field experiments conducted over 3 years, visual ratings and dry weights were used to phenotype drought stress-induced premature senescence in the RIL population. Kruskall-Wallis and multiple-QTL model mapping analysis were used to identify QTL associated with drought response phenotypes. Observed QTL were highly reproducible between stg and rdw under greenhouse conditions. Field studies confirmed all ten drought-response QTL observed under greenhouse conditions. Regions harboring drought-related QTL were observed on linkage groups 1, 2, 3, 5, 6, 7, 9, and 10 accounting for between 4.7 and 24.2% of the phenotypic variance (R(2)). Further, two QTL for maturity (R(2) = 14.4-28.9% and R(2) = 11.7-25.2%) mapped on linkage groups 7 and 8 separately from drought-related QTL. These results provide a platform for identification of genetic determinants of seedling drought tolerance in cowpea.

  16. Importância de caracteres na dissimilaridade de progênies de batata em gerações iniciais de seleção Importance of characters in the dissimilarity of potato progênies in early generations

    Directory of Open Access Journals (Sweden)

    Giovani Olegário da Silva

    2008-01-01

    Full Text Available O trabalho teve por objetivo verificar as implicações da utilização da análise de importância de caracteres na eliminação de caracteres avaliados para o cálculo da distância genética de progênies de batata (Solanum tuberosum L. nas primeiras gerações de seleção. Os experimentos foram desenvolvidos em casa plástica (geração de seedlings e em campo (primeira geração clonal, na Embrapa Clima Temperado, Pelotas, Estado do Rio Grande do Sul em outono de 2004 e outono de 2005. O estudo demonstrou que a análise de importância de caracteres foi eficiente para diminuir o número de caracteres necessários à classificação das progênies de batata em relação à dissimilaridade. O formato de tubérculo foi o caráter com maior eficiência para o estudo de dissimilaridade em progênies de batata.The objective of the present work was to access the implications of the use of analysis of importance of characters in the elimination of appraised characters for calculating genetic distance of potato (Solanum tuberosum L. progenies in early generations. The experiments were carried out in plastic house (seedling generation and in the field (first clonal generations at Embrapa Temperate Climate, Pelotas, Rio Grande do Sul State in autumn 2004 and 2005. The study was demonstrated the efficiency of the analysis in importance of characters for reducing the number of characters necessary for classifying potato progenies in relation to the dissimilarity. Tuber shape was the character with the largest efficiency for the dissimilarity study in potato progenies.

  17. Comparación de caracteres corporales y del veneno de Bothrops alternatus entre poblaciones de las provincias de Buenos Aires y Entre Ríos, Argentina

    Directory of Open Access Journals (Sweden)

    Rocco, Daniela Marisa

    2011-11-01

    Full Text Available Comparamos caracteres corporales y producción de veneno de ejemplares de Bothrops alternatus de una población aislada geográficamente (Olavarría, región de Tandilia, Buenos Aires con otra en su área de distribución continua de Concordia (Entre Ríos. Estudiamos el largo corporal, peso, separación entre dientes inoculadores, cantidad de veneno y de proteínas en el veneno por ejemplar. No se hallaron diferencias en los caracteres estudiados entre ambas poblaciones (p > 0.05. Las hembras fueron mayores que los machos en ambas muestras, entre un 12-18% (p 0.5; Olavarría: 142 ± 65 mg/animal, Concordia: 160 ± 80 mg/animal, aún ajustando la cantidad de veneno producida respecto al tamaño, mediante el cociente veneno/largo corporal (p >0.6. Tampoco hubo diferencias en el contenido proteico, siendo para ambas muestras de 0.697 ± 0.096 mg de proteínas/mg de veneno seco. Nuestros datos sugieren que los ejemplares de la población aislada de Tandilia no presentan variaciones en el tamaño corporal o en la cantidad de veneno producida, respecto a los ejemplares de Concordia. Some corporal characters and venom yield of adult specimens of Bothrops alternatus from the isolated region of Olavarría (Tandilian Region, Buenos Aires and the region of continuous distribution of Concordia (Entre Ríos were compared. Corporal length, weight, separation between fangs, venom yield by snake and the amount of protein in the venom were determined. No differences in the distinct characters from specimens from both regions were found (p > 0.05. Females were greater than males in both samples, 12-18% (p 0.5; Olavarría= 142 ± 65 mg / animal, Concordia= 161 ± 80 mg / animal even adjusting the venom yield with the corporal length by the relation mg of venom / corporal length (p > 0.6. No differences were observed in the protein content of the dry venom which was of 0.697 ± 0.096 mg of protein / mg of dry venom. From the study of these samples, it could be

  18. Identification of QTL with effects on fatty acid composition of meat in a Charolais x Holstein cross population.

    Science.gov (United States)

    Gutiérrez-Gil, B; Wiener, P; Richardson, R I; Wood, J D; Williams, J L

    2010-08-01

    A whole-genome scan was carried out to detect quantitative trait loci (QTL) influencing beef fatty acid composition using a CharolaisxHolstein population established using a balanced F2 and Backcross breeding design. The phenotypes considered in this study included a total of 24 fatty acid related traits determined in loin muscle samples of the 235 second-generation cross-bred bull calves of the herd. The QTL regression analysis performed, based on 165 microsatellite markers distributed across the 29 bovine autosomes, identified 34 QTL with F-ratios exceeding the 5% chromosome-wide significance threshold. Three of these QTL, one located on chromosome 1 (for the content on linoleic acid, C18:2n-6) and two on chromosome 10 (for the content of gamma-linoleic DPA-docosapentaenoic and DPA-docosapentaenoic, C20:3n-6 and C22:5n-3), also exceeded the 5% genome-wide significance level. A follow-up analysis correcting for intramuscular fat content showed that some of the QTL detected initially (e.g. those localised on chromosome 22) were influenced by fat deposition differences between the founder breeds. The coincident location of some of the linkage associations identified and QTL previously reported for beef fatty acid composition and other meat quality traits, in the same or other cattle populations, provides supporting evidence for the results reported here. PMID:20416790

  19. Mapping QTL associated with Verticillium dahliae resistance in the cultivated strawberry (Fragaria × ananassa).

    Science.gov (United States)

    Antanaviciute, L; Šurbanovski, N; Harrison, N; McLeary, K J; Simpson, D W; Wilson, F; Sargent, D J; Harrison, R J

    2015-01-01

    A biparental cross of octoploid strawberry segregating for resistance to Verticillium dahliae, the causative agent of Verticillium wilt, was screened under field conditions for three seasons. Average wilt scores were significantly associated with multiple QTL, which were mostly significant across all years. Markers significantly associated with the traits were used to screen material with known wilt resistance and susceptibility phenotypes. A clear and statistically significant relationship was observed between resistant, tolerant and susceptible material and the total number of markers present in the different resistance classes. In field situations resistance QTL appear to behave in an additive manner. These markers are abundant in the cultivated strawberry germplasm indicating that, despite the large number of markers, clear genetic gain is possible through marker-assisted breeding.

  20. Across Breed QTL Detection and Genomic Prediction in French and Danish Dairy Cattle Breeds

    DEFF Research Database (Denmark)

    van den Berg, Irene; Guldbrandtsen, Bernt; Hozé, C;

    Our objective was to investigate the potential benefits of using sequence data to improve across breed genomic prediction, using data from five French and Danish dairy cattle breeds. First, QTL for protein yield were detected using high density genotypes. Part of the QTL detected within breed was...... shared across breed. Second, sequence data was used to quantify the loss in prediction reliabilities that results from using genomic markers rather than the causal variants. 50, 100 or 250 causative mutations were simulated and different sets of prediction markers were used to predict genomic...... relationships at causative mutations. Prediction of genomic relationships at causative mutations was most accurate when predicted by a selective number of markers within 1 Kb of the causative mutations. Whole-genome sequence data can help to get closer to the causative mutations and therefore improve genomic...

  1. QTL mapping of inbreeding-related cold sensitivity and conditional lethality in Drosophila melanogaster

    DEFF Research Database (Denmark)

    Vermeulen, Corneel J.; Bijlsma, R.; Loeschcke, Volker

    2008-01-01

    . Whenever the expression of deleterious alleles is conditional, this can result in extreme environmental sensitivity in certain inbred lineages. Analysis of conditional lethal effects can reveal some of the loci that are sensitive to inbreeding. We performed a QTL (quantitative trait locus) mapping study...... of inbreeding-related and conditionally expressed lethality in Drosophila melanogaster. The lethal effect was triggered by exposure to a cold shock. We used a North Carolina crossing Design 3 to establish the mapping population, as well as to estimate the average dominance ratio and heritability. We found two...... QTL on the major autosomes carrying recessive lethals that caused male mortality, one of which also affected female mortality. More detailed study of these loci will provide information on the mechanistic basis and environmental sensitivity of inbreeding depression....

  2. QTL analysis of crown rust resistance in perennial ryegrass under conditions of natural and artificial infection

    DEFF Research Database (Denmark)

    Schejbel, Britt; Jensen, Louise Friis Bach; Xing, Yongzhong;

    2007-01-01

    Crown rust is an economically devastating disease of perennial ryegrass. Both artificial crown rust inoculations, with the possibility of several selection cycles in one year, as well as marker-assisted selection can be used for more efficient breeding of new resistant cultivars. The objective...... of this study was to map quantitative trait loci (QTL) for response to crown rust infection in perennial ryegrass. In order to identify relevant markers for response to crown rust infection, QTL mapping was performed on a ryegrass mapping population which was evaluated for resistance in the field for two years...... as well as by artificial pathogen inoculations using a detached leaf assessment. The broad sense heritability values for the field, detached leaf and combined assays were 0.42, 0.56, and 0.64, respectively, indicating a good potential for selection for crown rust resistance. A total of six QTLs were...

  3. Mapping QTL associated with Verticillium dahliae resistance in the cultivated strawberry (Fragaria × ananassa).

    Science.gov (United States)

    Antanaviciute, L; Šurbanovski, N; Harrison, N; McLeary, K J; Simpson, D W; Wilson, F; Sargent, D J; Harrison, R J

    2015-01-01

    A biparental cross of octoploid strawberry segregating for resistance to Verticillium dahliae, the causative agent of Verticillium wilt, was screened under field conditions for three seasons. Average wilt scores were significantly associated with multiple QTL, which were mostly significant across all years. Markers significantly associated with the traits were used to screen material with known wilt resistance and susceptibility phenotypes. A clear and statistically significant relationship was observed between resistant, tolerant and susceptible material and the total number of markers present in the different resistance classes. In field situations resistance QTL appear to behave in an additive manner. These markers are abundant in the cultivated strawberry germplasm indicating that, despite the large number of markers, clear genetic gain is possible through marker-assisted breeding. PMID:26504565

  4. Characterization and mapping of QTL used in breeding of Scots pine (Pinus sylvestris L.)

    OpenAIRE

    Nowicka, Aleksandra; Ukalska, Joanna; Simińska, Joanna; Szyp-Borowska, Iwona

    2013-01-01

    This paper reports the construction a map based on Amplified Fragment Length Polymorphic DNA (AFLP) in Scots pine (Pinus sylvestris L.). The main purpose of map construction was its application to quantitative traits loci (QTL) mapping for breeding traits economically important in Scots pine breeding program such as tree height and diameter at breast height, number of needles and their length, width, and area. Genomic DNA of needles and haploid megagamethophytes from seeds originating from a ...

  5. Genetic and QTL analysis of resistance to Xiphinema index in a grapevine cross.

    Science.gov (United States)

    Xu, K; Riaz, S; Roncoroni, N C; Jin, Y; Hu, R; Zhou, R; Walker, M A

    2008-01-01

    Resistance to the dagger nematode Xiphinema index has been an important objective in grape rootstock breeding programs. This nematode not only causes severe feeding damage to the root system, but it also vectors grapevine fanleaf virus (GFLV), the causal agent of fanleaf degeneration and one of the most severe viral diseases of grape. The established screening procedures for dagger nematode resistance are time consuming and can produce inconsistent results. A fast and reliable greenhouse-based system for screening resistance to X. index that is suitable for genetic studies and capable of evaluating breeding populations is needed. In this report, the dynamics of nematode numbers, gall formation, and root weight loss were investigated using a variety of soil mixes and pot sizes over a 52-week period. Results indicated that the number of galls formed was correlated with the size of the nematode population and with the degree of root weight loss. After inoculation with 100 nematodes, gall formation could be reliably evaluated in 4-8 weeks in most plant growth conditions and results were obtained 6 months more rapidly than past evaluation methods. This modified X. index resistance screening method was successfully applied to 185 of the 188 F(1) progeny from a cross of D8909-15 x F8909-17 (the 9621 population), which segregates for a form of X. index resistance originally derived from Vitis arizonica. Quantitative trait loci (QTL) analysis was carried out on both parental genetic maps of 255 markers using MapQTL 4.0. Results revealed that X. index resistance is controlled by a major QTL, designated Xiphinema index Resistance 1 (XiR1), near marker VMC5a10 on chromosome 19. The XiR1 QTL was supported by a LOD score of 36.9 and explained 59.9% of the resistance variance in the mapping population.

  6. QTL Mapping of Genome Regions Controlling Temephos Resistance in Larvae of the Mosquito Aedes aegypti

    OpenAIRE

    Guadalupe Del Carmen Reyes-Solis; Karla Saavedra-Rodriguez; Adriana Flores Suarez; Black, William C.

    2014-01-01

    Introduction The mosquito Aedes aegypti is the principal vector of dengue and yellow fever flaviviruses. Temephos is an organophosphate insecticide used globally to suppress Ae. aegypti larval populations but resistance has evolved in many locations. Methodology/Principal Findings Quantitative Trait Loci (QTL) controlling temephos survival in Ae. aegypti larvae were mapped in a pair of F3 advanced intercross lines arising from temephos resistant parents from Solidaridad, México and temephos s...

  7. Joint QTL analysis of three connected F2-crosses in pigs

    OpenAIRE

    Bennewitz Jörn; Rückert Christine

    2010-01-01

    Abstract Background Numerous QTL mapping resource populations are available in livestock species. Usually they are analysed separately, although the same founder breeds are often used. The aim of the present study was to show the strength of analysing F2-crosses jointly in pig breeding when the founder breeds of several F2-crosses are the same. Methods Three porcine F2-crosses were generated from three founder breeds (i.e. Meishan, Pietrain and wild boar). The crosses were analysed jointly, u...

  8. A Bayesian partition method for detecting pleiotropic and epistatic eQTL modules.

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    Wei Zhang

    2010-01-01

    Full Text Available Studies of the relationship between DNA variation and gene expression variation, often referred to as "expression quantitative trait loci (eQTL mapping", have been conducted in many species and resulted in many significant findings. Because of the large number of genes and genetic markers in such analyses, it is extremely challenging to discover how a small number of eQTLs interact with each other to affect mRNA expression levels for a set of co-regulated genes. We present a Bayesian method to facilitate the task, in which co-expressed genes mapped to a common set of markers are treated as a module characterized by latent indicator variables. A Markov chain Monte Carlo algorithm is designed to search simultaneously for the module genes and their linked markers. We show by simulations that this method is more powerful for detecting true eQTLs and their target genes than traditional QTL mapping methods. We applied the procedure to a data set consisting of gene expression and genotypes for 112 segregants of S. cerevisiae. Our method identified modules containing genes mapped to previously reported eQTL hot spots, and dissected these large eQTL hot spots into several modules corresponding to possibly different biological functions or primary and secondary responses to regulatory perturbations. In addition, we identified nine modules associated with pairs of eQTLs, of which two have been previously reported. We demonstrated that one of the novel modules containing many daughter-cell expressed genes is regulated by AMN1 and BPH1. In conclusion, the Bayesian partition method which simultaneously considers all traits and all markers is more powerful for detecting both pleiotropic and epistatic effects based on both simulated and empirical data.

  9. Network-based group variable selection for detecting expression quantitative trait loci (eQTL

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    Zhang Xuegong

    2011-06-01

    Full Text Available Abstract Background Analysis of expression quantitative trait loci (eQTL aims to identify the genetic loci associated with the expression level of genes. Penalized regression with a proper penalty is suitable for the high-dimensional biological data. Its performance should be enhanced when we incorporate biological knowledge of gene expression network and linkage disequilibrium (LD structure between loci in high-noise background. Results We propose a network-based group variable selection (NGVS method for QTL detection. Our method simultaneously maps highly correlated expression traits sharing the same biological function to marker sets formed by LD. By grouping markers, complex joint activity of multiple SNPs can be considered and the dimensionality of eQTL problem is reduced dramatically. In order to demonstrate the power and flexibility of our method, we used it to analyze two simulations and a mouse obesity and diabetes dataset. We considered the gene co-expression network, grouped markers into marker sets and treated the additive and dominant effect of each locus as a group: as a consequence, we were able to replicate results previously obtained on the mouse linkage dataset. Furthermore, we observed several possible sex-dependent loci and interactions of multiple SNPs. Conclusions The proposed NGVS method is appropriate for problems with high-dimensional data and high-noise background. On eQTL problem it outperforms the classical Lasso method, which does not consider biological knowledge. Introduction of proper gene expression and loci correlation information makes detecting causal markers more accurate. With reasonable model settings, NGVS can lead to novel biological findings.

  10. Resolving candidate genes of mouse skeletal muscle QTL via RNA-Seq and expression network analyses

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    Lionikas Arimantas

    2012-11-01

    Full Text Available Abstract Background We have recently identified a number of Quantitative Trait Loci (QTL contributing to the 2-fold muscle weight difference between the LG/J and SM/J mouse strains and refined their confidence intervals. To facilitate nomination of the candidate genes responsible for these differences we examined the transcriptome of the tibialis anterior (TA muscle of each strain by RNA-Seq. Results 13,726 genes were expressed in mouse skeletal muscle. Intersection of a set of 1061 differentially expressed transcripts with a mouse muscle Bayesian Network identified a coherent set of differentially expressed genes that we term the LG/J and SM/J Regulatory Network (LSRN. The integration of the QTL, transcriptome and the network analyses identified eight key drivers of the LSRN (Kdr, Plbd1, Mgp, Fah, Prss23, 2310014F06Rik, Grtp1, Stk10 residing within five QTL regions, which were either polymorphic or differentially expressed between the two strains and are strong candidates for quantitative trait genes (QTGs underlying muscle mass. The insight gained from network analysis including the ability to make testable predictions is illustrated by annotating the LSRN with knowledge-based signatures and showing that the SM/J state of the network corresponds to a more oxidative state. We validated this prediction by NADH tetrazolium reductase staining in the TA muscle revealing higher oxidative potential of the SM/J compared to the LG/J strain (p Conclusion Thus, integration of fine resolution QTL mapping, RNA-Seq transcriptome information and mouse muscle Bayesian Network analysis provides a novel and unbiased strategy for nomination of muscle QTGs.

  11. QTL and candidate gene mapping for polyphenolic composition in apple fruit

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    Chagné David

    2012-01-01

    Full Text Available Abstract Background The polyphenolic products of the phenylpropanoid pathway, including proanthocyanidins, anthocyanins and flavonols, possess antioxidant properties that may provide health benefits. To investigate the genetic architecture of control of their biosynthesis in apple fruit, various polyphenolic compounds were quantified in progeny from a 'Royal Gala' × 'Braeburn' apple population segregating for antioxidant content, using ultra high performance liquid chromatography of extracts derived from fruit cortex and skin. Results Construction of genetic maps for 'Royal Gala' and 'Braeburn' enabled detection of 79 quantitative trait loci (QTL for content of 17 fruit polyphenolic compounds. Seven QTL clusters were stable across two years of harvest and included QTLs for content of flavanols, flavonols, anthocyanins and hydroxycinnamic acids. Alignment of the parental genetic maps with the apple whole genome sequence in silico enabled screening for co-segregation with the QTLs of a range of candidate genes coding for enzymes in the polyphenolic biosynthetic pathway. This co-location was confirmed by genetic mapping of markers derived from the gene sequences. Leucoanthocyanidin reductase (LAR1 co-located with a QTL cluster for the fruit flavanols catechin, epicatechin, procyanidin dimer and five unknown procyanidin oligomers identified near the top of linkage group (LG 16, while hydroxy cinnamate/quinate transferase (HCT/HQT co-located with a QTL for chlorogenic acid concentration mapping near the bottom of LG 17. Conclusion We conclude that LAR1 and HCT/HQT are likely to influence the concentration of these compounds in apple fruit and provide useful allele-specific markers for marker assisted selection of trees bearing fruit with healthy attributes.

  12. Mapping QTL associated with Verticillium dahliae resistance in the cultivated strawberry (Fragaria × ananassa)

    OpenAIRE

    L Antanaviciute; Šurbanovski, N; Harrison, N.; K J McLeary; Simpson, D. W.; Wilson, F.; Sargent, D.J.; Harrison, R. J.

    2015-01-01

    A biparental cross of octoploid strawberry segregating for resistance to Verticillium dahliae, the causative agent of Verticillium wilt, was screened under field conditions for three seasons. Average wilt scores were significantly associated with multiple QTL, which were mostly significant across all years. Markers significantly associated with the traits were used to screen material with known wilt resistance and susceptibility phenotypes. A clear and statistically significant relationship w...

  13. Vacuolar invertase regulates elongation of Arabidopsis thaliana roots as revealed by QTL and mutant analysis

    OpenAIRE

    Sergeeva, L.I.; Keurentjes, J. J. B.; Bentsink, L.; Vonk, J.; Plas, van der, M..; Koornneef, M; Vreugdenhil, D.

    2006-01-01

    The possible role of the sucrose-splitting enzymes sucrose synthase and invertase in elongating roots and hypocotyls of Arabidopsis was tested by using a combination of histochemical methods and quantitative trait locus (QTL) analysis. Lengths of roots and hypocotyls correlated better with invertase activities than with sucrose synthase activities. The highest correlations were observed with activities in the elongating zones of roots. The genetic basis of these correlations was studied by us...

  14. A Complete Solution for Dissecting Pure Main and Epistatic Effects of QTL in Triple Testcross Design

    OpenAIRE

    He, Xiao-Hong; Zhang, Yuan-Ming

    2011-01-01

    Epistasis plays an important role in genetics, evolution and crop breeding. To detect the epistasis, triple test cross (TTC) design had been developed several decades ago. Classical procedures for the TTC design use only linear transformations Z1, Z2 and Z3, calculated from the TTC family means of quantitative trait, to infer the nature of the collective additive, dominance and epistatic effects of all the genes. Although several quantitative trait loci (QTL) mapping approaches in the TTC des...

  15. Mapping QTL influencing gastrointestinal nematode burden in Dutch Holstein-Friesian dairy cattle

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    Georges Michel

    2009-03-01

    Full Text Available Abstract Background Parasitic gastroenteritis caused by nematodes is only second to mastitis in terms of health costs to dairy farmers in developed countries. Sustainable control strategies complementing anthelmintics are desired, including selective breeding for enhanced resistance. Results and Conclusion To quantify and characterize the genetic contribution to variation in resistance to gastro-intestinal parasites, we measured the heritability of faecal egg and larval counts in the Dutch Holstein-Friesian dairy cattle population. The heritability of faecal egg counts ranged from 7 to 21% and was generally higher than for larval counts. We performed a whole genome scan in 12 paternal half-daughter groups for a total of 768 cows, corresponding to the ~10% most and least infected daughters within each family (selective genotyping. Two genome-wide significant QTL were identified in an across-family analysis, respectively on chromosomes 9 and 19, coinciding with previous findings in orthologous chromosomal regions in sheep. We identified six more suggestive QTL by within-family analysis. An additional 73 informative SNPs were genotyped on chromosome 19 and the ensuing high density map used in a variance component approach to simultaneously exploit linkage and linkage disequilibrium in an initial inconclusive attempt to refine the QTL map position.

  16. The application of the entropy-based statistic for genomic association study of QTL

    Institute of Scientific and Technical Information of China (English)

    Yang Xiang; Yumei Li; Zaiming Liu; Zhenqiu Sun

    2008-01-01

    An entropy-based statistic TPE has been proposed for genomic association study for disease-susceptibility locus.The statistic TPE may be directly adopted and/or extended to quantitative-trait locus (QTL)mapping for quantitative traits.In this article,the statistic TPE was extended and applied to quantitative trait for association analysis of QTL by means of selective genotyping.The statistical properties (the type I error rate and the power) were examined under a range of parameters and population-sampling strategies (e.g.,various genetic models,various heritabilities,and various sample-selection threshold values) by simulation studies.The results indicated that the statistic Tee is robust and powerful for genomic association study of QTL.A simulation study based on the haplotype frequencies of 10 single nucleotide polymorphisms (SNPs) of angiotensin-I converting enzyme genes was conducted to evaluate the performance of the statistic TPE for genetic association study.

  17. Advanced technologies for genomic analysis in farm animals and its application for QTL mapping.

    Science.gov (United States)

    Hu, Xiaoxiang; Gao, Yu; Feng, Chungang; Liu, Qiuyue; Wang, Xiaobo; Du, Zhuo; Wang, Qingsong; Li, Ning

    2009-06-01

    Rapid progress in farm animal breeding has been made in the last few decades. Advanced technologies for genomic analysis in molecular genetics have led to the identification of genes or markers associated with genes that affect economic traits. Molecular markers, large-insert libraries and RH panels have been used to build the genetic linkage maps, physical maps and comparative maps in different farm animals. Moreover, EST sequencing, genome sequencing and SNPs maps are helping us to understand how genomes function in various organisms and further areas will be studied by DNA microarray technologies and proteomics methods. Because most economically important traits in farm animals are controlled by multiple genes and the environment, the main goal of genome research in farm animals is to map and characterize genes determining QTL. There are two main strategies to identify trait loci, candidate gene association tests and genome scan approaches. In recent years, some new concepts, such as RNAi, miRNA and eQTL, have been introduced into farm animal research, especially for QTL mapping and finding QTN. Several genes that influence important traits have already been identified or are close to being identified, and some of them have been applied in farm animal breeding programs by marker-assisted selection.

  18. Association studies in QTL regions linked to bovine trypanotolerance in a West African crossbred population.

    Science.gov (United States)

    Dayo, G K; Gautier, M; Berthier, D; Poivey, J P; Sidibe, I; Bengaly, Z; Eggen, A; Boichard, D; Thevenon, S

    2012-04-01

    African animal trypanosomosis is a parasitic blood disease transmitted by tsetse flies and is widespread in sub-Saharan Africa. West African taurine breeds have the ability, known as trypanotolerance, to limit parasitaemia and anaemia and remain productive in enzootic areas. Several quantitative trait loci (QTL) underlying traits related to trypanotolerance have been identified in an experimentally infected F(2) population resulting from a cross between taurine and zebu cattle. Although this information is highly valuable, the QTL remain to be confirmed in populations subjected to natural conditions of infection, and the corresponding regions need to be refined. In our study, 360 West African cattle were phenotyped for the packed cell volume control under natural conditions of infection in south-western Burkina Faso. Phenotypes were assessed by analysing data from previous cattle monitored over 2 years in an area enzootic for trypanosomosis. We further genotyped for 64 microsatellite markers mapping within four previously reported QTL on BTA02, BTA04, BTA07 and BTA13. These data enabled us to estimate the heritability of the phenotype using the kinship matrix between individuals computed from genotyping data. Thus, depending on the estimators considered and the method used, the heritability of anaemia control ranged from 0.09 to 0.22. Finally, an analysis of association identified an allele of the MNB42 marker on BTA04 as being strongly associated with anaemia control, and a candidate gene, INHBA, as being close to that marker. PMID:22404348

  19. QTL affecting fitness of hybrids between wild and cultivated soybeans in experimental fields.

    Science.gov (United States)

    Kuroda, Yosuke; Kaga, Akito; Tomooka, Norihiko; Yano, Hiroshi; Takada, Yoshitake; Kato, Shin; Vaughan, Duncan

    2013-07-01

    The objective of this study was to identify quantitative trait loci (QTL) affecting fitness of hybrids between wild soybean (Glycine soja) and cultivated soybean (Glycine max). Seed dormancy and seed number, both of which are important for fitness, were evaluated by testing artificial hybrids of G. soja × G. max in a multiple-site field trial. Generally, the fitness of the F1 hybrids and hybrid derivatives from self-pollination was lower than that of G. soja due to loss of seed dormancy, whereas the fitness of hybrid derivatives with higher proportions of G. soja genetic background was comparable with that of G. soja. These differences were genetically dissected into QTL for each population. Three QTLs for seed dormancy and one QTL for total seed number were detected in the F2 progenies of two diverse cross combinations. At those four QTLs, the G. max alleles reduced seed number and severely reduced seed survival during the winter, suggesting that major genes acquired during soybean adaptation to cultivation have a selective disadvantage in natural habitats. In progenies with a higher proportion of G. soja genetic background, the genetic effects of the G. max alleles were not expressed as phenotypes because the G. soja alleles were dominant over the G. max alleles. Considering the highly inbreeding nature of these species, most hybrid derivatives would disappear quickly in early self-pollinating generations in natural habitats because of the low fitness of plants carrying G. max alleles.

  20. ANÁLISIS DE ASOCIACIÓN DE CARACTERES EN EL CULTIVO DE ARROZ (Oryza sativa L. EMPLEANDO TÉCNICAS MULTIVARIADAS

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    R. Morejón

    2005-01-01

    Full Text Available El trabajo se desarrolló en áreas de la Estación Experimental del Arroz "Los Palacios", perteneciente al Instituto Nacional de Ciencias Agrícolas (INCA, con el objetivo de proporcionar a las personas encargadas del manejo y la conservación de las colecciones de recursos fitogenéticos las herramientas necesarias para el análisis de la asociación de caracteres en genotipos de arroz y, de esta forma, obtener la mayor información y comprensión posible de estos a partir de técnicas multivariadas. Las asociaciones entre variables que fueron identificadas por la matriz de correlaciones, por el grado de discriminación identificado en el Análisis de Componentes Principales y confirmadas por el Análisis de Conglomerados para los 65 genotipos de arroz utilizados, constituyen una información de utilidad para los programas de mejoramiento genético en este cultivo.

  1. Variabilidade genética e correlações entre caracteres de feijão-caupi = Genetic variability and correlations between characters in cowpea

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    Agenor Martinho Correa

    2015-03-01

    Full Text Available Objetivou-se com este trabalho estimar a variabilidade genética em uma população de feijão-caupi com base em caracteres de interesse agronômico e definir caracteres a serem utilizados na seleção de genótipos superiores. O experimento foi conduzido na Universidade Estadual de Mato Grosso do Sul, em Aquidauana, no período da “seca” do ano de 2009. Os tratamentos consistiram de 20 genótipos de feijão-caupi, sendo 11 cultivares (Canapuzinho, Canapuzinho-2, Inhuma, Pingo-de-ouro-1-2, Pingo-de-ouro-2, Paulistinha, Patativa, BRS-Paraguassu, BRS-Milênio, BR17-Gurguéia e BRS-Marataoã e 9 linhagens (MNC99- 510F-16-1, MNC99-510F-16-3, MNC99-537F-14-2, MNC01-611F-11, MNC01-614F-15, MNC01-631F-11, MNC01-631F-15, MNC01-631F-20-5, MNC01-649E-2. O delineamento experimental adotado foi o de blocos inteiramente casualizados, com 4 repetições. Foram avaliados os caracteres: início de florescimento, início de maturação, massa de 100 grãos, comprimento de vagem verde, massa de vagem verde, número de grãos por vagem e produtividade de grãos secos. Para verificar a existência de variabilidade entre os genótipos, os dados foram submetidos à análise de variância pelo teste F. Posteriormente, foram determinados os seguintes parâmetros genéticos: variância ambiental, fenotípica e genotípica; coeficiente de variação experimental e genotípico; coeficiente de determinação genotípico; quociente b; correlações ambientais, fenotípicas e genotípicas. A população apresenta variabilidade genética e potencial para o melhoramento genético. Com base nos parâmetros avaliados, os programas de melhoramento genético em feijão-caupi podem realizar a seleção de genótipos baseados nos caracteres: dias para maturação, massa verde de vagens, número de grãos por vagem e produtividade de grãos. = Abstract: The study aimed to estimate the genetic variability in a population of cowpea based on agronomically important traits and see

  2. DIVERSIDAD DE MAÍCES CRIOLLOS DE NUEVO LEÓN, MÉXICO, MEDIANTE AFLP Y CARACTERES MORFOLÓGICOS

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    Gilberto Rodr\\u00EDguez-P\\u00E9rez

    2012-01-01

    Full Text Available Diversidad de maíces criollos de Nuevo León, México, mediante AFLP y caracteres morfológicos. El presente trabajo tuvo como objetivo identifi car la variabilidad fenotípica y molecular entre poblaciones de maíz Pinto Amarillo y Liebre en Nuevo León, México. En la caracterización fenotípica se estableció un experimento en primavera 2009. Las variables registradas fueron altura de planta, días a fl oración masculina y femenina, número de hileras por mazorca, granos por hilera de mazorca, longitud y diámetro de mazorca. Para la caracterización molecular, las treinta poblaciones se sembraron en febrero del 2010 en macetas con peat-moss, después de treinta días se colectaron todas las hojas de la plántula, para la técnica AFLP; se realizó un análisis conglomerados utilizando el método de UPGMA. Se identifi caron tres grupos; doce poblaciones de Pinto Amarillo y tres de Liebre agrupando genotipos comunes. Los grupos se asociaron más a la raza de maíz que al lugar de colectas.

