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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.

    Directory of Open Access Journals (Sweden)

    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. Variabilidade genética de caracteres forrageiros em Paspalum

    Directory of Open Access Journals (Sweden)

    Emerson André Pereira

    2012-10-01

    Full Text Available O objetivo deste trabalho foi determinar a variabilidade genética e a expressão de caracteres de interesse forrageiro em espécies de Paspalum. Os experimentos foram conduzidos em diferentes locais e anos de cultivo, em delineamento de blocos ao acaso, com três repetições. Foram avaliados cinco acessos de P. nicorae e dois de P. guenoarum, além da cultivar Pensacola (P. notatum, utilizada como testemunha. Foram quantificados os seguintes caracteres: relação folha/colmo, índice de colheita e massa de matéria seca total, de folhas e de colmo. Tanto os efeitos principais (genótipos, anos e locais de cultivo quanto a interação entre os fatores tiveram influência significativa sobre os caracteres avaliados. Os acessos avaliados apresentam variabilidade genética em caracteres de interesse forrageiro, bem como desempenho variável de acordo com o local e o ano de cultivo. A produção de matéria seca total e de folhas são os caracteres que mais contribuem para a detecção da variabilidade genética observada, independentemente do ano de avaliação.

  3. 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)

  4. Discovering genes underlying QTL

    Energy Technology Data Exchange (ETDEWEB)

    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. 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.

  6. Statistical Methods for Mapping Multiple QTL

    OpenAIRE

    2008-01-01

    Since Lander and Botstein proposed the interval mapping method for QTL mapping data analysis in 1989, tremendous progress has been made in the last many years to advance new and powerful statistical methods for QTL analysis. Recent research progress has been focused on statistical methods and issues for mapping multiple QTL together. In this article, we review this progress. We focus the discussion on the statistical methods for mapping multiple QTL by maximum likelihood and Bayesian methods ...

  7. 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

  8. Sistema de Reconocimiento de Caracteres Orientado a Sistemas Android

    OpenAIRE

    Segura Morales, Oriol

    2014-01-01

    Este proyecto trata sobre un sistema de reconocimiento de caracteres que se implementa para sistemas Android en forma de aplicación para móvil y Tablet. La aplicación está orientada para que los niños aprendan a escribir de una forma más amena. El sistema utiliza el patrón de diseño Modelo-Vista-Controlador para separar la lógica del sistema de la interfaz visual. En la interfaz, el sistema pide que se escriba un carácter utilizando la pantalla táctil y una vez el usuario lo ha escrito el sis...

  9. 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. ...

  10. QTL Information Table: 732 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available qtl12.1 Resistance or Tolerance Drought tolerance Plant heigh at maturity SSR C)Interval F3 Way Rare...m Vandana A RM28048 RM28166 pha Bernier, J., Kumar, A., Ramaiah, V., Spaner, D., and Atlin, G. (2007). A Lar...ge-Effect QTL for Grain Yield under Reproductive-Stage Drought Stress in Upland Rice. Crop

  11. 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...

  12. qtl.outbred: Interfacing outbred line cross data with the R/qtl mapping software

    Science.gov (United States)

    2011-01-01

    Background qtl.outbred is an extendible interface in the statistical environment, R, for combining quantitative trait loci (QTL) mapping tools. It is built as an umbrella package that enables outbred genotype probabilities to be calculated and/or imported into the software package R/qtl. Findings Using qtl.outbred, the genotype probabilities from outbred line cross data can be calculated by interfacing with a new and efficient algorithm developed for analyzing arbitrarily large datasets (included in the package) or imported from other sources such as the web-based tool, GridQTL. Conclusion qtl.outbred will improve the speed for calculating probabilities and the ability to analyse large future datasets. This package enables the user to analyse outbred line cross data accurately, but with similar effort than inbred line cross data. PMID:21615912

  13. Validación de métodos analíticos no cuantitativos

    OpenAIRE

    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...

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

    Directory of Open Access Journals (Sweden)

    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.

  15. 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...

  16. 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.

  17. QTL Information Table: 119 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Physiological trait Flowering heading date RFLP C)Interval BC1F9 Nipponbare Kasalath A R2171 R21 ... d temperature: a QTL analysis using a phenological model . Theor Appl Genet 110, 778-786. ...

  18. QTL Information Table: 692 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available qTRA7 Resistance or Tolerance Other stress resistance tolerance to disturbance trampling toleran ... , M., and Sano, Y. (2007). A QTL Cluster for Plant Architecture ... and Its Ecological Significance in Asian Wild Rice ...

  19. QTL Information Table: 181 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Glu6 Physiological trait Eating quality glutelin subunit polypeptides A)Physical OSJNBa0083F15 p ... . QTL mapping of the root traits in rice seedling. Yi ... Chuan Xue Bao 28, 433-438. ...

  20. QTL Information Table: 468 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Morphological trait Root Root / Shoot Ratio of Dry Weight RFLP C)Interval DHL ZYQ8 Jingxi 17 B R ... . QTL mapping of the root traits in rice seedling. Yi ... Chuan Xue Bao 28, 433-438. ...

  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: 444 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Resistance or Tolerance Insect resistance Green ... rice hopper RFLP C)Interval RIL Asominori IR24 B ... Yoshimura, A. (1999). QTL mapping of antibiosis to green ... leafhopper, Nephotettix virescens Distant and gree ...

  3. 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

  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: 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

  6. 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

  7. 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 ...

  8. 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 ...

  9. 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 ...

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

    Directory of Open Access Journals (Sweden)

    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

  11. QTL Information Table: 730 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available qtl12.1 Resistance or Tolerance Drought tolerance Harvest index SSR C)Interval F3 W...ay Rarem Vandana A RM7195 RM28166 pha Bernier, J., Kumar, A., Ramaiah, V., Spaner, D., and Atlin, G. (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 ...

  12. QTL Information Table: 729 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available qtl12.1 Resistance or Tolerance Drought tolerance Biomass yield SSR C)Interval F3 Way Rare...m Vandana A RM28048 RM28166 pha Bernier, J., Kumar, A., Ramaiah, V., Spaner, D., and Atlin, G. (2007). A Lar...ge-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 ...

  13. QTL Information Table: 728 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available qtl12.1 Resistance or Tolerance Drought tolerance Grain yield SSR C)Interval F3 Way Rare...m Vandana A RM28048 RM511 pha Bernier, J., Kumar, A., Ramaiah, V., Spaner, D., and Atlin, G. (2007). A Lar...ge-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 ...

  14. 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...

  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. QTL detection for physicochemical characteristics of cashew apple

    Directory of Open Access Journals (Sweden)

    Francisco Herbeth Costa dos Santos

    2011-08-01

    Full Text Available The identification of quantitative trait loci (QTL and marker-assisted selection have aroused great interest inbreeding programs aiming at fruit quality. The objective of this study was to detect QTL related to the quality of the cashew apple.The physicochemical characteristics oligomeric phenolics, total soluble solids, total titrable acidity and vitamin C contents wereanalyzed in the mapped cashew population. QTL were detected by QTL interval and multiple QTL mapping. The results showedhigh phenotypic variation in the segregating F1 generation for all traits. Eighteen QTL associated with cashew quality wereidentified: three for oligomeric phenolics, five for total soluble solids, six for total acidity and four for vitamin C. QTL are promisingfor marker-assisted selection since they have the greatest phenotypic effects and contribution to phenotypic variation.

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

    Directory of Open Access Journals (Sweden)

    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

  18. 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...

  19. QTL Information Table: 324 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available qSdn-5 Physiological trait Germination/dormancy germination percentage SSR d)Co-seg... J.M. (2004). Comparative mapping of QTL for seed dormancy in cultivated rice: N22 among three populations. Rice Genetics Newsletter 21, 46-49. ...

  20. 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. ...

  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: 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. ...

  3. QTL Information Table: 687 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available qSPR4 Morphological trait Panicle/flower spreading of panicle at maturity stage RFLP C)Interval ... , M., and Sano, Y. (2007). A QTL Cluster for Plant Architecture ... and Its Ecological Significance in Asian Wild Rice ...

  4. QTL Information Table: 690 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available qAHL6 Morphological trait Panicle/flower apiculus hair length at seed traits SSR C)Interval RIL ... , M., and Sano, Y. (2007). A QTL Cluster for Plant Architecture ... and Its Ecological Significance in Asian Wild Rice ...

  5. QTL Information Table: 689 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available qSW5 Morphological trait Seed seed width at seed traits RFLP C)Interval RIL A58 W107 (o. rufipog ... , M., and Sano, Y. (2007). A QTL Cluster for Plant Architecture ... and Its Ecological Significance in Asian Wild Rice ...

  6. QTL Information Table: 686 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available q2LSL3 Morphological trait Shoot/Seedling leaf sheath length st seedling stage SSR C)Interval RI ... , M., and Sano, Y. (2007). A QTL Cluster for Plant Architecture ... and Its Ecological Significance in Asian Wild Rice ...

  7. QTL Information Table: 691 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available qLT12 Resistance or Tolerance Cold tolerance low-temperature tolerance SSR C)Interval RIL A58 W1 ... , M., and Sano, Y. (2007). A QTL Cluster for Plant Architecture ... and Its Ecological Significance in Asian Wild Rice ...

  8. QTL Information Table: 688 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available qSH1 Morphological trait Panicle/flower shattring habit at maturity stage SSR C)Interval RIL A58 ... , M., and Sano, Y. (2007). A QTL Cluster for Plant Architecture ... and Its Ecological Significance in Asian Wild Rice ...

  9. QTL Information Table: 467 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Morphological trait Root Maximum Root Length RFLP C)Interval DHL ZYQ8 Jingxi 17 B C711 G103 pha ... . QTL mapping of the root traits in rice seedling. Yi ... Chuan Xue Bao 28, 433-438. ...

  10. QTL Information Table: 210 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Morphological trait Seed Grain yi eld RFLP C)Interval RIL Zhenshan 97B Milyang 46 RG138 RZ398 pha ... .L. (2001). Comparison of the detection of QTL for yi eld traits in different generations of a rice cross ... using two mapping approaches. Yi ... Chuan Xue Bao 28, 458-464. ...

  11. QTL Information Table: 211 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Morphological trait Seed 1000-grain weight RFLP C)Interval RIL Zhenshan 97B Milyang 46 RZ811 RG5 ... .L. (2001). Comparison of the detection of QTL for yi eld traits in different generations of a rice cross ... using two mapping approaches. Yi ... Chuan Xue Bao 28, 458-464. ...

  12. QTL Information Table: 422 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available qH2O21 Others Others H2O2 content RFLP C)Interval BIL Nipponbare Kasalath B C86 C813 pha Yang, Q ... , J.M. (2003). QTL and epistatic interaction underlyi ng leaf chlorophyll and H2O2 content variation in r ... ice (Oryza sativa L.). Yi ... Chuan Xue Bao 30, 245-250. ...

  13. QTL Information Table: 209 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Physiological trait Source activity spikelet fertility RFLP C)Interval RIL Zhenshan 97B Milyang ... .L. (2001). Comparison of the detection of QTL for yi eld traits in different generations of a rice cross ... using two mapping approaches. Yi ... Chuan Xue Bao 28, 458-464. ...

  14. QTL Information Table: 207 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Morphological trait Culm/leaf number of panicle RFLP C)Interval RIL Zhenshan 97B Milyang 46 RG65 ... .L. (2001). Comparison of the detection of QTL for yi eld traits in different generations of a rice cross ... using two mapping approaches. Yi ... Chuan Xue Bao 28, 458-464. ...

  15. QTL Information Table: 88 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available qGP4 Morphological trait Panicle/flower grain number RFLP d)Co-segregated CSSL Asominori IR24 B ... ng, C.M., Wan, J.M., and Zhu, J.G. (2005). QTL for yi eld and its components responded to elevated CO2 in ... rice (Oryza sativa L.). Yi ... Chuan Xue Bao 32, 1066-1073. ...

  16. QTL Information Table: 206 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Physiological trait Source activity number of filled grains per panicle RFLP C)Interval RIL Zhen ... .L. (2001). Comparison of the detection of QTL for yi eld traits in different generations of a rice cross ... using two mapping approaches. Yi ... Chuan Xue Bao 28, 458-464. ...

  17. QTL Information Table: 421 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available qChll1a Morphological trait Culm/leaf Chlorophyll contents RFLP C)Interval BIL Nipponbare Kasala ... , J.M. (2003). QTL and epistatic interaction underlyi ng leaf chlorophyll and H2O2 content variation in r ... ice (Oryza sativa L.). Yi ... Chuan Xue Bao 30, 245-250. ...

  18. QTL Information Table: 208 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Morphological trait Panicle/flower total number of spikelets per panicle RFLP C)Interval RIL Zhe ... .L. (2001). Comparison of the detection of QTL for yi eld traits in different generations of a rice cross ... using two mapping approaches. Yi ... Chuan Xue Bao 28, 458-464. ...

  19. QTL Information Table: 3 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available rb2 Physiological trait Eating quality ... Rice bran SSR C)Interval DH from BC3F1 Caiapo Oryza glabe ... n, C., and Oard, J.H. (2004). QTL mapping of grain quality ... traits from the interspecific cross Oryza sativa x ...

  20. QTL Information Table: 287 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Physiological trait Eating quality ... gel consistency RFLP C)Interval DHL IR64 Azucena A RG331 RG81 ... ui, H.R., and Shu, Q.Y. (2002). QTL for rice grain quality ... based on a DH population derived from parents with ...

  1. 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. ...

  2. 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

  3. 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

  4. 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

  5. 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. ...

  6. 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. ...

  7. 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

  8. 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. ...

  9. QTL Information Table: 383 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Pi32(t) Resistance or Tolerance Blast resistance RFLP C)Interval DHL IR64 Azucena A C449 pha Sal ... st-resistant rice variety IR64 using a QTL mapping strategy . Theor Appl Genet 106, 794-803. ...

  10. QTL Information Table: 751 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available ri B RM257 RM242 pha Miyata, M., Yamamoto, T., Komori, T., and Nitta, N. (2007). Marker-assisted selection and evaluation... of the QTL for stigma exsertion under japonica rice genetic background. Theor Appl Genet 114, 539-548. ... ...qGL9 Morphological trait Seed Grain length Mixture C)Interval F2 98SQ1496 Koshihika

  11. QTL Information Table: 749 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Koshihikari B R1943 R2976 pha Miyata, M., Yamamoto, T., Komori, T., and Nitta, N. (2007). Marker-assisted selection and evaluation... of the QTL for stigma exsertion under japonica rice genetic background. Theor Appl Genet 114, 539-548. ... ...qDTH8 Physiological trait Flowering Days-to-heading Mixture C)Interval F2 98SQ1496

  12. QTL Information Table: 752 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available i B C706 C12534S pha Miyata, M., Yamamoto, T., Komori, T., and Nitta, N. (2007). Marker-assisted selection and evaluation... of the QTL for stigma exsertion under japonica rice genetic background. Theor Appl Genet 114, 539-548. ... ...qGW3 Morphological trait Seed Grain width Mixture C)Interval F2 98SQ1496 Koshihikar

  13. 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 ...

  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: 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. ...

  16. 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. ...

  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: 450 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Morphological trait Seed grain yield RFLP C)Interval RIL Zhenshan 97B Milyang 46 RG138 RZ398 rgn ... Y.Y., Wu, J.L., Xia, Y.W., and Zheng, K.L. (2000). Comparison ... of QTL detection for yield traits using F2 and rec ...

  20. QTL Information Table: 607 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Morphological trait Shoot/Seedling root length SSR C)Interval RIL Lemont Teqing B OSR19 RM225 ph ... .-S., Wan, S., Chen, L.-H., and Zhu, Y.-G. (2005). Comparison ... of QTL Controlling Seedling Vigour under Different ...

  1. QTL Information Table: 605 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available qSV-3-1 Morphological trait Shoot/Seedling dry weight SSR C)Interval RIL Lemont Teqing A RM156 R ... .-S., Wan, S., Chen, L.-H., and Zhu, Y.-G. (2005). Comparison ... of QTL Controlling Seedling Vigour under Different ...

  2. QTL Information Table: 608 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available qSV-3-1 Morphological trait Shoot/Seedling shoot length SSR C)Interval RIL Lemont Teqing A RM156 ... .-S., Wan, S., Chen, L.-H., and Zhu, Y.-G. (2005). Comparison ... of QTL Controlling Seedling Vigour under Different ...

  3. QTL Information Table: 453 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Physiological trait Source activity spikelet fertility RFLP C)Interval RIL Zhenshan 97B Milyang ... Y.Y., Wu, J.L., Xia, Y.W., and Zheng, K.L. (2000). Comparison ... of QTL detection for yield traits using F2 and rec ...

  4. QTL Information Table: 451 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Physiological trait Source activity number of filled grain per paniucle RFLP C)Interval RIL Zhen ... Y.Y., Wu, J.L., Xia, Y.W., and Zheng, K.L. (2000). Comparison ... of QTL detection for yield traits using F2 and rec ...

  5. QTL Information Table: 606 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available qSV-3-2 Physiological trait Germination/dormancy germination rate SSR C)Interval RIL Lemont Teqi ... .-S., Wan, S., Chen, L.-H., and Zhu, Y.-G. (2005). Comparison ... of QTL Controlling Seedling Vigour under Different ...

  6. QTL Information Table: 452 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Morphological trait Panicle/flower total number of spikelets per panicle RFLP C)Interval RIL Zhe ... Y.Y., Wu, J.L., Xia, Y.W., and Zheng, K.L. (2000). Comparison ... of QTL detection for yield traits using F2 and rec ...