  3. Quantitative ultrasound for the detection and management of osteoporosis Ultrasonido cuantitativo para la detección y manejo de osteoporosis

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    Didier Hans

    2009-01-01

    Full Text Available Quantitative ultrasound (QUS appears to be developing into an acceptable, low-cost and readily-accessible alternative to dual X-ray absorptiometry (DXA measurements of bone mineral density (BMD in the detection and management of osteoporosis. Perhaps the major difficulty with their widespread use is that many different QUS devices exist that differ substantially from each other, in terms of the parameters they measure and the strength of empirical evidence supporting their use. But another problem is that virtually no data exist outside of Caucasian or Asian populations. In general, heel QUS appears to be most tested and most effective. Some, but not all heel QUS devices are effective assessing fracture risk in some, but not all populations, the evidence being strongest for Caucasian females > 55 years old, though some evidence exists for Asian females > 55 and for Caucasian and Asian males > 70. Certain devices may allow to estimate the likelihood of osteoporosis, but very limited evidence exists supporting QUS use during the initiation or monitoring of osteoporosis treatment. Likely, QUS is most effective when combined with an assessment of clinical risk factors (CRF; with DXA reserved for individuals who are not identified as either high or low risk using QUS and CRF. However, monitoring and maintenance of test and instrument accuracy, precision and reproducibility are essential if QUS devices are to be used in clinical practice; and further scientific research in non-Caucasian, non-Asian populations clearly is compulsory to validate this tool for more widespread use.El ultrasonido cuantitativo (QUS es una alternativa para la detección y manejo de la osteoporosis de bajo costo y uso práctico, si se compara con las densitometrías de rayos X de doble haz de baja energía (DXA que determinan densidad mineral ósea (BMD. La mayor dificultad para el uso generalizado del QUS por un lado es que existen muchos instrumentos que son

  4. Genotype x environment interaction of agronomic and processing quality traits in potato Interação genótipo x ambiente em caracteres agronômicos e qualidade de processamento em batata

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    Lizete Augustin

    2012-03-01

    foram: i identificar clones com alto potencial produtivo e com qualidade industrial para as condições de cultivo de outono e de primavera na região norte/nordeste do RS; ii estimar os efeitos da interação genótipo x ambiente e de ambiente na expressão dos caracteres agronômicos e de qualidade de processamento, visando estabelecer a melhor estratégia para o melhoramento. Nesse trabalho, 170 clones de nove famílias clonais foram desenvolvidos e comparados às cultivares Atlantic, Baronesa, Catucha, Ciclamen, Hertha, Lady Roseta, Macaca, Monalisa e Vivaldi e, ao clone SMIJ 461-1, no outono e na primavera de 2006, em Passo Fundo, região norte do Rio Grande do Sul. Os caracteres avaliados foram número de tubérculos por planta, massa fresca média de tubérculos, produtividade por planta, profundidade dos olhos, teor de massa seca e coloração dos chips. Foi observada interação genótipo x ambiente significativa para todos os caracteres sendo os caracteres de qualidade de processamento, principalmente coloração dos chips, mais influenciados pela época de cultivo. A expressão do potencial genético dos clones, para os caracteres relacionados à produção, foi maximizada na primavera. Foi possível identificar clones que expressaram caracteres superiores nos dois cultivos. Os caracteres profundidade de olhos e massa seca apresentaram alta correlação entre as duas épocas de cultivo, podendo ser selecionados tanto no outono quanto na primavera.

  5. Search for QTL affecting the shape of the egg laying curve of the Japanese quail

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    Gourichon David

    2006-05-01

    Full Text Available Abstract Background Egg production is of critical importance in birds not only for their reproduction but also for human consumption as the egg is a highly nutritive and balanced food. Consequently, laying in poultry has been improved through selection to increase the total number of eggs laid per hen. This number is the cumulative result of the oviposition, a cyclic and repeated process which leads to a pattern over time (the egg laying curve which can be modelled and described individually. Unlike the total egg number which compounds all variations, the shape of the curve gives information on the different phases of egg laying, and its genetic analysis using molecular markers might contribute to understand better the underlying mechanisms. The purpose of this study was to perform the first QTL search for traits involved in shaping the egg laying curve, in an F2 experiment with 359 female Japanese quail. Results Eight QTL were found on five autosomes, and six of them could be directly associated with egg production traits, although none was significant at the genome-wide level. One of them (on CJA13 had an effect on the first part of the laying curve, before the production peak. Another one (on CJA06 was related to the central part of the curve when laying is maintained at a high level, and the four others (on CJA05, CJA10 and CJA14 acted on the last part of the curve where persistency is determinant. The QTL for the central part of the curve was mapped at the same position on CJA06 than a genome-wide significant QTL for total egg number detected previously in the same F2. Conclusion Despite its limited scope (number of microsatellites, size of the phenotypic data set, this work has shown that it was possible to use the individual egg laying data collected daily to find new QTL which affect the shape of the egg laying curve. Beyond the present results, this new approach could also be applied to longitudinal traits in other species, like growth

  6. Investigation of QTL regions on Chromosome 17 for genes associated with meat color in the pig.

    Science.gov (United States)

    Fan, B; Glenn, K L; Geiger, B; Mileham, A; Rothschild, M F

    2008-08-01

    Previous studies have uncovered several significant quantitative trait loci (QTL) relevant to meat colour traits mapped at the end of SSC17 in the pig. Furthermore, results released from the porcine genome sequencing project have identified genes underlying the entire QTL regions and can further contribute to mining the region for likely causative genes. Ten protein coding genes or novel transcripts located within the QTL regions were screened for single nucleotide polymorphisms (SNPs). Linkage mapping and association studies were carried out in the ISU Berkshire x Yorkshire (B x Y) pig resource family. The total length of the new SSC17 linkage map was 126.6 cM and additional markers including endothelin 3 (EDN3) and phosphatase and actin regulator 3 (PHACTR3) genes were assigned at positions 119.4 cM and 122.9 cM, respectively. A new QTL peak was noted at approximately 120 cM, close to the EDN3 gene, and for some colour traits QTL exceeded the 5% chromosome-wise significance threshold. The association analyses in the B x Y family showed that the EDN3 BslI and PHACTR3 PstI polymorphisms were strongly associated with the subjective colour score and objective colour reflectance measures in the loin, as well as average drip loss percentage and pH value. The RNPC1 DpnII and CTCFL HpyCH4III polymorphisms were associated with some meat colour traits. No significant association between CBLN4, TFAP2C, and four novel transcripts and meat colour traits were detected. The association analyses conducted in one commercial pig line found that both EDN3 BslI and PHACTR3 PstI polymorphisms were associated with meat colour reflectance traits such as centre loin hue angle and Minolta Lightness score. The present findings suggested that the EDN3 and PHACTR3 genes might have potential effects on meat colour in pigs, and molecular mechanisms of their functions are worth exploring.

  7. Sodium exclusion QTL associated with improved seedling growth in bread wheat under salinity stress.

    Science.gov (United States)

    Genc, Y; Oldach, K; Verbyla, A P; Lott, G; Hassan, M; Tester, M; Wallwork, H; McDonald, G K

    2010-09-01

    Worldwide, dryland salinity is a major limitation to crop production. Breeding for salinity tolerance could be an effective way of improving yield and yield stability on saline-sodic soils of dryland agriculture. However, this requires a good understanding of inheritance of this quantitative trait. In the present study, a doubled-haploid bread wheat population (Berkut/Krichauff) was grown in supported hydroponics to identify quantitative trait loci (QTL) associated with salinity tolerance traits commonly reported in the literature (leaf symptoms, tiller number, seedling biomass, chlorophyll content, and shoot Na(+) and K(+) concentrations), understand the relationships amongst these traits, and determine their genetic value for marker-assisted selection. There was considerable segregation within the population for all traits measured. With a genetic map of 527 SSR-, DArT- and gene-based markers, a total of 40 QTL were detected for all seven traits. For the first time in a cereal species, a QTL interval for Na(+) exclusion (wPt-3114-wmc170) was associated with an increase (10%) in seedling biomass. Of the five QTL identified for Na(+) exclusion, two were co-located with seedling biomass (2A and 6A). The 2A QTL appears to coincide with the previously reported Na(+) exclusion locus in durum wheat that hosts one active HKT1;4 (Nax1) and one inactive HKT1;4 gene. Using these sequences as template for primer design enabled mapping of at least three HKT1;4 genes onto chromosome 2AL in bread wheat, suggesting that bread wheat carries more HKT1;4 gene family members than durum wheat. However, the combined effects of all Na(+) exclusion loci only accounted for 18% of the variation in seedling biomass under salinity stress indicating that there were other mechanisms of salinity tolerance operative at the seedling stage in this population. Na(+) and K(+) accumulation appear under separate genetic control. The molecular markers wmc170 (2A) and cfd080 (6A) are expected to

  8. Effects of Phaseolus vulgaris QTL in controlling host-bacteria interactions under two levels of nitrogen fertilization

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    Souza Alessandra A.

    2000-01-01

    Full Text Available Molecular markers were used to estimate the effect of mineral nitrogen on the phenotypic expression of quantitative trait loci (QTL controlling the number of Rhizobium nodules (NN and resistance to Xanthomonas axonopodis pv. phaseoli in the common bean. Recombinant inbred lines derived from a BAT-93 x Jalo EEP558 cross were grown in a greenhouse in the absence or presence (5 mM NH4NO3 of nitrogen. Resistance to Xanthomonas was assessed as diseased leaf area (DLA and the number of nodules was obtained by direct counting. Analyses of variance were used to detect significant associations between 85 marker loci from 12 linkage groups (LG and quantitative traits. In the absence of nitrogen, 15 and 11 markers, distributed over 7 and 5 LG, showed a significant association with NN and DLA, respectively. The combined percentage of phenotypic variance explained by the marker-loci and QTL associations was 34% for NN and 42% for DLA. In the presence of nitrogen, there were only five significant associations for NN and eight for DLA, which explained 28 and 26% of the total phenotypic variance, respectively. The effects of some QTL were detected only at a certain level of nitrogen. The contribution of parental alleles at two NN QTL was dependent on the level of nitrogen. Four QTL were associated with both the number of Rhizobium nodules and resistance to Xanthomonas, suggesting a common genetic control of responses to bacterial infections in the common bean. Despite the dramatic environmental interactions noted with some QTL, in other cases the phenotypic effects were not affected by the amount of nitrogen. The stability of the latter QTL may be relevant when breeding cultivars adapted to variable soil fertility.

  9. Genetic, physiological, and gene expression analyses reveal that multiple QTL enhance yield of rice mega-variety IR64 under drought.

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    B P Mallikarjuna Swamy

    Full Text Available BACKGROUND: Rice (Oryza sativa L. is a highly drought sensitive crop, and most semi dwarf rice varieties suffer severe yield losses from reproductive stage drought stress. The genetic complexity of drought tolerance has deterred the identification of agronomically relevant quantitative trait loci (QTL that can be deployed to improve rice yield under drought in rice. Convergent evidence from physiological characterization, genetic mapping, and multi-location field evaluation was used to address this challenge. METHODOLOGY/PRINCIPAL FINDINGS: Two pairs of backcross inbred lines (BILs from a cross between drought-tolerant donor Aday Sel and high-yielding but drought-susceptible rice variety IR64 were produced. From six BC4F3 mapping populations produced by crossing the +QTL BILs with the -QTL BILs and IR64, four major-effect QTL--one each on chromosomes 2, 4, 9, and 10--were identified. Meta-analysis of transcriptome data from the +QTL/-QTL BILs identified differentially expressed genes (DEGs significantly associated with QTL on chromosomes 2, 4, 9, and 10. Physiological characterization of BILs showed increased water uptake ability under drought. The enrichment of DEGs associated with root traits points to differential regulation of root development and function as contributing to drought tolerance in these BILs. BC4F3-derived lines with the QTL conferred yield advantages of 528 to 1875 kg ha⁻¹ over IR64 under reproductive-stage drought stress in the targeted ecosystems of South Asia. CONCLUSIONS/SIGNIFICANCE: Given the importance of rice in daily food consumption and the popularity of IR64, the BC4F3 lines with multiple QTL could provide higher livelihood security to farmers in drought-prone environments. Candidate genes were shortlisted for further characterization to confirm their role in drought tolerance. Differential yield advantages of different combinations of the four QTL reported here indicate that future research should include

  10. A general and efficient method for estimating continuous IBD functions for use in genome scans for QTL

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    Carlborg Örjan

    2007-11-01

    Full Text Available Abstract Background Identity by descent (IBD matrix estimation is a central component in mapping of Quantitative Trait Loci (QTL using variance component models. A large number of algorithms have been developed for estimation of IBD between individuals in populations at discrete locations in the genome for use in genome scans to detect QTL affecting various traits of interest in experimental animal, human and agricultural pedigrees. Here, we propose a new approach to estimate IBD as continuous functions rather than as discrete values. Results Estimation of IBD functions improved the computational efficiency and memory usage in genome scanning for QTL. We have explored two approaches to obtain continuous marker-bracket IBD-functions. By re-implementing an existing and fast deterministic IBD-estimation method, we show that this approach results in IBD functions that produces the exact same IBD as the original algorithm, but with a greater than 2-fold improvement of the computational efficiency and a considerably lower memory requirement for storing the resulting genome-wide IBD. By developing a general IBD function approximation algorithm, we show that it is possible to estimate marker-bracket IBD functions from IBD matrices estimated at marker locations by any existing IBD estimation algorithm. The general algorithm provides approximations that lead to QTL variance component estimates that even in worst-case scenarios are very similar to the true values. The approach of storing IBD as polynomial IBD-function was also shown to reduce the amount of memory required in genome scans for QTL. Conclusion In addition to direct improvements in computational and memory efficiency, estimation of IBD-functions is a fundamental step needed to develop and implement new efficient optimization algorithms for high precision localization of QTL. Here, we discuss and test two approaches for estimating IBD functions based on existing IBD estimation algorithms. Our

  11. Linkage mapping and identification of QTL affecting deoxynivalenol (DON) content (Fusarium resistance) in oats (Avena sativa L.).

    Science.gov (United States)

    He, Xinyao; Skinnes, Helge; Oliver, Rebekah E; Jackson, Eric W; Bjørnstad, Asmund

    2013-10-01

    Mycotoxins caused by Fusarium spp. is a major concern on food and feed safety in oats, although Fusarium head blight (FHB) is often less apparent than in other small grain cereals. Breeding resistant cultivars is an economic and environment-friendly way to reduce toxin content, either by the identification of resistance QTL or phenotypic evaluation. Both are little explored in oats. A recombinant-inbred line population, Hurdal × Z595-7 (HZ595, with 184 lines), was used for QTL mapping and was phenotyped for 3 years. Spawn inoculation was applied and deoxynivalenol (DON) content, FHB severity, days to heading and maturity (DH and DM), and plant height (PH) were measured. The population was genotyped with DArTs, AFLPs, SSRs and selected SNPs, and a linkage map of 1,132 cM was constructed, covering all 21 oat chromosomes. A QTL for DON on chromosome 17A/7C, tentatively designated as Qdon.umb-17A/7C, was detected in all experiments using composite interval mapping, with phenotypic effects of 12.2–26.6 %. In addition, QTL for DON were also found on chromosomes 5C, 9D, 13A, 14D and unknown_3, while a QTL for FHB was found on 11A. Several of the DON/FHB QTL coincided with those for DH, DM and/or PH. A half-sib population of HZ595, Hurdal × Z615-4 (HZ615, with 91 lines), was phenotyped in 2011 for validation of QTL found in HZ595, and Qdon.umb-17A/7C was again localized with a phenotypic effect of 12.4 %. Three SNPs closely linked to Qdon.umb-17A/7C were identified in both populations, and one each for QTL on 5C, 11A and 13A were identified in HZ595. These SNPs, together with those yet to be identified, could be useful in marker-assisted selection to pyramiding resistance QTL.

  12. IMPACTO DE LA ELIMINACIÓN DE LOS CAT Y DEL OTORGAMIENTO DE OTROS INCENTIVOS DE POLÍTICA COMERCIAL: UN ANÁLISIS CUANTITATIVO DE EQUILIBRIO GENERAL COMPUTABLE

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    Marco Vinicio Sánchez C.

    2011-08-01

    Full Text Available Es bien sabido por todos que los exportadores de productos no tradicionales que se han beneficiado con el otorgamiento del Certificado de Abono Tributario (CAT, dejarán de hacerlo a partir del año 2000. El objetivo de este artículo es analizar, de una forma cuantitativa, el impacto potencial que la eliminación de dicho incentivo podría tener sobre la producción, el empleo y la generación de ingreso. Complementariamente, se busca determinar los posibles impactos de otros instrumentos como los impuestos a las exportaciones y las tarifas a las importaciones en su papel de incentivos de política comercial para compensar la eliminación de los CAT. Como bien se explica más adelante, la metodología utilizada para desarrollar el análisis cuantitativo es un modelo computable de equilibrio general.

  13. Fine mapping QTL for resistance to VNN disease using a high-density linkage map in Asian seabass.

    Science.gov (United States)

    Liu, Peng; Wang, Le; Wong, Sek-Man; Yue, Gen Hua

    2016-01-01

    Asian seabass has suffered from viral nervous necrosis (VNN) disease. Our previous study has mapped quantitative trait loci (QTL) for resistance to VNN disease. To fine map these QTL and identify causative genes, we identified 6425 single nucleotide polymorphisms (SNPs) from 85 dead and 94 surviving individuals. Combined with 155 microsatellites, we constructed a genetic map consisting of 24 linkage groups (LGs) containing 3000 markers, with an average interval of 1.27 cM. We mapped one significant and three suggestive QTL with phenotypic variation explained (PVE) of 8.3 to 11.0%, two significant and two suggestive QTL with PVE of 7.8 to 10.9%, for resistance in three LGs and survival time in four LGs, respectively. Further analysis one QTL with the largest effect identified protocadherin alpha-C 2-like (Pcdhac2) as the possible candidate gene. Association study in 43 families with 1127 individuals revealed a 6 bp insertion-deletion was significantly associated with disease resistance. qRT-PCR showed the expression of Pcdhac2 was significantly induced in the brain, muscle and skin after nervous necrosis virus (NNV) infection. Our results could facilitate marker-assisted selection (MAS) for resistance to NNV in Asian seabass and set up the basis for functional analysis of the potential causative gene for resistance.

  14. Sequence-based Association Analysis Reveals an MGST1 eQTL with Pleiotropic Effects on Bovine Milk Composition

    Science.gov (United States)

    Littlejohn, Mathew D.; Tiplady, Kathryn; Fink, Tania A.; Lehnert, Klaus; Lopdell, Thomas; Johnson, Thomas; Couldrey, Christine; Keehan, Mike; Sherlock, Richard G.; Harland, Chad; Scott, Andrew; Snell, Russell G.; Davis, Stephen R.; Spelman, Richard J.

    2016-01-01

    The mammary gland is a prolific lipogenic organ, synthesising copious amounts of triglycerides for secretion into milk. The fat content of milk varies widely both between and within species, and recent independent genome-wide association studies have highlighted a milk fat percentage quantitative trait locus (QTL) of large effect on bovine chromosome 5. Although both EPS8 and MGST1 have been proposed to underlie these signals, the causative status of these genes has not been functionally confirmed. To investigate this QTL in detail, we report genome sequence-based imputation and association mapping in a population of 64,244 taurine cattle. This analysis reveals a cluster of 17 non-coding variants spanning MGST1 that are highly associated with milk fat percentage, and a range of other milk composition traits. Further, we exploit a high-depth mammary RNA sequence dataset to conduct expression QTL (eQTL) mapping in 375 lactating cows, revealing a strong MGST1 eQTL underpinning these effects. These data demonstrate the utility of DNA and RNA sequence-based association mapping, and implicate MGST1, a gene with no obvious mechanistic relationship to milk composition regulation, as causally involved in these processes. PMID:27146958

  15. Detecting parent of origin and dominant QTL in a two-generation commercial poultry pedigree using variance component methodology

    Directory of Open Access Journals (Sweden)

    Haley Christopher S

    2009-01-01

    Full Text Available Abstract Introduction Variance component QTL methodology was used to analyse three candidate regions on chicken chromosomes 1, 4 and 5 for dominant and parent-of-origin QTL effects. Data were available for bodyweight and conformation score measured at 40 days from a two-generation commercial broiler dam line. One hundred dams were nested in 46 sires with phenotypes and genotypes on 2708 offspring. Linear models were constructed to simultaneously estimate fixed, polygenic and QTL effects. Different genetic models were compared using likelihood ratio test statistics derived from the comparison of full with reduced or null models. Empirical thresholds were derived by permutation analysis. Results Dominant QTL were found for bodyweight on chicken chromosome 4 and for bodyweight and conformation score on chicken chromosome 5. Suggestive evidence for a maternally expressed QTL for bodyweight and conformation score was found on chromosome 1 in a region corresponding to orthologous imprinted regions in the human and mouse. Conclusion Initial results suggest that variance component analysis can be applied within commercial populations for the direct detection of segregating dominant and parent of origin effects.

  16. Confirmation and fine-mapping of clinical mastitis and somatic cell score QTL in Nordic Holstein cattle.

    Science.gov (United States)

    Sahana, G; Guldbrandtsen, B; Thomsen, B; Lund, M S

    2013-12-01

    A genome-wide association study of 2098 progeny-tested Nordic Holstein bulls genotyped for 36 387 SNPs on 29 autosomes was conducted to confirm and fine-map quantitative trait loci (QTL) for mastitis traits identified earlier using linkage analysis with sparse microsatellite markers in the same population. We used linear mixed model analysis where a polygenic genetic effect was fitted as a random effect and single SNPs were successively included as fixed effects in the model. We detected 143 SNP-by-trait significant associations (P mastitis-related traits. Among them, 21 SNP-by-trait combinations exceeded the genome-wide significant threshold. For 12 chromosomes, both the present association study and the previous linkage study detected QTL, and of these, six were in the same chromosomal locations. Strong associations of SNPs with mastitis traits were observed on bovine autosomes 6, 13, 14 and 20. Possible candidate genes for these QTL were identified. Identification of SNPs in linkage disequilibrium with QTL will enable marker-based selection for mastitis resistance. The candidate genes identified should be further studied to detect candidate polymorphisms underlying these QTL.

  17. Quantitative trait locus analysis of seed germination and seedling vigour in Brassica rapa reveals QTL hotspots and epistatic interactions

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    Ram Kumar Basnet

    2015-12-01

    Full Text Available The genetic basis of seed germination and seedling vigour is largely unknown in Brassica species. We performed a study to evaluate the genetic basis of these important traits in a B. rapa doubled haploid population from a cross of a yellow-seeded oil-type yellow sarson and a black-seeded vegetable-type pak choi. We identified 26 QTL regions across all 10 linkage groups for traits related to seed weight, seed germination and seedling vigour under non-stress and salt stress conditions illustrating the polygenic nature of these traits. QTLs for multiple traits co-localized and we identified eight hotspots for quantitative trait loci (QTL of seed weight, seed germination, and root and shoot lengths. A QTL hotspot for seed germination on A02 mapped at the B. rapa FLOWERING LOCUS C (BrFLC2. Another hotspot on A05 with salt stress specific QTLs co-located with the B. rapa FATTY ACID DESATURASE 2 (BrFAD2 locus. Epistatic interactions were observed between QTL hotspots for seed germination on A02 and A10 and with a salt tolerance QTL on A05. These results contribute to the understanding of the genetics of seed quality and seeding vigour in B. rapa and can offer tools for Brassica breeding.

  18. Seleção em gerações iniciais para caracteres agronômicos em batata Selection in early generations to agronomic characters in potatoes

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    Giovani O da Silva

    2011-12-01

    Full Text Available A presente revisão objetivou fazer algumas considerações sobre a seleção nas gerações iniciais (geração de plântula, primeira e segunda geração clonal e as implicações no melhoramento genético de batata. Em batata, onde milhares de plântulas têm que ser avaliadas para possibilitar a identificação de um genótipo superior e, considerando os elevados custos com o processo de melhoramento da cultura, é imprescindível o aprimoramento das técnicas de seleção pela utilização de informações provenientes da experimentação. A exclusão dos genótipos inferiores o mais cedo possível, por meio da seleção em gerações iniciais, evita que genótipos inferiores sejam mantidos nos ensaios de campo, proporcionando reduções consideráveis de custos pela menor utilização de insumos, área de plantio e mão de obra. Apesar de serem encontrados na literatura consultada alguns casos indicando a baixa eficiência na seleção de genótipos de batata em gerações precoces, principalmente para caracteres quantitativos; pode-se também observar situações onde este tipo de seleção mostrou-se eficiente. Pôde-se concluir que há evidências que a seleção nas gerações iniciais, começando na geração de plântula, seja uma opção viável, possibilitando maior versatilidade e eficiência aos programas de melhoramento de batata. No entanto, devem ser definidos os caracteres mais eficazes de serem selecionados e a pressão de seleção a ser aplicada, para não correr o risco de eliminar materiais que deveriam ser mantidos na população.This review aimed to make some considerations about the selection in early generations (seedling generation, first and second clonal generations and its implications for the potato breeding, which requires the evaluation of thousands of seedlings in order to identify the best genotypes. Considering the high costs of the breeding process, the constant improvement of the selection techniques by

  19. Estudio de razas de palomas españolas a partir del análisis de caracteres morfológicos cualitativos

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    Pere-Miquel Parés C

    2010-12-01

    Full Text Available Objetivo. Evaluar una posible base morfológica que sustente una clasificación racional y no arbitraria de razas de palomo, se estudió la relación fenética entre diferentes razas. Materiales y métodos. Se sometieron para su estudio morfológico comparativo un total de 29 razas españolas de palomas, considerándose cada raza como Operational Taxonomic Unit (OTU y agrupadas a priori en grupos de afinidad funcional y morfológica: buchones, razas catalanas, razas baleáricas, palomos de morfología. Se realizó un análisis de coordenadas (ACo sobre la base de la matriz de distancias de similitud de Gower entre OTUs a partir del análisis de 29 caracteres. A fin de conocer cuáles eran las variables responsables de las similitudes y/o disimilitudes observadas se aplicó igualmente un análisis de correspondencia (ACrr. Resultados. En el ACo se reflejó que la variabilidad representada por los dos primeros vectores Eigen no es alta. El ACrr demostró que muchas variables están fuertemente correlacionadas. Conclusiones. La distribución de las razas en el ACo apunta a una distribución bastante buena en los 4 grupos establecidos. El ACrr mostró que las variables más discriminantes pueden ser reducidas a nueve: grosor y longitud del pico, desarrollo de las carúnculas nasales y oculares, longitud del cuello, tamaño y colgado de buche, longitud relativa de la cola y posición de las alas en reposo respecto de la cola.

  20. Effects of the number of markers per haplotype and clustering of haplotypes on the accuracy of QTL mapping and prediction of genomic breeding values

    NARCIS (Netherlands)

    Calus, M.P.L.; Meuwissen, T.H.E.; Windig, J.J.; Knol, E.F.; Schrooten, C.; Vereijken, A.L.J.; Veerkamp, R.F.

    2009-01-01

    The aim of this paper was to compare the effect of haplotype definition on the precision of QTL-mapping and on the accuracy of predicted genomic breeding values. In a multiple QTL model using identity-by-descent (IBD) probabilities between haplotypes, various haplotype definitions were tested i.e. i

  1. Integration of QTL detection and marker assisted selection for improving resistance to Fusarium head blight and important agronomic traits in wheat

    Institute of Scientific and Technical Information of China (English)

    Chao; Lv; Yanxia; Song; Lifeng; Gao; Qin; Yao; Ronghua; Zhou; Rugen; Xu; Jizeng; Jia

    2014-01-01

    Fusarium head blight(FHB), caused by Fusarium graminearum, is one of the most destructive wheat(Triticum aestivum L.) diseases worldwide. Identification of quantitative trait loci(QTL) conferring FHB resistance followed by marker assisted selection(MAS) is an efficient approach to breed FHB-resistant varieties. In this study, 38 additive QTL and 18 pairs of epistatic QTL for FHB resistance were detected in four environments using a population of recombinant inbred lines(RILs) derived from varieties Neixiang 188 and Yanzhan 1. Six QTL clusters were located on chromosomes 2D, 4B, 4D, 5A, 5D and 7B, suggesting possible polytrophic functions. Six elite lines with good FHB resistance and agronomic traits were selected from the same population using the associated markers. Our results suggest that MAS of multiple QTL will be effective and efficient in wheat breeding.

  2. Integration of QTL detection and marker assisted selection for improving resistance to Fusarium head blight and important agronomic traits in wheat

    Directory of Open Access Journals (Sweden)

    Chao Lv

    2014-02-01

    Full Text Available Fusarium head blight (FHB, caused by Fusarium graminearum, is one of the most destructive wheat (Triticum aestivum L. diseases worldwide. Identification of quantitative trait loci (QTL conferring FHB resistance followed by marker assisted selection (MAS is an efficient approach to breed FHB-resistant varieties. In this study, 38 additive QTL and 18 pairs of epistatic QTL for FHB resistance were detected in four environments using a population of recombinant inbred lines (RILs derived from varieties Neixiang 188 and Yanzhan 1. Six QTL clusters were located on chromosomes 2D, 4B, 4D, 5A, 5D and 7B, suggesting possible polytrophic functions. Six elite lines with good FHB resistance and agronomic traits were selected from the same population using the associated markers. Our results suggest that MAS of multiple QTL will be effective and efficient in wheat breeding.

  3. Identification of Quantitative Trait Loci (QTL) and Candidate Genes for Cadmium Tolerance in Populus

    Energy Technology Data Exchange (ETDEWEB)

    Induri, Brahma R [West Virginia University; Ellis, Danielle R [West Virginia University; Slavov, Gancho [West Virginia University; Yin, Tongming [ORNL; Muchero, Wellington [ORNL; Tuskan, Gerald A [ORNL; DiFazio, Stephen P [West Virginia University

    2012-01-01

    Knowledge of genetic variation in response of Populus to heavy metals like cadmium (Cd) is an important step in understanding the underlying mechanisms of tolerance. In this study, a pseudo-backcross pedigree of Populus trichocarpa and Populus deltoides was characterized for Cd exposure. The pedigree showed significant variation for Cd tolerance thus enabling the identification of relatively tolerant and susceptible genotypes for intensive characterization. A total of 16 QTLs at logarithm of odds (LOD) ratio > 2.5, were found to be associated with total dry weight, its components, and root volume. Four major QTLs for total dry weight were mapped to different linkage groups in control (LG III) and Cd conditions (LG XVI) and had opposite allelic effects on Cd tolerance, suggesting that these genomic regions were differentially controlled. The phenotypic variation explained by Cd QTL for all traits under study varied from 5.9% to 11.6% and averaged 8.2% across all QTL. Leaf Cd contents also showed significant variation suggesting the phytoextraction potential of Populus genotypes, though heritability of this trait was low (0.22). A whole-genome microarray study was conducted by using two genotypes with extreme responses for Cd tolerance in the above study and differentially expressed genes were identified. Candidate genes including CAD2 (CADMIUM SENSITIVE 2), HMA5 (HEAVY METAL ATPase5), ATGTST1 (Arabidopsis thaliana Glutathione S-Transferase1), ATGPX6 (Glutathione peroxidase 6), and ATMRP 14 (Arabidopsis thaliana Multidrug Resistance associated Protein 14) were identified from QTL intervals and microarray study. Functional characterization of these candidate genes could enhance phytoremediation capabilities of Populus.

  4. QTL consistency for agronomic traits across three generations and potential applications in popcorn

    Institute of Scientific and Technical Information of China (English)

    DONG Yong-bin; ZHANG Zhong-wei; SHI Qing-ling; WANG Qi-lei; ZHOU Qiang; DENG Fei; MA Zhi-yan; QIAO Da-he; LI Yu-ling

    2015-01-01

    Favorable agronomic traits are important to improve productivity of popcorn. In this study, a recombinant inbred line (RIL) population consisting of 258 lines was evaluated to identify quantitative trait loci (QTLs) for nine agronomic traits (plant height, ear height, top height (plant height subtracted ear height), top height/plant height, number of leaves above the top ear, leaf area, stalk diameter, number of tassel branches and the length of tassel) under three environments. Meta-anal-ysis was conducted then to integrate QTLs identiifed across three generations (RIL, F2:3 and BC2F2) developed from the same crosses. In total, 179 QTLs and 36 meta-QTLs (mQTL) were identiifed. The percentage of phenotypic variation (R2) explained by any single QTL varied from 3.86 to 28.4%, and 24 QTLs with contributions over 15%. Nine common QTLs located in the same or similar chromosome regions were detected across three generations. Five meta-QTLs were identiifed including QTLs in three independent studies. Seven important mQTLs were composed of 11–26 QTLs for 4–7 traits, respectively. Only 11 mQTLs were commonly identiifed in the same or similar chromosome regions across agronomic traits, popping characteristics (popping fold, popping volume and popping rate) and grain yield components (ear weight per plant, grain weight per plant, 100-grain weight, ear length, kernel number per row, ear diameter, row number per ear and kernel ratio) by meta-QTL analysis. In conclusion, we identiifed a list of QTLs, some of which with much higher contributions to agronomic traits should be valuable for further study in improving both popping characteristics and grain yield components in popcorn.

  5. Genetic analysis and QTL mapping for fruit skin anthocyanidin in grape (vitis vinifera)

    International Nuclear Information System (INIS)

    In this study, an F1 population was created by the cross 87-1*9-22. The female parent 87-1 was a black purple cultivar and the male parent was an excellent breeding line with green pericarp. the skin color separation of population and distribution, and determined the content of each individual fruit peel pigment. On the basis of the genetic map of Vitis vinifera L. We carried out the grape skin pigment content quantitative trait locus (QTL) analyses. The results show that the fruit color performance for continuous variation and the inheritance of fruit skin anthocyanidin content was a quantitative inheritance. The color of offspring ranges from green and black-blue and existing distribution. Using SSR and SRAP molecular markers to construct 188 female parent maps,175 male parent maps and 251 consensus maps, and the total map distance is 1047.5 cM,1100.2 cM and 1264.2 cM respectively. The result of QTL showed that there were more QTLs exist in the linkage group of 1, 2, 3, 4, 9, 13, 14, 16 and 19 and in the linkage group of 3, 4, 13 and 14, we detected QTLs in the similar position with the result of the study in the year of 2011 and 2012, and based on this we will conduct the fine QTL location in the future, this result will lay a good foundation for the grape in the department of molecular assistant breeding in the future. (author)

  6. Sherlock: detecting gene-disease associations by matching patterns of expression QTL and GWAS.

    Science.gov (United States)

    He, Xin; Fuller, Chris K; Song, Yi; Meng, Qingying; Zhang, Bin; Yang, Xia; Li, Hao

    2013-05-01

    Genetic mapping of complex diseases to date depends on variations inside or close to the genes that perturb their activities. A strong body of evidence suggests that changes in gene expression play a key role in complex diseases and that numerous loci perturb gene expression in trans. The information in trans variants, however, has largely been ignored in the current analysis paradigm. Here we present a statistical framework for genetic mapping by utilizing collective information in both cis and trans variants. We reason that for a disease-associated gene, any genetic variation that perturbs its expression is also likely to influence the disease risk. Thus, the expression quantitative trait loci (eQTL) of the gene, which constitute a unique "genetic signature," should overlap significantly with the set of loci associated with the disease. We translate this idea into a computational algorithm (named Sherlock) to search for gene-disease associations from GWASs, taking advantage of independent eQTL data. Application of this strategy to Crohn disease and type 2 diabetes predicts a number of genes with possible disease roles, including several predictions supported by solid experimental evidence. Importantly, predicted genes are often implicated by multiple trans eQTL with moderate associations. These genes are far from any GWAS association signals and thus cannot be identified from the GWAS alone. Our approach allows analysis of association data from a new perspective and is applicable to any complex phenotype. It is readily generalizable to molecular traits other than gene expression, such as metabolites, noncoding RNAs, and epigenetic modifications.

  7. QTL Mapping for Hull Thickness and Related Traits in Hybrid Rice Xieyou 9308

    Institute of Scientific and Technical Information of China (English)

    LUO Li-li; ZHANG Ying-xin; CHEN Dai-bo; ZHAN Xiao-deng; SHEN Xi-hong; CHENG Shi-hua; CAO Li-yong

    2014-01-01

    We conducted a quantitative trait locus (QTL) analysis of 165 rice recombinant inbred lines derived from a cross between Zhonghui 9308 (Z9308) and Xieqingzao B (XB) in Hainan and Hangzhou, China. Grain thickness (GT), brown rice thickness (BRT), hull thickness (HT) and milling quality were used for QTL mapping. HT was significantly and positively correlated with GT and BRT. Twenty-nine QTLs were detected with phenotypic effects ranging from 2.80% to 21.27%. Six QTLs, qGT3, qBRT3, qBRT4, qHT6.1, qHT8 and qHT11, were detected repeatedly across two environments. Inherited from XB, qHT6.1, qHT8 and qHT11 showed stable expression, explaining 9.92%, 21.27% and 10.83% of the phenotypic variances in Hainan and 9.61%, 6.40%and 6.71%in Hangzhou, respectively. Additionally, the QTL cluster between RM5944 and RM5626 on chromosome 3 was probably responsible for GT and milling quality. The cluster between RM6992 and RM6473 on chromosome 4 played an important role in grain filling. Three near isogenic lines (NILs), X345, X338 and X389, were selected because they contained homozygous fragments from Zhonghui 9308, corresponding to qHT6.1, qHT8 and qHT11, respectively. The hull of XB was thicker than those of X345, X338 and X389. In all the lines, qHT6.1, qHT8 and qHT11 that regulated rice HT were stably inherited with obvious genetic effects.

  8. Fine-mapping of muscle weight QTL in LG/J and SM/J intercrosses.

    Science.gov (United States)

    Lionikas, A; Cheng, R; Lim, J E; Palmer, A A; Blizard, D A

    2010-09-01

    Genetic variation plays a substantial role in variation in strength, but the underlying mechanisms remain poorly understood. The objective of the present study was to examine the mechanisms underlying variation in muscle mass, a predictor of strength, between LG/J and SM/J strains, which are the inbred progeny of mice selected, respectively, for high and low body weight. We measured weight of five hindlimb muscles in LG/J and SM/J males and females, in F(1) and F(2) intercrosses, and in an advanced intercross (AI), F(34), between the two. F(2) mice were genotyped using 162 SNPs throughout the genome; F(34) mice were genotyped at 3,015 SNPs. A twofold difference in muscle mass between the LG/J and SM/J mouse strains was observed. Integrated genome-wide association analysis in the combined population of F(2) and AI identified 22 quantitative trait loci (QTL; genome-wide P LG/J allele conferred greater muscle weight in all cases. The 1.5-LOD QTL support intervals ranged between 0.3 and 13.4 Mb (median 3.7 Mb) restricting the list of candidates to between 5 and 97 genes. Selection for body weight segregated the alleles affecting skeletal muscle, the most abundant tissue in the body. Combination of analyses in an F(2) and AI was an effective strategy to detect and refine the QTL in a genome-wide manner. The achieved resolution facilitates further elucidation of the underlying genetic mechanisms affecting muscle mass.

  9. Correlações fenotípicas entre caracteres avaliados nos estádios juvenil e adulto de açaizeiros Juvenile-mature correlations in assai palms

    Directory of Open Access Journals (Sweden)

    Marilene Leão Alves Bovi

    1990-01-01

    Full Text Available São apresentados coeficientes de correlações fenotípicas obtidos entre diferentes idades de alguns caracteres relacionados ao desenvolvimento vegetativo de açaizeiros (Euterpe oleracea Mart. Visa-se auxiliar na identificação de caracteres que possam ser utilizados para a seleção precoce de plantas superiores dessas palmeiras com vistas ao melhoramento genético. Correlações entre os caracteres mensurados em diferentes estádios foram estatisticamente significativas para a quase totalidade das avaliações efetuadas, com magnitude aumentando gradativamente com o tempo. Dada a taxa crescente apresentada pelos coeficientes de correlação e as estimativas de ganho esperado por seleção praticada, especialmente sobre o caráter circunferência da planta, sugere-se que a seleção em açaizeiros possa ter início logo aos 17 meses após o plantio, com maior probabilidade de selecionar genótipos superiores dessas palmeiras a partir do segundo ano de campo.Juvenile-mature correlation coefficients relating two vegetative traits of Euterpe oleracea Mart. are presented as an aid to early and indirect selection for heart of palm yield in breeding work with this palm. Significant age to age correlation coefficients were found for almost all paired comparison for plant girth and tillering number, with increasing values overtime. This fact together with the expected gain obtained by selection practiced, especially over palm girth, suggest that indirect phenotypic selection on this palm could start as early as seventeen months, with greater probability of selecting superior genotypes after two years after planting.

  10. Construction of chromosome segment substitution lines enables QTL mapping for flowering and morphological traits in Brassica rapa

    Directory of Open Access Journals (Sweden)

    Xiaonan eLi

    2015-06-01

    Full Text Available Chromosome segment substitution lines (CSSLs represent a powerful method for precise quantitative trait loci (QTL detection of complex agronomical traits in plants. In this study, we used a marker-assisted backcrossing strategy to develop a population consisting of 63 CSSLs, derived from backcrossing of the F1 generated from a cross between two Brassica rapa subspecies: ‘Chiifu’ (ssp. pekinensis, the Brassica A genome-represented line used as the donor, and ‘49caixin’ (ssp. parachinensis, a non-heading cultivar used as the recipient. The 63 CSSLs covered 87.95% of the B. rapa genome. Among them, 39 lines carried a single segment; 15 lines, two segments; and nine lines, three or more segments of the donor parent chromosomes. To verify the potential advantage of these CSSL lines, we used them to locate QTL for six morphology-related traits. A total of 58 QTL were located on eight chromosomes for all six traits: 17 for flowering time, 14 each for bolting time and plant height, 6 for plant diameter, 2 for leaf width, and 5 for flowering stalk diameter. Co-localized QTL were mainly distributed on eight genomic regions in A01, A02, A05, A06, A08, A09, and A10, present in the corresponding CSSLs. Moreover, new chromosomal fragments that harbored QTL were identified using the findings of previous studies. The CSSL population constructed in our study paves the way for fine mapping and cloning of candidate genes involved in late bolting, flowering, and plant architecture-related traits in B. rapa. Furthermore, it has great potential for future marker-aided gene/QTL pyramiding of other interesting traits in B. rapa breeding.

  11. Identification of carcass and meat quality QTL in an F2 Duroc x Pietrain pig resource population using different least-squares analysis models

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    Igseo eChoi

    2011-05-01

    Full Text Available A three-generation resource population was constructed by crossing pigs from the Duroc and Pietrain breeds. In this study, 954 F2 animals were used to identify quantitative trait loci (QTL affecting carcass and meat quality traits. Based on results of the first scan analyzed with a line-cross model using 124 microsatellite markers and 510 F2 animals, 9 chromosomes were selected for genotyping of additional markers. Twenty additional markers were genotyped for 954 F2 animals and 20 markers used in the first scan were genotyped for 444 additional F2 animals. Three different Mendelian models using least-squares for QTL analysis were applied for the second scan: a line-cross model, a half-sib model, and a combined line-cross and half-sib model. Significance thresholds were determined by false discovery rate (FDR. In total, 50 QTL using the line-cross model, 38 QTL using the half-sib model and 3 additional QTL using the combined line-cross and half-sib model were identified (q < 0.05. The line-cross and half-sib models revealed strong evidence for QTL regions on SSC6 for carcass traits (e.g., 10th-rib backfat; q < 0.0001 and on SSC15 for meat quality traits (e.g., tenderness, color, pH; q < 0.01, respectively. QTL for pH (SSC3, dressing percent (SSC7, marbling score and moisture percent (SSC12, CIE a* (SSC16 and carcass length and spareribs weight (SSC18 were also significant (q < 0.01. Additional marker and animal genotypes increased the statistical power for QTL detection, and applying different analysis models allowed confirmation of QTL and detection of new QTL.

  12. Meta-analysis for heritability estimates of vegetative and reproductive traits of Coffea arabica L.Meta-análise para estimativas de herdabilidade de caracteres vegetativos e reprodutivos de Coffea arabica L.

    Directory of Open Access Journals (Sweden)

    Danielle Pereira Baliza

    2012-08-01

    Full Text Available The compilation of informations resulting from independent studies has been difficulted in almost all scientific fields, mainly due to the great number of scientific papers published in recent years. As a result, summarizing information became a need. In this context, a meta-analysis was conducted with the objective of summarizing the estimates for the heritability for vegetative and reproductive traits of coffee (Coffea arabica L.. Heritability estimates were appraised regarding the following traits: average height of plant, average diameter of the canopy, vegetative vigor, production of processed coffee, yield and rust. The data regarding the heritability estimates are from scientific articles published in national and international journals, congress annals, PhD thesis and Master dissertations. The technique of meta-analysis summarized the estimates heritability from different studies and made possible to conclude that all of the appraised traits are highly inherited, reflecting the great genetic variety of coffee plants, and that is possible to reach satisfactory genetic gains in improvement programs in which those traits are evaluated. A compilação de informações advindas de estudos independentes tem sido dificultada em quase todos os campos da ciência, devido principalmente, ao grande número de trabalhos científicos publicados nos últimos anos. Assim, sumarizar informações tornou-se uma necessidade. Neste contexto, uma meta-análise foi conduzida com o objetivo de sistematizar as estimativas para a herdabilidade de caracteres vegetativos e reprodutivos de cafeeiros (Coffea arabica L.. Foram avaliadas as estimativas de herdabilidade referentes aos seguintes caracteres: altura média da planta, diâmetro médio da copa, vigor vegetativo, produção de café beneficiado, rendimento e resistência a ferrugem. Os dados referentes às estimativas de herdabilidade são provenientes de artigos científicos publicados em revistas

  13. Comparación de la composición química, caracteres organolépticos y grado de aceptabilidad entre un helado estándar y un helado funcional

    OpenAIRE

    Colella, Gloria

    2011-01-01

    La leche funcional con altas concentraciones de ácido linoleico conjugado (CLA) presenta propiedades beneficiosas sobre la salud. El objetivo del presente trabajo es determinar las diferencias en la composición química, caracteres organolépticos y grado de aceptabilidad entre un helado elaborado con leche estándar y un helado elaborado con leche funcional, y la transferencia de AG CLA de la leche al helado. En él, se observa que el 97% de las personas encuestadas consumen helad...

  14. Caracteres morfológicos de vainilla (Vanilla planifolia J.) utilizados por el agricultor en la selección de material reproductivo en cuatro municipios del Totonacapan, México.

    OpenAIRE

    Baltazar Nieto, Pablo

    2010-01-01

    El objetivo de este estudio fue conocer los caracteres morfológicos de la planta de vainilla (Vanilla planifolia J.) de hoja, tallo, fruto y esqueje que el productor usa en la selección de su material de reproducción y comprender su importancia en la conservación de la especie en cuatro municipios de la región del Totonacapan, México. Los municipios en los que se hizo el estudio fueron: Venustiano Carranza y Caxhuacan del estado de Puebla y de Papantla de Olarte y Gutiérrez Zamora del estado ...

  15. Revisiting QTL Affecting Clinical Mastitis by High-Density GWAS and Resequencing in the Finnish Ayrshire Dairy Cattle

    DEFF Research Database (Denmark)

    Vilkki, Johanna; Iso-Touru, Terhi; Schulman, Nina F;

    Mastitis is the most common disease of dairy cattle, causing high economic losses each year. Studies to locate QTL affecting clinical mastitis and milk somatic cell counts have been carried out to increase our understanding of the disease. As part of the EU FP7 Quantomics project, we have used most...... recent genomic tools to characterize QTL affecting mastitis incidence in the Finnish Ayrshire cattle. Clinical mastitis diagnoses from -15 to 50 days and 51 to 300 days of first lactation and SCC (geometric mean of SCS observations between 5 to 170 days of first lactation) were included. In total, 1920...

  16. Identification of Candidate Genes Associated with Beef Marbling Using QTL and Pathway Analysis in Hanwoo (Korean Cattle)

    OpenAIRE

    Park, Hyesun; Seo, Seongwon; Cho, Yong Min; Oh, Sung Jong; Seong, Hwan-Hoo; Lee, Seung Hwan; Lim, Dajeong

    2012-01-01

    Marbling from intramuscular fat is an important trait of meat quality and has an economic benefit for the beef industry. Quantitative trait loci (QTL) fine mapping was performed to identify the marbling trait in 266 Hanwoo steers using a 10K single nucleotide polymorphism panel with the combined linkage and linkage disequilibrium method. As a result, we found nine putative QTL regions for marbling: three on BTA6, two on BTA17, two on BTA22, and two on BTA29. We detected candidate genes for ma...

  17. A high-resolution linkage map for comparative genome analysis and QTL fine mapping in Asian seabass, Lates calcarifer

    Directory of Open Access Journals (Sweden)

    Feng Felicia

    2011-04-01

    Full Text Available Abstract Background High density linkage maps are essential for comparative analysis of synteny, fine mapping of quantitative trait loci (QTL, searching for candidate genes and facilitating genome sequence assembly. However, in most foodfish species, marker density is still low. We previously reported a first generation linkage map with 240 DNA markers and its application to preliminarily map QTL for growth traits in Asian seabass (Lates calcarifer. Here, we report a high-resolution linkage map with 790 microsatellites and SNPs, comparative analysis of synteny, fine-mapping of QTL and the identification of potential candidate genes for growth traits. Results A second generation linkage map of Asian seabass was developed with 790 microsatellite and SNP markers. The map spanned a genetic length of 2411.5 cM, with an average intermarker distance of 3.4 cM or 1.1 Mb. This high density map allowed for comparison of the map with Tetraodon nigroviridis genome, which revealed 16 synteny regions between the two species. Moreover, by employing this map we refined QTL to regions of 1.4 and 0.2 cM (or 400 and 50 kb in linkage groups 2 and 3 in a population containing 380 progeny; potential candidate genes for growth traits in QTL regions were further identified using comparative genome analysis, whose effects on growth traits were investigated. Interestingly, a QTL cluster at Lca371 underlying growth traits of Asian seabass showed similarity to the cathepsin D gene of human, which is related to cancer and Alzheimer's disease. Conclusions We constructed a high resolution linkage map, carried out comparative mapping, refined the positions of QTL, identified candidate genes for growth traits and analyzed their effects on growth. Our study developed a framework that will be indispensable for further identification of genes and analysis of molecular variation within the refined QTL to enhance understanding of the molecular basis of growth and speed up genetic

  18. Identification of QTL-s for drought tolerance in maize, II: Yield and yield components

    Directory of Open Access Journals (Sweden)

    Nikolić Ana

    2013-01-01

    Full Text Available Grain yield is the primary trait of interest in maize breeding programs. Worldwide, drought is the most pervasive limitation to the achievement of yield potential in maize. Drought tolerance of maize has been considerably improved through conventional breeding. Traditional breeding methods have numerous limitations, so development of new molecular genetics techniques could help in elucidation of genetic basis of drought tolerance .In order to map QTLs underlying yield and yield components under drought 116 F3 families of DTP79xB73 cross were evaluated in the field trials. Phenotypic correlations calculated using Pearson’s coefficients were high and significant. QTL detection was performed using composite interval mapping option in WinQTL Cartographer v 2.5. Over all nine traits 45 QTLs were detected: five for grain yield per plant and 40 for eight yield components. These QTLs were distributed on all chromosomes except on chromosome 9. Percent of phenotypic variability determined for the identified QTLs for all the traits was in the range from 27.46 to 95.85%. Different types of gene action were found for the QTLs identified for analyzed traits. [Projekat Ministarstva nauke Republike Srbije, br. TR31068

  19. Teamwork: improved eQTL mapping using combinations of machine learning methods.

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    Marit Ackermann

    Full Text Available Expression quantitative trait loci (eQTL mapping is a widely used technique to uncover regulatory relationships between genes. A range of methodologies have been developed to map links between expression traits and genotypes. The DREAM (Dialogue on Reverse Engineering Assessments and Methods initiative is a community project to objectively assess the relative performance of different computational approaches for solving specific systems biology problems. The goal of one of the DREAM5 challenges was to reverse-engineer genetic interaction networks from synthetic genetic variation and gene expression data, which simulates the problem of eQTL mapping. In this framework, we proposed an approach whose originality resides in the use of a combination of existing machine learning algorithms (committee. Although it was not the best performer, this method was by far the most precise on average. After the competition, we continued in this direction by evaluating other committees using the DREAM5 data and developed a method that relies on Random Forests and LASSO. It achieved a much higher average precision than the DREAM best performer at the cost of slightly lower average sensitivity.

  20. Mouse pulmonary adenoma susceptibility 1 locus is an expression QTL modulating Kras-4A.

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    Alice Dassano

    2014-04-01

    Full Text Available Pulmonary adenoma susceptibility 1 (Pas1 is the major locus responsible for lung tumor susceptibility in mice; among the six genes mapping in this locus, Kras is considered the best candidate for Pas1 function although how it determines tumor susceptibility remains unknown. In an (A/J × C57BL/6F4 intercross population treated with urethane to induce lung tumors, Pas1 not only modulated tumor susceptibility (LOD score = 48, 69% of phenotypic variance explained but also acted, in lung tumor tissue, as an expression quantitative trait locus (QTL for Kras-4A, one of two alternatively spliced Kras transcripts, but not Kras-4B. Additionally, Kras-4A showed differential allelic expression in lung tumor tissue of (A/J × C57BL/6F4 heterozygous mice, with significantly higher expression from the A/J-derived allele; these results suggest that cis-acting elements control Kras-4A expression. In normal lung tissue from untreated mice of the same cross, Kras-4A levels were also highly linked to the Pas1 locus (LOD score = 23.2, 62% of phenotypic variance explained and preferentially generated from the A/J-derived allele, indicating that Pas1 is an expression QTL in normal lung tissue as well. Overall, the present findings shed new light on the genetic mechanism by which Pas1 modulates the susceptibility to lung tumorigenesis, through the fine control of Kras isoform levels.

  1. Multi-trait QTL analysis for agronomic and quality characters of Agaricus bisporus (button mushrooms).

    Science.gov (United States)

    Gao, Wei; Baars, Johan J P; Maliepaard, Chris; Visser, Richard G F; Zhang, Jinxia; Sonnenberg, Anton S M

    2016-12-01

    The demand for button mushrooms of high quality is increasing. Superior button mushroom varieties require the combination of multiple traits to maximize productivity and quality. Very often these traits are correlated and should, therefore, be evaluated together rather than as single traits. In order to unravel the genetic architecture of multiple traits of Agaricus bisporus and the genetic correlations among traits, we have investigated a total of six agronomic and quality traits through multi-trait QTL analyses in a mixed-model. Traits were evaluated in three heterokaryon sets. Significant phenotypic correlations were observed among traits. For instance, earliness (ER) correlated to firmness (FM), cap color, and compost colonization, and FM correlated to scales (SC). QTLs of different traits located on the same chromosomes genetically explains the phenotypic correlations. QTL detected on chromosome 10 mainly affects three traits, i.e., ER, FM and SC. It explained 31.4 % phenotypic variation of SC on mushroom cap (heterokaryon Set 1), 14.9 % that of the FM (heterokaryon Set 3), and 14.2 % that of ER (heterokaryon Set 3). High value alleles from the wild parental line showed beneficial effects for several traits, suggesting that the wild germplasm is a valuable donor in terms of those traits. Due to the limitations of recombination pattern, we only made a start at understanding the genetic base for several agronomic and quality traits in button mushrooms. PMID:27620731

  2. Conditional QTL Mapping of Sedimentation Volume on Seven Quality Traits in Common Wheat

    Institute of Scientific and Technical Information of China (English)

    DENG Zhi-ying; ZHAO Liang; LIU Bin; ZHANG Kun-pu; CHEN Jian-sheng; QU Hou-lan; SUN Cai-ling; ZHANG Yong-xiang; TIAN Ji-chun

    2013-01-01

    To evaluate the possible genetic interrelationships between lfour components and the sedimentation volume (SD), a doubled haploid (DH) population comprising 168 lines were used to identify the conditional quantitative trait loci (QTLs) for SD in three environments. Ten additive QTLs and 15 pairs of epistatic QTLs were detected for SD through unconditional and conditional QTL mapping. Three major additive QTLs were detected for SD conditioned on the seven quality traits. Two additive QTLs were found to be independent of these traits. Three additive QTLs were suppressed by three of the seven traits because of non-detection in unconditional mapping.Three pairs of epistatic QTLs were completely affected by the seven traits because of detection in unconditional mapping but no-detection in conditional mapping. Twelve pairs of epistatic QTLs were detected in conditional mapping. Our results indicated that conditional mapping could contribute to a better understanding of the interdependence of different and closely correlated traits at the QTL molecular level, especially some minor QTLs were found. The conditional mapping approach provides new insights that will make it possible to avoid the disadvantages of different traits by breeding through molecular design.

  3. QTL molecular marker location of powdery mildew resistance in cucumber (Cucumis sativus L.)

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    The cucumber lines, S94 (Northern China open-field type, powdery mildew (PM) susceptible) and S06 (European greenhouse type, PM resistant), and their F6:7 populations were used to investigate PM re-sistance under seedling spray inoculation in 2005/Autumn and 2006/Spring. QTL analysis was under-taken based on a constructed molecular linkage map of the corresponding F6 population using com-posite interval mapping. A total of four QTLs (pm1.1, pm2.1, pm4.1 and pm6.1) for PM resistance were identified and located on LG 1, 2, 4 and 6, respectively, explaining 5.2%-21.0% of the phenotypic variation. Three consistent QTLs (pm1.1, pm2.1 and pm4.1) were detected under the two test conditions. The QTL pm6.1 was only identified in 2005/Autumn. The total phenotypic variation explained by the QTLs was 52.0% and 42.0% in 2005/Autumn and 2006/Spring, respectively. Anchor markers tightly linked to those loci (<5 cM) could lay a basis for both molecular marker-assisted breeding and map-based gene cloning of the PM-resistance gene in cucumber.

  4. QTL mapping of soybean oil content for marker-assisted selection in plant breeding program.

    Science.gov (United States)

    Leite, D C; Pinheiro, J B; Campos, J B; Di Mauro, A O; Unêda-Trevisoli, S H

    2016-03-18

    The present study was undertaken to detect and map the quantitative trait loci (QTL) related to soybean oil content. We used 244 progenies derived from a bi-parental cross of the Lineage 69 (from Universidade Estadual Paulista "Júlio de Mesquita Filho"/Faculdade de Ciências Agrárias e Veterinárias - Breeding Program) and Tucunaré cultivar. A total of 358 simple sequence repeat (SSR; microsatellite) markers were used to investigate the polymorphism between the parental lines, and for the polymorphic lines all the F2 individuals were tested. Evaluation of the oil content and phenotype was performed with the aid of a Tango equipment by near infra-red reflectance spectroscopy, using single F2 seeds and F2:3 progenies, in triplicate. The data were analyzed by QTL Cartographer program for 56 SSR polymorphic markers. Two oil-content related QTLs were detected on K and H linkage groups. The total phenotypic variation explained by QTLs ranged from 7.8 to 46.75% for oil content. New QTLs were identified for the oil content in addition to those previously identified in other studies. The results reported in this study show that regions different from those already known could be involved in the genetic control of soybean oil content.

  5. Genetic diversity of table grape based on morphoagronomic traits Diversidade genética de acessos de uvas de mesa baseada em caracteres morfoagronômicos

    Directory of Open Access Journals (Sweden)

    Patrícia Coelho de Souza Leão

    2011-02-01

    Full Text Available The conservation and characterization of grape (Vitis spp genetic resources in germplasm banks have been the basis of its use in breeding programs that result in development of new cultivars. There are at least 10,000 grape cultivars kept in germplasm collection. The genetic diversity in 136 table grape accessions from the state of Bahia, Brazil, was evaluated. Continuous and discrete morphoagronomic traits were assessed. The clustering analysis by the Tocher otimization method resulted in 30 clusters (considering continuous morphoagronomic traits, and 9 clusters (taking into consideration multicategorical traits. There was no agreement between clusters obtained by both, continuous or discrete phenotypic descriptors, independent of the cluster method analysis used. A satisfactory genetic variability among the table grape accessions was observed.A conservação e caracterização dos recursos genéticos de videira (Vitis spp. em bancos de germoplasma tem sido a base para a sua utilização nos programas de melhoramento, que resultam no desenvolvimento de novas cultivares, estimando-se a existência de pelo menos 10.000 cultivares de uva mantidos em coleções de germoplasma. Avaliou-se a diversidade genética presente em 136 acessos de uvas de mesa de uma coleção de germoplasma do estado da Bahia, com base em caraterísticas morfoagronômicas de variação contínua e discreta. A análise de agrupamento pelo método de Tocher resultou na formação de 30 grupos utilizando-se descritores morfo-agronômicos de variação contínua e 9 grupos, com base em caracteres multicategóricos. Não houve concordância entre os grupos obtidos pela análise de descritores fenotípicos contínuos e discretos, independente do método de agrupamento utilizado. Detectou-se a existência de variabilidade genética satisfatória entre os acessos de uvas de mesa da coleção.

  6. Confirmation and fine-mapping of a major QTL for resistance to infectious pancreatic necrosis in Atlantic salmon (Salmo salar: population-level associations between markers and trait

    Directory of Open Access Journals (Sweden)

    Moen Thomas

    2009-08-01

    Full Text Available Abstract Background Infectious pancreatic necrosis (IPN is one of the most prevalent and economically devastating diseases in Atlantic salmon (Salmo salar farming worldwide. The disease causes large mortalities at both the fry- and post-smolt stages. Family selection for increased IPN resistance is performed through the use of controlled challenge tests, where survival rates of sib-groups are recorded. However, since challenge-tested animals cannot be used as breeding candidates, within-family selection is not performed and only half of the genetic variation for IPN resistance is being exploited. DNA markers linked to quantitative trait loci (QTL affecting IPN resistance would therefore be a powerful selection tool. The aim of this study was to identify and fine-map QTL for IPN-resistance in Atlantic salmon, for use in marker-assisted selection to increase the rate of genetic improvement for this trait. Results A genome scan was carried out using 10 large full-sib families of challenge-tested Atlantic salmon post-smolts and microsatellite markers distributed across the genome. One major QTL for IPN-resistance was detected, explaining 29% and 83% of the phenotypic and genetic variances, respectively. This QTL mapped to the same location as a QTL recently detected in a Scottish Atlantic salmon population. The QTL was found to be segregating in 10 out of 20 mapping parents, and subsequent fine-mapping with additional markers narrowed the QTL peak to a 4 cM region on linkage group 21. Challenge-tested fry were used to show that the QTL had the same effect on fry as on post-smolt, with the confidence interval for QTL position in fry overlapping the confidence interval found in post-smolts. A total of 178 parents were tested for segregation of the QTL, identifying 72 QTL-heterozygous parents. Genotypes at QTL-heterozygous parents were used to determine linkage phases between alleles at the underlying DNA polymorphism and alleles at single markers or

  7. Correlações entre caracteres da planta e do cacho em bananeira (Musa spp Correlations among characters of the plant and of the bunch in banana (Musa spp.

    Directory of Open Access Journals (Sweden)

    Sérgio Luiz Rodrigues Donato

    2006-02-01

    Full Text Available Os caracteres observados em áreas experimentais têm natureza fenotípica e suas correlações são estimadas visando mensurar alterações em um caráter quando se altera outro relacionado. Objetivou-se com este trabalho, quantificar a relação entre os caracteres da planta e do cacho observados na época do florescimento e da colheita de 13 genótipos (variedades e híbridos de bananeira (Musa spp., em dois ciclos de produção, em Guanambi, Bahia. Foram utilizadas as variedades Prata anã, Pacovan (AAB, Grande naine e Nanicão (AAA, e os híbridos PA42-44, PV42-85, PV42-142, PV42-68 e ST12-31 (AAAB e Ambrosia, Calipso, Bucaneiro e FHIA02 (AAAA, selecionados na Embrapa Mandioca e Fruticultura. Consideraram-se os caracteres: altura da planta; perímetro do pseudocaule; número de folhas vivas no florescimento e na colheita; número de dias do plantio ao florescimento e à colheita; intervalo florescimento à colheita; peso do cacho, da ráquis e da pencas; comprimento e diâmetro do engaço; número de pencas e de frutos; peso da segunda penca; peso, comprimento e diâmetro do fruto e espessura da casca. As correlações entre o peso do cacho e os demais caracteres estudados, variaram entre genótipos e ciclos. As associações entre o peso do cacho e os caracteres da planta, de forma geral foram não-significativas, e entre o peso do cacho e os caracteres do cacho significativas e positivas para a maioria dos genótipos, nos ciclos avaliados. As correlações entre os caracteres envolvendo todos os genótipos ao longo dos dois ciclos foram predominantemente positivas e não- significativas, entretanto, as associações entre os caracteres do cacho foram em maioria significativas, positivas e com valores expressivos.The characters observed in a experimental areas has phenotypic nature and their correlations are estimated with the purpose to verify alterations in one character when is altered another. The objectives of this work were to

  8. The Genetic Architecture of Flowering Time and Photoperiod Sensitivity in Maize as Revealed by QTL Review and Meta Analysis

    Institute of Scientific and Technical Information of China (English)

    Jie Xu; Tingzhao Rong; Yaxi Liu; Jian Liu; Moju Cao; Jing Wang; Hai Lan; Yunbi Xu; Yanli Lu; Guangtang Pan

    2012-01-01

    The control of flowering is not only important for reproduction,but also plays a key role in the processes of domestication and adaptation.To reveal the genetic architecture for flowering time and photoperiod sensitivity,a comprehensive evaluation of the relevant literature was performed and followed by meta analysis.A total of 25 synthetic consensus quantitative trait loci (QTL) and four hot-spot genomic regions were identified for photoperiod sensitivity including 11 genes related to photoperiod response or flower morphogenesis and development.Besides,a comparative analysis of the QTL for flowering time and photoperiod sensitivity highlighted the regions containing shared and unique QTL for the two traits.Candidate genes associated with maize flowering were identified through integrated analysis of the homologous genes for flowering time in plants and the consensus QTL regions for photoperiod sensitivity in maize (Zea mays L.).Our results suggest that the combination of literature review,meta-analysis and homologous blast is an efficient approach to identify new candidate genes and create a global view of the genetic architecture for maize photoperiodic flowering.Sequences of candidate genes can be used to develop molecular markers for various models of marker-assisted selection,such as marker-assisted recurrent selection and genomic selection that can contribute significantly to crop environmental adaptation.

  9. Utility assessment of published microsatellite markers for fiber length and bundle strength QTL in a cotton breeding program

    Science.gov (United States)

    Marker-assisted selection (MAS) may help mitigate some of the current challenges regarding the genetic improvement of cotton fiber quality, such as low genetic diversity and the negative association between fiber quality and lint yield. A multitude of quantitative trait loci (QTL) for fiber length a...

  10. Mapping quantitative trait loci (QTL in sheep. IV. Analysis of lactation persistency and extended lactation traits in sheep

    Directory of Open Access Journals (Sweden)

    Lam Mary K

    2011-06-01

    Full Text Available Abstract Background In sheep dairy production, total lactation performance, and length of lactation of lactation are of economic significance. A more persistent lactation has been associated with improved udder health. An extended lactation is defined by a longer period of milkability. This study is the first investigation to examine the presence of quantitative trait loci (QTL for extended lactation and lactation persistency in sheep. Methods An (Awassi × Merino × Merino single-sire backcross family with 172 ewes was used to map QTL for lactation persistency and extended lactation traits on a framework map of 189 loci across all autosomes. The Wood model was fitted to data from multiple lactations to estimate parameters of ovine lactation curves, and these estimates were used to derive measures of lactation persistency and extended lactation traits of milk, protein, fat, lactose, useful yield, and somatic cell score. These derived traits were subjected to QTL analyses using maximum likelihood estimation and regression analysis. Results Overall, one highly significant (LOD > 3.0, four significant (2.0 Conclusion This study identified ten novel QTL for lactation persistency and extended lactation in sheep, but results suggest that lactation persistency and extended lactation do not have a major gene in common. These results provide a basis for further validation in extended families and other breeds as well as targeting regions for genome-wide association mapping using high-density SNP arrays.