  7. QTL Information Table: 449 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Morphological trait Seed 1000 grain weight RFLP C)Interval F2 Zhenshan 97B Milyang 46 RG543 RG81 ... Y.Y., Wu, J.L., Xia, Y.W., and Zheng, K.L. (2000). Comparison ... of QTL detection for yield traits using F2 and rec ...

  8. QTL Information Table: 821 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Resistance or Tolerance Other soil stress tolerance Plant height (High N level, Soi...l culture , Maturity ) RFLP C)Interval RIL IR64 Azucena B RZ730 RZ801 pha Fang, P., and Wu, P. (2001). QTL × N-level

  9. QTL Information Table: 825 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Resistance or Tolerance Other soil stress tolerance Plant height (Low N level, Soil... culture , Maturity ) RFLP C)Interval RIL IR64 Azucena B RZ730 RZ801 pha Fang, P., and Wu, P. (2001). QTL × N-level

  10. 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.

  11. 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.

  12. 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.

  13. 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

    conformation trait in dairy cattle. Several QTL were detected for which the QTL status (homozygous or heterozygous for the QTL) was inferred for each individual. Subsequently, the inferred QTL status was used in a concordance analysis to reduce the number of candidate mutations. Methods Twenty QTL for rear leg...... status was concordant with the QTL status were kept as candidate causative mutations. Results QTL status could be inferred for 15 of the 20 QTL. The number of concordant polymorphisms differed between QTL and depended on the number of QTL statuses that could be inferred and the linkage disequilibrium in......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...

  14. 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 PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods QTL list Data de...Policy | Contact Us QTL list - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive ...

  15. 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...... 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 of...... milk production in the Czech Fleckvieh cattle....

  16. QTL Information Table: 750 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available 96 Koshihikari A R1943 R2976 pha Miyata, M., Yamamoto, T., Komori, T., and Nitta, N. (2007). Marker-assisted selection and evaluation... of the QTL for stigma exsertion under japonica rice genetic background. Theor Appl Genet 114, 539-548. ... ...qPL8 Morphological trait Panicle/flower Panicle length Mixture C)Interval F2 98SQ14

  17. QTL Information Table: 848 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Morphological trait Culm/leaf Leaf area RFLP d)Co-segregated BC1F7 Nipponbare Kasalath A R565 pha Ishimar...ison between QTLs and expressed sequence tags. TAG Theoretical...d the mapping of physiological and agronomic characters on a rice function map: QTL analysis and compar...u, K., Yano, M., Aoki, N., Ono, K., Hirose, T., Lin, S.Y., Monna, L., Sasaki, T., and Ohsugi, R. (2001). Towar

  18. QTL Information Table: 576 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available 1.2 Resistance or Tolerance Blast resistance Lesion area RFLP d)Co-segregated RIL B...ala Azucena A C1370 pha Talukder, Z.I., McDonald, A.J., and Price, A.H. (2005). Loci controlling partial res...istance to rice blast do not show marked QTL x environment interaction when plant nitrogen status alters disease severity. New Phytol 168, 455-464. ...

  19. QTL Information Table: 841 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available p: QTL analysis and comparison between QTLs and expressed sequence tags. TAG Theore...Physiological trait Source activity Decreased Chl. content RFLP d)Co-segregated BC1F7 Nipponbare... Kasalath B C607 pha Ishimaru, K., Yano, M., Aoki, N., Ono, K., Hirose, T., Lin, S.Y., Monna, L...., Sasaki, T., and Ohsugi, R. (2001). Toward the mapping of physiological and agronomic characters on a rice function ma

  20. QTL Information Table: 846 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available p: QTL analysis and comparison between QTLs and expressed sequence tags. TAG Theore...Morphological trait Dwarf Elongation of plant height RFLP d)Co-segregated BC1F7 Nipponbare... Kasalath A C506 pha Ishimaru, K., Yano, M., Aoki, N., Ono, K., Hirose, T., Lin, S.Y., Monna, L., Sas...aki, T., and Ohsugi, R. (2001). Toward the mapping of physiological and agronomic characters on a rice function ma

  1. QTL Information Table: 849 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Physiological trait Germination/dormancy Seed dormancy RFLP d)Co-segregated BC1F7 Nipponbare...p: QTL analysis and comparison between QTLs and expressed sequence tags. TAG Theore... Kasalath A C1488 pha Ishimaru, K., Yano, M., Aoki, N., Ono, K., Hirose, T., Lin, S.Y., Monna, L., ...Sasaki, T., and Ohsugi, R. (2001). Toward the mapping of physiological and agronomic characters on a rice function ma

  2. QTL Information Table: 844 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available p: QTL analysis and comparison between QTLs and expressed sequence tags. TAG Theore...Morphological trait Dwarf Plant height (middle stage) RFLP d)Co-segregated BC1F7 Nipponbare... Kasalath B R2414 pha Ishimaru, K., Yano, M., Aoki, N., Ono, K., Hirose, T., Lin, S.Y., Monna, L., S...asaki, T., and Ohsugi, R. (2001). Toward the mapping of physiological and agronomic characters on a rice function ma

  3. 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...

  4. 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.

  5. Caracteres anatômicos de folha e caule de Piper mikanianum (Kunth) Steud., Piperaceae

    OpenAIRE

    Duarte, Márcia do Rocio; Siebenrock, Maria C.N.

    2010-01-01

    O gênero Piper L. (Piperaceae) ocorre em regiões tropicais e subtropicais, e inclui várias espécies de importância na medicina popular, podendo-se destacar Piper mikanianum (Kunth) Steud. Denominada de pariparoba e jaborandi, essa planta é empregada como antisséptico, hepatoprotetor e emenagogo. Este trabalho investigou a anatomia foliar e caulinar dessa potencial droga vegetal, a fim de estabelecer caracteres estruturais para a identificação microscópica e para a diferenciação de outras e...

  6. 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...

  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. 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...

  9. 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...... field fitness at different environmental temperatures with genotypic variation in a QTL for thermal tolerance. Graphical abstract...

  10. 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.

  11. 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

  12. QTL Information Table: 839 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Others Others Ratoon RFLP d)Co-segregated BC1F7 Nipponbare Kasalath A C901 pha Ishimar...ison between QTLs and expressed sequence tags. TAG Theoretical and Applied Genetics 102, 793-800. http://dx.doi.org/10.1007/s001220000467 ... ...u, K., Yano, M., Aoki, N., Ono, K., Hirose, T., Lin, S.Y., Monna, L., Sasaki, T., and Ohsugi, R. (2001). Toward the ma...pping of physiological and agronomic characters on a rice function map: QTL analysis and compar

  13. QTL Information Table: 838 [Q-TARO

    Lifescience Database Archive (English)

    Full Text Available Morphological trait Seed Yield RFLP d)Co-segregated BC1F7 Nipponbare Kasalath A C136 pha Ishimar...ison between QTLs and expressed sequence tags. TAG Theoretical and Applied Genetics 102, 793-800. http://dx.doi.org/10.1007/s001220000467 ... ...u, K., Yano, M., Aoki, N., Ono, K., Hirose, T., Lin, S.Y., Monna, L., Sasaki, T., and Ohsugi, R. (2001). Toward the ma...pping of physiological and agronomic characters on a rice function map: QTL analysis and compar

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

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

    OpenAIRE

    van der Knaap Esther; Buels Robert M; Menda Naama; Tecle Isaak Y; Mueller Lukas A

    2010-01-01

    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...

  20. 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

  1. 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...

  2. La agenda de investigación del turismo mediante el Análisis Cuantitativo de Redes Sociales (QSNA)

    OpenAIRE

    Merinero Rodríguez, Rafael

    2015-01-01

    El trabajo realiza un recorrido por la literatura aparecida en los últimos años en las revistas científicas y libros que han utilizado el Análisis Cuantitativo de Redes Sociales (QSNA, en inglés) para el estudio del turismo. Se presenta de forma sistemática todas las aportaciones científicas que han usado los métodos y técnicas propias del QSNA para el análisis del turismo, lo que permitirá que cualquier investigador pueda disponer de las referencias oportunas con el objeto de ...

  3. Aplicación de parámetros cuantitativos en el estudio de Aloysia citrodora Palau (Verbenaceae)

    OpenAIRE

    Albrecht, Roxana A.; Bassols, Graciela B.; Gurni, Alberto Angel

    2005-01-01

    Aloysia citrodora Palau (Verbenaceae) es vulgarmente conocida como "cedrón", "hierba Luisa" y "poleo de Castilla". Las hojas se emplean en forma de infusión como digestivas, sedantes, carminativas y tónicas. El objetivo de este trabajo es estimar los índices de empalizada, de venación y de estomas como parámetro cuantitativo para el control de calidad, especialmente para hojas fragmentadas. El método empleado es una diafanización con hidrato de cloral y posterior tinción con safranina. Los re...

  4. 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...

  5. Higiene de manos como estrategia fundamental en el control de infección hospitalaria. Un estudio cuantitativo.

    OpenAIRE

    M.S. Coelho; Silva Arruda, C.; Faria Simões, Sonia Mara

    2011-01-01

    La infección hospitalaria sigue constituyendo un grave problema de salud pública en todo el mundo. Entre sus principales medidas de prevención y control está el lavado de manos, que según Semmelweis y Florence Nightingale, es un instrumento importante para la reducción de sus índices. Por lo tanto, este estudio descriptivo de carácter cuantitativo tuvo un enfoque destinado a analizar la frecuencia de lavado de manos por las enfermeras en un Hospital de la Universidad ubicado en la ciudad de N...

  6. 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.

  7. 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

  8. 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.

  9. 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.

  10. 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...

  11. 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...

  12. 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.

  13. GENE LINKAGE MAPPING OF THE PORCINE CHROMOSOME X REGION HARBOURING QTL FOR FAT DEPOSITION

    Science.gov (United States)

    The QTL for backfat thickness and intramuscular fat content on SSCX is well documented in Meishan x Western breed pedigrees. The QTL has been mapped to the chromosome region between microsatellites SW2456 and SW1943. In the French pedigree with more than 1,100 F2 animals the QTL mapped at position 7...

  14. 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.

  15. Métodos cuantitativos en las contribuciones a los simposios de la SEIEM en 2001-2010

    OpenAIRE

    Miguel R. Wilhelmi; Lacasta, Eduardo

    2011-01-01

    Se toma como campo de observación las contribuciones a los simposios de la Sociedad Española de Investigación en Educación Matemática (SEIEM) en las que aparecen métodos cuantitativos. Se motiva la necesidad de un control previo a la recogida de datos y su tratamiento. Se justifica entonces la función que la ingeniería didáctica como método de investigación puede aquí cumplir. Asimismo, se realiza un análisis sistemático de una contribución de tipo experimental cuyo método privilegiado es cua...

  16. 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.

  17. 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.

  18. 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.

  19. 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...

  20. 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

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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...

  6. 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.

  7. 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

  8. 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

  9. 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% for...

  10. Fast and efficient QTL mapper for thousands of molecular phenotypes

    Science.gov (United States)

    Ongen, Halit; Buil, Alfonso; Brown, Andrew Anand; Dermitzakis, Emmanouil T.; Delaneau, Olivier

    2016-01-01

    Motivation: In order to discover quantitative trait loci, multi-dimensional genomic datasets combining DNA-seq and ChiP-/RNA-seq require methods that rapidly correlate tens of thousands of molecular phenotypes with millions of genetic variants while appropriately controlling for multiple testing. Results: We have developed FastQTL, a method that implements a popular cis-QTL mapping strategy in a user- and cluster-friendly tool. FastQTL also proposes an efficient permutation procedure to control for multiple testing. The outcome of permutations is modeled using beta distributions trained from a few permutations and from which adjusted P-values can be estimated at any level of significance with little computational cost. The Geuvadis & GTEx pilot datasets can be now easily analyzed an order of magnitude faster than previous approaches. Availability and implementation: Source code, binaries and comprehensive documentation of FastQTL are freely available to download at http://fastqtl.sourceforge.net/ Contact: emmanouil.dermitzakis@unige.ch or olivier.delaneau@unige.ch Supplementary information: Supplementary data are available at Bioinformatics online. PMID:26708335

  11. Análise de associação quanto à produtividade e seus caracteres componentes em linhagens e cultivares de arroz de terras altas

    OpenAIRE

    2014-01-01

    O objetivo deste trabalho foi identificar, por meio da análise de mapeamento associativo, os marcadores moleculares relacionados à produtividade do arroz de terras altas e aos seus caracteres componentes. Foram usadas 113 linhagens e cultivares de arroz de terras altas, da Coleção Nuclear de Arroz da Embrapa, com reduzido vínculo genético entre si. Os seguintes caracteres componentes da produtividade foram avaliados: número de panículas por metro, número de grãos por panícula e peso de 100 gr...

  12. 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.

  13. 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?

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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 the...... 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...

  19. Fine Mapping of a Major-Effect QTL Controlling Rhizomatous Growth in Perennial Wildrye Hyrbrids

    OpenAIRE

    Clements, Jenny L.

    2016-01-01

    Quantitative trait loci (QTL) analysis is the science of discovering genes or chromosome regions that influence the expression of quantitative traits. Statistical methods for doing this have evolved from single marker analysis of variance (ANOVA) to more complex approaches such as interval mapping and multiple QTL mapping. The goal of this project was to refine a previously identified QTL chromosome region responsible for rhizome growth in grass hybrids developed from two species of the Triti...

  20. eQTL Viewer: visualizing how sequence variation affects genome-wide transcription

    OpenAIRE

    Zeng Zhao-Bang; Aylor David L; Zou Wei

    2007-01-01

    Abstract Background Expression Quantitative Trait Locus (eQTL) mapping methods have been used to identify the genetic basis of gene expression variations. To map eQTL, thousands of expression profiles are related with sequence polymorphisms across the genome through their correlated variations. These eQTL distribute in many chromosomal regions, each of which can include many genes. The large number of mapping results produced makes it difficult to consider simultaneously the relationships bet...

  1. Identificazione e trasferimento di QTL coinvolti nell’accumulo di antiossidanti nel frutto di pomodoro

    OpenAIRE

    Lombardi, Nadia

    2011-01-01

    L’obiettivo del progetto ha riguardato la combinazione di QTL coinvolti nell’incremento del contenuto in antiossidanti nel frutto di pomodoro. A tale scopo sono state utilizzate le linee di introgressione (IL) di pomodoro. Tali IL sono particolarmente utili per la dissezione di caratteri complessi e consentono l’individuazione ed il mappaggio di QTL di interesse su specifici cromosomi. Il trasferimento dei QTL e la loro combinazione in nuovi genotipi è stato perseguito eseguendo incroci tra l...

  2. 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 ...

  3. 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...

  4. Separation of base allele and sampling term effects gives new insights in variance component QTL analysis

    OpenAIRE

    Carlborg Örjan; Rönnegård Lars

    2007-01-01

    Abstract Background Variance component (VC) models are commonly used for Quantitative Trait Loci (QTL) mapping in outbred populations. Here, the QTL effect is given as a random effect and a critical part of the model is the relationship between the phenotypic values and the random effect. In the traditional VC model, each individual has a unique QTL effect and the relationship between these random effects is given as a covariance structure (known as the identity-by-descent (IBD) matrix). Resu...

  5. 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 ...

  6. 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

  7. 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

  8. Tamanho de amostra para a estimação da média de caracteres morfológicos e produtivos de nabo forrageiro

    Directory of Open Access Journals (Sweden)

    Alberto Cargnelutti Filho

    2014-02-01

    Full Text Available O objetivo deste trabalho foi determinar o tamanho de amostra (número de plantas para a estimação da média de caracteres morfológicos e produtivos de nabo forrageiro (Raphanus sativus L.. Em um experimento a campo, foram selecionadas, aleatoriamente, 300 plantas e mensurados os caracteres morfológicos (estatura de planta e número de folhas aos 21, 35, 48, 55, 62, 70, 77 e 91 dias após a semeadura e os produtivos (massas verde e seca, de raízes, de caule, de folhas e total aos 91 dias após a semeadura. Foram calculadas medidas de tendência central e de variabilidade, verificada a normalidade e calculado o tamanho de amostra. Para estimar a média, com mesma precisão, o tamanho de amostra dos caracteres produtivos é maior que dos morfológicos. Para os caracteres morfológicos e produtivos estudados, 231 plantas são suficientes para um erro de estimação máximo de 10% da média estimada, com grau de confiança de 95%.

  9. 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.

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

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    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.

  11. 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.

  12. 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.

  13. Divergência genética em germoplasma de aveias silvestres com base em caracteres multicategóricos e quantitativos

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    Simone Meredith Scheffer-Basso

    2012-10-01

    Full Text Available As aveias silvestres são importantes fontes de genes para programas de melhoramento e sua caracterização é fundamental para a efetiva conservação e uso. Por isso, o objetivo deste estudo foi avaliar a divergência genética em uma coleção de 71 subamostras de aveias silvestres, do Banco de Germoplasma da Embrapa Trigo, com base em caracteres multicategóricos e quantitativos. Procederam-se às análises de variância, para os caracteres quantitativos, e multivariada, para ambos os tipos de caracteres. Os métodos de agrupamento UPGMA, a partir da distância euclidiana média (caracteres multicategóricos, e de ligação completa, com base na distância de Mahalanobis (caracteres quantitativos, foram os mais adequados para ilustrar a relação entre as subamostras. A pilosidade da base dos grãos foi o caractere com maior contribuição relativa para divergência genética (32,16% e a menor contribuição foi da pilosidade do nó superior (0,081%. As subamostras divergiram quanto a vinte caracteres: pilosidade da bainha da folha inferior, bordas da lâmina imediatamente abaixo da folha bandeira, nó superior, face externa do lema e base do grão; posição da folha bandeira e das ramificações na panícula; frequência de plantas com folha bandeira recurvada; intensidade da pilosidade do nó superior e da cerosidade do lema; orientação das ramificações na panícula; comprimento dos pelos basais do grão, ráquila, panícula, glumas e planta; cor do lema, tipo de arista, número de grãos por espigueta e ciclo. O germoplasma apresenta elevada variabilidade genética e genes de interesse para o melhoramento de aveias.