  11. In-silico QTL mapping of postpubertal mammary ductal development in the mouse uncovers potential human breast cancer risk loci

    Science.gov (United States)

    Genetic background plays a dominant role in mammary gland development and breast cancer (BrCa). Despite this, the role of genetics is only partially understood. This study used strain-dependent variation in an inbred mouse mapping panel, to identify quantitative trait loci (QTL) underlying structura...

  12. A weighted AMMI Algorithm to Study Genotype-by-Environment Interaction and QTL-by-Environment Interaction

    NARCIS (Netherlands)

    Rodrigues, P.C.; Malosetti, M.; Gauch, H.G.

    2014-01-01

    Genotype-by-environment (G × E) interaction (GEI) and quantitative trait locus (QTL)-by-environment interaction (QEI) are common phenomena in multiple-environment trials and represent a major challenge to breeders. The additive main effects and multiplicative interaction (AMMI) model is a widely use

  13. Mapping the quantitative trait loci (QTL) controlling seed morphology and disk diameter in sunflower (Helianthus annuus L.)

    Science.gov (United States)

    Several seed morphological traits, along with disk diameter, differ greatly between oilseed and confection sunflower types, which are bred for different end-use purposes. This paper reports the results of analyzing the quantitative trait loci (QTL) underlying seed morphological traits and disk diam...

  14. Genome wide association analysis of the 16th QTL- MAS Workshop dataset using the Random Forest machine learning approach

    Science.gov (United States)

    2014-01-01

    Background Genome wide association studies are now widely used in the livestock sector to estimate the association among single nucleotide polymorphisms (SNPs) distributed across the whole genome and one or more trait. As computational power increases, the use of machine learning techniques to analyze large genome wide datasets becomes possible. Methods The objective of this study was to identify SNPs associated with the three traits simulated in the 16th MAS-QTL workshop dataset using the Random Forest (RF) approach. The approach was applied to single and multiple trait estimated breeding values, and on yield deviations and to compare them with the results of the GRAMMAR-CG method. Results The two QTL mapping methods used, GRAMMAR-CG and RF, were successful in identifying the main QTLs for trait 1 on chromosomes 1 and 4, for trait 2 on chromosomes 1, 4 and 5 and for trait 3 on chromosomes 1, 2 and 3. Conclusions The results of the RF approach were confirmed by the GRAMMAR-CG method and validated by the effective QTL position, even if their approach to unravel cryptic genetic structure is different. Furthermore, both methods showed complementary findings. However, when the variance explained by the QTL is low, they both failed to detect significant associations. PMID:25519518

  15. Epigenetic regulation of the ELOVL6 gene is associated with a major QTL effect on fatty acid composition in pigs

    NARCIS (Netherlands)

    Corominas, J.; Marchesi, J.A.; Puig-Oliveras, A.; Revilla, M.; Estelle, J.; Alves, E.; Folch, J.M.; Ballester, M.

    2015-01-01

    BACKGROUND: In previous studies on an Iberian x Landrace cross, we have provided evidence that supported the porcine ELOVL6 gene as the major causative gene of the QTL on pig chromosome 8 for palmitic and palmitoleic acid contents in muscle and backfat. The single nucleotide polymorphism (SNP) ELOVL

  16. Correlação fenotípica entre caracteres de híbridos diploides (AA de bananeira Phenotypic correlation between characters in banana (AA diploid hybrids

    Directory of Open Access Journals (Sweden)

    Lauro Saraiva Lessa

    2012-12-01

    Full Text Available O estudo de correlação tem como propósito mensurar a alteração em um caráter quando se altera outro. Neste trabalho, objetivou-se estimar correlações fenotípicas entre o número de frutos por cacho e 22 caracteres avaliados em híbridos diploides (AA de bananeira. No experimento, conduzido na Embrapa Mandioca e Fruticultura, em blocos casualizados com quatro repetições, foram avaliados 11 híbridos diploides (AA de bananeira. Os caracteres avaliados foram: altura de plantas, diâmetro do pseudocaule, número de filhos, número de folhas na floração, período do plantio ao florescimento, presença de pólen, peso do cacho e da ráquis, sigatoka-amarela no florescimento, número de folhas na colheita, Sigatoka-amarela na colheita do cacho, número de dias do florescimento à colheita, comprimento e diâmetro do engaço, peso da segunda penca, número de pencas e de frutos por cacho, fragilidade do pedicelo, comprimento e diâmetro do fruto e comprimento do pedicelo, além de presença de semente. Após a tabulação, procederam-se a estudos de correlação entre o número de frutos e os demais caracteres da planta. Essas correlações variaram entre os genótipos, sendo assim, observado que as associações entre o número de frutos e os caracteres vegetativos da planta foram, de forma geral, não significativas. Já as relações entre o número de frutos por cacho e os outros caracteres produtivos foram, predominantemente, significativas.The objective of the present study was to estimate the phenotypic correlations between the number of fruits per bunch and 22 characters evaluated in banana (AA diploid hybrids. The experiment was carried out at Embrapa Cassava and Fruits in randomized blocks with four repetitions and 11 (AA banana diploid hybrids were evaluated. The following characteristics were evaluated: plant height, pseudostem diameter, number of suckers, number of leaves during flowering, plant cycle until emission of the

  17. Diferenciação de espécies daninhas aquáticas pela análise multivariada de caracteres estruturais foliares Differentiation of aquatic weeds by multivariate analysis of foliar structural characters

    Directory of Open Access Journals (Sweden)

    N.V. Costa

    2006-01-01

    Full Text Available Algumas espécies de plantas aquáticas têm-se tornado problemáticas em reservatórios hidrelétricos no Brasil, devido a sua grande capacidade de reprodução. O objetivo destes trabalho foi diferenciar Brachiaria mutica, Brachiaria subquadripara, Panicum repens, Eichhornia crassipes, Heteranthera reniformis, Typha ubulata e Enhydra anagallis, utilizando-se 19 caracteres estruturais quantitativos do limbo foliar, que se relacionassem com a penetração e translocação de herbicidas. Amostras do terço médio do limbo foram fixadas em FAA 50, cortadas transversalmente em micrótomo com 8 mm de espessura e coradas com azul-de-toluidina. Foram quantificados (% os seguintes caracteres estruturais da nervura central (NC e da região internervural (IN: epidermes adaxial e abaxial, feixe vascular, bainha do feixe vascular, esclerênquima, parênquima e lacunas do aerênquima, além da espessura da folha, do número de estômatos e do número de tricomas nas faces adaxial e abaxial. Os 19 caracteres estruturais foram submetidos à Análise de Agrupamento e Análise de Componentes Principais. Houve a formação de três grupos principais: grupo 1 B. mutica, B. subquadripara e P. repens (Poaceae; grupo 2 E. crassipes e H. reniformis (Pontederiaceae e E. anagallis (Asteraceae; e grupo 3 apenas T. subulata (Typhaceae. Os caracteres com maior poder discriminatório foram: porcentagem de epiderme adaxial (IN; porcentagem de epiderme abaxial; feixe vascular; bainha do feixe vascular; esclerênquima e lacunas do aerênquima (NC e IN; espessura da folha e número de estômatos das faces adaxial e abaxial. Concluiu-se que os caracteres estruturais quantitativos permitiram diferenciar essas espécies daninhas aquáticas em fase vegetativa.Some aquatic plant species have caused great damage to hydroelectric power dams in Brazil, due to their great capacity of reproduction. Nineteen quantitative structural characters of leaf blades were used to differentiate

  18. Relação entre caracteres da planta e do palmito de açaizeiros Phenotypic relationship between non-destructive traits and palmito yield of assai palms

    Directory of Open Access Journals (Sweden)

    Marilene Leão Alves Bovi

    1990-01-01

    Full Text Available Estudaram-se caracteres vegetativos da planta e do palmito de açaizeiros (Euterpe oleracea Mart cultivados na Estação Experimental de Ubatuba, litoral norte do Estado de São Paulo, Brasil, com o objetivo principal de identificar caracteres não-destrutíveis que possam ser utilizados na seleção de plantas superiores no programa de melhoramento genético dessa palmeira. Entre os dez caracteres estudados, o número de perfilhos, o peso bruto do palmito e os pesos do resíduo basal e do palmito mostraram maior variabilidade (CV acima de 40%. Menor variabilidade foi encontrada para os caracteres número de folhas e circunferência da planta-mãe (CV entre 14 e 18%. O peso, os diâmetros e o comprimento do palmito mostraram-se positivamente correlacionados com a circunferência da planta. Correlação negativa foi evidenciada entre peso bruto do palmito e número de perfilhos e entre esta última variável e o peso do resíduo basal. O número de folhas mostrou correlação parcial significativa apenas com o diâmetro médio do palmito e com o peso do palmito bruto. Entre os caracteres vegetativos não-destrutíveis avaliados, a circunferência da planta foi o que mais contribuiu para a variação apresentada pelo palmito bruto e liquído (peso, diâmetro e comprimento, sendo responsável por mais de 65% da variação do peso bruto, 35% do peso líquido e em tomo de 50% de seu diâmetro. Constitui-se, assim, em um caráter útil, além de não-destrutível e facilmente mensurável, para orientar a seleção de plantas superiores de açaizeiro num programa de melhoramento genético de palmeiras desta espécie.Three vegetative characters and palmito yield components of assai palms (Euterpe oleracea Mart. were studied in an experiment at Ubatuba, State of São Paulo, Brazil, in order to identify non-destructive traits that could be used to estimate yield in superior material evaluation and selection. Partial correlation coefficients showed

  19. Divergência genética entre acessos de batata-doce utilizando caracteres fenotípicos de raiz Genetic divergence among sweet potato accessions based on root traits

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    Giovani O da Silva

    2012-12-01

    Full Text Available Estudos de quantificação da divergência genética entre acessos e caracterização dos recursos genéticos têm sido de grande importância em programas de melhoramento, auxiliando na identificação de genitores e no conhecimento do material genético disponível. Os objetivos do presente trabalho foram: (1 avaliar os acessos de batata-doce pertencentes ao banco de germoplasma da Embrapa com base em caracteres de raiz; (2 calcular a importância relativa dos caracteres morfo-agronômicos quantitativos na discriminação dos acessos e, (3 obter indicações das combinações híbridas mais promissoras para cruzamentos. Foi avaliada uma coleção de 11 clones pertencentes ao Banco Ativo de Germoplasma da Embrapa por meio de um experimento conduzido na Embrapa SPM/EN, em Canoinhas-SC. Os acessos foram cultivados em condições de campo no delineamento em blocos ao acaso com quatro repetições, onde a parcela experimental foi composta por 10 plantas. As plantas de cada parcela foram colhidas e avaliadas para 12 caracteres fenotípicos de raiz. O estudo indicou que os caracteres número e massa total de raízes e peso específico foram os que mais contribuíram para a divergência genética. A maioria dos acessos é bastante similar quanto aos caracteres quantitativos avaliados. Porém, há a possibilidade de ganhos com a heterose, geração de variabilidade genética e de progênies superiores cruzando-se os acessos dos diferentes grupamentos formados; pois os genótipos mais contrastantes '1228', '051-1' e '1270' foram agrupados entre os melhores para várias características como massa e número total de raízes, massa comercial de raízes; os dois primeiros apresentaram elevado peso específico e o '1270' apresentou coloração alaranjada intensa, indicativo de alto teor de β-caroteno.The estimation of the genetic divergence among accessions of a germplasm bank, as well as their characterization are very important in breeding programs in

  20. Genetic dissection of fruit quality traits in the octoploid cultivated strawberry highlights the role of homoeo-QTL in their control.

    Science.gov (United States)

    Lerceteau-Köhler, E; Moing, A; Guérin, G; Renaud, C; Petit, A; Rothan, C; Denoyes, Béatrice

    2012-04-01

    Fruit quality traits are major breeding targets in the Rosaceae. Several of the major Rosaceae species are current or ancient polyploids. To dissect the inheritance of fruit quality traits in polyploid fleshy fruit species, we used a cultivated strawberry segregating population comprising a 213 full-sibling F1 progeny from a cross between the variety 'Capitola' and the genotype 'CF1116'. We previously developed the most comprehensive strawberry linkage map, which displays seven homoeology groups (HG), including each four homoeology linkage groups (Genetics 179:2045-2060, 2008). The map was used to identify quantitative trait loci (QTL) for 19 fruit traits related to fruit development, texture, colour, anthocyanin, sugar and organic acid contents. Analyses were carried out over two or three successive years on field-grown plants. QTL were detected for all the analysed traits. Because strawberry is an octopolyploid species, QTL controlling a given trait and located at orthologous positions on different homoeologous linkage groups within one HG are considered as homoeo-QTL. We found that, for various traits, about one-fourth of QTL were putative homoeo-QTL and were localised on two linkage groups. Several homoeo-QTL could be detected the same year, suggesting that several copies of the gene underlying the QTL are functional. The detection of some other homoeo-QTL was year-dependent. Therefore, changes in allelic expression could take place in response to environmental changes. We believe that, in strawberry as in other polyploid fruit species, the mechanisms unravelled in the present study may play a crucial role in the variations of fruit quality.

  1. QTL Analysis of Fiber Yield and Quality and Resistance to Verticillium Wilt Using Gossypium hirsutum and G.barbadense Advanced Backcross Populations

    Institute of Scientific and Technical Information of China (English)

    LI Ai-guo; WANG Tao; YUAN You-lu; LIU Guang-ping; ZHANG Bao-cai; LI Jun-wen; SHI Yu-zhen; LIU Ai-ying; YANG Ze-mao; LIU Zhi; YU Xiao-nan

    2008-01-01

    @@ To introgress elite QTL alleles of Gossypium barbadense L.for fiber yield and quality and resistance to Verticillium wilt into G.hirsutum L.,enlarge the genetic base of G.hirsutum,and provide new germplasm resources for the variety development,the cultivars Zhongmiansuo 36,G.hirsutum,and Hai 1,G.barbadense,were used as recurrent and donor parent,respectively,to produce BC1 F1,BC1S1,and BC2F1 populations.QTL analyses of fiber quality,yield-related,Key words: interspecific backcrosss; AB-QTL; fiber quality; yield; Verticillium wilt resistance

  2. QTL Mapping of Agronomic Waterlogging Tolerance Using Recombinant Inbred Lines Derived from Tropical Maize (Zea mays L) Germplasm

    Science.gov (United States)

    Zaidi, Pervez Haider; Rashid, Zerka; Vinayan, Madhumal Thayil; Almeida, Gustavo Dias; Phagna, Ramesh Kumar; Babu, Raman

    2015-01-01

    Waterlogging is an important abiotic stress constraint that causes significant yield losses in maize grown throughout south and south-east Asia due to erratic rainfall patterns. The most economic option to offset the damage caused by waterlogging is to genetically incorporate tolerance in cultivars that are grown widely in the target agro-ecologies. We assessed the genetic variation in a population of recombinant inbred lines (RILs) derived from crossing a waterlogging tolerant line (CAWL-46-3-1) to an elite but sensitive line (CML311-2-1-3) and observed significant range of variation for grain yield (GY) under waterlogging stress along with a number of other secondary traits such as brace roots (BR), chlorophyll content (SPAD), % stem and root lodging (S&RL) among the RILs. Significant positive correlation of GY with BR and SPAD and negative correlation with S&RL indicated the potential use of these secondary traits in selection indices under waterlogged conditions. RILs were genotyped with 331 polymorphic single nucleotide polymorphism (SNP) markers using KASP (Kompetitive Allele Specific PCR) Platform. QTL mapping revealed five QTL on chromosomes 1, 3, 5, 7 and 10, which together explained approximately 30% of phenotypic variance for GY based on evaluation of RIL families under waterlogged conditions, with effects ranging from 520 to 640 kg/ha for individual genomic regions. 13 QTL were identified for various secondary traits associated with waterlogging tolerance, each individually explaining from 3 to 14% of phenotypic variance. Of the 22 candidate genes with known functional domains identified within the physical intervals delimited by the flanking markers of the QTL influencing GY and other secondary traits, six have previously been demonstrated to be associated with anaerobic responses in either maize or other model species. A pair of flanking SNP markers has been identified for each of the QTL and high throughput marker assays were developed to facilitate

  3. Genetic mapping and QTL analysis of growth-related traits in Pinctada fucata using restriction-site associated DNA sequencing.

    Directory of Open Access Journals (Sweden)

    Yaoguo Li

    Full Text Available The pearl oyster, Pinctada fucata (P. fucata, is one of the marine bivalves that is predominantly cultured for pearl production. To obtain more genetic information for breeding purposes, we constructed a high-density linkage map of P. fucata and identified quantitative trait loci (QTL for growth-related traits. One F1 family, which included the two parents, 48 largest progeny and 50 smallest progeny, was sampled to construct a linkage map using restriction site-associated DNA sequencing (RAD-Seq. With low coverage data, 1956.53 million clean reads and 86,342 candidate RAD loci were generated. A total of 1373 segregating SNPs were used to construct a sex-average linkage map. This spanned 1091.81 centimorgans (cM, with 14 linkage groups and an average marker interval of 1.41 cM. The genetic linkage map coverage, Coa, was 97.24%. Thirty-nine QTL-peak loci, for seven growth-related traits, were identified using the single-marker analysis, nonparametric mapping Kruskal-Wallis (KW test. Parameters included three for shell height, six for shell length, five for shell width, four for hinge length, 11 for total weight, eight for soft tissue weight and two for shell weight. The QTL peak loci for shell height, shell length and shell weight were all located in linkage group 6. The genotype frequencies of most QTL peak loci showed significant differences between the large subpopulation and the small subpopulation (P<0.05. These results highlight the effectiveness of RAD-Seq as a tool for generation of QTL-targeted and genome-wide marker data in the non-model animal, P. fucata, and its possible utility in marker-assisted selection (MAS.

  4. QTL IciMapping:Integrated software for genetic linkage map construction and quantitative trait locus mapping in biparental populations

    Institute of Scientific and Technical Information of China (English)

    Lei Meng; Huihui Li; Luyan Zhang; Jiankang Wang

    2015-01-01

    QTL IciMapping is freely available public software capable of building high-density linkage maps and mapping quantitative trait loci (QTL) in biparental populations. Eight func-tionalities are integrated in this software package: (1) BIN:binning of redundant markers;(2) MAP: construction of linkage maps in biparental populations; (3) CMP: consensus map construction from multiple linkage maps sharing common markers; (4) SDL: mapping of segregation distortion loci;(5) BIP:mapping of additive, dominant, and digenic epistasis genes;(6) MET:QTL-by-environment interaction analysis;(7) CSL:mapping of additive and digenic epistasis genes with chromosome segment substitution lines; and (8) NAM: QTL mapping in NAM populations. Input files can be arranged in plain text, MS Excel 2003, or MS Excel 2007 formats. Output files have the same prefix name as the input but with different extensions. As examples, there are two output files in BIN, one for summarizing the identified bin groups and deleted markers in each bin, and the other for using the MAP functionality. Eight output files are generated by MAP, including summary of the completed linkage maps, Mendelian ratio test of individual markers, estimates of recombination frequencies, LOD scores, and genetic distances, and the input files for using the BIP, SDL, and MET functionalities. More than 30 output files are generated by BIP, including results at all scanning positions, identified QTL, permutation tests, and detection powers for up to six mapping methods. Three supplementary tools have also been developed to display completed genetic linkage maps, to estimate recombination frequency between two loci, and to perform analysis of variance for multi-environmental trials.

  5. QTL IciMapping:Integrated software for genetic linkage map construction and quantitative trait locus mapping in biparental populations

    Institute of Scientific and Technical Information of China (English)

    Lei; Meng; Huihui; Li; Luyan; Zhang; Jiankang; Wang

    2015-01-01

    QTL Ici Mapping is freely available public software capable of building high-density linkage maps and mapping quantitative trait loci(QTL) in biparental populations. Eight functionalities are integrated in this software package:(1) BIN: binning of redundant markers;(2) MAP: construction of linkage maps in biparental populations;(3) CMP: consensus map construction from multiple linkage maps sharing common markers;(4) SDL: mapping of segregation distortion loci;(5) BIP: mapping of additive, dominant, and digenic epistasis genes;(6) MET: QTL-by-environment interaction analysis;(7) CSL: mapping of additive and digenic epistasis genes with chromosome segment substitution lines; and(8) NAM: QTL mapping in NAM populations. Input files can be arranged in plain text, MS Excel 2003, or MS Excel 2007 formats. Output files have the same prefix name as the input but with different extensions. As examples, there are two output files in BIN, one for summarizing the identified bin groups and deleted markers in each bin, and the other for using the MAP functionality. Eight output files are generated by MAP, including summary of the completed linkage maps, Mendelian ratio test of individual markers, estimates of recombination frequencies, LOD scores, and genetic distances, and the input files for using the BIP, SDL,and MET functionalities. More than 30 output files are generated by BIP, including results at all scanning positions, identified QTL, permutation tests, and detection powers for up to six mapping methods. Three supplementary tools have also been developed to display completed genetic linkage maps, to estimate recombination frequency between two loci,and to perform analysis of variance for multi-environmental trials.

  6. Identification of a major QTL allele from wild soybean (Glycine soja Sieb. & Zucc.) for increasing alkaline salt tolerance in soybean.

    Science.gov (United States)

    Tuyen, D D; Lal, S K; Xu, D H

    2010-07-01

    Salt-affected soils are generally classified into two main categories, sodic (alkaline) and saline. Our previous studies showed that the wild soybean accession JWS156-1 (Glycine soja) from the Kinki area of Japan was tolerant to NaCl salt, and the quantitative trait locus (QTL) for NaCl salt tolerance was located on soybean linkage group N (chromosome 3). Further investigation revealed that the wild soybean accession JWS156-1 also had a higher tolerance to alkaline salt stress. In the present study, an F(6) recombinant inbred line mapping population (n = 112) and an F(2) population (n = 149) derived from crosses between a cultivated soybean cultivar Jackson and JWS156-1 were used to identify QTL for alkaline salt tolerance in soybean. Evaluation of soybean alkaline salt tolerance was carried out based on salt tolerance rating (STR) and leaf chlorophyll content (SPAD value) after treatment with 180 mM NaHCO(3) for about 3 weeks under greenhouse conditions. In both populations, a significant QTL for alkaline salt tolerance was detected on the molecular linkage group D2 (chromosome 17), which accounted for 50.2 and 13.0% of the total variation for STR in the F(6) and the F(2) populations, respectively. The wild soybean contributed to the tolerance allele in the progenies. Our results suggest that QTL for alkaline salt tolerance is different from the QTL for NaCl salt tolerance found previously in this wild soybean genotype. The DNA markers closely associated with the QTLs might be useful for marker-assisted selection to pyramid tolerance genes in soybean for both alkaline and saline stresses.

  7. Dissection of two soybean QTL conferring partial resistance to Phytophthora sojae through sequence and gene expression analysis

    Directory of Open Access Journals (Sweden)

    Wang Hehe

    2012-08-01

    Full Text Available Abstract Background Phytophthora sojae is the primary pathogen of soybeans that are grown on poorly drained soils. Race-specific resistance to P. sojae in soybean is gene-for-gene, although in many areas of the US and worldwide there are populations that have adapted to the most commonly deployed resistance to P. sojae ( Rps genes. Hence, this system has received increased attention towards identifying mechanisms and molecular markers associated with partial resistance to this pathogen. Several quantitative trait loci (QTL have been identified in the soybean cultivar ‘Conrad’ that contributes to the expression of partial resistance to multiple P. sojae isolates. Results In this study, two of the Conrad QTL on chromosome 19 were dissected through sequence and expression analysis of genes in both resistant (Conrad and susceptible (‘Sloan’ genotypes. There were 1025 single nucleotide polymorphisms (SNPs in 87 of 153 genes sequenced from Conrad and Sloan. There were 304 SNPs in 54 genes sequenced from Conrad compared to those from both Sloan and Williams 82, of which 11 genes had SNPs unique to Conrad. Eleven of 19 genes in these regions analyzed with qRT-PCR had significant differences in fold change of transcript abundance in response to infection with P. sojae in lines with QTL haplotype from the resistant parent compared to those with the susceptible parent haplotype. From these, 8 of the 11 genes had SNPs in the upstream, untranslated region, exon, intron, and/or downstream region. These 11 candidate genes encode proteins potentially involved in signal transduction, hormone-mediated pathways, plant cell structural modification, ubiquitination, and basal resistance. Conclusions These findings may indicate a complex defense network with multiple mechanisms underlying these two soybean QTL conferring resistance to P. sojae. SNP markers derived from these candidate genes can contribute to fine mapping of QTL and marker assisted breeding for

  8. Análisis de la expresión transcripcional del receptor de estrógeno en ovario de ovejas prepúberes de razas Texel y Criolla Araucana mediante RT-PCR cuantitativo en tiempo real

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    M Flores

    2015-01-01

    Full Text Available El estado morfofuncional del sistema reproductivo de las ovejas es determinado por las hormonas sexuales, que actúan por medio de receptores específicos, desencadenando una serie de cambios celulares, metabólicos y proliferativos dependientes de la expresión de numerosos genes. A diferencia de otros mamíferos, las ovejas presentan en el endometrio y posiblemente otros órganos del sistema reproductivo receptores de estrógenos fisiológicamente activos desde la etapa prepuberal cuya función aún no está esclarecida. La información sobre la expresión de receptores de hormonas sexuales en el aparato reproductor es muy escasa, sobre todo en el ovario y no existen estudios que correlacionen la raza con la expresión de estos receptores. Generalmente los criadores privilegian razas de mayor nivel de prolificidad y esto podría estar relacionado con el nivel de expresión de los receptores de estrógeno en el sistema reproductivo. El objetivo del presente trabajo fue evaluar comparativamente la expresión transcripcional del receptor de estrógeno en el ovario de ovejas prepúberes de raza Texel de alta prolificidad y de raza Criolla Araucana de prolificidad estándar, mediante análisis de RT-PCR en tiempo real cuantitativo.

  9. La calidad de la Universidad en España. Autoevaluación del Departamento de Métodos Cuantitativos para la Economía de la USP-CEU.

    Directory of Open Access Journals (Sweden)

    Casas Guillén, Mercedes

    2001-01-01

    Full Text Available La entrada de España en la Unión Europea ha significado su integración en todos los ámbitos, y en particular en la enseñanza universitaria. Para lograr una coordinación en la Enseñanza Superior Europea es preciso realizar una evaluación previa de su calidad. Con este fin, en el ámbito europeo se han implantado sistemas homogéneos de evaluación de la calidad de la enseñanza superior. En España, el Consejo de Universidades impulsó en 1995 el establecimiento del Plan Nacional de Evaluación de la Calidad de las Universidades. La Universidad San Pablo-CEU se ha incorporado a este Plan desde sus inicios, siendo evaluada en el pasado curso la Facultad de Ciencias Económicas y Empresariales, implicando a todas las Titulaciones que se imparten en la misma. El Departamento de Métodos Cuantitativos para la Economía ha realizado un Informe de Autoevaluación de la Calidad en la que se han recogido los aspectos relativos a la docencia y a la investigación. En este Trabajo ponemos de manifiesto cómo ha afectado la autoevaluación de la calidad de la docencia en las asignaturas de Matemáticas y Estadística.

  10. Association mapping of common bacterial blight resistance QTL in Ontario bean breeding populations

    Directory of Open Access Journals (Sweden)

    Navabi Alireza

    2011-03-01

    Full Text Available Abstract Background Common bacterial blight (CBB, incited by Xanthomonas axonopodis pv. phaseoli (Xap, is a major yield-limiting factor of common bean (Phaseolus vulgaris L. production around the world. Host resistance is practically the most effective and environmentally-sound approach to control CBB. Unlike conventional QTL discovery strategies, in which bi-parental populations (F2, RIL, or DH need to be developed, association mapping-based strategies can use plant breeding populations to synchronize QTL discovery and cultivar development. Results A population of 469 dry bean lines of different market classes representing plant materials routinely developed in a bean breeding program were used. Of them, 395 lines were evaluated for CBB resistance at 14 and 21 DAI (Days After Inoculation in the summer of 2009 in an artificially inoculated CBB nursery in south-western Ontario. All lines were genotyped using 132 SNPs (Single Nucleotide Polymorphisms evenly distributed across the genome. Of the 132 SNPs, 26 SNPs had more than 20% missing data, 12 SNPs were monomorphic, and 17 SNPs had a MAF (Minor Allelic Frequency of less than 0.20, therefore only 75 SNPs were used for association study, based on one SNP per locus. The best possible population structure was to assign 36% and 64% of the lines into Andean and Mesoamerican subgroups, respectively. Kinship analysis also revealed complex familial relationships among all lines, which corresponds with the known pedigree history. MLM (Mixed Linear Model analysis, including population structure and kinship, was used to discover marker-trait associations. Eighteen and 22 markers were significantly associated with CBB rating at 14 and 21 DAI, respectively. Fourteen markers were significant for both dates and the markers UBC420, SU91, g321, g471, and g796 were highly significant (p ≤ 0.001. Furthermore, 12 significant SNP markers were co-localized with or close to the CBB-QTLs identified previously in bi

  11. QTL mapping of partial resistance in winter wheat to Stagonospora nodorum blotch.

    Science.gov (United States)

    Czembor, Pawel C; Arseniuk, Edward; Czaplicki, Andrzej; Song, Qijiang; Cregan, Perry B; Ueng, Peter P

    2003-08-01

    Stagonospora nodorum blotch is an important foliar and glume disease in cereals. Inheritance of resistance in wheat appears to be quantitative. To date, breeding of partially resistant cultivars has been the only effective way to combat this pathogen. The partial resistance components, namely length of incubation period, disease severity, and length of latent period, were evaluated on a population of doubled haploids derived from a cross between the partially resistant Triticum aestivum 'Liwilla' and susceptible Triticum aestivum 'Begra'. Experiments were conducted in a controlled environment and the fifth leaf was examined. Molecular analyses were based on bulked segregant analyses using 240 microsatellite markers. Four QTLs were significantly associated with partial resistance components and were located on chromosomes 2B, 3B, 5B, and 5D. The percentage of phenotypic variance explained by a single QTL ranged from 14 to 21% for incubation period, from 16 to 37% for disease severity, and from 13 to 28% for latent period,

  12. Detection of differentially expressed candidate genes for a fatty liver QTL on mouse chromosome 12

    OpenAIRE

    Kobayashi, Misato; Suzuki, Miyako; Ohno, Tamio; Tsuzuki, Kana; Taguchi, Chie; Tateishi, Soushi; Kawada, Teruo; Kim, Young-Il; Murai, Atsushi; Horio, Fumihiko

    2016-01-01

    Background The SMXA-5 mouse is an animal model of high-fat diet-induced fatty liver. The major QTL for fatty liver, Fl1sa on chromosome 12, was identified in a SM/J × SMXA-5 intercross. The SMXA-5 genome consists of the SM/J and A/J genomes, and the A/J allele of Fl1sa is a fatty liver-susceptibility allele. The existence of the responsible genes for fatty liver within Fl1sa was confirmed in A/J-12SM consomic mice. The aim of this study was to identify candidate genes for Fl1sa, and to invest...

  13. QTL analysis by sequencing of Water Use Efficiency (WUE) in potato

    DEFF Research Database (Denmark)

    Kaminski, Kacper Piotr; Sønderkær, Mads; Sørensen, Kirsten Kørup;

    2013-01-01

    The traditional approach to potato breeding, the classical “mate and phenotype” approach is relatively costly and because phenotyping and growth capacity is limited, this are being slowly replaced by Marker Assisted Selection (MAS) breeding schemes. MAS is based on the presence of DNA polymorphic...... markers closely associated with trait of interest and as such allows screening of much larger effective populations in a cost-effective manner already at the seed or seedling stages. However, it requires discovery and development of relevant molecular markers, which up to recently has been both costly...... and time consuming process. Here, a novel method for Quantitative Trait Locus (QTL) analysis has been developed, that allows for development of specific markers by use of genomic sequence reads and the recently published reference genome sequence for potato. Prior to sequencing the mapping population...

  14. QTL analysis of cadmium and zinc accumulation in the heavy metal hyperaccumulator Thlaspi caerulescens.

    Science.gov (United States)

    Deniau, A X; Pieper, B; Ten Bookum, W M; Lindhout, P; Aarts, M G M; Schat, H

    2006-09-01

    Thlaspi caerulescens (Tc; 2n = 14) is a natural Zn, Cd and Ni hyperaccumulator species belonging to the Brassicaceae family. It shares 88% DNA identity in the coding regions with Arabidopsis thaliana (At) (Rigola et al. 2006). Although the physiology of heavy metal (hyper)accumulation has been intensively studied, the molecular genetics are still largely unexplored. We address this topic by constructing a genetic map based on AFLP markers and expressed sequence tags (ESTs). To establish a genetic map, an F(2) population of 129 individuals was generated from a cross between a plant from a Pb/Cd/Zn-contaminated site near La Calamine, Belgium, and a plant from a comparable site near Ganges (GA), France. These two accessions show different degrees of Zn and, particularly, Cd accumulation. We analyzed 181 AFLP markers (of which 4 co-dominant) and 13 co-dominant EST sequences-based markers and mapped them to seven linkage groups (LGs), presumably corresponding to the seven chromosomes of T. caerulescens. The total length of the genetic map is 496 cM with an average density of one marker every 2.5 cM. This map was used for Quantitative Trait Locus (QTL) mapping in the F(2). For Zn as well as Cd concentration in root we mapped two QTLs. Three QTLs and one QTL were mapped for Zn and Cd concentration in shoot, respectively. These QTLs explain 23.8-60.4% of the total variance of the traits measured. We found only one common locus (LG6) for Zn and Cd (concentration in root) and one common locus for shoot and root concentrations of Zn (LG1) and of Cd (LG3). For all QTLs, the GA allele increased the trait value except for two QTLs for Zn accumulation in shoot (LG1 and LG4) and one for Zn concentration in root (LG1). PMID:16850314

  15. [The construction of the genetic map and QTL locating analysis on chromosome 2 in swine].

    Science.gov (United States)

    Qu, Yan-Chun; Deng, Chang-Yan; Xiong, Yuan-Zhu; Zheng, Rong; Yu, Li; Su, Yu-Hong; Liu, Gui-Lan

    2002-01-01

    The study constructed the genetic linkage map of porcine chromosome 2 and further analysis of quantitative trait loci was conducted. The results of the study demonstrated that all 7 microsatellite loci we chose were with relatively high polymorphism, and its polymorphic information content was from 0.40182 to 0.58477. The genetic map we constructed for resource family was 152.9 cM in length, with the order of all loci highly consistent with the USDA map. All marker intervals were longer than USDA map with the interval between marker Sw2516 and Sw1201 as an exception. Furthermore, we conducted QTLs locating analysis by combining the genetic map with the phenotypic data. QTLs affecting lively estimated traits such as lean meat percentage, were located at 60-65 cM on chromosome 2, while QTLs for the height and marbling of Longissmus dorsi muscle were located at 20 cM and 55 cM, respectively Among them, QTL for estimated lean meat percentage was significant at chromosome-wise level (P < 0.01) and was responsible for 21.55% of the phenotypic variance. QTLs for the height and marbling of Longissmus dorsi muscle were responsible for 10.12% and 10.97% of the phenotypic variance, respectively. The additive and dominance effect of lively estimated traits were in the inverse tendency, while the QTL for the height of Longissmus dorsi muscle had its additive and dominance effect in the same tendency and was with advantageous allele in Large White. The QTLs we detected had relatively large effect on phenotype and built a basis for molecular marker assisted selection and breeding.

  16. QTL associated with horizontal resistance to soybean cyst nematode in Glycine soja PI464925B.

    Science.gov (United States)

    Winter, Shawn M J; Shelp, Barry J; Anderson, Terry R; Welacky, Tom W; Rajcan, Istvan

    2007-02-01

    Soybean cyst nematode (Heterodera glycines Ichinohe; SCN) is the primary disease responsible for yield loss of soybean [Glycine max (L.) Merr.]. Resistant cultivars are an effective management tool; however, the sources currently available have common resistant genes. Glycine soja Sieb. and Zucc., the wild ancestor of domesticated soybean, represents a diverse germplasm pool with known SCN resistance. The objectives of this research were to: (1) determine the genetic variation and inheritance of SCN resistance in a G. max ('S08-80') x G. soja (PI464925B) F (4:5) recombinant inbred line (RIL) population; and (2) identify and evaluate quantitative trait loci (QTL) associated with SCN resistance. Transgressive segregation for resistance was observed, although neither parent was resistant to the Chatham and Ruthven SCN isolates. Broad sense heritability was 0.81 for the Ruthven and 0.91 for the Chatham isolate. Root dry weight was a significant covariate that influenced cyst counts. One RIL [female index (FI) = 5.2 +/- 1.11] was identified as resistant to the Chatham isolate (FI soja, were identified on linkage groups I, K, and O, and individually explained 8, 7 and 5% (LOD = 2.1-2.7) of the total phenotypic variation, respectively. Significant epistatic interactions were found between pairs of SSR markers that individually may or may not have been associated with SCN resistance, which explained between 10 and 15% of the total phenotypic variation. Best-fit regression models explained 21 and 31% of the total phenotypic variation in the RIL population to the Chatham and Ruthven isolates, respectively. The results of this study help to improve the understanding of the genetic control of SCN resistance in soybean caused by minor genes resulting in horizontal resistance. The incorporation of the novel resistance QTL from G. soja could increase the durability of SCN-resistance in soybean cultivars, especially if major gene resistance breaks down.

  17. Development of selective markers linked to a major QTL for parthenocarpy in eggplant (Solanum melongena L.).

    Science.gov (United States)

    Miyatake, Koji; Saito, Takeo; Negoro, Satomi; Yamaguchi, Hirotaka; Nunome, Tsukasa; Ohyama, Akio; Fukuoka, Hiroyuki

    2012-05-01

    Parthenocarpy, the ability to set fruits without pollination, is a useful trait for setting fruit under unfavorable conditions. To identify the loci controlling parthenocarpy in eggplant (Solanum melongena L.), we constructed linkage maps by using co-dominant simple sequence repeat and single nucleotide polymorphism markers in F(2) populations derived from intraspecific crosses between two non-parthenocarpic lines (LS1934 and Nakate-Shinkuro) and a parthenocarpic line (AE-P03). Total map distances were 1,414.6 cM (ALF2: LS1934 x AE-P03) and 1,153.8 cM (NAF2: Nakate-Shinkuro x AE-P03), respectively. Quantitative trait locus (QTL) analyses revealed two QTLs on chromosomes 3 and 8, which we denoted as Controlling parthenocarpy3.1 (Cop3.1) and Cop8.1, respectively. The percentage of phenotypic variance explained (PVE) of Cop3.1 was 6.3% in ALF2 (LOD = 4.2) and 10.6% in NAF2 (LOD = 3.0). The PVE of Cop8.1 was 45.7% in ALF2 (LOD = 23.8) and 29.7% in NAF2 (LOD = 7.9). Using a population of backcross inbred lines, we confirmed the effect of Cop8.1, but there was no evidence to support the contribution of Cop3.1. We need to verify the effect of Cop3.1 under various temperature conditions. In addition, we clarified the effectiveness of selective SSR markers, emf21H22 and emh11J10, mapped on each side of Cop8.1 in other F(2) populations derived from various parental combinations. This is the first report concerning QTL analysis of parthenocarpy in eggplant using molecular markers. It will be useful in marker-assisted selection and in revealing the genomic mechanism underlying parthenocarpy in eggplant. PMID:22301906

  18. [The construction of the genetic map and QTL locating analysis on chromosome 2 in swine].

    Science.gov (United States)

    Qu, Yan-Chun; Deng, Chang-Yan; Xiong, Yuan-Zhu; Zheng, Rong; Yu, Li; Su, Yu-Hong; Liu, Gui-Lan

    2002-01-01

    The study constructed the genetic linkage map of porcine chromosome 2 and further analysis of quantitative trait loci was conducted. The results of the study demonstrated that all 7 microsatellite loci we chose were with relatively high polymorphism, and its polymorphic information content was from 0.40182 to 0.58477. The genetic map we constructed for resource family was 152.9 cM in length, with the order of all loci highly consistent with the USDA map. All marker intervals were longer than USDA map with the interval between marker Sw2516 and Sw1201 as an exception. Furthermore, we conducted QTLs locating analysis by combining the genetic map with the phenotypic data. QTLs affecting lively estimated traits such as lean meat percentage, were located at 60-65 cM on chromosome 2, while QTLs for the height and marbling of Longissmus dorsi muscle were located at 20 cM and 55 cM, respectively Among them, QTL for estimated lean meat percentage was significant at chromosome-wise level (P < 0.01) and was responsible for 21.55% of the phenotypic variance. QTLs for the height and marbling of Longissmus dorsi muscle were responsible for 10.12% and 10.97% of the phenotypic variance, respectively. The additive and dominance effect of lively estimated traits were in the inverse tendency, while the QTL for the height of Longissmus dorsi muscle had its additive and dominance effect in the same tendency and was with advantageous allele in Large White. The QTLs we detected had relatively large effect on phenotype and built a basis for molecular marker assisted selection and breeding. PMID:12645259

  19. Genetic mapping and identification of QTL for earliness in the globe artichoke/cultivated cardoon complex

    Directory of Open Access Journals (Sweden)

    Portis Ezio

    2012-05-01

    Full Text Available Abstract Background The Asteraceae species Cynara cardunculus (2n = 2x = 34 includes the two fully cross-compatible domesticated taxa globe artichoke (var. scolymus L. and cultivated cardoon (var. altilis DC. As both are out-pollinators and suffer from marked inbreeding depression, linkage analysis has focussed on the use of a two way pseudo-test cross approach. Results A set of 172 microsatellite (SSR loci derived from expressed sequence tag DNA sequence were integrated into the reference C. cardunculus genetic maps, based on segregation among the F1 progeny of a cross between a globe artichoke and a cultivated cardoon. The resulting maps each detected 17 major linkage groups, corresponding to the species’ haploid chromosome number. A consensus map based on 66 co-dominant shared loci (64 SSRs and two SNPs assembled 694 loci, with a mean inter-marker spacing of 2.5 cM. When the maps were used to elucidate the pattern of inheritance of head production earliness, a key commercial trait, seven regions were shown to harbour relevant quantitative trait loci (QTL. Together, these QTL accounted for up to 74% of the overall phenotypic variance. Conclusion The newly developed consensus as well as the parental genetic maps can accelerate the process of tagging and eventually isolating the genes underlying earliness in both the domesticated C. cardunculus forms. The largest single effect mapped to the same linkage group in each parental maps, and explained about one half of the phenotypic variance, thus representing a good candidate for marker assisted selection.

  20. Seleção precoce de clones de batata para caracteres do tubérculo Early selection of potato clones for tuber characters

    Directory of Open Access Journals (Sweden)

    Geovani Bernardo Amaro

    2003-06-01

    Full Text Available Nos últimos anos, foi despertado um grande interesse para o processamento da batata na forma de fritura no Brasil. Visando à obtenção de cultivares nacionais que atendam aos padrões de qualidade culinária exigidos pelas indústrias de processamento, os programas de melhoramento de batata têm estabelecido estratégias para a redução de custos e de tempo. Realizou-se este trabalho com o objetivo de avaliar a eficiência da seleção precoce de clones de batata (Solanum tuberosum L. para características de importância ao processamento na forma de fritura. Os caracteres avaliados foram: peso específico de tubérculos, índices de formato de tubérculos e notas na glico-fita, mediante correlações entre as gerações seedling (S, primeira geração clonal (C-1 e segunda geração clonal (C-2, entre clones e entre famílias. Os experimentos foram conduzidos no sul do estado de Minas Gerais, Brasil. As correlações foram significativas na maioria dos casos, porém, baixas e geralmente apresentaram maiores valores quando consideradas entre famílias, indicando a baixa eficiência da seleção precoce entre clones. Assim, deve ser praticada somente para se eliminar as piores famílias. A correlação para o índice de formato de tubérculo (comprimento/diâmetro maior entre as gerações S e C-1 foi de 0,51 entre clones e 0,77 entre famílias e ambos os valores foram significativos, indicando uma razoável eficiência da seleção precoce para esse caráter tanto entre clones como entre famílias.The purpose of this research was to assess the effectiveness of early selection for tuber specific gravity, tuber shape index, and reducing sugars content in the tubers of potato (Solanum tuberosum L. clones. The experiments were conducted in the south of the State of Minas Gerais, Brazil. Correlation coefficients were determined for the seedling (S and first (FCG and second (SCG clonal generations at the clones and families levels. In general

  1. Los sistemas geotermales del Pirineo central. I. Caracteres geoquímicos y fisicoquímicos de los manantiales termales

    Directory of Open Access Journals (Sweden)

    Gómez, J.

    1996-08-01

    ás, comunes a los existentes en otros sistemas pirenaicos y característicos de la tipología de aguas termales alcalinas asociadas a materiales graníticos. Sin embargo y más específicamente, las concentraciones de Na y K en las aguas de Panticosa y Benasque son las más bajas de todas las definidas hasta el momento en este grupo de aguas termales alcalinas. Los valores de pH de los manantiales termales se encuentran relacionados con la temperatura de surgencia y, como ocurre en el resto de sistemas geotermales pirenaicos, dependen de la intensidad del proceso de enfriamiento durante el ascenso de la solución. Los cálculos de especiación en condiciones de surgencia indican que: los valores de presión parcial de CO2 de las soluciones son muy bajos; la sílice disuelta se encuentra parcialmente ionizada; y la especie Al(OH4- es la forma dominante de aluminio en solución. Los índices de saturación obtenidos demuestran que casi todas las aguas consideradas se encuentran sobresaturadas respecto a cuarzo (próximas al equilibrio con calcedonia, feldespato potásico y albita, minerales con los que factiblemente las soluciones establecen relaciones de equilibrio en el reservorio. Pero, además, todas las aguas se encuentran en situaciones de equilibrio respecto a calcita y caolinita en condiciones de surgencia, lo que demuestra la existencia de procesos de reequilibrio durante su ascenso hasta los manantiales y evidencia uno de los caracteres más importantes en la evolución geoquímica de este tipo de sistemas alcalinos.

  2. Relação entre diferentes caracteres de plantas jovens de seringueira Correlations and regressions studies among juvenile rubber tree characters

    Directory of Open Access Journals (Sweden)

    César Lavorenti

    1990-01-01

    Full Text Available O presente trabalho foi realizado com o objetivo de determinar a existência e as magnitudes de correlações e regressões lineares simples em plântulas jovens de seringueira (Hevea spp., para melhor condução de seleção nos futuros trabalhos de melhoramento. Foram utilizadas médias de produção de borracha seca por plântulas por corte, através do teste Hamaker-Morris-Mann (P; circunferência do caule (CC; espessura de casca (EC; número de anéis (NA; diâmetro dos vasos (DV; densidade dos vasos laticíleros (D e distância média entre anéis de vasos consecutivos (DMEAVC em um viveiro de cruzamento com três anos e meio de idade. Os resultados mostraram, entre outros fatores, que as correlações lineares simples de P com CC, EC, NA, D, DV e DMEAVC foram, respectivamente, r =t 0,61, 0,34, 0,28, 0,29, 0,43 e -0,13. As correlações de CC com EC, NA, D, DV e DMEAVC foram: 0,65, 0,22, 0,37, 0,33 e 0,096 respectivamente. Estudos de regressão linear simples de P com CC, EC, NA, DV, D e DMEAVC sugerem que CC foi o caráter independente mais significativo, contribuindo com 36% da variação em P. Em relação ao vigor, a regressão de CC com os respectivos caracteres sugere que EC foi o único caráter que contribuiu significativamente para a variação de CC com 42%. As altas correlações observadas da produção com circunferência do caule e com espessura de casca evidenciam a possibilidade de obter genótipos jovens de boa capacidade produtiva e grande vigor, através de seleção precoce dessas variáveis.This study was undertaken aiming to determine the existence of linear correlations, based on simple regression studies for a better improvement of young rubber tree (Hevea spp. breeding and selection. The characters studied were: yield of dry rubber per tapping by Hamaker-Morris-Mann test tapping (P, mean gurth (CC, bark thickness (EC, number of latex vessel rings (NA, diameter of latex vesseis (DV, density of latex vesseis per 5mm

  3. Comparative genetic analysis of quantitative traits in sunflower (Helianthus annuus L.). 2. Characterisation of QTL involved in developmental and agronomic traits.

    Science.gov (United States)

    Bert, P-F; Jouan, I; Tourvieille de Labrouhe, D; Serre, F; Philippon, J; Nicolas, P; Vear, F

    2003-06-01

    Seed weight and oil content are important properties of cultivated sunflower under complex genetic and environmental control, and associated with morphological and developmental characteristics such as plant height or flowering dates. Using a genetic map with 290 markers for a cross between two inbred sunflower lines and 2 years of observations on F3 families, QTL controlling seed weight, oil content, plant height, plant lodging, flowering dates, maturity dates and delay from flowering to maturity were detected. QTL detected were compared between the F2 and F3 generations and between the 2 years of testing for the F3 families in 1997 and 1999. Some of the QTL controlling seed weight overlapped with those controlling oil content. Several other co-localisations of QTL controlling developmental or morphological characteristics were observed and the relationships between the traits were also shown by correlation analyses. The relationships between all these traits and with resistance to Sclerotinia sclerotiorum and Diaporthe helianthi are discussed.

  4. Estimación bayesiana de componentes de (covarianza en Brangus argentino para caracteres de res mediante el algoritmo FCG Bayesian estimation of (co variance components in Argentinian Brangus for carcass traits using the FCG algorithm

    Directory of Open Access Journals (Sweden)

    R. J. C. Cantet

    2010-06-01

    Full Text Available Se emplearon los datos de 2273 toritos y vaquillonas Brangus para estimar las heredabilidades (h² y las correlaciones aditivas y ambientales de caracteres de calidad de carne medidos por ultrasonido. Los registros provenían del programa de evaluación genética de la Asociación Argentina de Brangus. Los caracteres medidos fueron el área del ojo del bife (AOB, el marmoreado (MB, la grasa dorsal (GD y la grasa de cadera (GC. La edad media de los animales al momento de la medición fue 641 días en machos y 685 días en hembras. Los parámetros genéticos y ambientales fueron estimados mediante un algoritmo bayesiano conjugado. Los valores estimados de h² fueron 0,22, 0,16, 0,12 y 0,21, para AOB, GD, CC y MB, respectivamente. En términos generales, las estimaciones de las correlaciones genéticas y ambientales se encontraron cercanas a la cifra media de la literatura. Si bien los valores estimados de h² fueron inferiores al promedio de la investigación realizada en vacunos para carne, la variabilidad encontrada es suficiente como para que la respuesta a la selección por estos caracteres - empleando predicciones de los valores de cría calculadas con los parámetros estimados - sea moderadamente efectiva.Data on 2273 Brangus young bulls and heifers were used to estimate heritabilities (h² and genetics and environmental correlations for ultrasound carcass measures. Records were from the genetic evaluation program of Asociación Argentina de Brangus. Traits measured were rib-eye area (AOB, marbling (MB, back-fat thickness (GD, and hip-fat thickness (GC. Average ages of measure were 641 days in males and 685 in females. The genetic and environmental dispersion parameters were estimated by a conjugate Bayesian algorithm (FCG. Estimates of h² were 0,22, 0,16, 0,12, and 0,21, for AOB, GD, CC, and MB, respectively. In general, estimates of genetic and environmental correlations were close to the average published values. Even tough estimates of

  5. A maximum likelihood QTL analysis reveals common genome regions controlling resistance to Salmonella colonization and carrier-state

    Directory of Open Access Journals (Sweden)

    Thanh-Son Tran

    2012-05-01

    Full Text Available Abstract Background The serovars Enteritidis and Typhimurium of the Gram-negative bacterium Salmonella enterica are significant causes of human food poisoning. Fowl carrying these bacteria often show no clinical disease, with detection only established post-mortem. Increased resistance to the carrier state in commercial poultry could be a way to improve food safety by reducing the spread of these bacteria in poultry flocks. Previous studies identified QTLs for both resistance to carrier state and resistance to Salmonella colonization in the same White Leghorn inbred lines. Until now, none of the QTLs identified was common to the two types of resistance. All these analyses were performed using the F2 inbred or backcross option of the QTLExpress software based on linear regression. In the present study, QTL analysis was achieved using Maximum Likelihood with QTLMap software, in order to test the effect of the QTL analysis method on QTL detection. We analyzed the same phenotypic and genotypic data as those used in previous studies, which were collected on 378 animals genotyped with 480 genome-wide SNP markers. To enrich these data, we added eleven SNP markers located within QTLs controlling resistance to colonization and we looked for potential candidate genes co-localizing with QTLs. Results In our case the QTL analysis method had an important impact on QTL detection. We were able to identify new genomic regions controlling resistance to carrier-state, in particular by testing the existence of two segregating QTLs. But some of the previously identified QTLs were not confirmed. Interestingly, two QTLs were detected on chromosomes 2 and 3, close to the locations of the major QTLs controlling resistance to colonization and to candidate genes involved in the immune response identified in other, independent studies. Conclusions Due to the lack of stability of the QTLs detected, we suggest that interesting regions for further studies are those that were

  6. Integrated Metabolo-Transcriptomics Reveals Fusarium Head Blight Candidate Resistance Genes in Wheat QTL-Fhb2

    Science.gov (United States)

    Dhokane, Dhananjay; Karre, Shailesh; Kushalappa, Ajjamada C.; McCartney, Curt

    2016-01-01

    Background Fusarium head blight (FHB) caused by Fusarium graminearum not only causes severe losses in yield, but also reduces quality of wheat grain by accumulating mycotoxins. Breeding for host plant resistance is considered as the best strategy to manage FHB. Resistance in wheat to FHB is quantitative in nature, involving cumulative effects of many genes governing resistance. The poor understanding of genetics and lack of precise phenotyping has hindered the development of FHB resistant cultivars. Though more than 100 QTLs imparting FHB resistance have been reported, none discovered the specific genes localized within the QTL region, nor the underlying mechanisms of resistance. Findings In our study recombinant inbred lines (RILs) carrying resistant (R-RIL) and susceptible (S-RIL) alleles of QTL-Fhb2 were subjected to metabolome and transcriptome profiling to discover the candidate genes. Metabolome profiling detected a higher abundance of metabolites belonging to phenylpropanoid, lignin, glycerophospholipid, flavonoid, fatty acid, and terpenoid biosynthetic pathways in R-RIL than in S-RIL. Transcriptome analysis revealed up-regulation of several receptor kinases, transcription factors, signaling, mycotoxin detoxification and resistance related genes. The dissection of QTL-Fhb2 using flanking marker sequences, integrating metabolomic and transcriptomic datasets, identified 4-Coumarate: CoA ligase (4CL), callose synthase (CS), basic Helix Loop Helix (bHLH041) transcription factor, glutathione S-transferase (GST), ABC transporter-4 (ABC4) and cinnamyl alcohol dehydrogenase (CAD) as putative resistance genes localized within the QTL-Fhb2 region. Conclusion Some of the identified genes within the QTL region are associated with structural resistance through cell wall reinforcement, reducing the spread of pathogen through rachis within a spike and few other genes that detoxify DON, the virulence factor, thus eventually reducing disease severity. In conclusion, we

  7. Characterization of QTL for unique agronomic traits of new-plant-type rice varieties using introgression lines of IR64

    Directory of Open Access Journals (Sweden)

    Analiza G. Tagle

    2016-02-01

    Full Text Available To enhance the yield potential of an elite indica rice cultivar, an introgression (BC3-derived line of IR64, YTH288, was developed using a new-plant-type cultivar, IR66215-44-2-3, as a donor parent. YTH288 has agronomically valuable characteristics such as large panicles, few unproductive tillers, and large leaves inherited from NPT. To identify the genetic basis of these traits, we used 167 F2 plants derived from a cross between IR64 and YTH288 to conduct QTL analysis for five agronomic traits: days to heading (DTH, culm length (CL, flag leaf length (FLL, flag leaf width (FLW, and filled spikelet number per panicle (FSN. Six putative QTL were detected: four on chromosome 4 (for CL, FLL, FLW, and FSN and two on chromosome 2 (for DTH and FLL. All QTL with the IR66215-44-2-3 allele, except that for FLL on chromosome 2, had positive effects on each trait. To confirm the effects of these putative QTL, we developed NILs with the IR64 genetic background by marker-assisted selection. We observed significant differences in several agronomic traits between IR64 and NILs that carried these QTL on chromosomes 2 and 4. Additionally, four IR64-NILs carrying chromosomal segments derived from different NPT varieties on the long arm of chromosome 4 exhibited similar pleiotropic effects for unique agronomic traits. These NILs can be used as research materials for studying each trait and as breeding materials for yield improvement of indica rice cultivars. Abbreviations NPT, new plant type; QTL, quantitative trait loci (locus; GF, grain fertility; DTH, days to heading; CL, culm length; PL, panicle length; LL, leaf length; FLL, flag leaf length; LW, leaf width; FLW, flag leaf width; FSN, filled spikelet number per panicle; TSN, total spikelet number per panicle; PN, panicle number per plant; IRRI, International Rice Research Institute; NIL, near-isogenic line; IL, introgression line; SSR, simple sequence repeat; PCR, polymerase chain reaction

  8. Animal QTLdb:an improved database tool for livestock animal QTL/association data dissemination in the post-genome era

    OpenAIRE

    Hu, Zhi-Liang; Park, Carissa A.; Wu, Xiao-Lin; Reecy, James M.

    2013-01-01

    The Animal QTL database (QTLdb; http://www.animalgenome.org/QTLdb) is designed to house all publicly available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. An earlier version was published in the Nucleic Acids Research Database issue in 2007. Since then, we have continued our efforts to develop new and improved database tools to allow more data types, parameters and functions. Our efforts have transformed the Animal QTLdb into a tool that actively ...

  9. Genome-wide QTL analysis of meat quality-related traits in a large F2 intercross between Landrace and Korean native pigs

    OpenAIRE

    Cho, In-Cheol; Yoo, Chae-Kyoung; Lee, Jae-Bong; Jung, Eun-Ji; Han, Sang-Hyun; Lee, Sung-Soo; Ko, Moon-Suck; Lim, Hyun-Tae; Park, Hee-Bok

    2015-01-01

    Background We conducted a genome-wide linkage analysis to identify quantitative trait loci (QTL) that influence meat quality-related traits in a large F2 intercross between Landrace and Korean native pigs. Thirteen meat quality-related traits of the m. longissimus lumborum et thoracis were measured in more than 830 F2 progeny. All these animals were genotyped with 173 microsatellite markers located throughout the pig genome, and the GridQTL program based on the least squares regression model ...

  10. Update History of This Database - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us ...PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods Update History o...URLs by Artio About This Database Database Description Download License Update History of This Database Site...f This Database Date Update contents 2014/10/10 PGDBj Registered plant list, Marker list, QTL list, Plant DB... Policy | Contact Us Update History of This Database - PGDBj Registered plant lis

  11. An Interspecific Backcross of Lycopersicon Esculentum X L. Hirsutum: Linkage Analysis and a Qtl Study of Sexual Compatibility Factors and Floral Traits

    OpenAIRE

    Bernacchi, D.; Tanksley, S D

    1997-01-01

    A BC(1) population of the self-compatible tomato Lycopersicon esculentum and its wild self-incompatible relative L. hirsutum f. typicum was used for restriction fragment length polymorphism linkage analysis and quantitative trait loci (QTL) mapping of reproductive behavior and floral traits. The self-incompatibility locus, S, on chromosome 1 harbored the only QTL for self-incompatibility indicating that the transition to self-compatibility in the lineage leading to the cultivated tomato was p...

  12. Utilizando as abordagens quantitativa e qualitativa na produção do conhecimento Utilizando los abordajes cuantitativo y cualitativo en la producción del conocimiento Using quantitative and qualitative approaches in knowledge production

    Directory of Open Access Journals (Sweden)

    Odaléa Maria Brüggemann

    2008-09-01

    Full Text Available O debate sobre as diferenças entre os métodos quantitativo e qualitativo é freqüente, havendo posições favoráveis e contrárias acerca da sua integração. Delinear uma pesquisa que contemple as duas abordagens gera dúvidas e inquietações sobre como utilizá-las sem ferir o rigor dos métodos, a especificidade, a sofisticação metodológica e reflexiva de cada uma delas. O objetivo é relatar e discutir a utilização da abordagem quantitativa (ensaio clínico controlado randomizado e qualitativa para avaliar e compreender a inserção do acompanhante de escolha da mulher durante o trabalho de parto/parto, desempenhando o papel de provedor de apoio. A utilização das duas abordagens possibilitou aproximar as múltiplas facetas envolvidas nessa prática e avaliá-la tanto na dimensão explicativa quanto na compreensiva, uma vez que pôde ser realizada com olhares complementares.El debate sobre las diferencias entre los métodos cuantitativo y cualitativo es frecuente, existiendo posiciones favorables y contrarias respecto a su integración. Delinear una investigación que contemple los dos abordajes genera dudas e inquietudes en relación a cómo utilizarlos sin herir el rigor de los métodos, la especificidad, la sofisticación metodológica y reflexiva de cada uno de ellos. El objetivo es relatar y discutir la utilización del abordaje cuantitativo (ensayo clínico controlado randomizado y cualitativo, para evaluar y comprender la inserción del acompañante elegido por la mujer durante el trabajo de parto y el parto, desempeñando el papel de proveedor de apoyo. La utilización de los dos abordajes hizo posible la aproximación de las múltiples facetas involucradas en esta práctica, así como evaluarlas tanto en la dimensión explicativa como en la comprensiva, debido a que puede ser realizada con visiones complementarias.The debate over the differences between quantitative and qualitative methods is frequent, holding favorable

  13. Combined QTL and selective sweep mappings with coding SNP annotation and cis-eQTL analysis revealed PARK2 and JAG2 as new candidate genes for adiposity regulation.

    OpenAIRE

    Roux, Pierre-François; Boitard, Simon; Blum, Anne; Parks, Brian; Montagner, Alexandra; Mouisel, Etienne; Djari, Anis; Esquerre, Diane; Désert, Colette; Boutin, Morgane; Leroux, Sophie; Lecerf, Frederic; Le Bihan-Duval, Elisabeth; Klopp, Christophe; Servin, Bertrand

    2015-01-01

    Very few causal genes have been identified by quantitative trait loci (QTLs) mapping because of the large size of QTLs, and most of them were identified thanks to functional links already known with the targeted phenotype. Here we propose to combine selection signature detection, coding SNP annotation, and cis-expression QTL analyses to identify potential causal genes underlying QTLs identified in divergent line designs. As a model, we chose experimental chicken lines divergently selected for...

  14. Genome-wide identification of QTL for seed yield and yield-related traits and construction of a high-density consensus map for QTL comparison in Brassica napus

    Directory of Open Access Journals (Sweden)

    Weiguo eZhao

    2016-01-01

    Full Text Available Seed yield (SY is the most important trait in rapeseed, which was determined by multiple seed yield-related traits (SYRTs and also easily subject to environmental influence. Lots of quantitative trait loci (QTL for SY and SYRTs were reported in Brassica napus. However, no studies have focused on SY and seven agronomic traits affecting SY simultaneous. Genome-wide QTL analysis for SY and seven SYRTs in eight environments was conducted in a doubled haploid population containing 348 lines. Totally, 18 and 208 QTLs for SY and SYRTs were observed, respectively, and then these QTLs were integrated into 144 consensus QTLs by a meta-analysis. Three major QTLs for SY were observed, including cqSY-C6-2 and cqSY-C6-3 that expressed stably in winter cultivation area for three years and cqSY-A2-2 only expressed in spring rapeseed area. Trait-by-trait meta-analysis revealed that the 144 consensus QTLs were integrated into 72 pleiotropic unique QTLs. Among them, all the unique QTLs affected SY, except for uq-A6-1, including uq.A2-3, uq.C1-2, uq.C1-3, uq.C6-1, uq.C6-5 and uq.C6-6 could also affect more than two SYRTs. According to high density consensus map construction and QTL comparison from literature, 36 QTLs from five populations were co-localized with QTLs identified in this study. In addition, 13 orthologs genes were observed, including five each genes for SY and SW, one each gene for BY, BH and PH, respectively. The genomic information of these QTLs would be valuable in hybrid cultivar breeding, and be helpful to analyze QTL expression in different environments.

  15. Capacidade de combinação multivariada para caracteres de tubérculo em gerações iniciais de seleção em batata Multivariate combining ability for tuber characters in potato early generation selection

    Directory of Open Access Journals (Sweden)

    Giovani Olegario da Silva

    2008-04-01

    Full Text Available A análise dialélica propicia estimativas de parâmetros úteis à seleção de genitores e ao entendimento dos efeitos genéticos envolvidos na determinação dos caracteres. O objetivo deste trabalho foi estimar a capacidade geral e específica de combinação multivariada de genótipos de batata em gerações iniciais de seleção. Foram avaliadas 20 famílias clonais de batata (5*4 de nove genótipos, em um esquema dialélico, por duas gerações sucessivas. Os experimentos foram conduzidos na Embrapa Clima Temperado, em Pelotas, RS (31°S, 52°W, na primavera de 2005 e no outono de 2006. Foram avaliados 14 caracteres morfológicos de tubérculo e selecionados os seis mais estáveis ou que melhor repetiram perante as gerações para outras análises. A análise de variância revelou diferença significativa para todos os caracteres. A análise de variância multivariada dialélica com componentes principais mostrou os genótipos "2CRI-1149-1-78", "Eliza", "C-1786-6-96" e "White Lady" com maior capacidade geral de combinação para os caracteres aparência, aspereza, sobrancelha, apontamento, curvatura e achatamento de tubérculo, contribuindo com efeitos aditivos nos cruzamentos. Os cruzamentos "C-1750-15-95"/"Agria", "C-1786-6-96"/ "Asterix" e "Eliza"/"Asterix" destacaram-se em capacidade específica de combinação para sobrancelha, apontamento, curvatura e achatamento de tubérculo, e "2CRI-1149-1-78"/ "Vivaldi", "Eliza"/"BP1" e "Eliza"/"Agria", para aparência, aspereza e sobrancelha de tubérculo.The diallel analysis provides estimates of useful parameters to parent selection and to the understanding of the genetic effects involved in a trait control. This research was aimed at estimating multivariate combining ability of potato parents in the initial generations of selection. Twenty potato clonal families (5*4 of nine genotypes in a partial diallel design were evaluated for two successive generations. The experiments were conducted at

  16. Correlação canônica entre caracteres de tubérculos para seleção precoce de clones de batata Canonical correlation for tuber trait to assist early selection of potato clones

    OpenAIRE

    Maria Helena Rigão; Lindolfo Storck; Dilson Antônio Bisognin; Sidinei José Lopes

    2009-01-01

    Uma das estratégias utilizadas pelos melhoristas de batata é a eliminação de um grande número de clones nas primeiras gerações de seleção, para reduzir os custos e o trabalho de manutenção e multiplicação destes. O objetivo deste trabalho foi avaliar o uso da correlação canônica entre caracteres de tubérculos plantados, relacionados com os colhidos, para auxiliar a seleção precoce de clones de batata. Foram conduzidos três ensaios em diferentes épocas, na área experimental do Departamento de ...