  14. 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.

  15. 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

  16. 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.

  17. 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

  18. 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...

  19. 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

  20. 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.

  1. Adaptive linear rank tests for eQTL studies.

    Science.gov (United States)

    Szymczak, Silke; Scheinhardt, Markus O; Zeller, Tanja; Wild, Philipp S; Blankenberg, Stefan; Ziegler, Andreas

    2013-02-10

    Expression quantitative trait loci (eQTL) studies are performed to identify single-nucleotide polymorphisms that modify average expression values of genes, proteins, or metabolites, depending on the genotype. As expression values are often not normally distributed, statistical methods for eQTL studies should be valid and powerful in these situations. Adaptive tests are promising alternatives to standard approaches, such as the analysis of variance or the Kruskal-Wallis test. In a two-stage procedure, skewness and tail length of the distributions are estimated and used to select one of several linear rank tests. In this study, we compare two adaptive tests that were proposed in the literature using extensive Monte Carlo simulations of a wide range of different symmetric and skewed distributions. We derive a new adaptive test that combines the advantages of both literature-based approaches. The new test does not require the user to specify a distribution. It is slightly less powerful than the locally most powerful rank test for the correct distribution and at least as powerful as the maximin efficiency robust rank test. We illustrate the application of all tests using two examples from different eQTL studies. PMID:22933317

  2. Mapping quantitative trait loci (QTL in sheep. I. A new male framework linkage map and QTL for growth rate and body weight

    Directory of Open Access Journals (Sweden)

    Attard Gina

    2009-04-01

    Full Text Available Abstract A male sheep linkage map comprising 191 microsatellites was generated from a single family of 510 Awassi-Merino backcross progeny. Except for ovine chromosomes 1, 2, 10 and 17, all other chromosomes yielded a LOD score difference greater than 3.0 between the best and second-best map order. The map is on average 11% longer than the Sheep Linkage Map v4.7 male-specific map. This map was employed in quantitative trait loci (QTL analyses on body-weight and growth-rate traits between birth and 98 weeks of age. A custom maximum likelihood program was developed to map QTL in half-sib families for non-inbred strains (QTL-MLE and is freely available on request. The new analysis package offers the advantage of enabling QTL × fixed effect interactions to be included in the model. Fifty-four putative QTL were identified on nine chromosomes. Significant QTL with sex-specific effects (i.e. QTL × sex interaction in the range of 0.4 to 0.7 SD were found on ovine chromosomes 1, 3, 6, 11, 21, 23, 24 and 26.

  3. Identification of CNV and QTL for productive and functional traits in dairy cattle using dense SNP chips

    OpenAIRE

    Bagnato, Alessandro

    2015-01-01

    The thesis identify CNV structural variants as possible markers for genomic selection and identify QTL regions for Fatty Acid Content in the Italian Brown Swiss population. Additionally it maps the QTL for mastitis resistance in the Valdostana Red Pied cattle.

  4. 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.

  5. 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

  6. 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.

  7. 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.

  8. 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

    Background: Microarray studies can supplement QTL studies by suggesting potential candidate. Microarray studies can supplement QTL studies by suggesting potential candidate genes in the QTL regions, which by themselves are too large to provide a limited selection of candidate genes. Here we provi...

  9. 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

  10. 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

  11. 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.

  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. 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 ma...

  14. 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.

  15. 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.

  16. 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...

  17. 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.

  18. Pathotype-specific QTL for stem rust resistance in Lolium perenne.

    Science.gov (United States)

    Pfender, W F; Slabaugh, M E

    2013-05-01

    A genetic map populated with RAD and SSR markers was created from F1 progeny of a stem rust-susceptible and stem rust-resistant parent of perennial ryegrass (Lolium perenne). The map supplements a previous map of this population by having markers in common with several other Lolium spp. maps including EST-SSR anchor markers from a consensus map published by other researchers. A QTL analysis was conducted with disease severity and infection type data obtained by controlled inoculation of the population with each of two previously characterized pathotypes of Puccinia graminis subsp. graminicola that differ in virulence to different host plant genotypes in the F1 population. Each pathotype activated a specific QTL on one linkage group (LG): qLpPg1 on LG7 for pathotype 101, or qLpPg2 on LG1 for pathotype 106. Both pathotypes also activated a third QTL in common, qLpPg3 on LG6. Anchor markers, present on a consensus map, were located in proximity to each of the three QTL. These QTL had been detected also in previous experiments in which a genetically heterogeneous inoculum of the stem rust pathogen activated all three QTL together. The results of this and a previous study are consistent with the involvement of the pathotype-specific QTL in pathogen recognition and the pathotype-nonspecific QTL in a generalized resistance response. By aligning the markers common to other published reports, it appears that two and possibly all three of the stem rust QTL reported here are in the same general genomic regions containing some of the L. perenne QTL reported to be activated in response to the crown rust pathogen (P. coronata). PMID:23361523

  19. 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

  20. Mapping quantitative trait loci (QTL in sheep. II. Meta-assembly and identification of novel QTL for milk production traits in sheep

    Directory of Open Access Journals (Sweden)

    Lam Mary K

    2009-10-01

    Full Text Available Abstract An (Awassi × Merino × Merino backcross family of 172 ewes was used to map quantitative trait loci (QTL for different milk production traits on a framework map of 200 loci across all autosomes. From five previously proposed mathematical models describing lactation curves, the Wood model was considered the most appropriate due to its simplicity and its ability to determine ovine lactation curve characteristics. Derived milk traits for milk, fat, protein and lactose yield, as well as percentage composition and somatic cell score were used for single and two-QTL approaches using maximum likelihood estimation and regression analysis. A total of 15 significant (P P http://crcidp.vetsci.usyd.edu.au/cgi-bin/gbrowse/oaries_genome/. Many of the QTL for milk production traits have been reported on chromosomes 1, 3, 6, 16 and 20. Those on chromosomes 3 and 20 are in strong agreement with the results reported here. In addition, novel QTL were found on chromosomes 7, 8, 9, 14, 22 and 24. In a cross-species comparison, we extended the meta-assembly by comparing QTL regions of sheep and cattle, which provided strong evidence for synteny conservation of QTL regions for milk, fat, protein and somatic cell score data between cattle and sheep.

  1. 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; Anistoroaei, Razvan Marian; Christensen, Knud; Fredholm, Merete; Nielsen, Vivi Hunnicke

    2011-01-01

    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 on......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...

  2. 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

  3. 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.

  4. 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

  5. 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...

  6. Estimativas de parâmetros genéticos de caracteres relacionados ao vigor de estacas em Lippia alba

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    Elcio Rodrigo Rufino

    2010-12-01

    Full Text Available A espécie Lippia alba da família Verbenaceae, aromática e medicinal, é um arbusto nativo com muito vigor e variabilidade genética. O principal interesse dos estudos com esta espécie são os óleos essenciais, cujas funções têm sido comprovadas cientificamente para aplicações nas indústrias de fármacos, cosmética, perfumaria e alimentícia. Apesar desta importância potencial, inexistem pesquisas sobre estimativas de parâmetros genéticos nesta espécie como forma de subsidiar o melhoramento que até o presente momento é incipiente. Este trabalho teve como objetivo, avaliar o potencial genético de Lippia alba, estimando parâmetros genéticos inicialmente em caracteres obtidos em nível de estacas, uma vez que é a forma tradicional de multiplicação da espécie. Os caracteres avaliados foram: sobrevivência (S%, comprimento de brotos (Cb e massa de brotos (Mb. Nesses estudos iniciais de parâmetros genéticos, envolvendo vigor de estacas, formaram-se três grupos de progênies com tamanhos efetivos de 30, 23 e 7. Excetuando-se S%, obtiveram-se altas herdabilidades, no sentido restrito, para os três tamanhos efetivos, variando de 90,2% a 94,5% para Mb e 95,2 %a 97,1% para Cb. Para S%, os valores de herdabilidade foram moderados, entre 50,0% e 56,0%. Os ganhos genéticos foram semelhantes também nos três grupos de progênies formados, refletindo ampla variabilidade genética mesmo para o grupo de reduzido tamanho efetivo de progênies. As correlações genéticas aditivas foram elevadas (87,9% a 99,9%, com predomínio nas correlações fenotípicas (G% entre 94,1% a 98,8%. Apesar das correlações elevadas de ambiente a proporção destes efeitos ambientais na correlação fenotípica foi baixa (E% entre 1,2% a 5,9%.

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

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    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.

  8. 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

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

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    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.

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

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    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.

  11. A consensus linkage map of oil palm and a major QTL for stem height.

    Science.gov (United States)

    Lee, May; Xia, Jun Hong; Zou, Zhongwei; Ye, Jian; Rahmadsyah; Alfiko, Yuzer; Jin, Jingjing; Lieando, Jessica Virginia; Purnamasari, Maria Indah; Lim, Chin Huat; Suwanto, Antonius; Wong, Limsoon; Chua, Nam-Hai; Yue, Gen Hua

    2015-01-01

    Oil palm (Elaeis guinensis Jacquin) is the most important source of vegetable oil and fat. Several linkage maps had been constructed using dominant and co-dominant markers to facilitate mapping of QTL. However, dominant markers are not easily transferable among different laboratories. We constructed a consensus linkage map for oil palm using co-dominant markers (i.e. microsatellite and SNPs) and two F1 breeding populations generated by crossing Dura and Pisifera individuals. Four hundreds and forty-four microsatellites and 36 SNPs were mapped onto 16 linkage groups. The map length was 1565.6 cM, with an average marker space of 3.72 cM. A genome-wide scan of QTL identified a major QTL for stem height on the linkage group 5, which explained 51% of the phenotypic variation. Genes in the QTL were predicted using the palm genome sequence and bioinformatic tools. The linkage map supplies a base for mapping QTL for accelerating the genetic improvement, and will be also useful in the improvement of the assembly of the genome sequences. Markers linked to the QTL may be used in selecting dwarf trees. Genes within the QTL will be characterized to understand the mechanisms underlying dwarfing. PMID:25648560

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

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    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. 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.

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

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    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.

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

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    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.

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

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    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.

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

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    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.

  18. Parámetros genéticos de caracteres biométricos en caballos Mangalarga

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    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.

  19. 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...

  20. Combining two Meishan F2 crosses improves the detection of QTL on pig chromosomes 2, 4 and 6

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    Bidanel Jean-Pierre

    2010-11-01

    Full Text Available Abstract Background In pig, a number of experiments have been set up to identify QTL and a multitude of chromosomal regions harbouring genes influencing traits of interest have been identified. However, the mapping resolution remains limited in most cases and the detected QTL are rather inaccurately located. Mapping accuracy can be improved by increasing the number of phenotyped and genotyped individuals and/or the number of informative markers. An alternative approach to overcome the limited power of individual studies is to combine data from two or more independent designs. Methods In the present study we report a combined analysis of two independent design (a French and a Dutch F2 experimental designs, with 2000 F2 individuals. The purpose was to further map QTL for growth and fatness on pig chromosomes 2, 4 and 6. Using QTL-map software, uni- and multiple-QTL detection analyses were applied separately on the two pedigrees and then on the combination of the two pedigrees. Results Joint analyses of the combined pedigree provided (1 greater significance of shared QTL, (2 exclusion of false suggestive QTL and (3 greater mapping precision for shared QTL. Conclusions Combining two Meishan x European breeds F2 pedigrees improved the mapping of QTL compared to analysing pedigrees separately. Our work was facilitated by the access to raw phenotypic data and DNA of animals from both pedigrees and the combination of the two designs with the addition of new markers allowed us to fine map QTL without phenotyping additional animals.

  1. QTL detection by multi-parent linkage mapping in oil palm (Elaeis guineensis Jacq.).

    OpenAIRE

    Billotte, N.; Jourjon, M-Francoise; Marseillac, N.; Berger, A; Flori, A.; Asmady, H.; Adon, B.; Singh, R.; Nouy, B.; Potier, F.; Cheah, S.C.; Rohde, W; Ritter, E; Courtois, B.; Charrier, A.

    2010-01-01

    A quantitative trait locus (QTL) analysis designed for a multi-parent population was carried out and tested in oil palm (Elaeis guineensis Jacq.), which is a diploid cross-fertilising perennial species. A new extension of the MCQTL package was especially designed for crosses between heterozygous parents. The algorithm, which is now available for any allogamous species, was used to perform and compare two types of QTL search for small size families, within-family analysis and across-family ana...

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

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    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.

  3. 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...

  4. 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...

  5. 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...

  6. QTL ANALYSIS OF FIBER COLOR AND FIBER QUALITY IN NATURALLY GREEN COLORED COTTON (Gossypium hirsutum L.)

    OpenAIRE

    SEMİZER-CUMING, Devrim; ALTAN, Filiz; AKDEMIR, Huseyin; TOSUN, Muzaffer; GUREL, Aynur; Tanyolac, Bahattin

    2015-01-01

    ABSTRACT Improving fiber quality of naturally colored cotton has become more important in recent years due to changes in the spinning technology and consumer demand. The identification of quantitative trait loci (QTL) closely linked to the fiber quality traits can allow marker assisted selection (MAS) which leads us to future’s improved cotton cultivars. In this study, we performed genetic mapping on F2 population of G. hirsutum (Yesil × Nazilli 84) intraspecific cross, and identified QTL for...

  7. 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.

  8. 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)

  9. 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.

  10. 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

  11. eQTL Viewer: visualizing how sequence variation affects genome-wide transcription

    Directory of Open Access Journals (Sweden)

    Zeng Zhao-Bang

    2007-01-01

    Full Text Available Abstract Background Expression Quantitative Trait Locus (eQTL mapping methods have been used to identify the genetic basis of gene expression variations. To map eQTL, thousands of expression profiles are related with sequence polymorphisms across the genome through their correlated variations. These eQTL distribute in many chromosomal regions, each of which can include many genes. The large number of mapping results produced makes it difficult to consider simultaneously the relationships between multiple genomic regions and multiple expressional profiles. There is a need for informative bioinformatics tools to assist the visualization and interpretation of these mapping results. Results We have developed a web-based tool, called eQTL Viewer, to visualize the relationships between the expression trait genes and the candidate genes in the eQTL regions using Scalable Vector Graphics. The plot generated by eQTL Viewer has the capacity to display mapping results with high resolutions at a variety of scales, and superimpose biological annotations onto the mapping results dynamically. Conclusion Our tool provides an efficient and intuitive way for biologists to explore transcriptional regulation patterns, and to generate hypotheses on the genetic basis of transcriptional regulations.

  12. 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.

  13. 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

  14. 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.

  15. 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.

  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. Complementary genetic and genomic approaches help characterize the linkage group I seed protein QTL in soybean

    Directory of Open Access Journals (Sweden)

    Weeks Nathan

    2010-03-01

    Full Text Available Abstract Background The nutritional and economic value of many crops is effectively a function of seed protein and oil content. Insight into the genetic and molecular control mechanisms involved in the deposition of these constituents in the developing seed is needed to guide crop improvement. A quantitative trait locus (QTL on Linkage Group I (LG I of soybean (Glycine max (L. Merrill has a striking effect on seed protein content. Results A soybean near-isogenic line (NIL pair contrasting in seed protein and differing in an introgressed genomic segment containing the LG I protein QTL was used as a resource to demarcate the QTL region and to study variation in transcript abundance in developing seed. The LG I QTL region was delineated to less than 8.4 Mbp of genomic sequence on chromosome 20. Using Affymetrix® Soy GeneChip and high-throughput Illumina® whole transcriptome sequencing platforms, 13 genes displaying significant seed transcript accumulation differences between NILs were identified that mapped to the 8.4 Mbp LG I protein QTL region. Conclusions This study identifies gene candidates at the LG I protein QTL for potential involvement in the regulation of protein content in the soybean seed. The results demonstrate the power of complementary approaches to characterize contrasting NILs and provide genome-wide transcriptome insight towards understanding seed biology and the soybean genome.

  18. 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.

  19. 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.

  20. Divergência genética entre progênies de pupunheira quanto a caracteres de palmito

    Directory of Open Access Journals (Sweden)

    Jacson Rondinelli da Silva Negreiros

    2013-05-01

    Full Text Available O objetivo deste trabalho foi estimar a divergência genética de progênies de pupunheira, com base em variáveis agronômicas do palmito. O delineamento experimental em blocos ao acaso foi utilizado em látice triplo 10x10, com 100 tratamentos (progênies e três repetições. Foram feitas as seguintes avaliações: massa da base do palmito, produtividade do palmito de primeira e de segunda qualidade, número de plantas por parcela e diâmetro do palmito. A divergência genética foi estimada pela distância generalizada de Mahalanobis, como medida de dissimilaridade, e pelo método de otimização de Tocher e variáveis canônicas, na formação de grupos. As progênies formaram 26 grupos distintos. A variância acumulada pelas três primeiras variáveis canônicas foi de 75,12%. Planta por parcela e massa do palmito de segunda, indiretamente relacionada à massa do palmito de primeira, foram os caracteres mais importantes na discriminação das progênies, na primeira variável canônica (35,77%. A massa da base do palmito apresentou relação indireta com a produtividade do palmito de segunda e plantas por parcela, na segunda variável canônica (22.93%, e com a massa do palmito de primeira na terceira variável canônica (16,42%. Dezessete progênies de quatro grupos divergentes (G3, G5, G11 e G12 têm potencial para seleção quanto à produtividade de palmito no programa de melhoramento da pupunheira.

  1. 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.

  2. Differential gene expression in nearly isogenic lines with QTL for partial resistance to Puccinia hordei in barley

    Directory of Open Access Journals (Sweden)

    Marcel Thierry C

    2010-11-01

    Full Text Available Abstract Background The barley-Puccinia hordei (barley leaf rust pathosystem is a model for investigating partial disease resistance in crop plants and genetic mapping of phenotypic resistance has identified several quantitative trait loci (QTL for partial resistance. Reciprocal QTL-specific near-isogenic lines (QTL-NILs have been developed that combine two QTL, Rphq2 and Rphq3, the largest effects detected in a recombinant-inbred-line (RIL population derived from a cross between the super-susceptible line L94 and partially-resistant line Vada. The molecular mechanism underpinning partial resistance in these QTL-NILs is unknown. Results An Agilent custom microarray consisting of 15,000 probes derived from barley consensus EST sequences was used to investigate genome-wide and QTL-specific differential expression of genes 18 hours post-inoculation (hpi with Puccinia hordei. A total of 1,410 genes were identified as being significantly differentially expressed across the genome, of which 55 were accounted for by the genetic differences defined by QTL-NILs at Rphq2 and Rphq3. These genes were predominantly located at the QTL regions and are, therefore, positional candidates. One gene, encoding the transcriptional repressor Ethylene-Responsive Element Binding Factor 4 (HvERF4 was located outside the QTL at 71 cM on chromosome 1H, within a previously detected eQTL hotspot for defence response. The results indicate that Rphq2 or Rphq3 contains a trans-eQTL that modulates expression of HvERF4. We speculate that HvERF4 functions as an intermediate that conveys the response signal from a gene(s contained within Rphq2 or Rphq3 to a host of down-stream defense responsive genes. Our results also reveal that barley lines with extreme or intermediate partial resistance phenotypes exhibit a profound similarity in their spectrum of Ph-responsive genes and that hormone-related signalling pathways are actively involved in response to Puccinia hordei. Conclusions

  3. 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.

  4. Estabilidade e adaptabilidade de genótipos de algodão de fibra colorida quanto aos caracteres de fibra

    OpenAIRE

    Luiz Paulo de Carvalho; Caio Césio Salgado; Francisco José Correia Farias; Vinícius Quintão Carneiro

    2015-01-01

    O objetivo deste trabalho foi verificar a presença de interação genótipo x ambiente (G x A) e determinar a adaptabilidade e estabilidade fenotípica de linhagens de algodão de fibra marrom, utilizando o modelo de Ebehart & Russell. Foram conduzidos sete experimentos nos estados de CE, GO, MS e RN, em 2010 e 2011, em regime irrigado e de sequeiro. O delineamento utilizado foi blocos casualizados com quatro repetições. Foram avaliados 11 genótipos, segundo sete caracteres relativos à fibra. A in...

  5. 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...

  6. 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.

  7. 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

  8. 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.

  9. 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

  10. 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

  11. Plant DB link - 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 Plant DB link Da... Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive ...

  12. 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

  13. 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...

  14. 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...

  15. 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...

  16. 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.

  17. 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/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. PMID:27031623

  18. 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.

  19. 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.

  20. 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

  1. Co-localization of growth QTL with differentially expressed candidate genes in rainbow trout.

    Science.gov (United States)

    Kocmarek, Andrea L; Ferguson, Moira M; Danzmann, Roy G

    2015-09-01

    We tested whether genes differentially expressed between large and small rainbow trout co-localized with familial QTL regions for body size. Eleven chromosomes, known from previous work to house QTL for weight and length in rainbow trout, were examined for QTL in half-sibling families produced in September (1 XY male and 1 XX neomale) and December (1 XY male). In previous studies, we identified 108 candidate genes for growth expressed in the liver and white muscle in a subset of the fish used in this study. These gene sequences were BLASTN aligned against the rainbow trout and stickleback genomes to determine their location (rainbow trout) and inferred location based on synteny with the stickleback genome. Across the progeny of all three males used in the study, 63.9% of the genes with differential expression appear to co-localize with the QTL regions on 6 of the 11 chromosomes tested in these males. Genes that co-localized with QTL in the mixed-sex offspring of the two XY males primarily showed up-regulation in the muscle of large fish and were related to muscle growth, metabolism, and the stress response. PMID:26360524

  2. Ancestral QTL Alleles from Wild Emmer Wheat Improve Drought Resistance and Productivity in Modern Wheat Cultivars

    Science.gov (United States)

    Merchuk-Ovnat, Lianne; Barak, Vered; Fahima, Tzion; Ordon, Frank; Lidzbarsky, Gabriel A.; Krugman, Tamar; Saranga, Yehoshua

    2016-01-01

    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. PMID:27148287

  3. An efficient hierarchical generalized linear mixed model for mapping QTL of ordinal traits in crop cultivars.

    Directory of Open Access Journals (Sweden)

    Jian-Ying Feng

    Full Text Available 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 estimation of parameters, the pseudo data normal approximation of likelihood function and empirical Bayes approach were adopted. A series of Monte Carlo simulation experiments were performed to confirm the reliability of new method. The result showed that new method works well with satisfactory statistical power and precision. The new method was also adopted to dissect the genetic basis of soybean alkaline-salt tolerance in 257 soybean cultivars obtained, by stratified random sampling, from 6 geographic ecotypes in China. As a result, 6 main-effect QTL and 3 QTL-by-environment interactions were identified.

  4. 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 ...

  5. 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.

  6. Genetic analysis of arsenic accumulation in maize using QTL mapping.

    Science.gov (United States)

    Fu, Zhongjun; Li, Weihua; Xing, Xiaolong; Xu, Mengmeng; Liu, Xiaoyang; Li, Haochuan; Xue, Yadong; Liu, Zonghua; Tang, Jihua

    2016-01-01

    Arsenic (As) is a toxic heavy metal that can accumulate in crops and poses a threat to human health. The genetic mechanism of As accumulation is unclear. Herein, we used quantitative trait locus (QTL) mapping to unravel the genetic basis of As accumulation in a maize recombinant inbred line population derived from the Chinese crossbred variety Yuyu22. The kernels had the lowest As content among the different maize tissues, followed by the axes, stems, bracts and leaves. Fourteen QTLs were identified at each location. Some of these QTLs were identified in different environments and were also detected by joint analysis. Compared with the B73 RefGen v2 reference genome, the distributions and effects of some QTLs were closely linked to those of QTLs detected in a previous study; the QTLs were likely in strong linkage disequilibrium. Our findings could be used to help maintain maize production to satisfy the demand for edible corn and to decrease the As content in As-contaminated soil through the selection and breeding of As pollution-safe cultivars. PMID:26880701

  7. 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.

  8. Prioritization of candidate genes in “QTL-hotspot” region for drought tolerance in chickpea (Cicer arietinum L.)

    Science.gov (United States)

    Kale, Sandip M; Jaganathan, Deepa; Ruperao, Pradeep; Chen, Charles; Punna, Ramu; Kudapa, Himabindu; Thudi, Mahendar; Roorkiwal, Manish; Katta, Mohan AVSK; Doddamani, Dadakhalandar; Garg, Vanika; Kishor, P B Kavi; Gaur, Pooran M; Nguyen, Henry T; Batley, Jacqueline; Edwards, David; Sutton, Tim; Varshney, Rajeev K

    2015-01-01

    A combination of two approaches, namely QTL analysis and gene enrichment analysis were used to identify candidate genes in the “QTL-hotspot” region for drought tolerance present on the Ca4 pseudomolecule in chickpea. In the first approach, a high-density bin map was developed using 53,223 single nucleotide polymorphisms (SNPs) identified in the recombinant inbred line (RIL) population of ICC 4958 (drought tolerant) and ICC 1882 (drought sensitive) cross. QTL analysis using recombination bins as markers along with the phenotyping data for 17 drought tolerance related traits obtained over 1–5 seasons and 1–5 locations split the “QTL-hotspot” region into two subregions namely “QTL-hotspot_a” (15 genes) and “QTL-hotspot_b” (11 genes). In the second approach, gene enrichment analysis using significant marker trait associations based on SNPs from the Ca4 pseudomolecule with the above mentioned phenotyping data, and the candidate genes from the refined “QTL-hotspot” region showed enrichment for 23 genes. Twelve genes were found common in both approaches. Functional validation using quantitative real-time PCR (qRT-PCR) indicated four promising candidate genes having functional implications on the effect of “QTL-hotspot” for drought tolerance in chickpea. PMID:26478518

  9. 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.

  10. 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.

  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. QTL analysis of ICA Bunsi-derived resistance to white mold in a pinto x navy bean cross

    Science.gov (United States)

    Breeding for genetic resistance to white mold [Sclerotinia sclerotiorum (Lib.) de Bary] in dry bean (Phaseolus vulgaris L.) is difficult because of low heritability. To facilitate breeding, researchers have sought to identify QTL underpinning genetic resistance to white mold. We identified two QTL ...

  13. Some quantity aspects of the solar radiation in Mexicali, B.C., Mexico; Algunos aspectos cuantitativos de la radiacion solar en Mexicali, B.C., Mexico

    Energy Technology Data Exchange (ETDEWEB)

    Garcia Cueto; Rafael [Instituto de Ingenieria, U.A.B.C., Mexicali, Baja California (Mexico)

    2000-07-01

    Study of the global solar radiation is very useful for assesing the potential efficiency of systems designed for solar energy utilization. This paper explore some aspects of solar in Mexicali, B.C., Mexico, analysis of the monthly averages global solar radiation and general atmospheric transparency for the year 1998 are discussed. The statistical distribution of the clearness index is determined using histograms of frequencies. The percentage number of days with solar radiation values bellow a certain value is analyzed and discussed. The period of successive days having radiation less than 10 MJ/m{sup 2} dia-1 and 13 MJ/m{sup 2} dia{sup -}1 is examined and presented graphically. [Spanish] El estudio de la radiacion solar global es muy util para evaluar la eficiencia potencial de sistemas que en su diseno esten basados en la utilizacion de energia solar. En particular, en este articulo se exploran algunos aspectos cuantitativos de la radiacion solar en Mexicali, B.C., Mexico: se analizan los promedios mensuales de radiacion solar global y la transparencia atmosferica para el ano de 1998. Se determina la distribucion estadistica del indice de claridad usando histogramas de frecuencias. Se analizan y discuten el porcentaje de dias con valores de radiacion solar inferiores a cierto valor y se presentan graficamente el periodo de dias sucesivos que tienen valores de radiacion menores a 10 MJ/m{sup 2} dia{sup -}1 y 13MJ/m{sup 2} dia{sup -}1.

  14. 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.

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

    Directory of Open Access Journals (Sweden)

    Mariana Marcos

    2015-01-01

    Full Text Available 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 2010, georeferenciado mediante Sistemas de Información Geográfica (SIG. El análisis se basa en la construcción de mapas temáticos y el cálculo de indicadores estadísticos de distribución espacial. Se observa que los extranjeros que residen en la AGBA han desarrollado pautas de localización particulares, cuyas formas se vinculan con distancias y proximidades que se construyen en el campo social. Lo que se propone aquí es rescatar al espacio como una dimen-sión esencial para comprender los procesos sociales, entendiendo que juega un rol fundamental como producto y productor de las relaciones y conflictos sociales que lo atraviesan.

  16. Mapping of QTL for resistance to powdery mildew and resistance gene analogues in perennial ryegrass

    DEFF Research Database (Denmark)

    Schejbel, B; Jensen, L B; Asp, T; Xing, Y; Lübberstedt, T

    2008-01-01

    The objective of this study was to map resistance gene analogues (RGA) and quantitative trait loci (QTL) for powdery mildew resistance in perennial ryegrass (Lolium perenne L.). The mapping population consisted of 184 F2 genotypes produced from a cross between one genotype of a synthetic perennial...... the heritability was 71.7%. In total, two QTL for powdery mildew resistance were identified, and mapped to linkage groups (LG) LG3 and LG7. Individually, these QTL explained between 7.5% and 22.1% of the total phenotypic variation. Six RGA and three laccases were mapped to LG2, LG3, LG4, LG5 and LG7...

  17. 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.

  18. 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.

  19. 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.

  20. 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

  1. 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.

  2. 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

    Genome-wide association study was carried out in Nordic Holsteins, Nordic Red and Jersey breeds for functional traits using BovineHD Genotyping BreadChip (Illumina, San Diego, CA). The association analyses were carried out using both linear mixed model approach and a Bayesian variable selection...... 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...

  3. 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...

  4. A Statistical Framework for eQTL Mapping Using RNA-seq Data

    OpenAIRE

    Sun, Wei

    2011-01-01

    RNA-seq may replace gene expression microarrays in the near future. Using RNA-seq, the expression of a gene can be estimated using the total number of sequence reads mapped to that gene, known as the Total Read Count (TReC). Traditional eQTL mapping methods, such as linear regression, can be applied to TReC measurements after they are properly normalized. In this paper, we show that eQTL mapping, by directly modeling TReC using discrete distributions, has higher statistical power than the two...

  5. 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...... within families, the odds-ratio of having CP was approximately twice as high for the unfavourable allele compared to the favourable one. These QTL and closely linked markers show promise for the development of gene-specific markers associated with a reduced incidence of CP located on the dorso-caudal...

  6. 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

  7. 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

  8. Desarrollo y evaluación de un cuestionario semi-cuantitativo de frecuencias alimenticias para adolescentes bolivianos Development and testing of a semi-quantitative food frequency questionnaire for bolivian adolescents

    OpenAIRE

    Pérez-Cueto Eulert, F. J. A.; Roberfroid, D.; P. W. Kolsteren

    2006-01-01

    Introducción: Puesto que estudios previos sugieren que los patrones dietéticos y el estilo de vida durante la adolescencia tienen un impacto en la salud adulta, es pertinente monitorear y documentar los patrones alimenticios de los adolescentes. Objetivo: Desarrollar y evaluar la confiabilidad y la validez de un cuestionario semi-cuantitativo de frecuencias alimenticias para adolescentes Bolivianos. Metodología: Una muestra de conveniencia de 82 adolescentes de un colegio secundario de la ciu...

  9. 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.

  10. 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.

  11. Mapping main, epistatic and sex-specific QTL for body composition in a chicken population divergently selected for low or high growth rate

    Directory of Open Access Journals (Sweden)

    Vignal Alain

    2010-02-01

    Full Text Available Abstract Background Delineating the genetic basis of body composition is important to agriculture and medicine. In addition, the incorporation of gene-gene interactions in the statistical model provides further insight into the genetic factors that underlie body composition traits. We used Bayesian model selection to comprehensively map main, epistatic and sex-specific QTL in an F2 reciprocal intercross between two chicken lines divergently selected for high or low growth rate. Results We identified 17 QTL with main effects across 13 chromosomes and several sex-specific and sex-antagonistic QTL for breast meat yield, thigh + drumstick yield and abdominal fatness. Different sets of QTL were found for both breast muscles [Pectoralis (P major and P. minor], which suggests that they could be controlled by different regulatory mechanisms. Significant interactions of QTL by sex allowed detection of sex-specific and sex-antagonistic QTL for body composition and abdominal fat. We found several female-specific P. major QTL and sex-antagonistic P. minor and abdominal fatness QTL. Also, several QTL on different chromosomes interact with each other to affect body composition and abdominal fatness. Conclusions The detection of main effects, epistasis and sex-dimorphic QTL suggest complex genetic regulation of somatic growth. An understanding of such regulatory mechanisms is key to mapping specific genes that underlie QTL controlling somatic growth in an avian model.

  12. Mapping quantitative trait loci (QTL) in sheep. II. Meta-assembly and identification of novel QTL for milk production traits in sheep

    OpenAIRE

    Lam Mary K; Hobbs Matthew; McGill David; Jonas Elisabeth; Raadsma Herman W; Thomson Peter C

    2009-01-01

    Abstract An (Awassi × Merino) × Merino backcross family of 172 ewes was used to map quantitative trait loci (QTL) for different milk production traits on a framework map of 200 loci across all autosomes. From five previously proposed mathematical models describing lactation curves, the Wood model was considered the most appropriate due to its simplicity and its ability to determine ovine lactation curve characteristics. Derived milk traits for milk, fat, protein and lactose yield, as well as ...

  13. 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

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

    OpenAIRE

    Moeses Andrigo Danner; Maria do Carmo Bassols Raseira; Simone Aparecida Zolet Sasso; Idemir Citadin; Silvia Scariot

    2010-01-01

    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 ...

  15. 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.