  17. Estudio estadístico de palabras y caracteres en títulos de artículos científico-técnicos en español

    OpenAIRE

    Gutiérrez Múñoz, Francisco; Rey Guerrero, Alfredo del

    1986-01-01

    [ES] Se muestran los resultados de un estudio estadístico efectuado a partir de una colección de títulos de artículos científico-técnicos en español, procedentes de la base de datos del índice Español de Ciencia y Tecnología. En dicho estudio se h m determinado las longitudes de los títulos (número de palabras por título) y de las palabras (número de caracteres por palabro), y se h a relacionado con lar frecuencias de aparición de las palabras en los títulos y de lar letras en ...

  18. REPETIBILIDADE DE CARACTERES DO CACHO DE AÇAIZEIRO NAS CONDIÇÕES DE BELÉM-PA REPEATIBILITY OF CHARACTERS OF THE RACEME OF AÇAI PALM AT BELÉM-PA

    Directory of Open Access Journals (Sweden)

    MARIA DO SOCORRO PADILHA DE OLIVEIRA

    2001-12-01

    Full Text Available Estimou-se o coeficiente de repetibilidade em caracteres do cacho de açaizeiro (Euterpe oleracea Mart. nas condições de Belém-PA, com o intuito de determinar a capacidade de eles expressarem a variabilidade genética dessa fruteira. Para tanto, foram colhidos quatro cachos por planta, todos apresentando completa maturação, em 30 genótipos pertencentes à Coleção de Germoplasma de Açaí da Embrapa Amazônia Oriental, onde foram mensurados seis caracteres: peso total do cacho (PTC, peso de frutos por cacho (PFC, número de frutos por cacho (NFC, número de ráquilas por cacho (NRC, peso médio do fruto (PMF e rendimento de frutos por cacho (RFC. A análise da repetibilidade, do número de medições necessárias e do coeficiente de determinação para cada caráter foi obtida através do método da análise de variância, utilizando o modelo com dois fatores de variação. Verificou-se que todos os caracteres apresentaram diferenças significativas entre genótipos, com o número de frutos, número de ráquilas e peso médio do fruto, evidenciando diferenças ao nível de 1% de probabilidade. Porém, o maior coeficiente de repetibilidade foi registrado para peso médio do fruto, enquanto os demais caracteres apresentaram valores inexpressivos. Essa variável teve, também, o maior coeficiente de determinação; entretanto, o número de repetições desejável para esse caráter deve ser quase o triplo do usado nesse estudo. Pelo fato de o coeficiente de repetibilidade expressar o valor máximo de herdabilidade, conclui-se que o PMF pode ser usado como parâmetro de seleção em métodos de melhoramento menos rigorosos.Was considered the repeatibility coefficient in characters of raceme in açai palm (Euterpe oleracea Mart. at Belém-PA with the intention of determining their capacity to express the genetic variability of that fruit bowl. For that were picked four racemes by plant, all presenting complete maturation, in 30 genotypes

  19. Estimativa da repetibilidade em caracteres morfológicos e de produção de palmito em pupunheira (Bactris gasipaes Kunth Estimate of repeatability in morphological and heart of palm production characters in peach palm (Bactris gasipaes Kunth

    Directory of Open Access Journals (Sweden)

    Nilson César Corrêa Padilha

    2003-08-01

    Full Text Available No melhoramento da pupunheira, visando a produção de palmito, é primordial o conhecimento de parâmetros genéticos de caracteres produtivos associados aos morfológicos na seleção de plantas promissoras. Por ser uma palmeira perene com caráter de produção destrutivo, o coeficiente de repetibilidade consiste em uma estratégia desejável. Assim, estimou-se o coeficiente de repetibilidade entre oito caracteres morfológicos e oito de produção de palmito em pupunheiras da coleção de germoplasma da Embrapa Amazônia Oriental. Para tanto, foram avaliadas 65 plantas com variação para número de estipes por planta. O coeficiente de repetibilidade, o número de estipes a serem cortados e o coeficiente de determinação foram obtidos através da análise da variância com um fator de variação, com número variável de observações. Quatro caracteres morfológicos apresentaram coeficientes de repetibilidade variando de 0,5317 a 0,6716, o que indica regularidade no comportamento das plantas de uma avaliação para outra. No entanto, apenas o comprimento da ráquis foliar mostrou número de medições necessárias para se obter predições com 95% de confiança. Todos os caracteres produtivos tiveram baixas magnitudes de repetibilidade de (0,1030 a 0,2202, o que expressa irregularidades na superioridade das plantas, além de exibirem números de medições elevados. Portanto, o comprimento da ráquis foliar pode ser usado na seleção de pupunheiras para palmito.Understanding the genetic parameters of the productive characters associated to the morphological is of utmost importance in selecting promising plants for peach palm breeding aiming at heart palm production. Since Bactris gasipaes is a perennial palm tree with a destructive production character, the repeatability coefficient is a desirable strategy to apply. Thus, the repeatability coefficient was estimated among eight morphological characters and eight heart of palm production

  20. Comparación de dos índices cuantitativos de estimación del estado de desarrollo de la alfalfa Comparison of two quantitative indexes for the estimation of alfalfa development stages

    Directory of Open Access Journals (Sweden)

    M.L. Bernáldez

    2006-12-01

    Full Text Available El estado de desarrollo de la alfalfa (Medicago sativa L. es una variable de estudio común en evaluaciones de cultivares, dada su relación con la composición química y la tasa de crecimiento de la pastura. La determinación de los índices cuantitativos "estado medio por conteo" y "estado medio por peso" (EMC y EMP respectivamente permite la descripción del estado de desarrollo en pasturas de alfalfa de una manera objetiva y reproducible. Los índices EMC y EMP describen igualmente el estado de desarrollo de la alfalfa cuando la pastura se encuentra próxima al momento de utilización recomendado en la práctica. La ventaja de estimar EMC en relación a EMP, se basa en la rapidez operativa que ofrece la generación de datos para el cálculo del primero.The developmental stage of alfalfa (Medicago sativa L. is an usual variable of study when evaluating cultivars because of its relationship with chemical composition and pasture growth rate. Determination of quantitative indexes such as "mean stage by count" and "mean stage by weight" (MSC and MSW respectively makes it possible to describe the developmental phenological stages of alfalfa pastures in a more objective and reproducible way. Likewise, both the MSC and MSW indexes, describe the developmental stages of alfalfa when the pasture is close to the recommended utilisation time in practice. The advantage of estimating MSC in relation to MSW is based on the higher operative efficiency offered by the former in data generation for its calculation.

  1. Capacidade combinatória e parâmetros genéticos de genótipos de pinhão-manso quanto a caracteres morfoagronômicos

    Directory of Open Access Journals (Sweden)

    Ulisses Andrade Santana

    2013-11-01

    Full Text Available O objetivo deste trabalho foi determinar as capacidades geral e específica de combinação, os parâmetros genéticos e a correlação entre caracteres morfoagronômicos, em acessos de pinhão-manso (Jatropha curcas. Utilizou-se o delineamento experimental de blocos ao acaso, com três repetições. Foram avaliados os caracteres: PR, produção de sementes; AP, altura de planta; NRS, número de ramos secundários; NFF, número de flores femininas; DC, diâmetro de colo; P100, massa de 100 sementes; AR, altura de ramificação; e DCO, diâmetro de copa. A capacidade geral de combinação foi significativa para PR, NRS, DC, P100 e AR, enquanto a capacidade específica foi significativa apenas para NFF e NRS. As estimativas de herdabilidade foram superiores a 70%, em NRS, NFF, DC e AR. Observou-se correlações genotípicas positivas entre NRS e DC (0,942, NRS e AP (0,762, NRS e DCO (0,798, NRS e PR (0,759, DC e AP (0,738, DC e DCO (0,844, DC e PR (0,802, e DCO e PR (0,742; e negativas entre NRS e AR (-0,665, e DC e AR (-0,687. O NFF explicou mais de 50% da variação dos híbridos de pinhão-manso. A capacidade geral de combinação é preponderante na maioria das características avaliadas.

  2. Confirmation and fine-mapping of clinical mastitis and somatic cell score QTL in Nordic Holstein cattle

    DEFF Research Database (Denmark)

    Sahana, Goutam; Guldbrandtsen, Bernt; Thomsen, Bo;

    2013-01-01

    A genome-wide association study of 2098 progeny-tested Nordic Holstein bulls genotyped for 36 387 SNPs on 29 autosomes was conducted to confirm and fine-map quantitative trait loci (QTL) for mastitis traits identified earlier using linkage analysis with sparse microsatellite markers in the same...... population. We used linear mixed model analysis where a polygenic genetic effect was fitted as a random effect and single SNPs were successively included as fixed effects in the model. We detected 143 SNP-by-trait significant associations (P mastitis-related traits....... Among them, 21 SNP-by-trait combinations exceeded the genome-wide significant threshold. For 12 chromosomes, both the present association study and the previous linkage study detected QTL, and of these, six were in the same chromosomal locations. Strong associations of SNPs with mastitis traits were...

  3. Identification of gametes and treatment of linear dependencies in the gametic QTL-relationship matrix and its inverse

    Directory of Open Access Journals (Sweden)

    Reinsch Norbert

    2004-11-01

    Full Text Available Abstract The estimation of gametic effects via marker-assisted BLUP requires the inverse of the conditional gametic relationship matrix G. Both gametes of each animal can either be identified (distinguished by markers or by parental origin. By example, it was shown that the conditional gametic relationship matrix is not unique but depends on the mode of gamete identification. The sum of both gametic effects of each animal – and therefore its estimated breeding value – remains however unaffected. A previously known algorithm for setting up the inverse of G was generalized in order to eliminate the dependencies between columns and rows of G. In the presence of dependencies the rank of G also depends on the mode of gamete identification. A unique transformation of estimates of QTL genotypic effects into QTL gametic effects was proven to be impossible. The properties of both modes of gamete identification in the fields of application are discussed.

  4. THREE SELECTIONS ARE BETTER THAN ONE: CLINAL VARIATION OF THERMAL QTL FROM INDEPENDENT SELECTION EXPERIMENTS IN DROSOPHILA

    OpenAIRE

    Rand, David M.; Weinreich, Daniel M.; Lerman, Daniel; Folk, Donna; Gilchrist, George W

    2010-01-01

    We report the results of two independent selection experiments that have exposed distinct populations of Drosophila melanogaster to different forms of thermal selection. A recombinant population derived from Arvin California and Zimbabwe isofemale lines was exposed to laboratory natural selection at two temperatures (TAZ: 18°C and 28°C). Microsatellite mapping identified quantitative trait loci (QTL) on the X-chromosome between the replicate “Hot” and “Cold” populations. In a separate experim...

  5. A genome scan to detect QTL affecting dairy traits in a dairy sheep backcross Sarda x Lacaune population

    Directory of Open Access Journals (Sweden)

    L. Mura

    2011-03-01

    Full Text Available Recently in Mediterranean countries as France, Italy and Spain, dairy sheep selection has been efficiently oriented towards milk yield and milk composition. More attention has been now paid to traits related to the reduction of production costs (milkability, functional traits, longevity, health (resistance to mastitis or parasitic diseases, safety of food (reduction in contaminants and quality (milk fatty acids composition. Therefore, research combining classical quantitative approach and QTL detection is needed, either on-farm by implementing experimental recording schemes......

  6. Three QTL in the honey bee Apis mellifera L. suppress reproduction of the parasitic mite Varroa destructor

    OpenAIRE

    Behrens, Dieter; Huang, Qiang; Geßner, Cornelia; Rosenkranz, Peter; Frey, Eva; Locke, Barbara; Moritz, Robin F.A.; Kraus, F B

    2011-01-01

    Varroa destructor is a highly virulent ectoparasitic mite of the honey bee Apis mellifera and a major cause of colony losses for global apiculture. Typically, chemical treatment is essential to control the parasite population in the honey bee colony. Nevertheless a few honey bee populations survive mite infestation without any treatment. We used one such Varroa mite tolerant honey bee lineage from the island of Gotland, Sweden, to identify quantitative trait loci (QTL) controlling reduced mit...

  7. Identification of QTL for adult-plant resistance to powdery mildew in Chinese wheat landrace Pingyuan 50

    Institute of Scientific and Technical Information of China (English)

    Muhammad; Azeem; Asad; Bin; Bai; Caixia; Lan; Jun; Yan; Xianchun; Xia; Yong; Zhang; Zhonghu; He

    2014-01-01

    Powdery mildew caused by Blumeria graminis f. sp. tritici is one of the major wheat diseases worldwide. The Chinese wheat landrace Pingyuan 50 has shown adult-plant resistance(APR)to powdery mildew in the field for over 60 years. To dissect the genetic basis of APR to powdery mildew in this cultivar, a mapping population of 137 double haploid(DH) lines derived from Pingyuan 50/Mingxian 169 was evaluated in replicated field trials for two years in Beijing(2009–2010 and 2010–2011) and one year in Anyang(2009–2010). A total of 540 polymorphic SSR markers were genotyped on the entire population for construction of a linkage map and QTL analysis. Three QTL were mapped on chromosomes 2BS(QPm.caas-2BS.2), 3BS(QPm.caas-3BS),and 5AL(QPm.caas-5AL) with the resistance alleles contributed by Pingyuan 50 explaining 5.3%,10.2%, and 9.1% of the phenotypic variances, respectively, and one QTL on chromosome 3BL(QPm.caas-3BL) derived from Mingxian 169 accounting for 18.1% of the phenotypic variance.QPm.caas-3BS, QPm.caas-3BL, and QPm.caas-5AL appear to be new powdery mildew APR loci.QPm.caas-2BS.2 and QPm.caas-5AL are possibly pleiotropic or closely linked resistance loci to stripe rust resistance QTL. Pingyuan 50 could be a potential genetic resource to facilitate breeding for improved APR to both powdery mildew and stripe rust.

  8. Genetic effects of polymorphisms in candidate genes and the QTL region on chicken age at first egg

    Directory of Open Access Journals (Sweden)

    Zhou Min

    2011-04-01

    Full Text Available Abstract Background The age at first egg (AFE, an important indicator for sexual maturation in female chickens, is controlled by polygenes. Based on our knowledge of reproductive physiology, 6 genes including gonadotrophin releasing hormone-I (GnRH-I, neuropeptide Y (NPY, dopamine D2 receptor (DRD2, vasoactive intestinal polypeptide (VIP, VIP receptor-1 (VIPR-1, and prolactin (PRL, were selected as candidates for influencing AFE. Additionally, the region between ADL0201 and MCW0241 of chromosome Z was chosen as the candidate QTL region according to some QTL databases. The objective of the present study was to investigate the effects of mutations in candidate genes and the QTL region on chicken AFE. Results Marker-trait association analysis of 8 mutations in those 6 genes in a Chinese native population found a highly significant association (P G840327C of the GnRH-I gene with AFE, and it remained significant even with Bonferroni correction. Based on the results of the 2-tailed χ2 test, mutations T32742394C, T32742468C, G32742603A, and C33379782T in the candidate QTL region of chromosome Z were selected for marker-trait association analysis. The haplotypes of T32742394C and T32742468C were significantly associated (P T32742394C and T32742468C were located in the intron region of the SH3-domain GRB2-like 2 (SH3GL2 gene, which appeared to be associated in the endocytosis and development of the oocyte. Conclusion This study found that G840327C of the GnRH-I gene and the haplotypes of T32742394C-T32742468C of the SH3GL2 gene were associated with the chicken AFE.

  9. Genetic control of rhizomes and genomic localization of a major-effect growth habit QTL in perennial wildrye.

    Science.gov (United States)

    Yun, Lan; Larson, Steve R; Mott, Ivan W; Jensen, Kevin B; Staub, Jack E

    2014-06-01

    Rhizomes are prostrate subterranean stems that provide primitive mechanisms of vegetative dispersal, survival, and regrowth of perennial grasses and other monocots. The extent of rhizome proliferation varies greatly among grasses, being absent in cereals and other annuals, strictly confined in caespitose perennials, or highly invasive in some perennial weeds. However, genetic studies of rhizome proliferation are limited and genes controlling rhizomatous growth habit have not been elucidated. Quantitative trait loci (QTLs) controlling rhizome spreading were compared in reciprocal backcross populations derived from hybrids of rhizomatous creeping wildrye (Leymus triticoides) and caespitose basin wildrye (L. cinereus), which are perennial relatives of wheat. Two recessive QTLs were unique to the creeping wildrye backcross, one dominant QTL was unique to the basin wildrye backcross, and one additive QTL was detectable in reciprocal backcrosses with high log odds (LOD = 31.6) in the basin wildrye background. The dominant QTL located on linkage group (LG)-2a was aligned to a dominant rhizome orthogene (Rhz3) of perennial rice (Oryza longistamina) and perennial sorghum (Sorghum propinquum). Nonparametric 99 % confidence bounds of the 31.6-LOD QTL were localized to a distal 3.8-centiMorgan region of LG-6a, which corresponds to a 0.7-Mb region of Brachypodium Chromosome 3 containing 106 genes. An Aux/IAA auxin signal factor gene was located at the 31.6-LOD peak, which could explain the gravitropic and aphototropic behavior of rhizomes. Findings elucidate genetic mechanisms controlling rhizome development and architectural growth habit differences among plant species. Results have possible applications to improve perennial forage and turf grasses, extend the vegetative life cycle of annual cereals, such as wheat, or control the invasiveness of highly rhizomatous weeds such as quackgrass (Elymus repens). PMID:24509730

  10. La mineria en Galicia: analisis economico cuantitativo.

    OpenAIRE

    Rodriguez, X.A.

    1995-01-01

    Los romanos consideraban a Galicia como un "coto minero" de especial relevancia para el Imperio, por sus ricos yacimientos de oro, plata, hierro, cobre, estaño, plomo... que poblaban su territorio. En el contexto de las dos Guerras Mundiales, y con finalidades belicas, adquieren importante protagonismo las extracciones gallegas de wolframio y estaño. En la actualidad la "vocacion" minera de esta Comunidad, dentro de lo que se dio en llamar la "nueva mineria" (productos de cantera y minerales ...

  11. Genome-wide QTL mapping for three traits related to teat number in a White Duroc × Erhualian pig resource population

    Directory of Open Access Journals (Sweden)

    Ai Huashui

    2009-02-01

    Full Text Available Abstract Background Teat number is an important fertility trait for pig production, reflecting the mothering ability of sows. It is also a discrete and often canalized trait presenting bilateral symmetry with minor differences between the two sides, providing a potential power to evaluate fluctuating asymmetry and developmental instability. The knowledge of its genetic control is still limited. In this study, a genome-wide scan was performed with 183 microsatellites covering the pig genome to identify quantitative trait loci (QTL for three traits related to teat number including the total teat number (TTN, the teat number at the left (LTN and right (RTN sides in a large scale White Duroc × Erhualian resource population. Results A sex-average linkage map with a total length of 2350.3 cM and an average marker interval of 12.84 cM was constructed. Eleven genome-wide significant QTL for TTN were detected on 8 autosomes including pig chromosomes (SSC 1, 3, 4, 5, 6, 7, 8 and 12. Six suggestive QTL for this trait were detected on SSC6, 9, 13, 14 and 16. Eight chromosomal regions each on SSC1, 3, 4, 5, 6, 7, 8 and 12 showed significant associations with LTN. These regions were also evidenced as significant QTL for RTN except for those on SSC6 and SSC8. The most significant QTL for the 3 traits were all located on SSC7. Erhualian alleles at most of the identified QTL had positive additive effects except for three QTL on SSC1 and SSC7, at which White Duroc alleles increased teat numbers. On SSC1, 6, 9, 13 and 16, significant dominance effects were observed on TTN, and predominant imprinting effect on TTN was only detected on SSC12. Conclusion The results not only confirmed the QTL regions from previous experiments, but also identified five new QTL for the total teat number in swine. Minor differences between the QTL regions responsible for LTN and RTN were validated. Further fine mapping should be focused on consistently identified regions with small

  12. An ultra-high-density bin map facilitates high-throughput QTL mapping of horticultural traits in pepper (Capsicum annuum).

    Science.gov (United States)

    Han, Koeun; Jeong, Hee-Jin; Yang, Hee-Bum; Kang, Sung-Min; Kwon, Jin-Kyung; Kim, Seungill; Choi, Doil; Kang, Byoung-Cheorl

    2016-04-01

    Most agricultural traits are controlled by quantitative trait loci (QTLs); however, there are few studies on QTL mapping of horticultural traits in pepper (Capsicumspp.) due to the lack of high-density molecular maps and the sequence information. In this study, an ultra-high-density map and 120 recombinant inbred lines (RILs) derived from a cross betweenC. annuum'Perennial' andC. annuum'Dempsey' were used for QTL mapping of horticultural traits. Parental lines and RILs were resequenced at 18× and 1× coverage, respectively. Using a sliding window approach, an ultra-high-density bin map containing 2,578 bins was constructed. The total map length of the map was 1,372 cM, and the average interval between bins was 0.53 cM. A total of 86 significant QTLs controlling 17 horticultural traits were detected. Among these, 32 QTLs controlling 13 traits were major QTLs. Our research shows that the construction of bin maps using low-coverage sequence is a powerful method for QTL mapping, and that the short intervals between bins are helpful for fine-mapping of QTLs. Furthermore, bin maps can be used to improve the quality of reference genomes by elucidating the genetic order of unordered regions and anchoring unassigned scaffolds to linkage groups. PMID:26744365

  13. Cis-eQTL analysis and functional validation of candidate susceptibility genes for high-grade serous ovarian cancer

    Science.gov (United States)

    Lawrenson, Kate; Li, Qiyuan; Kar, Siddhartha; Seo, Ji-Heui; Tyrer, Jonathan; Spindler, Tassja J.; Lee, Janet; Chen, Yibu; Karst, Alison; Drapkin, Ronny; Aben, Katja K. H.; Anton-Culver, Hoda; Antonenkova, Natalia; Bowtell, David; Webb, Penelope M.; deFazio, Anna; Baker, Helen; Bandera, Elisa V.; Bean, Yukie; Beckmann, Matthias W.; Berchuck, Andrew; Bisogna, Maria; Bjorge, Line; Bogdanova, Natalia; Brinton, Louise A.; Brooks-Wilson, Angela; Bruinsma, Fiona; Butzow, Ralf; Campbell, Ian G.; Carty, Karen; Chang-Claude, Jenny; Chenevix-Trench, Georgia; Chen, Anne; Chen, Zhihua; Cook, Linda S.; Cramer, Daniel W.; Cunningham, Julie M.; Cybulski, Cezary; Dansonka-Mieszkowska, Agnieszka; Dennis, Joe; Dicks, Ed; Doherty, Jennifer A.; Dörk, Thilo; du Bois, Andreas; Dürst, Matthias; Eccles, Diana; Easton, Douglas T.; Edwards, Robert P.; Eilber, Ursula; Ekici, Arif B.; Fasching, Peter A.; Fridley, Brooke L.; Gao, Yu-Tang; Gentry-Maharaj, Aleksandra; Giles, Graham G.; Glasspool, Rosalind; Goode, Ellen L.; Goodman, Marc T.; Grownwald, Jacek; Harrington, Patricia; Harter, Philipp; Hasmad, Hanis Nazihah; Hein, Alexander; Heitz, Florian; Hildebrandt, Michelle A. T.; Hillemanns, Peter; Hogdall, Estrid; Hogdall, Claus; Hosono, Satoyo; Iversen, Edwin S.; Jakubowska, Anna; James, Paul; Jensen, Allan; Ji, Bu-Tian; Karlan, Beth Y.; Kruger Kjaer, Susanne; Kelemen, Linda E.; Kellar, Melissa; Kelley, Joseph L.; Kiemeney, Lambertus A.; Krakstad, Camilla; Kupryjanczyk, Jolanta; Lambrechts, Diether; Lambrechts, Sandrina; Le, Nhu D.; Lee, Alice W.; Lele, Shashi; Leminen, Arto; Lester, Jenny; Levine, Douglas A.; Liang, Dong; Lissowska, Jolanta; Lu, Karen; Lubinski, Jan; Lundvall, Lene; Massuger, Leon F. A. G.; Matsuo, Keitaro; McGuire, Valerie; McLaughlin, John R.; Nevanlinna, Heli; McNeish, Ian; Menon, Usha; Modugno, Francesmary; Moysich, Kirsten B.; Narod, Steven A.; Nedergaard, Lotte; Ness, Roberta B.; Azmi, Mat Adenan Noor; Odunsi, Kunle; Olson, Sara H.; Orlow, Irene; Orsulic, Sandra; Weber, Rachel Palmieri; Pearce, Celeste L.; Pejovic, Tanja; Pelttari, Liisa M.; Permuth-Wey, Jennifer; Phelan, Catherine M.; Pike, Malcolm C.; Poole, Elizabeth M.; Ramus, Susan J.; Risch, Harvey A.; Rosen, Barry; Rossing, Mary Anne; Rothstein, Joseph H.; Rudolph, Anja; Runnebaum, Ingo B.; Rzepecka, Iwona K.; Salvesen, Helga B.; Schildkraut, Joellen M.; Schwaab, Ira; Sellers, Thomas A.; Shu, Xiao-Ou; Shvetsov, Yurii B.; Siddiqui, Nadeem; Sieh, Weiva; Song, Honglin; Southey, Melissa C.; Sucheston, Lara; Tangen, Ingvild L.; Teo, Soo-Hwang; Terry, Kathryn L.; Thompson, Pamela J.; Timorek, Agnieszka; Tsai, Ya-Yu; Tworoger, Shelley S.; van Altena, Anne M.; Van Nieuwenhuysen, Els; Vergote, Ignace; Vierkant, Robert A.; Wang-Gohrke, Shan; Walsh, Christine; Wentzensen, Nicolas; Whittemore, Alice S.; Wicklund, Kristine G.; Wilkens, Lynne R.; Woo, Yin-Ling; Wu, Xifeng; Wu, Anna H.; Yang, Hannah; Zheng, Wei; Ziogas, Argyrios; Monteiro, Alvaro; Pharoah, Paul D.; Gayther, Simon A.; Freedman, Matthew L.

    2015-01-01

    Genome-wide association studies have reported 11 regions conferring risk of high-grade serous epithelial ovarian cancer (HGSOC). Expression quantitative trait locus (eQTL) analyses can identify candidate susceptibility genes at risk loci. Here we evaluate cis-eQTL associations at 47 regions associated with HGSOC risk (P≤10−5). For three cis-eQTL associations (P<1.4 × 10−3, FDR<0.05) at 1p36 (CDC42), 1p34 (CDCA8) and 2q31 (HOXD9), we evaluate the functional role of each candidate by perturbing expression of each gene in HGSOC precursor cells. Overexpression of HOXD9 increases anchorage-independent growth, shortens population-doubling time and reduces contact inhibition. Chromosome conformation capture identifies an interaction between rs2857532 and the HOXD9 promoter, suggesting this SNP is a leading causal variant. Transcriptomic profiling after HOXD9 overexpression reveals enrichment of HGSOC risk variants within HOXD9 target genes (P=6 × 10−10 for risk variants (P<10−4) within 10 kb of a HOXD9 target gene in ovarian cells), suggesting a broader role for this network in genetic susceptibility to HGSOC. PMID:26391404

  14. A bi-dimensional genome scan for prolificacy traits in pigs shows the existence of multiple epistatic QTL

    Directory of Open Access Journals (Sweden)

    Bidanel Jean P

    2009-12-01

    Full Text Available Abstract Background Prolificacy is the most important trait influencing the reproductive efficiency of pig production systems. The low heritability and sex-limited expression of prolificacy have hindered to some extent the improvement of this trait through artificial selection. Moreover, the relative contributions of additive, dominant and epistatic QTL to the genetic variance of pig prolificacy remain to be defined. In this work, we have undertaken this issue by performing one-dimensional and bi-dimensional genome scans for number of piglets born alive (NBA and total number of piglets born (TNB in a three generation Iberian by Meishan F2 intercross. Results The one-dimensional genome scan for NBA and TNB revealed the existence of two genome-wide highly significant QTL located on SSC13 (P SSC17 (P P P P P Conclusions The complex inheritance of prolificacy traits in pigs has been evidenced by identifying multiple additive (SSC13 and SSC17, dominant and epistatic QTL in an Iberian × Meishan F2 intercross. Our results demonstrate that a significant fraction of the phenotypic variance of swine prolificacy traits can be attributed to first-order gene-by-gene interactions emphasizing that the phenotypic effects of alleles might be strongly modulated by the genetic background where they segregate.

  15. Quantitative trait loci (QTL) mapping of resistance to strongyles and coccidia in the free-living Soay sheep (Ovis aries).

    Science.gov (United States)

    Beraldi, Dario; McRae, Allan F; Gratten, Jacob; Pilkington, Jill G; Slate, Jon; Visscher, Peter M; Pemberton, Josephine M

    2007-01-01

    A genome-wide scan was performed to detect quantitative trait loci (QTL) for resistance to gastrointestinal parasites and ectoparasitic keds segregating in the free-living Soay sheep population on St. Kilda (UK). The mapping panel consisted of a single pedigree of 882 individuals of which 588 were genotyped. The Soay linkage map used for the scans comprised 251 markers covering the whole genome at average spacing of 15cM. The traits here investigated were the strongyle faecal egg count (FEC), the coccidia faecal oocyst count (FOC) and a count of keds (Melophagus ovinus). QTL mapping was performed by means of variance component analysis so that the genetic parameters of the study traits were also estimated and compared with previous studies in Soay and domestic sheep. Strongyle FEC and coccidia FOC showed moderate heritability (h(2)=0.26 and 0.22, respectively) in lambs but low heritability in adults (h(2)scans were performed for the traits with moderate heritability and two genomic regions reached the level of suggestive linkage for coccidia FOC in lambs (logarithm of the odds=2.68 and 2.21 on chromosomes 3 and X, respectively). We believe this is the first study to report a QTL search for parasite resistance in a free-living animal population and therefore may represent a useful reference for similar studies aimed at understanding the genetics of host-parasite co-evolution in the wild.

  16. RiceGeneThresher: a web-based application for mining genes underlying QTL in rice genome.

    Science.gov (United States)

    Thongjuea, Supat; Ruanjaichon, Vinitchan; Bruskiewich, Richard; Vanavichit, Apichart

    2009-01-01

    RiceGeneThresher is a public online resource for mining genes underlying genome regions of interest or quantitative trait loci (QTL) in rice genome. It is a compendium of rice genomic resources consisting of genetic markers, genome annotation, expressed sequence tags (ESTs), protein domains, gene ontology, plant stress-responsive genes, metabolic pathways and prediction of protein-protein interactions. RiceGeneThresher system integrates these diverse data sources and provides powerful web-based applications, and flexible tools for delivering customized set of biological data on rice. Its system supports whole-genome gene mining for QTL by querying using DNA marker intervals or genomic loci. RiceGeneThresher provides biologically supported evidences that are essential for targeting groups or networks of genes involved in controlling traits underlying QTL. Users can use it to discover and to assign the most promising candidate genes in preparation for the further gene function validation analysis. The web-based application is freely available at http://rice.kps.ku.ac.th. PMID:18820292

  17. Re-sequencing data for refining candidate genes and polymorphisms in QTL regions affecting adiposity in chicken.

    Directory of Open Access Journals (Sweden)

    Pierre-François Roux

    Full Text Available In this study, we propose an approach aiming at fine-mapping adiposity QTL in chicken, integrating whole genome re-sequencing data. First, two QTL regions for adiposity were identified by performing a classical linkage analysis on 1362 offspring in 11 sire families obtained by crossing two meat-type chicken lines divergently selected for abdominal fat weight. Those regions, located on chromosome 7 and 19, contained a total of 77 and 84 genes, respectively. Then, SNPs and indels in these regions were identified by re-sequencing sires. Considering issues related to polymorphism annotations for regulatory regions, we focused on the 120 and 104 polymorphisms having an impact on protein sequence, and located in coding regions of 35 and 42 genes situated in the two QTL regions. Subsequently, a filter was applied on SNPs considering their potential impact on the protein function based on conservation criteria. For the two regions, we identified 42 and 34 functional polymorphisms carried by 18 and 24 genes, and likely to deeply impact protein, including 3 coding indels and 4 nonsense SNPs. Finally, using gene functional annotation, a short list of 17 and 4 polymorphisms in 6 and 4 functional genes has been defined. Even if we cannot exclude that the causal polymorphisms may be located in regulatory regions, this strategy gives a complete overview of the candidate polymorphisms in coding regions and prioritize them on conservation- and functional-based arguments.

  18. First evidence for family-specific QTL for temperature-dependent sex reversal in Nile tilapia (Oreochromis niloticus).

    Science.gov (United States)

    Lühmann, L M; Knorr, C; Hörstgen-Schwark, G; Wessels, S

    2012-01-01

    This study for the first time screens microsatellite markers for associations with the temperature-dependent sex of Oreochromis niloticus. Previous studies revealed markers on linkage groups (LG) 1, 3, and 23 to be linked to the phenotypic sex of Oreochromis spp. at normal rearing temperatures. Moreover, candidate genes for sex determination and differentiation have been mapped to these linkage groups. Here, 6 families of a temperature-treated genetically all-female (XX) F(1)-population were genotyped for 21 microsatellites on the 3 LGs. No population-wide QTL (quantitative trait loci) or marker trait associations could be detected. However, family-specific QTL were found on LG 1 flanked by UNH995 and UNH104, on LG 3 at the position of GM213, and on LG 23 next to GM283. Moreover, family-specific single marker associations for UNH995 and UNH104 on LG 1, GM213 on LG 3, as well as for UNH898 and GM283 on LG 23 were detected. Yet, marker trait associations could not explain the temperature-dependent sex of all fish in the respective families. The molecular cue for the temperature-dependent sex in Nile tilapia might partially coincide with allelic variants at major and minor genetic sex determining factors. Moreover, additional QTL contributing to variable liabilities towards temperature might persist on other LGs. PMID:22797471

  19. Meta-Analysis of Tenderness QTL in Swine%猪肉嫩度相关QTL整合定位与基因关联分析研究

    Institute of Scientific and Technical Information of China (English)

    刘璐; 苏玉虹; 王军; 赵会仁; 袁志发

    2012-01-01

    This study was conducted for the Quantitative Trait Loci (QTL) related to tenderness to estimate the number and refine the positions of QTL with Meta-analysis. Tenderness QTL were collected and projected to the swine linkage map of USDA-MARC 2.0 to establish an integrated map. Meta-QTL (MQTL) was obtained by meta-analysis which reduced the the 95% confidence interval. Positions of candidate genes and meta-QTL obtained in this study were compared to reckon the precision of meta-QTL. With the software BioMercator 2.1, 99 tenderness QTL were collected from 23 published papers since 2001 and an integrated map was established. 16 meta-QTL as well as their corresponding markers were obtained. The 95% confidence intervals of meta-QTL, with 8 of which were shrunk more than 50% and 6 of which were less than 10 cM, ranged from 2.42 cM to 25.18 cM. The 95% confidence interval of MQTL1 and MQTL2 was only 2.42 cM and 3.22 cM, and was merged with 9 and 20 initial QTL, respectively. Projected to the integrated map, the position of FABP3, MYPN and ANK1 gene was in the confidence interval of MQTL5, MQTL12 and MQTL16. These results could lead to more precise QTL position estimates, and offered a basis for gene mining and molecular breeding in swine.%为了优化猪肉嫩度相关数量性状位点(quantitative trait loci,QTL),为基因的精细定位和克隆奠定基础,通过Meta分析,利用数学模型整合猪肉嫩度相关QTL,分析已知候选基因与MQTL的关联性.收集猪肉嫩度相关QTL,将其逐一映射到美国肉畜研究中心(USDA-MARC 2.0)公布的猪遗传连锁图谱,构建整合图谱.进行Meta分析,得到精确性更高的MQTL,并将已知候选基因映射到整合图谱,比较候选基因与各MQTL的关联性.研究表明:99个猪肉嫩度相关QTL映射到参考图谱,构建成新的整合图谱.通过Meta分析,定位了16个MQTL,图距2.42~25.18 cM,29.21%~93.18%.值得一提的是MQTL1和MQTL2,图距仅为2.42 cM和3.22 cM,且分别由9

  20. Genetic Linkage Map Construction and QTL Analysis of Two Interspecific Reproductive Isolation Traits in Sponge Gourd.

    Science.gov (United States)

    Wu, Haibin; He, Xiaoli; Gong, Hao; Luo, Shaobo; Li, Mingzhu; Chen, Junqiu; Zhang, Changyuan; Yu, Ting; Huang, Wangping; Luo, Jianning

    2016-01-01

    The hybrids between Luffa acutangula (L.) Roxb. and L.cylindrica (L.) Roem. have strong heterosis effects. However, some reproductive isolation traits hindered their normal hybridization and fructification, which was mainly caused by the flowering time and hybrid pollen sterility. In order to study the genetic basis of two interspecific reproductive isolation traits, we constructed a genetic linkage map using an F2 population derived from a cross between S1174 [L. acutangula (L.) Roxb.] and 93075 [L. cylindrica (L.) Roem.]. The map spans 1436.12 CentiMorgans (cM), with an average of 8.11 cM among markers, and consists of 177 EST-SSR markers distributed in 14 linkage groups (LG) with an average of 102.58 cM per LG. Meanwhile, we conducted colinearity analysis between the sequences of EST-SSR markers and the genomic sequences of cucumber, melon and watermelon. On the basis of genetic linkage map, we conducted QTL mapping of two reproductive isolation traits in sponge gourd, which were the flowering time and hybrid male sterility. Two putative QTLs associated with flowering time (FT) were both detected on LG 1. The accumulated contribution of these two QTLs explained 38.07% of the total phenotypic variance (PV), and each QTL explained 15.36 and 22.71% of the PV respectively. Four QTLs for pollen fertility (PF) were identified on LG 1 (qPF1.1 and qPF1.2), LG 3 (qPF3) and LG 7 (qPF7), respectively. The percentage of PF explained by these QTLs varied from 2.91 to 16.79%, and all together the four QTLs accounted for 39.98% of the total PV. Our newly developed EST-SSR markers and linkage map are very useful for gene mapping, comparative genomics and molecular marker-assisted breeding. These QTLs for interspecific reproductive isolation will also contribute to the cloning of genes relating to interspecific reproductive isolation and the utilization of interspecific heterosis in sponge gourd in further studies. PMID:27458467

  1. Genetic Linkage Map Construction and QTL Analysis of Two Interspecific Reproductive Isolation Traits in Sponge Gourd

    Science.gov (United States)

    Wu, Haibin; He, Xiaoli; Gong, Hao; Luo, Shaobo; Li, Mingzhu; Chen, Junqiu; Zhang, Changyuan; Yu, Ting; Huang, Wangping; Luo, Jianning

    2016-01-01

    The hybrids between Luffa acutangula (L.) Roxb. and L.cylindrica (L.) Roem. have strong heterosis effects. However, some reproductive isolation traits hindered their normal hybridization and fructification, which was mainly caused by the flowering time and hybrid pollen sterility. In order to study the genetic basis of two interspecific reproductive isolation traits, we constructed a genetic linkage map using an F2 population derived from a cross between S1174 [L. acutangula (L.) Roxb.] and 93075 [L. cylindrica (L.) Roem.]. The map spans 1436.12 CentiMorgans (cM), with an average of 8.11 cM among markers, and consists of 177 EST-SSR markers distributed in 14 linkage groups (LG) with an average of 102.58 cM per LG. Meanwhile, we conducted colinearity analysis between the sequences of EST-SSR markers and the genomic sequences of cucumber, melon and watermelon. On the basis of genetic linkage map, we conducted QTL mapping of two reproductive isolation traits in sponge gourd, which were the flowering time and hybrid male sterility. Two putative QTLs associated with flowering time (FT) were both detected on LG 1. The accumulated contribution of these two QTLs explained 38.07% of the total phenotypic variance (PV), and each QTL explained 15.36 and 22.71% of the PV respectively. Four QTLs for pollen fertility (PF) were identified on LG 1 (qPF1.1 and qPF1.2), LG 3 (qPF3) and LG 7 (qPF7), respectively. The percentage of PF explained by these QTLs varied from 2.91 to 16.79%, and all together the four QTLs accounted for 39.98% of the total PV. Our newly developed EST-SSR markers and linkage map are very useful for gene mapping, comparative genomics and molecular marker-assisted breeding. These QTLs for interspecific reproductive isolation will also contribute to the cloning of genes relating to interspecific reproductive isolation and the utilization of interspecific heterosis in sponge gourd in further studies. PMID:27458467

  2. QTL Analysis for Seven Quality Traits of RIL Population in Japonica Rice Based on Three Genetic Statistical Models

    Institute of Scientific and Technical Information of China (English)

    LIU Qiang-ming; JIANG Jian-hua; NIU Fu-an; HE Ying-jun; HONG De-lin

    2013-01-01

    QTL mapping for seven quality traits was conducted by using 254 recombinant inbred lines (RIL) derived from a japonica-japonica rice cross of Xiushui 791C Bao.The seven traits investigated were grain length (GL),grain length to width ratio (LWR),chalk grain rate (CGR),chalkiness degree (CD),gelatinization temperature (GT),amylose content (AC) and gel consistency (GC) of head rice.Three mapping methods employed were composite interval mapping in QTLMapper 2.0 software based on mixed linear model (MCIM),inclusive composite interval mapping in QTL IciMapping 3.0 software based on stepwise regression linear model (ICIM) and multiple interval mapping with regression forward selection in Windows QTL Cartographer 2.5 based on multiple regression analysis (MIMR).Results showed that five QTLs with additive effect (A-QTLs) were detected by all the three methods simultaneously,two by two methods simultaneously,and 23 by only one method.Five A-QTLs were detected by MCIM,nine by ICIM and 28 by MIMR.The contribution rates of single A-QTL ranged from 0.89% to 38.07%.All the QTLs with epistatic effect (E-QTLs) detected by MIMR were not detected by the other two methods.Fourteen pairs of E-QTLs were detected by both MCIM and ICIM,and 142 pairs of E-QTLs were detected by only one method.Twenty-five pairs of E-QTLs were detected by MCIM,141 pairs by ICIM and four pairs by MIMR.The contribution rates of single pair of E-QTL were from 2.60% to 23.78%.In the Xiu-Bao RIL population,epistatic effect played a major role in the variation of GL and CD,and additive effect was the dominant in the variation of LWR,while both epistatic effect and additive effect had equal importance in the variation of CGR,AC,GT and GC.QTLs detected by two or more methods simultaneously were highly reliable,and could be applied to improve the quality traits in japonica hybrid rice.

  3. Identification and Verification of QTL Associated with Frost Tolerance Using Linkage Mapping and GWAS in Winter Faba Bean.

    Science.gov (United States)

    Sallam, Ahmed; Arbaoui, Mustapha; El-Esawi, Mohamed; Abshire, Nathan; Martsch, Regina

    2016-01-01

    Frost stress is one of the abiotic stresses that causes a significant reduction in winter faba bean yield in Europe. The main objective of this work is to genetically improve frost tolerance in winter faba bean by identifying and validating QTL associated with frost tolerance to be used in marker-assisted selection (MAS). Two different genetic backgrounds were used: a biparental population (BPP) consisting of 101 inbred lines, and 189 genotypes from single seed descent (SSD) from the Gottingen Winter bean Population (GWBP). All experiments were conducted in a frost growth chamber under controlled conditions. Both populations were genotyped using the same set of 189 SNP markers. Visual scoring for frost stress symptoms was used to define frost tolerance in both populations. In addition, leaf fatty acid composition (FAC) and proline content were analyzed in BPP as physiological traits. QTL mapping (for BPP) and genome wide association studies (for GWBP) were performed to detect QTL associated with frost tolerance. High genetic variation between genotypes, and repeatability estimates, were found for all traits. QTL mapping and GWAS identified new putative QTL associated with promising frost tolerance and related traits. A set of 54 SNP markers common in both genetic backgrounds showed a high genetic diversity with polymorphic information content (PIC) ranging from 0.31 to 0.37 and gene diversity ranging from 0.39 to 0.50. This indicates that these markers may be polymorphic for many faba bean populations. Five SNP markers showed a significant marker-trait association with frost tolerance and related traits in both populations. Moreover, synteny analysis between Medicago truncatula (a model legume) and faba bean genomes was performed to identify candidate genes for these markers. Collinearity was evaluated between the faba bean genetic map constructed in this study and the faba bean consensus map, resulting in identifying possible genomic regions in faba bean which may

  4. Identification and Verification of QTL Associated with Frost Tolerance Using Linkage Mapping and GWAS in Winter Faba Bean

    Science.gov (United States)

    Sallam, Ahmed; Arbaoui, Mustapha; El-Esawi, Mohamed; Abshire, Nathan; Martsch, Regina

    2016-01-01

    Frost stress is one of the abiotic stresses that causes a significant reduction in winter faba bean yield in Europe. The main objective of this work is to genetically improve frost tolerance in winter faba bean by identifying and validating QTL associated with frost tolerance to be used in marker-assisted selection (MAS). Two different genetic backgrounds were used: a biparental population (BPP) consisting of 101 inbred lines, and 189 genotypes from single seed descent (SSD) from the Gottingen Winter bean Population (GWBP). All experiments were conducted in a frost growth chamber under controlled conditions. Both populations were genotyped using the same set of 189 SNP markers. Visual scoring for frost stress symptoms was used to define frost tolerance in both populations. In addition, leaf fatty acid composition (FAC) and proline content were analyzed in BPP as physiological traits. QTL mapping (for BPP) and genome wide association studies (for GWBP) were performed to detect QTL associated with frost tolerance. High genetic variation between genotypes, and repeatability estimates, were found for all traits. QTL mapping and GWAS identified new putative QTL associated with promising frost tolerance and related traits. A set of 54 SNP markers common in both genetic backgrounds showed a high genetic diversity with polymorphic information content (PIC) ranging from 0.31 to 0.37 and gene diversity ranging from 0.39 to 0.50. This indicates that these markers may be polymorphic for many faba bean populations. Five SNP markers showed a significant marker-trait association with frost tolerance and related traits in both populations. Moreover, synteny analysis between Medicago truncatula (a model legume) and faba bean genomes was performed to identify candidate genes for these markers. Collinearity was evaluated between the faba bean genetic map constructed in this study and the faba bean consensus map, resulting in identifying possible genomic regions in faba bean which may

  5. Genetic mapping of two QTL from the wild tomato Solanum pimpinellifolium L. controlling resistance against two-spotted spider mite (Tetranychus urticae Koch).

    Science.gov (United States)

    Salinas, María; Capel, Carmen; Alba, Juan Manuel; Mora, Blanca; Cuartero, Jesús; Fernández-Muñoz, Rafael; Lozano, Rafael; Capel, Juan

    2013-01-01

    A novel source of resistance to two-spotted spider mite (Tetranychus urticae Koch) was found in Solanum pimpinellifolium L. accession TO-937 and thereby a potential source of desirable traits that could be introduced into new tomato varieties. This resistance was found to be controlled by a major locus modulated by minor loci of unknown location in the genome of this wild tomato. We first applied a bulked segregant analysis (BSA) approach in an F(4) population as a method for rapidly identifying a genomic region of 17 cM on chromosome 2, flanked by two simple sequence repeat markers, harboring Rtu2.1, one of the major QTL involved in the spider mite resistance. A population of 169 recombinant inbred lines was also evaluated for spider mite infestation and a highly saturated genetic map was developed from this population. QTL mapping corroborated that chromosome 2 harbored the Rtu2.1 QTL in the same region that our previous BSA findings pointed out, but an even more robust QTL was found in the telomeric region of this chromosome. This QTL, we termed Rtu2.2, had a LOD score of 15.43 and accounted for more than 30% of the variance of two-spotted spider mite resistance. Several candidate genes involved in trichome formation, synthesis of trichomes exudates and plant defense signaling have been sequenced. However, either the lack of polymorphisms between the parental lines or their map position, away from the QTL, led to their rejection as candidate genes responsible for the two-spotted spider mite resistance. The Rtu2 QTL not only serve as a valuable target for marker-assisted selection of new spider mite-resistant tomato varieties, but also as a starting point for a better understanding of the molecular genetic functions underlying the resistance to this pest.

  6. Genetic control of soybean seed oil: I. QTL and genes associated with seed oil concentration in RIL populations derived from crossing moderately high-oil parents.

    Science.gov (United States)

    Eskandari, Mehrzad; Cober, Elroy R; Rajcan, Istvan

    2013-02-01

    Soybean seed is a major source of oil for human consumption worldwide and the main renewable feedstock for biodiesel production in North America. Increasing seed oil concentration in soybean [Glycine max (L.) Merrill] with no or minimal impact on protein concentration could be accelerated by exploiting quantitative trait loci (QTL) or gene-specific markers. Oil concentration in soybean is a polygenic trait regulated by many genes with mostly small effects and which is negatively associated with protein concentration. The objectives of this study were to discover and validate oil QTL in two recombinant inbred line (RIL) populations derived from crosses between three moderately high-oil soybean cultivars, OAC Wallace, OAC Glencoe, and RCAT Angora. The RIL populations were grown across several environments over 2 years in Ontario, Canada. In a population of 203 F(3:6) RILs from a cross of OAC Wallace and OAC Glencoe, a total of 11 genomic regions on nine different chromosomes were identified as associated with oil concentration using multiple QTL mapping and single-factor ANOVA. The percentage of the phenotypic variation accounted for by each QTL ranged from 4 to 11 %. Of the five QTL that were tested in a population of 211 F(3:5) RILs from the cross RCAT Angora × OAC Wallace, a "trait-based" bidirectional selective genotyping analysis validated four QTL (80 %). In addition, a total of seven two-way epistatic interactions were identified for oil concentration in this study. The QTL and epistatic interactions identified in this study could be used in marker-assisted introgression aimed at pyramiding high-oil alleles in soybean cultivars to increase oil concentration for biodiesel as well as edible oil applications.

  7. Tamanho de amostra para a estimação da média de caracteres de pêssego na colheita e após o armazenamento refrigerado Sample size to estimate the average peach characters at harvest and after cold storage

    Directory of Open Access Journals (Sweden)

    Marcos Toebe

    2012-02-01

    Full Text Available O objetivo deste trabalho foi determinar o tamanho de amostra necessário para avaliar caracteres de frutos de pêssego na colheita e após o armazenamento refrigerado. Foram colhidos frutos de um pomar comercial. No laboratório, separaram-se, aleatoriamente, duas amostras de 120 frutos de pêssego, sendo uma amostra avaliada na colheita e a outra armazenada a -0,5°C por 30 dias, mais cinco dias a 20°C. Foram mensurados 11 caracteres em cada fruto na colheita e 12 caracteres após o armazenamento refrigerado, sendo calculadas medidas de tendência central e de dispersão e verificada a normalidade. Posteriormente, compararam-se as médias e verificou-se a homogeneidade de variâncias dos caracteres avaliados na colheita e após o armazenamento refrigerado. A seguir, foi determinado o tamanho de amostra para cada caractere. São necessários 169 frutos para estimar a firmeza de polpa, 34 frutos para estimar a massa, a acidez e o ratio, 11 frutos para avaliar a suculência e seis frutos para estimar os demais caracteres na colheita e após o armazenamento refrigerado, com erro de estimação de 5% da média.The aim of this research was to determine the sample size needed to evaluate peach fruit characters at harvest and after cold storage. Fruits were collected from a commercial orchard. In the laboratory, split randomly, two samples of 120 fruits each, one sample assessed at harvest and one stored at -0.5°C for 30 days, and then for five additional days at 20°C. Eleven characters were measured on each fruit at harvest and twelve after cold storage, being the central tendency measures and dispersion calculated and normality checked. After, it was compared the average and the homogeneity of variance at harvest and after cold storage and calculated the sample size for each character. In peach, 169 fruits are needed to estimate the pulp firmness, 34 fruits to estimate the weight, acidity and ratio, 11 fruits to assess fruit juiciness and six

  8. QTL Analysis of the Oil Content and the Hull Content in Brassica napus L.

    Institute of Scientific and Technical Information of China (English)

    JIN Meng-yang; LI Jia-na; FU Fu-you; ZHANG Zheng-sheng; ZHANG Xue-kun; LIU Lie-zhao

    2007-01-01

    The QTLs of the oil content and the hull content were analyzed in Brassica napus L. By constructing the linkage map. The F2:6 RIL population with 188 lines, derived from the cross of GH06 × P147, was used as the mapping population. The SRAP, SSR, AFLP, and TRAP markers were used to construct the linkage map, and the composite interval mapping (CIM) to identify the quantitative trait loci associated with the oil content and the hull content. 300 markers were integrated into 19 linkage groups, covering 1 248.5 cM in total. Seven QTLs were found to be responsible for the oil content with the single contribution to phenotypic variance ranging from 3.73 to 10.46%; four QTLs were found for the hull content with the single contribution to phenotypic variance ranging from 4.89 to 6.84%. The yellow-seeded Brassica napus L. Has the advantage of higher oil content and the hull content has a significant effect on the oil content. In addition, the SRAP marker is good for detecting QTL.

  9. QTL analysis of leaf photosynthesis rate and related physiological traits in Brassica napus

    Institute of Scientific and Technical Information of China (English)

    YAN Xing-ying; QU Cun-min; LI Jia-na; CHEN Li; LIU Lie-zhao

    2015-01-01

    Rapeseed (Brassica napus L.) oil is the crucial source of edible oil in China. In addition, it can become a major renewable and sustainable feedstock for biodiesel production in the future. It is known that photosynthesis products are the primary sources for dry matter accumulation in rapeseed. Therefore, increasing the photosynthetic efifciency is desirable for the raise of rapeseed yield. The objective of the present study was to identify the genetic mechanism of photosynthesis based on the description of relationships between different photosynthetic traits and their quantitative trait loci (QTL) by using a recombinant inbred line (RIL) population with 172 lines. Speciifcal y, correlation analysis in this study showed that internal CO2 concentration has negative correlations with other three physiological traits under two different stages. Total y, 11 and 12 QTLs of the four physiological traits measured at the stages 1 and 2 were detected by using a high-density single nu-cleotidepolymorphism (SNP) markers linkage map with composite interval mapping (CIM), respectively. Three co-localized QTLs on A03 were detected at stage 1 with 5, 5, and 10%of the phenotypic variation, respectively. Other two co-localized QTLs were located on A05 at stage 2, which explained up to 12 and 5%of the phenotypic variation, respectively. The results are beneifcial for our understanding of genetic control of photosynthetic physiological characterizations and improvement of rapeseed yield in the future.

  10. Comparative QTL Mapping of Resistance to Gray Leaf Spot in Maize Based on Bioinformatics

    Institute of Scientific and Technical Information of China (English)

    SHI Li-yu; LI Xin-hai; HAO Zhuan-fang; XIE Chuan-xiao; JI Hai-lian; L(U) Xiang-ling; ZHANG Shi-huang; PAN Guang-tang

    2007-01-01

    The integration QTL map for gray leaf spot resistance in maize was constructed by compiling a total of 57 QTLs available with genetic map IBM2 2005 neighbors as reference.Twenty-six "real QTLs" and seven consensus QTLs were identified by refining these 57 QTLs using overview and meta-analysis approaches.Seven consensus QTLs were found on chromosomes 1.06,2.06,3.04,4.06,4.08,5.03,and 8.06,and the map coordinates were 552.53,425.72,279.20,368.97,583.21,308.68 and 446.14 cM,respectively.Using a synteny conservation approach based on comparative mapping between the maize genetic map and rice physical map,a total of 69 rice and maize resistance genes collected from websites Gramene and MaizeGDB were projected onto the maize genetic map IBM2 2005 neighbors,and 2(Rgene32,ht1),4(Rgene5,rp3,scmv2,wsm2),and 4(ht2,Rgene6,Rgene8 and Rgene7)positional candidate genes were found in three consensus QTLs on chromosomes 2.06,3.04,and 8.06,respectively.The results suggested that the combination of meta-analysis of gray leaf spot in maize and sequence homologous comparison between maize and rice could be an efficient strategy for identifying major QTLs and corresponding candidate genes for the gray leaf spot.

  11. Identification of QTL in soybean underlying resistance to herbivory by Japanese beetles (Popillia japonica, Newman).

    Science.gov (United States)

    Yesudas, C R; Sharma, H; Lightfoot, D A

    2010-07-01

    Soybean [Glycine max (L.) Merr.] was one of the most important legume crops in the world in 2010. Japanese beetles (JB; Popillia japonica, Newman) in the US were an introduced and potentially damaging insect pest for soybean. JBs are likely to spread across the US if global warming occurs. Resistance to JB in soybean was previously reported only in plant introductions. The aims here were to identify loci underlying resistance to JB herbivory in recombinant inbred lines (RILs) derived from the cross of Essex x Forrest cultivars (EF94) and to correlate those with loci with factors that confer insect resistance in soybean cultivars. The RIL population was used to map 413 markers, 238 satellite markers and 177 other DNA markers. Field data were from two environments over 2 years. Pest severity (PS) measured defoliation on a 0-9 scale. Pest incidence (PI) was the percentage of plants within each RIL with beetles on them. Antibiosis and antixenosis data were from feeding assays with detached leaves in petri plates. Five QTL were detected for the mean PS field trait (16% root knot nematode (LG F) but not other major loci underlying resistance to nematode or insect pests (LGs G, H and M).

  12. Modular network construction using eQTL data: an analysis of computational costs and benefits

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    Yen-Yi eHo

    2014-02-01

    Full Text Available Background: In this paper, we consider analytic methods for the integrated analysis of genomic DNA variation and mRNA expression (also named as eQTL data, to discover genetic networks that are associated with a complex trait of interest. Our focus is the systematic evaluation of the trade-off between network size and network search efficiency in the construction of these networks. Results: We developed a modular approach to network construction, building from smaller networks to larger ones, thereby reducing the search space while including more variables in the analysis. The goal is achieving a lower computational cost while maintaining high confidence in the resulting networks. As demonstrated in our simulation results, networks built in this way have low node/edge false discovery rate (FDR and high node/edge sensitivity comparing to greedy search. We further demonstrate our method in a data set of cellular responses to two chemotherapeutic agents: docetaxel and 5-fluorouracil (5-FU, and identify biologically plausible networks that might describe resistances to these drugs.Conclusions: In this study, we suggest that guided comprehensive searches for parsimonious networks should be considered as an alternative to greedy network searches.

  13. Estudio cuali-cuantitativo sobre la atención de salud de niños menores de tres años en establecimientos de salud de nueve regiones pobres del Perú

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    Luis Germán Cordero Muñoz

    2016-01-01

    Full Text Available Objetivos. Evaluar cinco elementos importantes de la calidad de atención (espacio físico, equipamiento, personal, tiempo para la atención, y consejería en servicios de crecimiento y desarrollo (CRED de 18 establecimientos de salud (EE. SS. en nueve regiones con altos índices de pobreza en Perú. Materiales y métodos. Estudio cuali-cuantitativo realizado en Amazonas, Apurímac, Ayacucho, Cajamarca, Cusco, Huánuco, Huancavelica, Puno y Ucayali, que incluyó la observación directa (OD durante la atención de CRED, grupos focales (GF con usuarios (uno por establecimiento de salud, y entrevistas en profundidad (EEP con trabajadores de salud (dos por establecimiento de salud. Resultados. Se realizaron 18 OD para la verificación de ambientes y equipos, 23 OD de turnos completos de atención, 67 acompañamientos a usuarios de los servicios de CRED, 18 GF (118 madres participantes, y 36 EEP. Las madres y los profesionales de salud coincidieron en que existen limitaciones de infraestructura, equipamiento, materiales y personal que afectarían una atención de CRED de calidad. La demora en la atención, el incumplimiento de horarios, y la falta de calidez en la atención son los aspectos que generaron mayor insatisfacción en los usuarios. Solo en 24,3% del tiempo total de los turnos observados se realizaron actividades que generaron beneficio al usuario. Por su parte, la consejería estaría cumpliendo el objetivo de promover el mejoramiento de las prácticas de cuidado del niño. Conclusiones. El estudio ha permitido identificar debilidades y áreas de oportunidad para reorientar los servicios de CRED, en el marco de la política de fortalecimiento del primer nivel de atención del sector Salud.

  14. Mapping QTLs and QTL x environment interaction for CIMMYT maize drought stress program using factorial regression and partial least squares methods.

    Science.gov (United States)

    Vargas, Mateo; van Eeuwijk, Fred A; Crossa, Jose; Ribaut, Jean-Marcel

    2006-04-01

    The study of QTL x environment interaction (QEI) is important for understanding genotype x environment interaction (GEI) in many quantitative traits. For modeling GEI and QEI, factorial regression (FR) models form a powerful class of models. In FR models, covariables (contrasts) defined on the levels of the genotypic and/or environmental factor(s) are used to describe main effects and interactions. In FR models for QTL expression, considerable numbers of genotypic covariables can occur as for each putative QTL an additional covariable needs to be introduced. For large numbers of genotypic and/or environmental covariables, least square estimation breaks down and partial least squares (PLS) estimation procedures become an attractive alternative. In this paper we develop methodology for analyzing QEI by FR for estimating effects and locations of QTLs and QEI and interpreting QEI in terms of environmental variables. A randomization test for the main effects of QTLs and QEI is presented. A population of F2 derived F3 families was evaluated in eight environments differing in drought stress and soil nitrogen content and the traits yield and anthesis silking interval (ASI) were measured. For grain yield, chromosomes 1 and 10 showed significant QEI, whereas in chromosomes 3 and 8 only main effect QTLs were observed. For ASI, QTL main effects were observed on chromosomes 1, 2, 6, 8, and 10, whereas QEI was observed only on chromosome 8. The assessment of the QEI at chromosome 1 for grain yield showed that the QTL main effect explained 35.8% of the QTL + QEI variability, while QEI explained 64.2%. Minimum temperature during flowering time explained 77.6% of the QEI. The QEI analysis at chromosome 10 showed that the QTL main effect explained 59.8% of the QTL + QEI variability, while QEI explained 40.2%. Maximum temperature during flowering time explained 23.8% of the QEI. Results of this study show the possibilities of using FR for mapping QTL and for dissecting QEI in terms

  15. Combined analysis of data from two granddaughter designs: A simple strategy for QTL confirmation and increasing experimental power in dairy cattle

    Directory of Open Access Journals (Sweden)

    Blümel Jürgen

    2003-05-01

    Full Text Available Abstract A joint analysis of five paternal half-sib Holstein families that were part of two different granddaughter designs (ADR- or Inra-design was carried out for five milk production traits and somatic cell score in order to conduct a QTL confirmation study and to increase the experimental power. Data were exchanged in a coded and standardised form. The combined data set (JOINT-design consisted of on average 231 sires per grandsire. Genetic maps were calculated for 133 markers distributed over nine chromosomes. QTL analyses were performed separately for each design and each trait. The results revealed QTL for milk production on chromosome 14, for milk yield on chromosome 5, and for fat content on chromosome 19 in both the ADR- and the Inra-design (confirmed within this study. Some QTL could only be mapped in either the ADR- or in the Inra-design (not confirmed within this study. Additional QTL previously undetected in the single designs were mapped in the JOINT-design for fat yield (chromosome 19 and 26, protein yield (chromosome 26, protein content (chromosome 5, and somatic cell score (chromosome 2 and 19 with genomewide significance. This study demonstrated the potential benefits of a combined analysis of data from different granddaughter designs.

  16. Effects of the number of markers per haplotype and clustering of haplotypes on the accuracy of QTL mapping and prediction of genomic breeding values.

    Science.gov (United States)

    Calus, Mario P L; Meuwissen, Theo H E; Windig, Jack J; Knol, Egbert F; Schrooten, Chris; Vereijken, Addie L J; Veerkamp, Roel F

    2009-01-15

    The aim of this paper was to compare the effect of haplotype definition on the precision of QTL-mapping and on the accuracy of predicted genomic breeding values. In a multiple QTL model using identity-by-descent (IBD) probabilities between haplotypes, various haplotype definitions were tested i.e. including 2, 6, 12 or 20 marker alleles and clustering base haplotypes related with an IBD probability of > 0.55, 0.75 or 0.95. Simulated data contained 1100 animals with known genotypes and phenotypes and 1000 animals with known genotypes and unknown phenotypes. Genomes comprising 3 Morgan were simulated and contained 74 polymorphic QTL and 383 polymorphic SNP markers with an average r2 value of 0.14 between adjacent markers. The total number of haplotypes decreased up to 50% when the window size was increased from two to 20 markers and decreased by at least 50% when haplotypes related with an IBD probability of > 0.55 instead of > 0.95 were clustered. An intermediate window size led to more precise QTL mapping. Window size and clustering had a limited effect on the accuracy of predicted total breeding values, ranging from 0.79 to 0.81. Our conclusion is that different optimal window sizes should be used in QTL-mapping versus genome-wide breeding value prediction.

  17. Effects of the number of markers per haplotype and clustering of haplotypes on the accuracy of QTL mapping and prediction of genomic breeding values

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    Schrooten Chris

    2009-01-01

    Full Text Available Abstract The aim of this paper was to compare the effect of haplotype definition on the precision of QTL-mapping and on the accuracy of predicted genomic breeding values. In a multiple QTL model using identity-by-descent (IBD probabilities between haplotypes, various haplotype definitions were tested i.e. including 2, 6, 12 or 20 marker alleles and clustering base haplotypes related with an IBD probability of > 0.55, 0.75 or 0.95. Simulated data contained 1100 animals with known genotypes and phenotypes and 1000 animals with known genotypes and unknown phenotypes. Genomes comprising 3 Morgan were simulated and contained 74 polymorphic QTL and 383 polymorphic SNP markers with an average r2 value of 0.14 between adjacent markers. The total number of haplotypes decreased up to 50% when the window size was increased from two to 20 markers and decreased by at least 50% when haplotypes related with an IBD probability of > 0.55 instead of > 0.95 were clustered. An intermediate window size led to more precise QTL mapping. Window size and clustering had a limited effect on the accuracy of predicted total breeding values, ranging from 0.79 to 0.81. Our conclusion is that different optimal window sizes should be used in QTL-mapping versus genome-wide breeding value prediction.

  18. Quantitative trait loci (QTL) associated with resistance to a monogenean parasite (Benedenia seriolae) in yellowtail (Seriola quinqueradiata) through genome wide analysis.

    Science.gov (United States)

    Ozaki, Akiyuki; Yoshida, Kazunori; Fuji, Kanako; Kubota, Satoshi; Kai, Wataru; Aoki, Jun-ya; Kawabata, Yumi; Suzuki, Junpei; Akita, Kazuki; Koyama, Takashi; Nakagawa, Masahiro; Hotta, Takurou; Tsuzaki, Tatsuo; Okamoto, Nobuaki; Araki, Kazuo; Sakamoto, Takashi

    2013-01-01

    Benedenia infections caused by the monogenean fluke ectoparasite Benedenia seriolae seriously impact marine finfish aquaculture. Genetic variation has been inferred to play a significant role in determining the susceptibility to this parasitic disease. To evaluate the genetic basis of Benedenia disease resistance in yellowtail (Seriola quinqueradiata), a genome-wide and chromosome-wide linkage analyses were initiated using F1 yellowtail families (n = 90 per family) based on a high-density linkage map with 860 microsatellite and 142 single nucleotide polymorphism (SNP) markers. Two major quantitative trait loci (QTL) regions on linkage groups Squ2 (BDR-1) and Squ20 (BDR-2) were identified. These QTL regions explained 32.9-35.5% of the phenotypic variance. On the other hand, we investigated the relationship between QTL for susceptibility to B. seriolae and QTL for fish body size. The QTL related to growth was found on another linkage group (Squ7). As a result, this is the first genetic evidence that contributes to detailing phenotypic resistance to Benedenia disease, and the results will help resolve the mechanism of resistance to this important parasitic infection of yellowtail. PMID:23750223

  19. Quantitative trait loci (QTL associated with resistance to a monogenean parasite (Benedenia seriolae in yellowtail (Seriola quinqueradiata through genome wide analysis.