  16. Variação de caracteres em híbridos de abacaxizeiro obtidos de diferentes cruzamentos Characters variation in pineapple hybrids obtained by different crosses

    Directory of Open Access Journals (Sweden)

    José Renato Santos Cabral

    2009-12-01

    Full Text Available A herança dos caracteres utilizados na seleção de híbridos de abacaxi é de suma importância para o sucesso dos programas de melhoramento genético desta fruteira. o trabalho teve como objetivo analisar as variações observadas nos principais caracteres utilizados na seleção de híbridos de abacaxi obtidos de diferentes cruzamentos. Foi realizada a análise de variância dos caracteres: altura da planta do solo até à base do fruto, comprimento do pedúnculo, peso do fruto sem coroa, peso da coroa, teor de sólidos solúveis e acidez titulável de 446 genótipos avaliados e 213 selecionados. observou-se uma diminuição do peso do fruto nos híbridos selecionados na maioria dos cruzamentos e aumento dos sólidos solúveis em todos os cruzamentos, quando comparados com todos os genótipos avaliados. Constatou-se correlação linear simples positiva significativa entre o peso do fruto e a altura da planta. Foi observada também correlação linear simples significativa, de baixa magnitude, positiva entre o peso do fruto e o peso da coroa, a altura da planta e o peso da coroa, a altura da planta e o teor de sólidos solúveis e negativa entre o teor de sólidos solúveis e ocomprimento do pedúnculo. Verificou-se diferença entre os cruzamentos na seleção de genótipos de abacaxi para os caracteres estudados.The inheritance of traits used for the selection of pineapple hybrids is very important for the success of the genetic breeding program of this fruit crop. The objective of the present work was to analyze the variations observed in main traits used for the selection of pineapple hybrids obtained by different crosses. The analysis of variance for 446 evaluated and 213 selected genotypes was carried out for the following traits: plant height from soil to the base of the fruit, peduncle length, weight of the fruit without the crown, weight of the crown, total soluble solids content and titrable acidity. in general, it was observed that

  17. 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.

  18. Use of the EM algorithm to detect QTL affecting multiple-traits in an across half-sib family analysis

    Directory of Open Access Journals (Sweden)

    McLachlan GM

    2005-01-01

    Full Text Available Abstract QTL detection experiments in livestock species commonly use the half-sib design. Each male is mated to a number of females, each female producing a limited number of progeny. Analysis consists of attempting to detect associations between phenotype and genotype measured on the progeny. When family sizes are limiting experimenters may wish to incorporate as much information as possible into a single analysis. However, combining information across sires is problematic because of incomplete linkage disequilibrium between the markers and the QTL in the population. This study describes formulæ for obtaining MLEs via the expectation maximization (EM algorithm for use in a multiple-trait, multiple-family analysis. A model specifying a QTL with only two alleles, and a common within sire error variance is assumed. Compared to single-family analyses, power can be improved up to fourfold with multi-family analyses. The accuracy and precision of QTL location estimates are also substantially improved. With small family sizes, the multi-family, multi-trait analyses reduce substantially, but not totally remove, biases in QTL effect estimates. In situations where multiple QTL alleles are segregating the multi-family analysis will average out the effects of the different QTL alleles.

  19. 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

  20. 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

  1. 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...

  2. 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.

  3. Association analyses of four genes within QTL for meat quality on q arm of SSC2

    Czech Academy of Sciences Publication Activity Database

    Čepica, Stanislav; Óvilo, C.; Masopust, Martin; Knoll, Aleš; Fernández, A.; López, A.; Rohrer, G. A.; Nonneman, D.

    Edinburgh : International Society for Animal Getics, 2010. s. 111-111. [32nd Conference of the International Society for Animal Genetics. 26.07.2010 - 30.07.2010, Edinburgh] R&D Projects: GA ČR GAP502/10/1216 Institutional research plan: CEZ:AV0Z50450515 Keywords : meat quality * QTL * IMF Subject RIV: GI - Animal Husbandry ; Breeding

  4. 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…

  5. High Resolution QTL Maps Of 31 Traits in Contemporary U.S. Holstein Cows

    Science.gov (United States)

    High-resolution QTL maps of 1586 SNPs affecting 31 dairy traits (top 100 effects per trait)were constructed based on a genome-wide association analysis of 1,654 contemporary U.S. Holstein cows genotyped with 45,878 SNPs. The 31 traits include net merit and its 8 compnent traits, 4 calving traits, an...

  6. Freezing tolerance-associated QTL in the Brundage × Coda wheat recombinant inbred line population

    Science.gov (United States)

    Freezing tolerance is an essential trait for winter wheat (Triticum aestivum L.) cultivars. A genetic analysis of a Brundage × Coda winter wheat recombinant inbred line (RIL) mapping population was undertaken to identify quantitative trait loci (QTL) associated with freezing tolerance. Five- to six...

  7. 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...

  8. 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

  9. 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

  10. 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

  11. 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

  12. A genome scan revealed significant associations of growth traits with a major QTL and GHR2 in tilapia

    OpenAIRE

    Feng Liu; Fei Sun; Jun Hong Xia; Jian Li; Gui Hong Fu; Grace Lin; Rong Jian Tu; Zi Yi Wan; Delia Quek; Gen Hua Yue

    2014-01-01

    Growth is an important trait in animal breeding. However, the genetic effects underpinning fish growth variability are still poorly understood. QTL mapping and analysis of candidate genes are effective methods to address this issue. We conducted a genome-wide QTL analysis for growth in tilapia. A total of 10, 7 and 8 significant QTLs were identified for body weight, total length and standard length at 140 dph, respectively. The majority of these QTLs were sex-specific. One major QTL for growt...

  13. 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.

  14. 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.

  15. Mapping of QTL affecting incidence of blood and meat inclusions in egg layers

    Directory of Open Access Journals (Sweden)

    Vennerström Pia

    2011-06-01

    Full Text Available Abstract Background Occurrence of blood and meat inclusions is an internal egg quality defect. Mass candling reveals most of the spots, but because brown eggshell hampers selection in brown chicken lines it has not been possible to eliminate the defect by selection. Estimated frequency of blood and meat inclusions in brown layers is about 18% whereas it is 0.5% in white egg layers. Several factors are known to increase the incidence of this fault: genetic background, low level of vitamin A and/or D, stress or infections, for instance. To study the genetic background of the defect, a mapping population of 1599 F2 hens from a cross of White Rock and Rhode Island Red lines was set up. Results Our histopathological analyses show that blood spots consist of mainly erythrocytes and that meat spots are accumulations of necrotic material. Linkage analysis of 27 chromosomes with 162 microsatellite markers revealed one significant quantitative trait locus (QTL affecting blood spot and meat spot frequency. We sequenced a fragment of a candidate gene within the region, ZO-2, coding for a tight junction protein. Nine polymorphisms were detected and two of them were included in fine-mapping and association analysis. Fine-mapping defined the QTL result. To further verify the QTL, association analyses were carried out in two independent commercial breeding lines with the marker MCW241 and surrounding SNPs. Association was found mainly in a 0.8 Mb-wide chromosomal area on GGAZ. Conclusions There was good agreement between the location of the QTL region on chromosome Z and the association results in the commercial breeds analyzed. Variations found in tight junction protein ZO-2 and microRNA gga-mir-1556 may predispose egg layers to blood and meat spot defects. This paper describes the first results of detailed QTL analyses of the blood and meat spots trait(s in chickens.

  16. 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

    2016-01-01

    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. PMID:27271557

  17. 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

  18. 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.

  19. 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

  20. Genetic variation, linkage mapping of QTL and correlation studies for yield, root, and agronomic traits for aerobic adaptation

    OpenAIRE

    Sandhu, Nitika; Jain, Sunita; Kumar, Arvind; Mehla, Balwant Singh; Jain, Rajinder

    2013-01-01

    Background Water scarcity and drought have seriously threatened traditional rice cultivation practices in several parts of the world, including India. Aerobic rice that uses significantly less water than traditional flooded systems has emerged as a promising water-saving technology. The identification of QTL conferring improved aerobic adaptation may facilitate the development of high-yielding aerobic rice varieties. In this study, experiments were conducted for mapping QTL for yield, root-re...

  1. 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.

  2. A high-resolution linkage map for comparative genome analysis and QTL fine mapping in Asian seabass, Lates calcarifer

    OpenAIRE

    Wang, Chun Ming; Bai, Zhi Yi; He, Xiao Ping; Lin, Grace; Xia, Jun Hong; Sun, Fei; Lo, Loong Chueng; Feng, Felicia; Zhu, Ze Yuan; Yue, Gen Hua

    2011-01-01

    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...

  3. 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

  4. 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.

  5. Caracterización mineralógica de materias primas cerámicas por métodos cuantitativos de difracción de rayos x

    OpenAIRE

    Rius, Jordi; Reventós, M. M.; Clausell, J. V.; Esteve, V; J. M. Delgado; Ochando, L. E.; Martí, F. J.; Amigó, J. M.

    2002-01-01

    [ES] El objetivo de este trabajo es la caracterización de fases minerales presentes en materias primas utilizadas en la industria cerámica. Para ello se utilizan dos métodos cuantitativos basados en la difracción de rayos X, el método de Rietveld y un método sin estándar. Los resultados obtenidos por difracción rayos X de estos materiales policristalinos se comparan con los correspondientes análisis químicos y la composición normativa calculada. La precisión y reproducibilidad de los...

  6. Análisis cuantitativo de cuarzo-alfa en mezclas de cemento portland anhidro y calcita sintética por difracción de rayos X con equipo Philips PW-1700

    OpenAIRE

    Sagrera-Moreno, J. L.

    1985-01-01

    In this article there are explained the necessary steps to make up a quantitative analysis of alpha-quartz applying the technique of rays X diffraction, in artificial mixtures of anhydrous portland cement and synthetic calcite, which contents are known.

    En el presente artículo se explican los pasos necesarios para realizar un análisis cuantitativo de cuarzo-alfa aplicando la técnica de difracción de rayos X en mezclas artificiales de cemento portland anhidro y calcita sinté...

  7. Análisis cuantitativo de cuarzo-alfa en mezclas de cemento portland anhidro y calcita sintética por difracción de rayos X con equipo Philips PW-1700

    Directory of Open Access Journals (Sweden)

    Sagrera-Moreno, J. L.

    1985-09-01

    Full Text Available In this article there are explained the necessary steps to make up a quantitative analysis of alpha-quartz applying the technique of rays X diffraction, in artificial mixtures of anhydrous portland cement and synthetic calcite, which contents are known.

    En el presente artículo se explican los pasos necesarios para realizar un análisis cuantitativo de cuarzo-alfa aplicando la técnica de difracción de rayos X en mezclas artificiales de cemento portland anhidro y calcita sintética, cuyos contenidos son conocidos.

  8. 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...

  9. 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...

  10. Estudio y análisis cuantitativo sobre las posibilidades didácticas de la Música Festera en el aula de secundaria. Una visión del profesorado

    OpenAIRE

    Botella Nicolás, Ana María; Martínez Gallego, Silvia; Fernández Maximiano, Rafael

    2014-01-01

    La presente comunicación trata de mostrar los resultados parciales de un estudio cuantitativo realizado sobre la aplicación didáctica de la Música Festera en el aula de enseñanza secundaria. La música de Moros y Cristianos, también llamada Música Festera, constituye una de las tradiciones musicales más ricas de la Comunidad Valenciana. Es una música incidental en constante evolución que se materializa en sus tres formas para el desfile: marchas moras, marchas cristianas y pasodoble.

  11. 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...

  12. 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 PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods Update History o...Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods is opened. Joomla SEF ...t, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive ... ... link & Genome analysis methods English archive site is opened. 2012/08/08 PGDBj ...f This Database Date Update contents 2014/10/10 PGDBj Registered plant list, Marker list, QTL list, Plant DB

  13. An interaction quantitative trait loci tool implicates epistatic functional variants in an apoptosis pathway in smallpox vaccine eQTL data.

    Science.gov (United States)

    Lareau, C A; White, B C; Oberg, A L; Kennedy, R B; Poland, G A; McKinney, B A

    2016-06-01

    Expression quantitative trait loci (eQTL) studies have functionalized nucleic acid variants through the regulation of gene expression. Although most eQTL studies only examine the effects of single variants on transcription, a more complex process of variant-variant interaction (epistasis) may regulate transcription. Herein, we describe a tool called interaction QTL (iQTL) designed to efficiently detect epistatic interactions that regulate gene expression. To maximize biological relevance and minimize the computational and hypothesis testing burden, iQTL restricts interactions such that one variant is within a user-defined proximity of the transcript (cis-regulatory). We apply iQTL to a data set of 183 smallpox vaccine study participants with genome-wide association study and gene expression data from unstimulated samples and samples stimulated by inactivated vaccinia virus. While computing only 0.15% of possible interactions, we identify 11 probe sets whose expression is regulated through a variant-variant interaction. We highlight the functional epistatic interactions among apoptosis-related genes, DIABLO, TRAPPC4 and FADD, in the context of smallpox vaccination. We also use an integrative network approach to characterize these iQTL interactions in a posterior network of known prior functional interactions. iQTL is an efficient, open-source tool to analyze variant interactions in eQTL studies, providing better understanding of the function of epistasis in immune response and other complex phenotypes. PMID:27052692

  14. 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...

  15. 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

  16. Genetic dissection of milk yield traits and mastitis resistance QTL on chromosome 20 in dairy cattle

    DEFF Research Database (Denmark)

    Kadri, Naveen Kumar; Guldbrandtsen, Bernt; Lund, Mogens Sandø;

    2015-01-01

    Intense selection to increase milk yield has had negative consequences for mastitis incidence in dairy cattle. Due to low heritability of mastitis resistance and an unfavorable genetic correlation with milk yield, a reduction in mastitis through traditional breeding has been difficult to achieve....... Here, we examined quantitative trait loci (QTL) that segregate for clinical mastitis (CM) and milk yield (MY) on Bos taurus autosome 20 (BTA20) to determine whether both traits are affected by a single polymorphism (pleiotropy) or by multiple closely linked polymorphisms. In the latter but not the...... (RDC) and Danish Jersey cattle (JER) with the goal of determining whether these QTL identified in Holsteins were segregating across breeds. Genotypes for 12,566 animals (5,966 HOL, 5,458 RDC, and 1,142 JER) were determined by using the Illumina Bovine SNP50 BeadChip (50k), which identifies 1,568 single...

  17. 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 ...

  18. QTL Mapping of Leafy Heads by Genome Resequencing in the RIL Population of Brassica rapa

    OpenAIRE

    Yu, Xiang; Wang, Han; ZHONG, WEILI; Bai, Jinjuan; Liu, Pinglin; He, Yuke

    2013-01-01

    Leaf heads of cabbage (Brassica oleracea), Chinese cabbage (B. rapa), and lettuce (Lactuca sativa) are important vegetables that supply mineral nutrients, crude fiber and vitamins in the human diet. Head size, head shape, head weight, and heading time contribute to yield and quality. In an attempt to investigate genetic basis of leafy head in Chinese cabbage (B. rapa), we took advantage of recent technical advances of genome resequencing to perform quantitative trait locus (QTL) mapping using...

  19. Fine mapping of a calving QTL on Bos taurus autosome 18 in Holstein cattle.

    Science.gov (United States)

    Mao, X; Kadri, N K; Thomasen, J R; De Koning, D J; Sahana, G; Guldbrandtsen, B

    2016-06-01

    Decreased calving performance not only directly impacts the economic efficiency of dairy cattle farming but also influences public concern for animal welfare. Previous studies have revealed a QTL on Bos taurus autosome (BTA) 18 that has a large effect on calving traits in Holstein cattle. In this study, fine mapping of this QTL was performed using imputed high-density SNP chip (HD) genotypes followed by imputed next-generation sequencing (NGS) variants. BTA18 was scanned for seven direct calving traits in 6113 bulls with imputed HD genotypes. SNP rs136283363 (BTA18: 57 548 213) was consistently the most significantly associated SNP across all seven traits [e.g. p-value = 2.04 × 10(-59) for birth index (BI)]. To finely map the QTL region and to explore pleiotropic effects, we studied NGS variants within the targeted region (BTA18: 57 321 450-57 625 355) for associations with direct calving traits and with three conformation traits. Significant variants were prioritized, and their biological relevance to the traits was interpreted. Considering their functional relationships with direct calving traits, SIGLEC12, CD33 and CEACAM18 were proposed as candidate genes. In addition, pleiotropic effects of this QTL region on direct calving traits and conformation traits were observed. However, the extent of linkage disequilibrium combined with the lack of complete annotation and potential errors in the Bos taurus genome assembly hampered our efforts to pinpoint the causal mutation. PMID:26486911

  20. Genome-wide SNP identification and QTL mapping for black rot resistance in cabbage

    OpenAIRE

    Lee, Jonghoon; Izzah, Nur Kholilatul; Jayakodi, Murukarthick; Perumal, Sampath; Joh, Ho Jun; Lee, Hyeon Ju; Lee, Sang-Choon; Park, Jee Young; Yang, Ki-Woung; Nou, Il-Sup; Seo, Joodeok; Yoo, Jaeheung; Suh, Youngdeok; Ahn, Kyounggu; Lee, Ji Hyun

    2015-01-01

    Background Black rot is a destructive bacterial disease causing large yield and quality losses in Brassica oleracea. To detect quantitative trait loci (QTL) for black rot resistance, we performed whole-genome resequencing of two cabbage parental lines and genome-wide SNP identification using the recently published B. oleracea genome sequences as reference. Results Approximately 11.5 Gb of sequencing data was produced from each parental line. Reference genome-guided mapping and SNP calling rev...

  1. 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...

  2. Quantitative genomics of voluntary exercise in mice: transcriptional analysis and mapping of expression QTL in muscle

    OpenAIRE

    Kelly, Scott A.; Nehrenberg, Derrick L.; Hua, Kunjie; Garland, Theodore; Pomp, Daniel

    2014-01-01

    Motivation and ability both underlie voluntary exercise, each with a potentially unique genetic architecture. Muscle structure and function are one of many morphological and physiological systems acting to simultaneously determine exercise ability. We generated a large (n = 815) advanced intercross line of mice (G4) derived from a line selectively bred for increased wheel running (high runner) and the C57BL/6J inbred strain. We previously mapped quantitative trait loci (QTL) contributing to v...

  3. 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...

  4. 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...

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Directory of Open Access Journals (Sweden)

    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.