    Directory of Open Access Journals (Sweden)

    Akiyuki Ozaki

    Full Text Available Benedenia infections caused by the monogenean fluke ectoparasite Benedenia seriolae seriously impact marine finfish aquaculture. Genetic variation has been inferred to play a significant role in determining the susceptibility to this parasitic disease. To evaluate the genetic basis of Benedenia disease resistance in yellowtail (Seriola quinqueradiata, a genome-wide and chromosome-wide linkage analyses were initiated using F1 yellowtail families (n = 90 per family based on a high-density linkage map with 860 microsatellite and 142 single nucleotide polymorphism (SNP markers. Two major quantitative trait loci (QTL regions on linkage groups Squ2 (BDR-1 and Squ20 (BDR-2 were identified. These QTL regions explained 32.9-35.5% of the phenotypic variance. On the other hand, we investigated the relationship between QTL for susceptibility to B. seriolae and QTL for fish body size. The QTL related to growth was found on another linkage group (Squ7. As a result, this is the first genetic evidence that contributes to detailing phenotypic resistance to Benedenia disease, and the results will help resolve the mechanism of resistance to this important parasitic infection of yellowtail.

  20. Characterization of the Main Effects, Epistatic Effects and Their Environmental Interactions of QTL on the Genetic Basis of Plant Height and Heading Date in Rice

    Institute of Scientific and Technical Information of China (English)

    JIANG Gong-hao; XU Cai-guo; LI Xiang-hua; HE Yu-qing

    2005-01-01

    Main-effect QTL, epistatic effects and their interactions with environment are important genetic components of quantitative traits. In this study, we analyzed the QTL, epistatic effects and QTL by environment interactions (QE) underlying plant height and heading date, using a doubled-haploid (DH) population consisting of 190 lines from the cross between an indica parent Zhenshan 97 and a japonica parent Wuyujing 2, and tested in two-year replicated field trials. A genetic linkage map with 179 SSR (simple sequence repeat) marker loci was constructed. A mixed linear model approach was applied to detect QTL, digenic interactions and QEs for the two traits. In total, 20 main-effect QTLs, 9 digenic interactions involving 18 loci, and 5 QTL by environment interactions were found to be responsible for the two traits. No interactions were detected between the digenic interaction and environment. The amounts of variations explained by QTLs of main effect were 53.9% for plant height and 57.8% for heading date, larger than that explained by epistasis and QEs. However,the epistasis and QE interactions sometimes accounted for a significant part of phenotypic variation and should not be disregarded.

  1. Variabilidade genética em trigos brasileiros a partir de caracteres componentes da qualidade industrial e produção de grãos Genetic variability for bread making quality and grain yield among Brazilian wheat genotypes

    Directory of Open Access Journals (Sweden)

    Douglas André Mallmann Schmidt

    2009-01-01

    Full Text Available O melhoramento genético para a qualidade industrial do trigo pode representar uma oportunidade de agregar valor de mercado aos produtos agrícolas, sendo o trigo um dos cereais com maior associação entre a qualidade intrínseca e a remuneração ao agricultor. O objetivo do trabalho foi o de determinar a variabilidade genética a partir de caracteres indicativos da qualidade industrial e o rendimento de grãos, e estimar o grau de associação entre estes caracteres em 22 genótipos de trigo. O experimento foi desenvolvido em área experimental pertencente à Universidade Federal de Pelotas, Capão do Leão (RS. Os resultados indicaram a provável existência de variabilidade genética para os caracteres em estudo, a qual pode auxiliar pesquisadores na escolha de genitores. Cruzamentos artificiais envolvendo os genótipos BRS 208, Rubi e Safira podem ser os mais promissores no intuito de incrementar o ganho genético, tanto para a qualidade industrial quanto para a produtividade de grãos. O rendimento de grãos manifestou correlação negativa com o conteúdo de proteína da farinha revelando que a superioridade genotípica para o rendimento de grãos pode afetar negativamente a proporção protéica. Entretanto, o conteúdo de proteína não evidenciou associação significativa com a força de glúten (indicador da qualidade industrial, revelando que a concentração de proteína da farinha não foi eficiente para predizer a qualidade industrial. Este resultado sugere a possibilidade de obtenção de genótipos superiores para o rendimento de grãos sem comprometer a qualidade industrial.The breeding for wheat bread making quality represents a great opportunity to incorporate commercial value to agricultural products. Wheat has one of the best relationship between end product quality and farmer earnings. Genetic variability among 22 different genotypes based on bread making quality traits and grain yield and the degree of their association

  2. Tamanho de amostra para avaliação de caracteres de cenoura em sistemas de cultivo agroecológico Sample size for evaluation of carrot traits in agroecologic cultivation systems

    Directory of Open Access Journals (Sweden)

    Giovani Olegário da Silva

    2009-06-01

    Full Text Available O correto dimensionamento de experimentos deve ser utilizado para que se possa reduzir o erro experimental e com isso, maximizar a precisão das informações obtidas. O objetivo deste trabalho foi estimar o número mínimo de famílias e de plantas por parcela para avaliação de caracteres de raiz em uma população de cenoura cultivada em sistema agroecológico. Os ensaios foram conduzidos no verão de 2006/2007 em duas propriedades com cultivo agroecológico em Brasília: Associação Mokiti Okada, que segue modelo de Agricultura Natural em Brazlândia-DF e Núcleo Rural Taguatinga, seguindo modelo de Agricultura Orgânica em Taguatinga-DF. Foram avaliadas 100 famílias de meio-irmãos de cenoura dispostas em delineamento de blocos casualizados com duas repetições e parcelas de 1 m². Foram colhidas 20 plantas competitivas por parcela e avaliadas individualmente para os caracteres comprimento de raiz, diâmetro da raiz, massa da raiz, diâmetro do xilema da raiz, relação diâmetro do xilema/diâmetro da raiz, tipo de ponta da raiz, tipo de ombro da raiz, parâmetro a* para os tecidos xilema e floema. Foi realizada análise de variância conjunta e para cada sistema, com informação entre e dentro de parcelas. Foram realizadas ainda análises de representatividade do número mínimo de famílias e de plantas para representar uma população de cenoura. Foi verificado que uma amostra de 18 plantas competitivas/parcela coletadas em ensaios com 2 repetições, bem como de 74 famílias, são suficientes para garantir uma adequada avaliação de famílias meio-irmãos de cenoura para os caracteres estudados.The correct experiment design should be used to reduce the experimental error and, with that, maximize the precision of the information obtained. The objective of this work was to estimate the minimum number of families and of plants per plot for evaluation of root traits in a carrot population cultivated in agroecologic systems. The

  3. Correlation among agronomic, physiological and phytochemical traits in Artemisia annua L. varieties Correlação entre caracteres agronômicos, fisiológicos e fitoquímicos em variedades de Artemisia annua L

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    C.O. Bolina

    2013-01-01

    Full Text Available The aim of this study was to estimate the correlations among agronomic, physiological and phytochemical traits of two varieties of Artemisia annua and to identify correlations that can be used in selection and breeding processes for this species. The design was completely randomized and the treatments were for Artemisia annua varieties 2/39x5x3M and 2/39x1V, which were subjected to agronomic, physiological and phytochemical evaluations. The relationship among the studied traits was estimated with Pearson's correlation coefficient, and the significance level of correlations was established by the t-test using Genes software. A significant positive correlation was found between the traits canopy volume and essential oil yield for 2/39x5x3M variety, showing that the selection of plants with a larger canopy volume would facilitate indirect selection of the trait essential oil yield. This correlation was not found for the 2/39x1V variety. In both varieties, there was a significant negative correlation between canopy volume and artemisinin content, which suggested that the selection of plants with a large canopy volume and a large number of branches should be avoided if the goal is to increase artemisinin content.O objetivo deste trabalho foi estimar as correlações existentes entre caracteres agronômicos, fisiológicos e fitoquímicos em duas variedades de Artemisia annua e identificar correlações que possam ser utilizadas em processos de seleção e melhoramento da espécie. O delineamento foi inteiramente casualizado e os tratamentos foram às variedades 2/39x5x3M e 2/39x1V de Artemisia annua, submetidas a avaliações agronômicas, fisiológicas e fitoquímicas. A relação existente entre os caracteres estudados foi estimada através do coeficiente de correlação de Pearson e o nível de significância das correlações pelo teste t, realizadas no programa Genes. Encontrou-se correlação positiva e significativa entre os caracteres volume

  4. Correlação canônica entre caracteres de tubérculos para seleção precoce de clones de batata Canonical correlation for tuber trait to assist early selection of potato clones

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    Maria Helena Rigão

    2009-11-01

    Full Text Available Uma das estratégias utilizadas pelos melhoristas de batata é a eliminação de um grande número de clones nas primeiras gerações de seleção, para reduzir os custos e o trabalho de manutenção e multiplicação destes. O objetivo deste trabalho foi avaliar o uso da correlação canônica entre caracteres de tubérculos plantados, relacionados com os colhidos, para auxiliar a seleção precoce de clones de batata. Foram conduzidos três ensaios em diferentes épocas, na área experimental do Departamento de Fitotecnia da Universidade Federal de Santa Maria. Foram avaliados os tubérculos-semente e aqueles colhidos de 10 progênies de batata. Os caracteres utilizados para a análise da correlação canônica foram: o comprimento, o maior e o menor diâmetro e a massa fresca. Com o uso da correlação canônica, observou-se que há relação das diferentes características dos tubérculos plantados e daqueles colhidos. O comprimento apresentou a maior associação entre os tubérculos plantados e colhidos. Tubérculos compridos resultam na produção de tubérculos alongados.A potato breeding strategy is applied in early selection to discard the majority of potato clones, to reduce costs and efforts for maintenance and multiplication. The objective of this research was to test the canonical correlation of seeded tuber traits and harvested tubers to assist the early selection of potato clones. Three experiments in different seasons were carried out in the experimental area of the Horticultural Department of the Federal University of Santa Maria. Seeded and harvested tubers of ten potato progeny were evaluated. The tuber traits length, larger and smaller diameter, and fresh weight were submitted to canonical correlation analysis. The canonical correlation showed a trait relationship between potato seeds and their production. The largest association was tuber length. Therefore, long seed tubers produce elongated tubers as well.

  5. Configuración de la materia troncal de Métodos Cuantitativos de Organización Industrial en las universidades españolas||Configuration of the Core Subject of Quantitative Methods for Industrial Organization in the Spanish Universities

    OpenAIRE

    Mula Bru, Josefa; Poler Escoto, Raúl

    2007-01-01

    El objetivo principal de este trabajo es analizar la materia troncal de Métodos Cuantitativos de Organización Industrial (MCOI) como disciplina de estudio en la titulación de Ingeniería de Organización Industrial (IOI) en las universidades españolas. El núcleo central de este trabajo se basa en realizar el recorrido histórico de los contenidos de los MCOI y analizar su docencia en las universidades españolas. Con ello, se pretende estructurar el conocimiento de esta materia para que pueda ser...

  6. Whole-Genome Mapping Reveals Novel QTL Clusters Associated with Main Agronomic Traits of Cabbage (Brassica oleracea var. capitata L.)

    Science.gov (United States)

    Lv, Honghao; Wang, Qingbiao; Liu, Xing; Han, Fengqing; Fang, Zhiyuan; Yang, Limei; Zhuang, Mu; Liu, Yumei; Li, Zhansheng; Zhang, Yangyong

    2016-01-01

    We describe a comprehensive quantitative trait locus (QTL) analysis for 24 main agronomic traits of cabbage. Field experiments were performed using a 196-line double haploid population in three seasons in 2011 and 2012 to evaluate important agronomic traits related to plant type, leaf, and head traits. In total, 144 QTLs with LOD threshold >3.0 were detected for the 24 agronomic traits: 25 for four plant-type-related traits, 64 for 10 leaf-related traits, and 55 for 10 head-related traits; each QTL explained 6.0–55.7% of phenotype variation. Of the QTLs, 95 had contribution rates higher than 10%, and 51 could be detected in more than one season. Major QTLs included Ph 3.1 (max R2 = 55.7, max LOD = 28.2) for plant height, Ll 3.2 (max R2 = 31.7, max LOD = 13.95) for leaf length, and Htd 3.2 (max R2 = 28.5, max LOD = 9.49) for head transverse diameter; these could all be detected in more than one season. Twelve QTL clusters were detected on eight chromosomes, and the most significant four included Indel481–scaffold18376 (3.20 Mb), with five QTLs for five traits; Indel64–scaffold35418 (2.22 Mb), six QTLs for six traits; scaffold39782–Indel84 (1.78 Mb), 11 QTLs for 11 traits; and Indel353–Indel245 (9.89 Mb), seven QTLs for six traits. Besides, most traits clustered within the same region were significantly correlated with each other. The candidate genes at these regions were also discussed. Robust QTLs and their clusters obtained in this study should prove useful for marker-assisted selection (MAS) in cabbage breeding and in furthering our understanding of the genetic control of these traits.

  7. Quantitative trait loci (QTL study identifies novel genomic regions associated to Chiari-like malformation in Griffon Bruxellois dogs.

    Directory of Open Access Journals (Sweden)

    Philippe Lemay

    Full Text Available Chiari-like malformation (CM is a developmental abnormality of the craniocervical junction that is common in the Griffon Bruxellois (GB breed with an estimated prevalence of 65%. This disease is characterized by overcrowding of the neural parenchyma at the craniocervical junction and disturbance of cerebrospinal fluid (CSF flow. The most common clinical sign is pain either as a direct consequence of CM or neuropathic pain as a consequence of secondary syringomyelia. The etiology of CM remains unknown but genetic factors play an important role. To investigate the genetic complexity of the disease, a quantitative trait locus (QTL approach was adopted. A total of 14 quantitative skull and atlas measurements were taken and were tested for association to CM. Six traits were found to be associated to CM and were subjected to a whole-genome association study using the Illumina canine high density bead chip in 74 GB dogs (50 affected and 24 controls. Linear and mixed regression analyses identified associated single nucleotide polymorphisms (SNPs on 5 Canis Familiaris Autosomes (CFAs: CFA2, CFA9, CFA12, CFA14 and CFA24. A reconstructed haplotype of 0.53 Mb on CFA2 strongly associated to the height of the cranial fossa (diameter F and an haplotype of 2.5 Mb on CFA14 associated to both the height of the rostral part of the caudal cranial fossa (AE and the height of the brain (FG were significantly associated to CM after 10 000 permutations strengthening their candidacy for this disease (P = 0.0421, P = 0.0094 respectively. The CFA2 QTL harbours the Sall-1 gene which is an excellent candidate since its orthologue in humans is mutated in Townes-Brocks syndrome which has previously been associated to Chiari malformation I. Our study demonstrates the implication of multiple traits in the etiology of CM and has successfully identified two new QTL associated to CM and a potential candidate gene.

  8. A Kelch Motif-Containing Serine/Threonine Protein Phosphatase Determines the Large Grain QTL Trait in Rice

    Institute of Scientific and Technical Information of China (English)

    Zejun Hu; Haohua He; Shiyong Zhang; Fan Sun; Xiaoyun Xin; Wenxiang Wang; Xi Qian; Jingshui Yang; Xiaojin Luo

    2012-01-01

    A thorough understanding of the genetic basis of rice grain traits is critical for the improvement of rice (Oryza sativa L.) varieties.In this study,we generated an F2 population by crossing the large-grain japonica cultivar CW23 with Peiai 64 (PA64),an elite indica small-grain cultivar.Using QTL analysis,17 QTLs for five grain traits were detected on four different chromosomes.Eight of the QTLs were newly-identified in this study.In particular,qGL3-1,a newly-identified grain length QTL with the highest LOD value and largest phenotypic variation,was fine-mapped to the 17 kb region of chromosome 3.A serine/threonine protein phosphatase gene encoding a repeat domain containing two Kelch motifs was identified as the unique candidate gene corresponding to this QTL.A comparison of PA64 and CW23 sequences revealed a single nucleotide substitution (C→A) at position 1092 in exon 10,resulting in replacement of Asp (D) in PA64 with Glu (E) in CW23 for the 364th amino acid.This variation is located at the D position of the conserved sequence motif AVLDT of the Kelch repeat.Genetic analysis of a near-isogenic line (NIL) for qGL3-1 revealed that the allele qGL3-1 from CW23 has an additive or partly dominant effect,and is suitable for use in molecular marker-assisted selection.

  9. Whole-Genome Mapping Reveals Novel QTL Clusters Associated with Main Agronomic Traits of Cabbage (Brassica oleracea var. capitata L.).

    Science.gov (United States)

    Lv, Honghao; Wang, Qingbiao; Liu, Xing; Han, Fengqing; Fang, Zhiyuan; Yang, Limei; Zhuang, Mu; Liu, Yumei; Li, Zhansheng; Zhang, Yangyong

    2016-01-01

    We describe a comprehensive quantitative trait locus (QTL) analysis for 24 main agronomic traits of cabbage. Field experiments were performed using a 196-line double haploid population in three seasons in 2011 and 2012 to evaluate important agronomic traits related to plant type, leaf, and head traits. In total, 144 QTLs with LOD threshold >3.0 were detected for the 24 agronomic traits: 25 for four plant-type-related traits, 64 for 10 leaf-related traits, and 55 for 10 head-related traits; each QTL explained 6.0-55.7% of phenotype variation. Of the QTLs, 95 had contribution rates higher than 10%, and 51 could be detected in more than one season. Major QTLs included Ph 3.1 (max R (2) = 55.7, max LOD = 28.2) for plant height, Ll 3.2 (max R (2) = 31.7, max LOD = 13.95) for leaf length, and Htd 3.2 (max R (2) = 28.5, max LOD = 9.49) for head transverse diameter; these could all be detected in more than one season. Twelve QTL clusters were detected on eight chromosomes, and the most significant four included Indel481-scaffold18376 (3.20 Mb), with five QTLs for five traits; Indel64-scaffold35418 (2.22 Mb), six QTLs for six traits; scaffold39782-Indel84 (1.78 Mb), 11 QTLs for 11 traits; and Indel353-Indel245 (9.89 Mb), seven QTLs for six traits. Besides, most traits clustered within the same region were significantly correlated with each other. The candidate genes at these regions were also discussed. Robust QTLs and their clusters obtained in this study should prove useful for marker-assisted selection (MAS) in cabbage breeding and in furthering our understanding of the genetic control of these traits. PMID:27458471

  10. Genetic architecture of aluminum tolerance in rice (Oryza sativa determined through genome-wide association analysis and QTL mapping.

    Directory of Open Access Journals (Sweden)

    Adam N Famoso

    2011-08-01

    Full Text Available Aluminum (Al toxicity is a primary limitation to crop productivity on acid soils, and rice has been demonstrated to be significantly more Al tolerant than other cereal crops. However, the mechanisms of rice Al tolerance are largely unknown, and no genes underlying natural variation have been reported. We screened 383 diverse rice accessions, conducted a genome-wide association (GWA study, and conducted QTL mapping in two bi-parental populations using three estimates of Al tolerance based on root growth. Subpopulation structure explained 57% of the phenotypic variation, and the mean Al tolerance in Japonica was twice that of Indica. Forty-eight regions associated with Al tolerance were identified by GWA analysis, most of which were subpopulation-specific. Four of these regions co-localized with a priori candidate genes, and two highly significant regions co-localized with previously identified QTLs. Three regions corresponding to induced Al-sensitive rice mutants (ART1, STAR2, Nrat1 were identified through bi-parental QTL mapping or GWA to be involved in natural variation for Al tolerance. Haplotype analysis around the Nrat1 gene identified susceptible and tolerant haplotypes explaining 40% of the Al tolerance variation within the aus subpopulation, and sequence analysis of Nrat1 identified a trio of non-synonymous mutations predictive of Al sensitivity in our diversity panel. GWA analysis discovered more phenotype-genotype associations and provided higher resolution, but QTL mapping identified critical rare and/or subpopulation-specific alleles not detected by GWA analysis. Mapping using Indica/Japonica populations identified QTLs associated with transgressive variation where alleles from a susceptible aus or indica parent enhanced Al tolerance in a tolerant Japonica background. This work supports the hypothesis that selectively introgressing alleles across subpopulations is an efficient approach for trait enhancement in plant breeding programs

  11. QTL analysis and candidate gene mapping for the polyphenol content in cider apple.

    Directory of Open Access Journals (Sweden)

    Cindy F Verdu

    Full Text Available Polyphenols have favorable antioxidant potential on human health suggesting that their high content is responsible for the beneficial effects of apple consumption. They control the quality of ciders as they predominantly account for astringency, bitterness, color and aroma. In this study, we identified QTLs controlling phenolic compound concentrations and the average polymerization degree of flavanols in a cider apple progeny. Thirty-two compounds belonging to five groups of phenolic compounds were identified and quantified by reversed phase liquid chromatography on both fruit extract and juice, over three years. The average polymerization degree of flavanols was estimated in fruit by phloroglucinolysis coupled to HPLC. Parental maps were built using SSR and SNP markers and used for the QTL analysis. Sixty-nine and 72 QTLs were detected on 14 and 11 linkage groups of the female and male maps, respectively. A majority of the QTLs identified in this study are specific to this population, while others are consistent with previous studies. This study presents for the first time in apple, QTLs for the mean polymerization degree of procyanidins, for which the mechanisms involved remains unknown to this day. Identification of candidate genes underlying major QTLs was then performed in silico and permitted the identification of 18 enzymes of the polyphenol pathway and six transcription factors involved in the apple anthocyanin regulation. New markers were designed from sequences of the most interesting candidate genes in order to confirm their co-localization with underlying QTLs by genetic mapping. Finally, the potential use of these QTLs in breeding programs is discussed.

  12. QTL Mapping for Adult Plant Resistance to Powdery Mildew in Italian Wheat cv. Strampelli

    Institute of Scientific and Technical Information of China (English)

    Asad Muhammad Azeem; BAI Bin; LAN Cai-xia; YAN Jun; XIA Xian-chun; ZHANG Yong; HE Zhong-hu

    2013-01-01

    The Italian wheat cv. Strampelli displays high resistance to powdery mildew caused by Blumeria graminis f. sp. tritici. The objective of this study was to map quantitative trait loci (QTLs) for resistance to powdery mildew in a population of 249 F2:3 lines from Strampelli/Huixianhong. Adult plant powdery mildew tests were conducted over 2 yr in Beijing and 1 yr in Anyang and simple sequence repeat (SSR) markers were used for genotyping. QTLs Qpm.caas-3BS, Qpm.caas-5BL.1, and Qpm.caas-7DS were consistent across environments whereas, Qpm.caas-2BS.1 found in two environments, explained 0.4-1.6, 5.5-6.9, 27.1-34.5, and 1.0-3.5%of the phenotypic variation respectively. Qpm.caas-7DS corresponded to the genomic location of Pm38/Lr34/Yr18. Qpm.caas-4BL was identified in Anyang 2010 and Beijing 2011, accounting for 1.9-3.5%of phenotypic variation. Qpm.caas-2BS.1 and Qpm.caas-5BL.1 contributed by Strampelli and Qpm.caas-3BS by Huixianhong, seem to be new QTL for powdery mildew resistance. Qpm.caas-4BL, Qpm.caas-5BL.3, and Qpm.caas-7DS contributed by Strampelli appeared to be in the same genomic regions as those mapped previously for stripe rust resistance in the same population, indicating that these loci conferred resistance to both stripe rust and powdery mildew. Strampelli could be a valuable genetic resource for improving durable resistance to both powdery mildew and stripe rust in wheat.

  13. The use of genome-wide eQTL associations in lymphoblastoid cell lines to identify novel genetic pathways involved in complex traits.

    Directory of Open Access Journals (Sweden)

    Josine L Min

    Full Text Available The integrated analysis of genotypic and expression data for association with complex traits could identify novel genetic pathways involved in complex traits. We profiled 19,573 expression probes in Epstein-Barr virus-transformed lymphoblastoid cell lines (LCLs from 299 twins and correlated these with 44 quantitative traits (QTs. For 939 expressed probes correlating with more than one QT, we investigated the presence of eQTL associations in three datasets of 57 CEU HapMap founders and 86 unrelated twins. Genome-wide association analysis of these probes with 2.2 m SNPs revealed 131 potential eQTLs (1,989 eQTL SNPs overlapping between the HapMap datasets, five of which were in cis (58 eQTL SNPs. We then tested 535 SNPs tagging the eQTL SNPs, for association with the relevant QT in 2,905 twins. We identified nine potential SNP-QT associations (P<0.01 but none significantly replicated in five large consortia of 1,097-16,129 subjects. We also failed to replicate previous reported eQTL associations with body mass index, plasma low-density lipoprotein cholesterol, high-density lipoprotein cholesterol and triglycerides levels derived from lymphocytes, adipose and liver tissue. Our results and additional power calculations suggest that proponents may have been overoptimistic in the power of LCLs in eQTL approaches to elucidate regulatory genetic effects on complex traits using the small datasets generated to date. Nevertheless, larger tissue-specific expression data sets relevant to specific traits are becoming available, and should enable the adoption of similar integrated analyses in the near future.

  14. Quantitative Trait Locus Analysis of Seed Germination and Seedling Vigor in Brassica rapa Reveals QTL Hotspots and Epistatic Interactions

    OpenAIRE

    Basnet, Ram K.; Duwal, Anita; Tiwari, Dev N.; Xiao, Dong; Monakhos, Sokrat; Bucher, Johan; Visser, Richard G F; Groot, Steven P. C.; Bonnema, Guusje; Maliepaard, Chris

    2015-01-01

    The genetic basis of seed germination and seedling vigor is largely unknown in Brassica species. We performed a study to evaluate the genetic basis of these important traits in a B. rapa doubled haploid population from a cross of a yellow-seeded oil-type yellow sarson and a black-seeded vegetable-type pak choi. We identified 26 QTL regions across all 10 linkage groups for traits related to seed weight, seed germination and seedling vigor under non-stress and salt stress conditions illustratin...

  15. eQTL networks unveil enriched mRNA master integrators downstream of complex disease-associated SNPs.

    Science.gov (United States)

    Li, Haiquan; Pouladi, Nima; Achour, Ikbel; Gardeux, Vincent; Li, Jianrong; Li, Qike; Zhang, Hao Helen; Martinez, Fernando D; Garcia, Joe G N 'Skip'; Lussier, Yves A

    2015-12-01

    The causal and interplay mechanisms of Single Nucleotide Polymorphisms (SNPs) associated with complex diseases (complex disease SNPs) investigated in genome-wide association studies (GWAS) at the transcriptional level (mRNA) are poorly understood despite recent advancements such as discoveries reported in the Encyclopedia of DNA Elements (ENCODE) and Genotype-Tissue Expression (GTex). Protein interaction network analyses have successfully improved our understanding of both single gene diseases (Mendelian diseases) and complex diseases. Whether the mRNAs downstream of complex disease genes are central or peripheral in the genetic information flow relating DNA to mRNA remains unclear and may be disease-specific. Using expression Quantitative Trait Loci (eQTL) that provide DNA to mRNA associations and network centrality metrics, we hypothesize that we can unveil the systems properties of information flow between SNPs and the transcriptomes of complex diseases. We compare different conditions such as naïve SNP assignments and stringent linkage disequilibrium (LD) free assignments for transcripts to remove confounders from LD. Additionally, we compare the results from eQTL networks between lymphoblastoid cell lines and liver tissue. Empirical permutation resampling (pcomplex disease SNPs via eQTL associations are likely to be regulated by a larger number of SNPs than expected. We name this novel property mRNA hubness in eQTL networks, and further term mRNAs with high hubness as master integrators. mRNA master integrators receive and coordinate the perturbation signals from large numbers of polymorphisms and respond to the personal genetic architecture integratively. This genetic signal integration contrasts with the mechanism underlying some Mendelian diseases, where a genetic polymorphism affecting a single protein hub produces a divergent signal that affects a large number of downstream proteins. Indeed, we verify that this property is independent of the hubness in

  16. Identification and mapping of quantitative trait loci (QTL) conferring resistance to Fusarium graminearum from soybean PI 567301B

    OpenAIRE

    Acharya, Bhupendra; Lee, Sungwoo; M A Rouf Mian; Jun, Tae-Hwan; McHale, Leah K; Michel, Andrew P; Dorrance, Anne E.

    2015-01-01

    Key message A major novel QTL was identified in a recombinant inbred line population derived from a cross of ‘Wyandot’ × PI 567301B for Fusarium graminearum, a seed and seedling pathogen of soybean. Abstract Fusarium graminearum is now recognized as a primary pathogen of soybean, causing root, seed rot and seedling damping-off in North America. In a preliminary screen, ‘Wyandot’ and PI 567301B were identified with medium and high levels of partial resistance to F. graminearum, respectively. T...

  17. Polymorphism in the ELOVL6 gene is associated with a major QTL effect on fatty acid composition in pigs.

    Directory of Open Access Journals (Sweden)

    Jordi Corominas

    Full Text Available BACKGROUND: The ELOVL fatty acid elongase 6 (ELOVL6, the only elongase related to de novo lipogenesis, catalyzes the rate-limiting step in the elongation cycle by controlling the fatty acid balance in mammals. It is located on pig chromosome 8 (SSC8 in a region where a QTL affecting palmitic, and palmitoleic acid composition was previously detected, using an Iberian x Landrace intercross. The main goal of this work was to fine-map the QTL and to evaluate the ELOVL6 gene as a positional candidate gene affecting the percentages of palmitic and palmitoleic fatty acids in pigs. METHODOLOGY AND PRINCIPAL FINDINGS: The combination of a haplotype-based approach and single-marker analysis allowed us to identify the main, associated interval for the QTL, in which the ELOVL6 gene was identified and selected as a positional candidate gene. A polymorphism in the promoter region of ELOVL6, ELOVL6:c.-533C>T, was highly associated with the percentage of palmitic and palmitoleic acids in muscle and backfat. Significant differences in ELOVL6 gene expression were observed in backfat when animals were classified by the ELOVL6:c.-533C>T genotype. Accordingly, animals carrying the allele associated with a decrease in ELOVL6 gene expression presented an increase in C16:0 and C16:1(n-7 fatty acid content and a decrease of elongation activity ratios in muscle and backfat. Furthermore, a SNP genome-wide association study with ELOVL6 relative expression levels in backfat showed the strongest effect on the SSC8 region in which the ELOVL6 gene is located. Finally, different potential genomic regions associated with ELOVL6 gene expression were also identified by GWAS in liver and muscle, suggesting a differential tissue regulation of the ELOVL6 gene. CONCLUSIONS AND SIGNIFICANCE: Our results suggest ELOVL6 as a potential causal gene for the QTL analyzed and, subsequently, for controlling the overall balance of fatty acid composition in pigs.

  18. QTL analysis of Na+ and K+ concentrations in roots and shoots under different levels of NaCl stress in rice (Oryza sativa L..

    Directory of Open Access Journals (Sweden)

    Zhoufei Wang

    Full Text Available The key to plant survival under NaCl salt stress is maintaining a low Na(+ level or Na(+/K(+ ratio in the cells. A population of recombinant inbred lines (RILs, F(2:9 derived from a cross between the salt-tolerant japonica rice variety Jiucaiqing and the salt-sensitive indica variety IR26, was used to determine Na(+ and K(+ concentrations in the roots and shoots under three different NaCl stress conditions (0, 100 and 120 mM NaCl. A total of nine additive QTLs were identified by QTL Cartographer program using single-environment phenotypic values, whereas eight additive QTLs were identified by QTL IciMapping program. Among these additive QTLs, five were identified by both programs. Epistatic QTLs and QTL-by-environment interactions were detected by QTLNetwork program in the joint analyses of multi-environment phenotypic values, and one additive QTL and nine epistatic QTLs were identified. There were three epistatic QTLs identified for Na(+ in roots (RNC, three additive QTLs and two epistatic QTLs identified for Na(+ in shoots (SNC, four additive QTLs identified for K(+ in roots (RKC, four additive QTLs and three epistatic QTLs identified for K(+ in shoots (SKC and one additive QTL and one epistatic QTL for salt tolerance rating (STR. The phenotypic variation explained by each additive, epistatic QTL and QTL×environment interaction ranged from 8.5 to 18.9%, 0.5 to 5.3% and 0.7 to 7.5%, respectively. By comparing the chromosomal positions of these additive QTLs with those previously identified, five additive QTLs, qSNC9, qSKC1, qSKC9, qRKC4 and qSTR7, might represent novel salt tolerance loci. The identification of salt tolerance in selected RILs showed that a major QTL qSNC11 played a significant role in rice salt tolerance, and could be used to improve salt tolerance of commercial rice varieties with marker-assisted selection (MAS approach.

  19. Download - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us PGD...d 1 README README_e.html - 2 Registered plant list pgdbj_dna_marker_linkage_map_plant_species_list_en.zip (2...0.0 KB) Simple search and download 3 Marker list pgdbj_dna_marker_linkage_map_pla...nt_marker_list.zip (1.6 MB) Simple search and download 4 QTL list pgdbj_dna_marker_linkage_map_plant_qtl_lis...t.zip (22.6 KB) Simple search and download 5 Plant DB link pgdbj_dna_marker_linkage_map_plant_db_link_en.zip

  20. Evaluation of the porcine Melanocortin-4 receptor gene (MC4R) as a positional candidate gene for a fatness QTL in a cross between Landrace and Hamphire

    DEFF Research Database (Denmark)

    Bruun, C S; Jørgensen, C B; Nielsen, Vivi Hunnicke;

    2006-01-01

    Melanocortin 4 receptor (MC4R) is expressed in the appetite-regulating areas of the brain where it is central in the regulation of feed intake and energy balance. A mutation in MC4R causing an Asp298Asn substitution has been associated with fatness, high daily gain and feed intake in the pig....... In a previously performed genome scan based on a Hampshire x Landrace cross, we detected one quantitative trait loci (QTL) affecting carcass fat/meat ratio and one QTL affecting the biceps femoris muscle, both close to the position of MC4R on porcine chromosome 1. In this study, the two lines were found...