  7. Multiparental mapping of plant height and flowering time QTL in partially isogenic sorghum families.

    Science.gov (United States)

    Higgins, R H; Thurber, C S; Assaranurak, I; Brown, P J

    2014-09-01

    Sorghum varieties suitable for grain production at temperate latitudes show dwarfism and photoperiod insensitivity, both of which are controlled by a small number of loci with large effects. We studied the genetic control of plant height and flowering time in five sorghum families (A-E), each derived from a cross between a tropical line and a partially isogenic line carrying introgressions derived from a common, temperate-adapted donor. A total of 724 F2:3 lines were phenotyped in temperate and tropical environments for plant height and flowering time and scored at 9139 SNPs using genotyping-by-sequencing. Biparental mapping was compared with multiparental mapping in different subsets of families (AB, ABC, ABCD, and ABCDE) using both a GWAS approach, which fit each QTL as a single effect across all families, and using a joint linkage approach, which fit QTL effects as nested within families. GWAS using all families (ABCDE) performed best at the cloned Dw3 locus, whereas joint linkage using all families performed best at the cloned Ma1 locus. Both multiparental approaches yielded apparently synthetic associations due to genetic heterogeneity and were highly dependent on the subset of families used. Comparison of all mapping approaches suggests that a GA2-oxidase underlies Dw1, and that a mir172a gene underlies a Dw1-linked flowering time QTL. PMID:25237111

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

    Directory of Open Access Journals (Sweden)

    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.

  9. 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.

  10. 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

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

    Directory of Open Access Journals (Sweden)

    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.

  12. 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.

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

    Directory of Open Access Journals (Sweden)

    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

  14. Elementos de Análisis Cualitativo y Cuantitativo en Proteínas del Gluten de Trigo Qualitative and Quantitative Element Analyses of the Wheat Gluten Protein

    Directory of Open Access Journals (Sweden)

    Paola Díaz Dellavalle

    2006-12-01

    Full Text Available La calidad del trigo para pan (Triticum aestivum L. depende de la calidad y cantidad de las proteínas del gluten -gluteninas y gliadinas- las cuales constituyen 10 a 14% de las proteínas del grano. Varios parámetros cuantitativos, como el contenido total de proteínas de la harina, el contenido de proteínas poliméricas presentes en el grano y la proporción de gluteninas y gliadinas, están relacionados a la calidad panadera. En este trabajo se presenta la caracterización de las gluteninas de alto peso molecular (G-APM en geles de poliacrilamida en SDS (SDS-PAGE de 22 cultivares y líneas de mejoramiento de Uruguay. Fueron observadas 14 subunidades de G-APM correspondientes a 10 combinaciones alélicas. Por otra parte, se propone un método sencillo para agrupar y cuantificar las principales proteínas de reserva de trigo mediante cromatografía líquida de exclusión por tamaño de alta resolución (SE-HPLC. Los cromatogramas obtenidos mostraron una excelente separación de las proteínas del endospermo en tres picos principales correspondientes a proteínas poliméricas, monoméricas y no gluten, respectivamente. El área de integración de los cromatogramas así como la presencia de subunidades de los cultivares fueron analizados. Los genotipos estudiados mostraron diferencias cuantitativas en el contenido de gluteninas/gliadinas solubles en SDS, en la proporción de proteínas poliméricas y monoméricas. El cultivar INIA Gorrión, de buena calidad panadera y que presenta el alelo Glu-D1 5+10, mostró menor porcentaje de proteínas poliméricas solubles en SDS y mayor porcentaje de proteínas poliméricas insolubles en comparación con la línea experimental LE 2265, que tiene el par Glu-D1 2+12.The bread making quality of wheat (Triticum aestivum L. depends on the quality and quantity of the gluten proteins -glutenins and gliadins- which constitute 10 to 14% of the grain protein content. Various quantitative parameters, such as the

  15. Insight into the genetic components of community genetics: QTL mapping of insect association in a fast-growing forest tree.

    Science.gov (United States)

    DeWoody, Jennifer; Viger, Maud; Lakatos, Ferenc; Tuba, Katalin; Taylor, Gail; Smulders, Marinus J M

    2013-01-01

    Identifying genetic sequences underlying insect associations on forest trees will improve the understanding of community genetics on a broad scale. We tested for genomic regions associated with insects in hybrid poplar using quantitative trait loci (QTL) analyses conducted on data from a common garden experiment. The F2 offspring of a hybrid poplar (Populus trichocarpa x P. deltoides) cross were assessed for seven categories of insect leaf damage at two time points, June and August. Positive and negative correlations were detected among damage categories and between sampling times. For example, sap suckers on leaves in June were positively correlated with sap suckers on leaves (P<0.001) but negatively correlated with skeletonizer damage (P<0.01) in August. The seven forms of leaf damage were used as a proxy for seven functional groups of insect species. Significant variation in insect association occurred among the hybrid offspring, including transgressive segregation of susceptibility to damage. NMDS analyses revealed significant variation and modest broad-sense heritability in insect community structure among genets. QTL analyses identified 14 genomic regions across 9 linkage groups that correlated with insect association. We used three genomics tools to test for putative mechanisms underlying the QTL. First, shikimate-phenylpropanoid pathway genes co-located to 9 of the 13 QTL tested, consistent with the role of phenolic glycosides as defensive compounds. Second, two insect association QTL corresponded to genomic hotspots for leaf trait QTL as identified in previous studies, indicating that, in addition to biochemical attributes, leaf morphology may influence insect preference. Third, network analyses identified categories of gene models over-represented in QTL for certain damage types, providing direction for future functional studies. These results provide insight into the genetic components involved in insect community structure in a fast-growing forest tree

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

    Directory of Open Access Journals (Sweden)

    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.

  17. QTL mapping reveals a two-step model for the evolutionary reduction of inner microsporangia within the asteracean genus Microseris.

    Science.gov (United States)

    Gailing, O; Bachmann, K

    2003-09-01

    The reduction of inner (adaxial) pollen sacs (microsporangia, MS) as a diagnostic character for the three asteracean species, Microseris bigelovii, Microseris elegans and Microseris pygmaea, was analysed in an interspecific cross between Microseris douglasii and Microseris bigelovii with 4 MS and 2 MS, respectively, using the average number of MS per plant as a quantitative character. A previous QTL (Quantitative Trait Locus) analysis had revealed one major QTL (3B) and three modifier QTLs (3A, 4A, 7A) with epistatic effects only on the homozygous recessive 2 MS genotype of QTL 3B. Here we performed a bulked segregant analysis on four 2 MS and four 4 MS DNA-bulks with 407 EcoRI/ MseI AFLP-primer combinations each. In this way additional AFLP markers were mapped close to QTL 3B and QTL 3A. Three of them were converted to SCAR (Sequence Characterized Amplified region) markers. All markers were tested in natural populations of the disporangiate (2 MS) species M. bigelovii, M. elegans and M. pygmaea, and in different populations of tetrasporangiate (4 MS) M. douglasii. The marker distribution suggests that locus 3B mutated in a progenitor of the disporangiate species. QTL 3A has evolved in the 2 MS background of the major gene in the disporangiate species. Since M. pygmaea and M. bigelovii are the sister group to M. elegans, the 4 MS genotype for (markers of) QTL 3A in M. pygmaea populations is most likely due to a back mutation to the 4 MS state and could explain the slight instability of the 2 MS phenotype in this species. PMID:12838389

  18. 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

    Directory of Open Access Journals (Sweden)

    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.

  19. 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

  20. 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

  1. 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.

  2. 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

  3. 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

  4. Interactions Between QTL SAP6 and SU91 on Resistance to Common Bacterial Blight in Red Kidney Bean and Pinto Bean Populations

    Science.gov (United States)

    Resistance to common bacterial blight in common bean is a complex trait that is quantitatively inherited. We examined the interaction between two independent QTL, SAP6 and SU91, which condition resistance to CBB.The QTL were studied in a pinto bean F2 population a cross between Othello (sap6 sap6 //...

  5. 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

    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 assoc...

  6. Seleção recorrente para três caracteres do feijoeiro Recurrent selection for three characters in common bean

    Directory of Open Access Journals (Sweden)

    José Ângelo Nogueira de Menezes Júnior

    2008-12-01

    Full Text Available O objetivo deste trabalho foi estimar o progresso genético após três ciclos de seleção recorrente na cultura do feijoeiro. Em cada ciclo, as progênies foram avaliadas por três gerações S0:1, S0:2 e S0:3, no campo experimental do Departamento de Biologia da Universidade Federal de Lavras (UFLA, em Lavras, Minas Gerais, no período de 2001 a 2006. Nos experimentos, avaliaram-se a produtividade de grãos, a arquitetura da planta e o tipo de grão. Em todas as avaliações de progênies, foram realizadas as análises de variância e obtidas as estimativas de parâmetros genéticos e fenotípicos. Foi estimado o progresso por caráter e, posteriormente, para os três caracteres, simultaneamente, após a padronização das variáveis. Como os ciclos foram obtidos em anos diferentes, utilizou-se o desempenho de duas linhagens que estiveram presentes em todas as avaliações para atenuar o efeito do ambiente nas estimativas obtidas. A diferença entre os b's da regressão linear, entre o número de ciclos, variável independente (x e o desempenho médio do caráter sob seleção, variável dependente (y, das progênies e das testemunhas, forneceu a estimativa do progresso genético. Após três ciclos de seleção recorrente, o progresso genético foi de 3,1%, considerando os três caracteres simultaneamente. A existência de variabilidade genética entre as progênies evidencia a possibilidade de continuar obtendo sucesso com a seleção.The objective of this study was to estimate the genetic progress after three recurrent selection cycles in common bean. The progenies in each cycle were evaluated over three generations S0:1, S0:2 and S0:3 on the experimental field of the Department of Biology at the Federal University of Lavras (UFLA, in Lavras, Minas Gerais, from 2001 to 2006. In the experiments, grain yield, grain type and plant architecture were evaluated. Analyses of variance and the estimates of genetic and phenotypic parameters were

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

    Directory of Open Access Journals (Sweden)

    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

  8. 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.

  9. 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.

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

    Directory of Open Access Journals (Sweden)

    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

  11. 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

    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......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 < 0.0001) on 20 chromosomes affecting mastitis-related traits...

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

    Directory of Open Access Journals (Sweden)

    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.

  13. 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.

  14. QTL associated with WSSV-resistance and growth-related traits in the Chinese shrimp Fenneropenaeus chinensis

    Directory of Open Access Journals (Sweden)

    WANG Wei-Ji

    2008-12-01

    Full Text Available A virgin female Chinese shrimp Fenneropenaeus chinensis was selected from the fourth generation of a successively WSSV(White Spot Syndrome Virus resistance population and mated with a wild male through artificial insemination to produce the F1 and F2 generation. These shrimp were challenged with WSSV and the F2 generation were collected and scored for WSSV resistance, standard length, total body length and body weight. AFLP (Amplified Fragment Length Polymorphism markers were used to construct a linkage map of F.chinensis based on this F2 family. The MAPMAKER/QTL1.1 software was applied in QTL (Quantitative Traits Loci mapping of standard length, total body length, weight and WSSV-resistant of F.chinensis based on interval mapping method (IM. At the criterion of LOD (Limit of Detection >2.0, one QTL associated with standard length, two with total body length, two with body weight and two with WSSV-resistance were detected. These QTL were distributed on three linkage groups. The variance-explained value of QTLs were between 26.6% and 66.9%. Three QTL for body weight, total body length and WSSV-resistance were detected on LG11, two QTLs for standard length and total body length shared a same LG (Linkage Group, and two QTL of WSSV-resistance and body weight were distributed on another LG. These results suggested that the WSSV-resistance and the body shape traits of F.chinensis are correlated[Acta Zoologica Sinica 54(6: 1075 – 1081, 2008].

  15. Repetibilidade e número mínimo de medições para caracteres de cacho de bacabi (Oenocarpus mapora Repeatability and minimum number of measurements for characters of bacabi palm (Oenocarpus mapora racemes

    Directory of Open Access Journals (Sweden)

    Maria do Socorro Padilha de Oliveira

    2010-12-01

    Full Text Available A bacabi (Oenocarpus mapora H. Karsten é uma palmeira perene nativa da Amazônia, que produz cachos com centenas de frutos que apresentam grande potencialidade à agroindústria de polpa, mas tem sido pouco estudada. Os objetivos deste trabalho foram estimar os coeficientes de repetibilidade e determinar a previsibilidade e o número de medições necessárias para caracteres de cacho dessa palmeira. Foram avaliados 27 indivíduos de bacabi pertencentes ao Banco de Germoplasma de Oenocarpus/Jessenia da Embrapa Amazônia Oriental, em Belém-PA. De cada planta, foram colhidos três cachos em maturação completa para a mensuração de seis caracteres: peso total do cacho (PTC e de frutos por cacho (PFC, número de ráquilas por cacho (NRC, comprimento da ráquis por cacho (CRC, peso de 100 frutos (PCF e rendimento de frutos por cacho (RFC. As estimativas de repetibilidade foram obtidas pelos métodos estatísticos da análise de variância, componentes principais e análise estrutural. Em todos os caracteres, as estimativas de repetibilidade apresentaram valores muito semelhantes nos três métodos. As estimativas dos coeficientes de repetibilidade e as previsibilidades foram relativamente altas (r 0,60 e R² 81,7% para os caracteres número de ráquilas e rendimento de frutos por cacho, demonstrando regularidade dos genótipos nas várias medições (cachos, em todos os métodos. Para esses caracteres, o número mínimo de cachos necessários para a avaliação do real valor dos genótipos foi de treze (RFC e cinco (NRC cachos com confiabilidade de 95%, tornando-os factíveis no uso de inferências genéticas para as condições do estudo. Os demais caracteres exibiram repetibilidades e coeficientes de determinação de médias a baixas magnitudes, indicando necessidade de maior controle ambiental para suas mensurações.Bacabi (Oenocarpus mapora H. Karsten is a native Amazonian palm that produces racemes with hundreds of fruits with great

  16. 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.

  17. 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)

  18. 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.

  19. QTL mapping for yield and lodging resistance in an enhanced SSR-based map for tef.

    Science.gov (United States)

    Zeid, M; Belay, G; Mulkey, S; Poland, J; Sorrells, M E

    2011-01-01

    Tef is a cereal crop of cultural and economic importance in Ethiopia. It is grown primarily for its grain though it is also an important source of fodder. Tef suffers from lodging that reduces both grain yield and quality. As a first step toward executing a marker-assisted breeding program for lodging resistance and grain yield improvement, a linkage map was constructed using 151 F(9) recombinant inbred lines obtained by single-seed-descent from a cross between Eragrostis tef and its wild relative Eragrostis pilosa. The map was primarily based on microsatellite (SSR) markers that were developed from SSR-enriched genomic libraries. The map consisted of 30 linkage groups and spanned a total length of 1,277.4 cM (78.7% of the genome) with an average distance of 5.7 cM between markers. This is the most saturated map for tef to date, and for the first time, all of the markers are PCR-based. Using agronomic data from 11 environments and marker data, it was possible to map quantitative trait loci (QTL) controlling lodging, grain yield and 15 other related traits. The positive effects of the QTL identified from the wild parent were mainly for earliness, reduced culm length and lodging resistance. In this population, it is now possible to combine lodging resistance and grain yield using a marker-assisted selection program targeting the QTL identified for both traits. The newly developed SSR markers will play a key role in germplasm organization, fingerprinting and monitoring the success of the hybridization process in intra-specific crosses lacking distinctive morphological markers. PMID:20706706

  20. 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.

  1. 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

  2. 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...

  3. QTL mapping of agronomic traits in tef [Eragrostis tef (Zucc) Trotter

    OpenAIRE

    Breseghello Flavio; Graznak Elizabeth; Yu Ju-Kyung; Tefera Hailu; Sorrells Mark E

    2007-01-01

    Abstract Background Tef [Eragrostis tef (Zucc.) Trotter] is the major cereal crop in Ethiopia. Tef is an allotetraploid with a base chromosome number of 10 (2n = 4× = 40) and a genome size of 730 Mbp. The goal of this study was to identify agronomically important quantitative trait loci (QTL) using recombinant inbred lines (RIL) derived from an inter-specific cross between E. tef and E. pilosa (30-5). Results Twenty-two yield-related and morphological traits were assessed across eight differe...

  4. QTL and Candidate Genes for Growth Traits in Pinus Taeda L

    Energy Technology Data Exchange (ETDEWEB)

    Claire G. Williams

    2002-10-01

    The reason for the project is to find the genetic factors which control growth at ages closer to commercial harvest (also known as QTL detection). To date, efforts to find genetic factors which control growth have been limited to seedlings. Because tree breeders want to find molecular markers which are linked to traits of direct economic value, finding linkage to factors controlling older-tree growth is more critical than seedling growth. Our current research interest includes both absolute height at ages 10-13 years but also growth trajectory or the rate of growth from seedling to half-rotation.

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

    Directory of Open Access Journals (Sweden)

    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.

  6. 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...

  7. 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 ...

  8. Caracteres anatómicos de la vegetación costera del Río Salado (Noroeste de la provincia de Buenos Aires, Argentina) Anatomic features of Salado river coastal vegetation (Northwest of Buenos Aires Province, Argentina)

    OpenAIRE

    Nancy Mariel Apóstolo

    2005-01-01

    Veintiún especies (doce Dicotyledoneae y nueve Monocotyledoneae) pertenecientes a la vegetación costera del río Salado (noroeste de la provincia de Buenos Aires, Argentina) fueron estudiadas con el fin de determinar las características anatómicas relacionadas a estrategias adaptativas al medio. Dichas especies pertenecen a los humedales de la cuenca del Salado y, por lo tanto, están afectadas por inundación, sequía temporaria y alta salinidad en agua y suelo. Caracteres anatómicos típicos de ...

  9. Bañón, Antonio M. et alii (2011): Desafíos y estrategias comunicativas de las enfermedades raras: La investigación médica como referente. Estudio cuantitativo-discursivo de la prensa escrita impresa y digital española (2009-2010) [Ressenya

    OpenAIRE

    Pérez Mantero, José Luis

    2011-01-01

    Reseña de Bañón, Antonio M. et alii (2011): Desafíos y estrategias comunicativas de las enfermedades raras: La investigación médica como referente. Estudio cuantitativo-discursivo de la prensa escrita impresa y digital española (2009-2010)

  10. 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

  11. 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

  12. Integration of summary data from GWAS and eQTL studies predicts complex trait gene targets.

    Science.gov (United States)

    Zhu, Zhihong; Zhang, Futao; Hu, Han; Bakshi, Andrew; Robinson, Matthew R; Powell, Joseph E; Montgomery, Grant W; Goddard, Michael E; Wray, Naomi R; Visscher, Peter M; Yang, Jian

    2016-05-01

    Genome-wide association studies (GWAS) have identified thousands of genetic variants associated with human complex traits. However, the genes or functional DNA elements through which these variants exert their effects on the traits are often unknown. We propose a method (called SMR) that integrates summary-level data from GWAS with data from expression quantitative trait locus (eQTL) studies to identify genes whose expression levels are associated with a complex trait because of pleiotropy. We apply the method to five human complex traits using GWAS data on up to 339,224 individuals and eQTL data on 5,311 individuals, and we prioritize 126 genes (for example, TRAF1 and ANKRD55 for rheumatoid arthritis and SNX19 and NMRAL1 for schizophrenia), of which 25 genes are new candidates; 77 genes are not the nearest annotated gene to the top associated GWAS SNP. These genes provide important leads to design future functional studies to understand the mechanism whereby DNA variation leads to complex trait variation. PMID:27019110

  13. Teamwork: improved eQTL mapping using combinations of machine learning methods.

    Directory of Open Access Journals (Sweden)

    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.

  14. QTL mapping for protein content in soybean cultivated in two tropical environments Mapeamento de QTL quanto ao conteúdo de proteína em soja cultivada em dois ambientes tropicais

    Directory of Open Access Journals (Sweden)

    Taís Cristina Bastos Soares

    2008-11-01

    Full Text Available The objectives of this study were to detect quantitative trait loci (QTL for protein content in soybean grown in two distinct tropical environments and to build a genetic map for protein content. One hundred eighteen soybean recombinant inbred lines (RIL, obtained from a cross between cultivars BARC 8 and Garimpo, were used. The RIL were cultivated in two distinct Brazilian tropical environments: Cascavel county, in Paraná, and Viçosa county, in Minas Gerais (24º57'S, 53º27'W and 20º45'S, 42º52'W, respectively. Sixty-six SSR primer pairs and 65 RAPD primers were polymorphic and segregated at a 1:1 proportion. Thirty poorly saturated linkage groups were obtained, with 90 markers and 41 nonlinked markers. For the lines cultivated in Cascavel, three QTL were mapped in C2, E and N linkage groups, which explained 14.37, 10.31 and 7.34% of the phenotypic variation of protein content, respectively. For the lines cultivated in Viçosa, two QTL were mapped in linkage groups G and #1, which explained 9.51 and 7.34% of the phenotypic variation of protein content. Based on the mean of the two environments, two QTL were identified: one in the linkage group E (9.90% and other in the group L (7.11%. In order for future studies to consistently detect QTL effects of different environments, genotypes with greater stability should be used.Os objetivos deste trabalho foram detectar QTL relativos ao conteúdo de proteína, em soja cultivada em dois ambientes tropicais divergentes, e construir um mapa genético para o conteúdo de proteína em genótipos adaptados a condições tropicais. Foram usadas 118 linhagens recombinantes endogâmicas de soja, obtidas do cruzamento entre as cultivares BARC 8 e Garimpo. A população de linhagens recombinantes endogâmicas foi cultivada em dois ambientes contrastantes: Cascavel, PR, e Viçosa, MG (24º57'S, 53º27'W; e 20º45'S, 42º52'W, respectivamente. Sessenta e seis pares de iniciadores SSR e 65 iniciadores RAPD

  15. 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. PMID:22215248

  16. Genetic diversity of table grape based on morphoagronomic traits Diversidade genética de acessos de uvas de mesa baseada em caracteres morfoagronômicos

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    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.

  17. New Breeding Parents Containing Novel QTL for Rice Sheath Blight Resistance Identified by Combining Phenotypic and Molecular Characterizations

    Science.gov (United States)

    Rice Sheath Blight (SB) disease, caused by the necrotrophic Rhizoctonia solani Kühn, is a global and annual cause of rice yield losses. Several QTL with small individual impact must be combined to create rice varieties tolerant of SB infection because no single gene confers complete resistance. Mo...

  18. 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.

  19. Identifying QTL and genetic correlations between fur quality traits in mink (Neovison vison)

    DEFF Research Database (Denmark)

    Thirstrup, Janne Pia; Anistoroaei, Razvan Marian; Guldbrandtsen, Bernt; Christensen, Knud; Fredholm, Merete; Nielsen, Vivi Hunnicke

    2014-01-01

    Mapping of QTL affecting fur quality traits (guard hair length, guard hair thickness, density of wool, surface of the fur and quality) and skin length was performed in a three-generation mink population (F2 design). In the parental generation, Nordic Brown mink were crossed reciprocally with Amer...

  20. 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.

  1. 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...

  2. 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

  3. 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

  4. Divergência genética entre acessos de batata-doce utilizando caracteres fenotípicos de raiz Genetic divergence among sweet potato accessions based on root traits

    Directory of Open Access Journals (Sweden)

    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

  5. Mapping with RAD (restriction-site associated DNA) markers to rapidly identify QTL for stem rust resistance in Lolium perenne.

    Science.gov (United States)

    Pfender, W F; Saha, M C; Johnson, E A; Slabaugh, M B

    2011-05-01

    A mapping population was created to detect quantitative trait loci (QTL) for resistance to stem rust caused by Puccinia graminis subsp. graminicola in Lolium perenne. A susceptible and a resistant plant were crossed to produce a pseudo-testcross population of 193 F(1) individuals. Markers were produced by the restriction-site associated DNA (RAD) process, which uses massively parallel and multiplexed sequencing of reduced-representation libraries. Additional simple sequence repeat (SSR) and sequence-tagged site (STS) markers were combined with the RAD markers to produce maps for the female (738 cM) and male (721 cM) parents. Stem rust phenotypes (number of pustules per plant) were determined in replicated greenhouse trials by inoculation with a field-collected, genetically heterogeneous population of urediniospores. The F(1) progeny displayed continuous distribution of phenotypes and transgressive segregation. We detected three resistance QTL. The most prominent QTL (qLpPg1) is located near 41 cM on linkage group (LG) 7 with a 2-LOD interval of 8 cM, and accounts for 30-38% of the stem rust phenotypic variance. QTL were detected also on LG1 (qLpPg2) and LG6 (qLpPg3), each accounting for approximately 10% of phenotypic variance. Alleles of loci closely linked to these QTL originated from the resistant parent for qLpPg1 and from both parents for qLpPg2 and qLpPg3. Observed quantitative nature of the resistance may be due to partial-resistance effects against all pathogen genotypes, or qualitative effects completely preventing infection by only some genotypes in the genetically mixed inoculum. RAD markers facilitated rapid construction of new genetic maps in this outcrossing species and will enable development of sequence-based markers linked to stem rust resistance in L. perenne. PMID:21344184

  6. 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.

  7. 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.

  8. 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

  9. 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% < R (2) < 27%). The loci were within the intervals Satt632-A2D8 on linkage group (LG) A2 (chromosome 8); Satt583-Satt415 on LG B1 (11); Satt009-Satt530 on LG N (3); and close to two markers OB02_140 (LG E; 20 cM from Satt572) and OZ15_150 LG (19 cM from Satt291 C2). Two QTL were detected for the mean PI field trait (16% < R (2) < 18%) close to Satt385 on LG A1 and Satt440 on LG I. The no choice feeding studies detected three QTL that were significant; two for antixenosis (22% < R (2) < 24%) between Satt632-A2D8 on LG A2 (8) and Sat_039-Satt160 on LG F (13); and a major locus effect (R (2) = 54%) for antibiosis on LG D2 (17) between Satt464-Satt488. Therefore, loci underlying resistance to JB herbivory were a mixture of major and minor gene effects. Some loci were within regions underlying resistance to soybean cyst nematode (LGs A2 and I) and root knot nematode (LG F) but not other major loci underlying

  10. 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...

  11. 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 ...

  12. Registered plant 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 PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods Registered plant... simple search page) Genome analysis methods Presence or absence of Genome analysis methods information in t...his DB (link to the Genome analysis methods information in simple search page) Joomla SEF URLs by Artio Abou...base Site Policy | Contact Us Registered plant list - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive ...

  13. 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 PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods Download First o... (36.3 KB) Simple search and download 6 Genome analysis methods pgdbj_dna_marker_...linkage_map_genome_analysis_methods_en.zip (5.8 KB) Simple search and download Downlaod via FTP Joomla SEF U...Policy | Contact Us Download - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive ...

  14. 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...

  15. A high-resolution linkage map for comparative genome analysis and QTL fine mapping in Asian seabass, Lates calcarifer

    OpenAIRE

    Feng Felicia; Lo Loong; Sun Fei; Xia Jun; Lin Grace; He Xiao; Bai Zhi; Wang Chun; Zhu Ze; Yue Gen

    2011-01-01

    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...

  16. 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 ...

  17. Tratado de Derecho y Políticas de la Unión Europea. Tomo I, Desarrollo histórico y caracteres básicos de la Unión Europea. Naturaleza, valores, principios y competencias [book review

    OpenAIRE

    Huguet, Montserrat

    2009-01-01

    Este artículo reseña: José Mª Beneyto Pérez (dir.). "Tratado de Derecho y Políticas de la Unión Europea. Tomo I, Desarrollo histórico y caracteres básicos de la Unión Europea. Naturaleza, valores, principios y competencias". Navarra: Aranzadi, 2009. ISBN: 9788483559376

  18. QTL mapping of agronomic traits in tef [Eragrostis tef (Zucc Trotter

    Directory of Open Access Journals (Sweden)

    Breseghello Flavio

    2007-06-01

    Full Text Available Abstract Background Tef [Eragrostis tef (Zucc. Trotter] is the major cereal crop in Ethiopia. Tef is an allotetraploid with a base chromosome number of 10 (2n = 4× = 40 and a genome size of 730 Mbp. The goal of this study was to identify agronomically important quantitative trait loci (QTL using recombinant inbred lines (RIL derived from an inter-specific cross between E. tef and E. pilosa (30-5. Results Twenty-two yield-related and morphological traits were assessed across eight different locations in Ethiopia during the growing seasons of 1999 and 2000. Using composite interval mapping and a linkage map incorporating 192 loci, 99 QTLs were identified on 15 of the 21 linkage groups for 19 traits. Twelve QTLs on nine linkage groups were identified for grain yield. Clusters of more than five QTLs for various traits were identified on seven linkage groups. The largest cluster (10 QTLs was identified on linkage group 8; eight of these QTLs were for yield or yield components, suggesting linkage or pleotrophic effects of loci. There were 15 two-way interactions of loci to detect potential epistasis identified and 75% of the interactions were derived from yield and shoot biomass. Thirty-one percent of the QTLs were observed in multiple environments; two yield QTLs were consistent across all agro-ecology zones. For 29.3% of the QTLs, the alleles from E. pilosa (30-5 had a beneficial effect. Conclusion The extensive QTL data generated for tef in this study will provide a basis for initiating molecular breeding to improve agronomic traits in this staple food crop for the people of Ethiopia.

  19. 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

  20. [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

  1. 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.

  2. 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

  3. 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.

  4. 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

  5. Characterization of QTL for unique agronomic traits of new-plant-type rice varieties using introgression lines of IR64

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    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

  6. A maximum likelihood QTL analysis reveals common genome regions controlling resistance to Salmonella colonization and carrier-state

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    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

  7. 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

  8. CAPACIDAD COMBINATORIA PARA RENDIMIENTO DE GRANO Y CARACTERES DE CALIDAD MALTERA EN CEBADA (Hordeum vulgare L. Combining ability for grain yield and malting quality traits in barley (Hordeum vulgare L.

    Directory of Open Access Journals (Sweden)

    Rudy Rivas P.

    2002-07-01

    Full Text Available Se cruzaron seis genotipos de cebada de ciclo de desarrollo primaveral en un arreglo dialelo, con el fin de estudiar sus capacidades combinatorias para rendimiento de grano y doce caracteres de calidad maltera. El comportamiento de los híbridos F1 fue analizado utilizando el Modelo I, método 2 de Griffing. El análisis de capacidad combinatoria general (CCG, de capacidad combinatoria específica (CCE y la relación CCG/CCE, demostraron que ocho de los trece caracteres estudiados mostraron expresión asociada a efectos génicos de tipo aditivo, que fueron: peso de grano, extracto de malta, viscosidad, friabilidad, proteína de la malta, proteína soluble, índice de Kolbach y amino nitrógeno libre (FAN: free amino nitrogen. Por otra parte en la expresión de los caracteres calibre de grano, diferencia del extracto, e índice de Hartong fueron importantes tanto los efectos aditivos como los no aditivos, siendo los primeros de mayor magnitud. Solo el rendimiento de grano y el poder diastásico mostraron predominio de acción génica de tipo no aditivo (dominancia y sobredominancia, aunque los efectos aditivos también estuvieron presentes.Six spring barley (Hordeum vulgare L. genotypes were crossed in a diallel system to study combining ability for grain yield and twelve malting quality traits. The F1 hybrids behavior was analyzed using Griffing’s Model I, method 2. The analysis for general combining ability (CCG, specific combining ability (CCE and the relationship CCG/CCE showed that expression of eight out of the thirteen traits were associated with genes which were additive in their effects: grain weight, malt extract, viscosity, friability, malt protein, soluble protein, Kolbach index and free amino nitrogen (FAN. On the other hand, the expression of grain plumpness, extract difference and the Hartong index showed both additive and non-additive genetic control, the former being of greater magnitude. Only grain yield and diastatic power

  9. 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

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    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

  10. 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.

  11. 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

    Directory of Open Access Journals (Sweden)

    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.

  12. 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...

  13. 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.

  14. 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

  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. 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

  18. 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 ...

  19. 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.

  20. 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...... progeny tested bulls were genotyped with the Illumina BovineSNP50 chip. After quality control, 38473 SNPs were analyzed using a mixed linear model (software package DMU). Associations (5% Bonferroni threshold) were detected in 9 peaks on 5 chromosomes. A set of 238 of the bulls were re-genotyped with the...

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

    OpenAIRE

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

  2. Insight into the Genetic Components of Community Genetics: QTL Mapping of Insect Association in a Fast-Growing Forest Tree

    OpenAIRE

    DeWoody, J.; Viger, M.; Lakatos, F.; Tuba, K.; Taylor, G.; Smulders, M.J.M.

    2013-01-01

    Identifying genetic sequences underlying insect associations on forest trees will improve the understanding of community genetics on a broad scale. We tested for genomic regions associated with insects in hybrid poplar using quantitative trait loci (QTL) analyses conducted on data from a common garden experiment. The F2 offspring of a hybrid poplar (Populus trichocarpa x P. deltoides) cross were assessed for seven categories of insect leaf damage at two time points, June and August. Positive ...

  3. 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......

  4. IMPROVEMENT OF PHOTOSYNTHESIS BY SUB1 QTL IN RICE UNDER SUBMERGENCE: PROBED BY CHLOROPHYLL FLUORESCENCE OJIP TRANSIENTS

    OpenAIRE

    Panda Debabrata; Sarkar Ramani Kumar

    2011-01-01

    The influence of submergence on the photosynthetic activity in rice plants either possessing or not possessing Sub1 QTL i.e. Swarna and Swarna Sub1 cultivars (cv.) were evaluated under simulated complete submergence. The leaf photosynthetic rate and stomatal conductance decreased in both the cv. during the progression of submergence as compared to control plant but significant varietal differences was observed after 1 day (d) of submergence. Submergence also alters the photo-system (PS) II ac...

  5. Pedigree genotyping: a new pedigree-based approach of QTL identification and allele mining by exploiting breeding material

    OpenAIRE

    Weg, van de, H; Voorrips, R. E.; Finkers, H. J.; Kodde, L.P.; Meulenbroek, E.J.; Jansen, J; Bink, M.C.A.M.

    2005-01-01

    To date, molecular markers have been made available for many economically important traits. Unfortunately, lack of knowledge of their allelic variation hampers their full exploitation in commercial breeding programs. These markers have usually been identified in one single cross. Consequently, only one or two favourable alleles of the related QTL are identified and may be exploited for marker-assisted breeding (MAB), while a breeding program may include several alleles. Selection for only the...

  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. 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

  8. 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...

  9. Heading Date QTL in Winter Wheat (Triticum aestivum L.) Coincide with Major Developmental Genes VERNALIZATION1 and PHOTOPERIOD1

    OpenAIRE

    Guedira, Mohammed; Xiong, Mai; Hao, Yuan Feng; Johnson, Jerry; Harrison, Steve; Marshall, David; Brown-Guedira, Gina

    2016-01-01

    In wheat (Triticum aestivum L.), time from planting to spike emergence is influenced by genes controlling vernalization requirement and photoperiod response. Characterizing the available genetic diversity of known and novel alleles of VERNALIZATION1 (VRN1) and PHOTOPERIOD1 (PPD1) in winter wheat can inform approaches for breeding climate resilient cultivars. This study identified QTL for heading date (HD) associated with multiple VRN1 and PPD1 loci in a population developed from a cross betwe...

  10. 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.

  11. Identification of QTL for adult-plant resistance to powdery mildew in Chinese wheat landrace Pingyuan 50

    Directory of Open Access Journals (Sweden)

    Muhammad Azeem Asad

    2014-10-01

    Full Text Available 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.

  12. Multiple regression approach to mapping of quantitative trait loci (QTL) based on sib-pair data: a theoretical analysis

    OpenAIRE

    Xiong, Momiao; Guo, Sunwei

    2000-01-01

    The interval mapping method has been shown to be a powerful tool for mapping QTL. However, it is still a challenge to perform a simultaneous analysis of several linked QTLs, and to isolate multiple linked QTLs. To circumvent these problems, multiple regression analysis has been suggested for experimental species. In this paper, the multiple regression approach is extended to human sib-pair data through multiple regression of the squared difference in trait values between two...

  13. 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.

  14. 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

  15. 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

  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. Correlation analysis and QTL mapping for plant height and fibre quality of dwarf mutant in upland cotton (Gossypium hirsutum L.)

    International Nuclear Information System (INIS)

    Ari1327 was a dwarf mutant derived from Ari971 introduced from America and treated by 60Co γ-rays irradiation. Cross combination was created by Ari1327 and TM-1 which was a standard genetic line for Gossypium hirsutum. QTL analysis for plant height and fiber quality traits was conducted in the F2 population of the cross. 4 QTLs were identified for plant height, distributed on chromosome 3, 11, 14 and LG6, jointly explaining 74.53% of the plant height variance. 2 QTLs were identified for fiber strength, distributing on Chr. 23 and LG 5, explaining 4.85% and 9.85% of the fiber strength variance, respectively. One QTL was identified for micronaire, distributing on LG3 and explaining 7.28% of the fiber micronaire variance. One QTL was identified for fiber length, fiber uniformity and fiber elongation accordingly, distributing on LG3 altogether and explaining 9.86%, 28.35% and 28.26% of the variance, respectively. The correlation coefficients between plant height and fiber quality traits were all small and not significant, indicating that fiber quality traits maybe have little relative with plant height genetically, provides the theoretical foundation for simultaneous improvement of plant height and fiber quality in cotton breeding. (authors)

  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. Characterisation of QTL-linked and genome-wide restriction site-associated DNA (RAD markers in farmed Atlantic salmon

    Directory of Open Access Journals (Sweden)

    Houston Ross D

    2012-06-01

    Full Text Available Abstract Background Restriction site-associated DNA sequencing (RAD-Seq is a genome complexity reduction technique that facilitates large-scale marker discovery and genotyping by sequencing. Recent applications of RAD-Seq have included linkage and QTL mapping with a particular focus on non-model species. In the current study, we have applied RAD-Seq to two Atlantic salmon families from a commercial breeding program. The offspring from these families were classified into resistant or susceptible based on survival/mortality in an Infectious Pancreatic Necrosis (IPN challenge experiment, and putative homozygous resistant or susceptible genotype at a major IPN-resistance QTL. From each family, the genomic DNA of the two heterozygous parents and seven offspring of each IPN phenotype and genotype was digested with the SbfI enzyme and sequenced in multiplexed pools. Results Sequence was obtained from approximately 70,000 RAD loci in both families and a filtered set of 6,712 segregating SNPs were identified. Analyses of genome-wide RAD marker segregation patterns in the two families suggested SNP discovery on all 29 Atlantic salmon chromosome pairs, and highlighted the dearth of male recombination. The use of pedigreed samples allowed us to distinguish segregating SNPs from putative paralogous sequence variants resulting from the relatively recent genome duplication of salmonid species. Of the segregating SNPs, 50 were linked to the QTL. A subset of these QTL-linked SNPs were converted to a high-throughput assay and genotyped across large commercial populations of IPNV-challenged salmon fry. Several SNPs showed highly significant linkage and association with resistance to IPN, and population linkage-disequilibrium-based SNP tests for resistance were identified. Conclusions We used RAD-Seq to successfully identify and characterise high-density genetic markers in pedigreed aquaculture Atlantic salmon. These results underline the effectiveness of RAD

  1. QTL mapping in white spruce: gene maps and genomic regions underlying adaptive traits across pedigrees, years and environments

    Directory of Open Access Journals (Sweden)

    Meirmans Patrick G

    2011-03-01

    Full Text Available Abstract Background The genomic architecture of bud phenology and height growth remains poorly known in most forest trees. In non model species, QTL studies have shown limited application because most often QTL data could not be validated from one experiment to another. The aim of our study was to overcome this limitation by basing QTL detection on the construction of genetic maps highly-enriched in gene markers, and by assessing QTLs across pedigrees, years, and environments. Results Four saturated individual linkage maps representing two unrelated mapping populations of 260 and 500 clonally replicated progeny were assembled from 471 to 570 markers, including from 283 to 451 gene SNPs obtained using a multiplexed genotyping assay. Thence, a composite linkage map was assembled with 836 gene markers. For individual linkage maps, a total of 33 distinct quantitative trait loci (QTLs were observed for bud flush, 52 for bud set, and 52 for height growth. For the composite map, the corresponding numbers of QTL clusters were 11, 13, and 10. About 20% of QTLs were replicated between the two mapping populations and nearly 50% revealed spatial and/or temporal stability. Three to four occurrences of overlapping QTLs between characters were noted, indicating regions with potential pleiotropic effects. Moreover, some of the genes involved in the QTLs were also underlined by recent genome scans or expression profile studies. Overall, the proportion of phenotypic variance explained by each QTL ranged from 3.0 to 16.4% for bud flush, from 2.7 to 22.2% for bud set, and from 2.5 to 10.5% for height growth. Up to 70% of the total character variance could be accounted for by QTLs for bud flush or bud set, and up to 59% for height growth. Conclusions This study provides a basic understanding of the genomic architecture related to bud flush, bud set, and height growth in a conifer species, and a useful indicator to compare with Angiosperms. It will serve as a basic

  2. 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

  3. 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.

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

    Directory of Open Access Journals (Sweden)

    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.

  5. 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.

  6. 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.

  7. QTL mapping of leafy heads by genome resequencing in the RIL population of Brassica rapa.

    Science.gov (United States)

    Yu, Xiang; Wang, Han; Zhong, Weili; Bai, Jinjuan; Liu, Pinglin; He, Yuke

    2013-01-01

    Leaf heads of cabbage (Brassica oleracea), Chinese cabbage (B. rapa), and lettuce (Lactuca sativa) are important vegetables that supply mineral nutrients, crude fiber and vitamins in the human diet. Head size, head shape, head weight, and heading time contribute to yield and quality. In an attempt to investigate genetic basis of leafy head in Chinese cabbage (B. rapa), we took advantage of recent technical advances of genome resequencing to perform quantitative trait locus (QTL) mapping using 150 recombinant inbred lines (RILs) derived from the cross between heading and non-heading Chinese cabbage. The resequenced genomes of the parents uncovered more than 1 million SNPs. Genotyping of RILs using the high-quality SNPs assisted by Hidden Markov Model (HMM) generated a recombination map. The raw genetic map revealed some physical assembly error and missing fragments in the reference genome that reduced the quality of SNP genotyping. By deletion of the genetic markers in which recombination rates higher than 20%, we have obtained a high-quality genetic map with 2209 markers and detected 18 QTLs for 6 head traits, from which 3 candidate genes were selected. These QTLs provide the foundation for study of genetic basis of leafy heads and the other complex traits. PMID:24204591

  8. 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.

  9. 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.

  10. Modular network construction using eQTL data: an analysis of computational costs and benefits

    Directory of Open Access Journals (Sweden)

    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.

  11. Divergência genética entre acessos de cenoura pertencentes a grupos varietais distintos utilizando caracteres morfológicos Genetic divergence among carrot accessions belonging to different varietal groups using morphologic characters

    Directory of Open Access Journals (Sweden)

    Jairo Vidal Vieira

    2009-12-01

    Full Text Available A utilização de híbridos de cenoura tem aumentado consideravelmente na última década no Brasil. Estudos de determinação de divergência genética entre genótipos têm sido ferramentas de grande importância em programas de melhoramento, auxiliando na identificação de genitores com potencial heterótico. No entanto, pouco ainda se sabe sobre a capacidade combinatória de acessos de cenoura adaptados às regiões tropicais. Os objetivos do presente trabalho foram: (1 estimar parâmetros genéticos, (2 estimar a importância relativa de quatro caracteres morfológicos na discriminação de grupos varietais de cenoura e (3 obter indicação, a partir deste conjunto de dados morfológicos, de combinações promissoras para cruzamentos, visando utilização prática da heterose. Dois experimentos foram conduzidos em campo, nas primaveras de 2000 e 2001, no delineamento em blocos ao acaso com duas repetições. Foram avaliadas quinze plantas competitivas em cada parcela para os caracteres comprimento de folha, tamanho da raiz, diâmetro de raiz e massa fresca de raiz. Os dados foram submetidos às análises de variância, de dissimilaridade e da importância relativa dos caracteres. Todos os caracteres apresentaram valores de herdabilidade e da relação entre os coeficientes de variação genética e ambiental de medianos a altos. Os caracteres comprimento e diâmetro de raiz foram os que mais contribuíram para a diferenciação dos genótipos. O grupo mais divergente foi 'Imperator'. Desta forma, cruzamentos deste grupo com os demais acessos tendem a proporcionar maior efeito da heterose. Os acessos pertencentes ao grupo 'Brasília', podem ser cruzados com a maioria dos acessos (exceto para aqueles derivados dos grupos varietais 'Chantenay' e 'Danvers', com probabilidade de geração de populações superiores em relação à heterose.The utilization of carrot hybrids has increased in the last decade in Brazil. The estimative of genetic

  12. Relações entre caracteres de raiz e ganhos genéticos diretos e indiretos em populações de cenoura Relationships among root traits and direct and indirect genetic gains in carrot populations

    Directory of Open Access Journals (Sweden)

    Giovani O da Silva

    2013-03-01

    Full Text Available Informações sobre efeitos múltiplos da seleção para características específicas de raiz ainda são limitadas em cenoura. Neste contexto, os objetivos do trabalho foram: (1 verificar a possibilidade da utilização do efeito direto da análise de trilha em substituição à correlação genética nas estimativas de ganhos correlacionados; (2 identificar estratégias de seleção para a obtenção de ganhos correlacionados em massa de raiz, a seleção de raízes mais grossas ou mais compridas; (3 determinar quais tecidos da raiz possibilitam maiores ganhos para o aumento do diâmetro da raiz; e (4 verificar a possibilidade de obter ganhos positivos concomitantemente, para coloração da raiz e para os demais caracteres avaliados. Três populações de cenoura (derivadas da cv. Brasília foram cultivadas durante o período do verão no Distrito Federal. Aos 90 dias após a semeadura foram colhidas 25 raízes por parcela e avaliados individualmente os caracteres massa da raiz; comprimento de raiz; diâmetro da raiz e do xilema da raiz; espessura do floema e o valor do componente de cromaticidade a* do xilema e floema. Foi realizada análise de variância e calculadas as correlações genéticas entre os caracteres. Posteriormente foi realizada a análise de trilha, calculadas as respostas correlacionadas (baseadas na correlação genética e no efeito direto da análise de trilha, e estimação dos ganhos diretos com a seleção. Observou-se que a substituição das correlações genéticas pelos efeitos diretos da análise de trilha para o cálculo dos ganhos correlacionados proporcionou melhor estimação do efeito que a seleção para determinado caráter traria nos demais, após a retirada dos efeitos indiretos. Para massa de raiz não são esperados ganhos correlacionados pela seleção nos demais caracteres avaliados. Para diâmetro da raiz os maiores ganhos correlacionados foram observados pela seleção no caráter espessura do

  13. 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 ...

  14. 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

  15. 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

  16. Caracteres para identificação de genótipos de trigo sensíveis ao ácido giberélico Traits to identify the giberellic acid sensitivity of wheat genotypes

    Directory of Open Access Journals (Sweden)

    Paulo Cesar Canci

    1997-06-01

    Full Text Available Distintos caracteres foram utilizados para avaliar a sensibilidade de genótipos de trigo de diferentes estaturas ao ácido giberélico em laboratório e em casa de vegetação, visando a identificação de genótipos portadores de genes redutores da estatura de planta. Foram avaliadas a altura de planta, altura da inserção da lâmina da primeira e segunda folha, comprimento da lâmina da primeira e segunda folha e a diferença entre a altura de inserção da lâmina da segunda e primeira folha. As determinações foram realizadas aos 20 e 28 dias após a germinação em laboratório e em casa de vegetação, nos genótipos submetidos às doses de 0 e 100ppm de ácido giberélico. A diferença entre os tratamentos com e sem ácido giberélico, para todos os caracteres, foi utilizada para a análise a fim de garantir a inexistência da interação genótipo x ambiente. Foram obtidas correlações expressivas para altura da inserção da lâmina da segunda folha e diferença da altura de inserção da lâmina da segunda e primeira folha em casa de vegetação e entre estatura de planta e comprimento da segunda folha em laboratório. Os valores obtidos em casa de vegetação foram superiores aos de laboratório para a maioria dos caracteres avaliados, tendo o caráter estatura de planta proporcionado a separação mais efetiva dos genótipos de acordo com a estatura e sensibilidade ao ácido giberélico nos dois ambientes.Six traits were measured to analyze the gibberellic acid sensitivity of wheat genotypes in two environments: greenhouse and laboratory. Plant height first and second leaf height insertion, first and second leaf length and difference between second and first leaf height insertion. These traits were evaluated at 20 and 28 days after germination in genotypes treated with 0 and 100 PPM of gibberellic acid. Differences between treatments with and without gibberellic acid indicated no genotype x environment interaction. High

  17. The use of genome-wide eQTL associations in lymphoblastoid cell lines to identify novel genetic pathways involved in complex traits.

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    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.

  18. 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

    Directory of Open Access Journals (Sweden)

    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.

  19. 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.

  20. 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.

  1. 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

  2. Combining mouse mammary gland gene expression and comparative mapping for the identification of candidate genes for QTL of milk production traits in cattle

    Directory of Open Access Journals (Sweden)

    Shani Moshe

    2007-06-01

    Full Text Available Abstract Background Many studies have found segregating quantitative trait loci (QTL for milk production traits in different dairy cattle populations. However, even for relatively large effects with a saturated marker map the confidence interval for QTL location by linkage analysis spans tens of map units, or hundreds of genes. Combining mapping and arraying has been suggested as an approach to identify candidate genes. Thus, gene expression analysis in the mammary gland of genes positioned in the confidence interval of the QTL can bridge the gap between fine mapping and quantitative trait nucleotide (QTN determination. Results We hybridized Affymetrix microarray (MG-U74v2, containing 12,488 murine probes, with RNA derived from mammary gland of virgin, pregnant, lactating and involuting C57BL/6J mice in a total of nine biological replicates. We combined microarray data from two additional studies that used the same design in mice with a total of 75 biological replicates. The same filtering and normalization was applied to each microarray data using GeneSpring software. Analysis of variance identified 249 differentially expressed probe sets common to the three experiments along the four developmental stages of puberty, pregnancy, lactation and involution. 212 genes were assigned to their bovine map positions through comparative mapping, and thus form a list of candidate genes for previously identified QTLs for milk production traits. A total of 82 of the genes showed mammary gland-specific expression with at least 3-fold expression over the median representing all tissues tested in GeneAtlas. Conclusion This work presents a web tool for candidate genes for QTL (cgQTL that allows navigation between the map of bovine milk production QTL, potential candidate genes and their level of expression in mammary gland arrays and in GeneAtlas. Three out of four confirmed genes that affect QTL in livestock (ABCG2, DGAT1, GDF8, IGF2 were over expressed in the

  3. AB-QTL analysis reveals new alleles associated to proline accumulation and leaf wilting under drought stress conditions in barley (Hordeum vulgare L.

    Directory of Open Access Journals (Sweden)

    Sayed Mohammed A

    2012-07-01

    Full Text Available Abstract Background Land plants have evolved several measures to maintain their life against abiotic stresses. The accumulation of proline is the most generalized response of plants under drought, heat or salt stress conditions. It is known as an osmoprotectant which also acts as an instant source of energy during drought recovery process. But, both its role and genetic inheritance are poorly understood in agriculture crops. In the present work, advanced backcross quantitative trait locus (AB-QTL analysis was performed to elucidate genetic mechanisms controlling proline accumulation and leaf wilting in barley under drought stress conditions. Results The analysis revealed eight QTL associated to proline content (PC and leaf wilting (WS. QTL for PC were localized on chromosome 3H, 4H, 5H and 6H. The strongest QTL effect QPC.S42.5H was detected on chromosome 5H where drought inducible exotic allele was associated to increase PC by 54%. QTL effects QPC.S42.3H, QPC.S42.4H and QPC.S42.6H were responsible to heighten PC due to the preeminence of elite alleles over the exotic alleles which ranged from 26% to 43%. For WS, QTL have been localized on chromosome 1H, 2H, 3H and 4H. Among these, QWS.S42.1H and QWS.S42.4H were associated to decrease in WS due to the introgression of exotic alleles. In addition, two digenic epistatic interaction effects were detected for WS where the additive effect of exotic alleles imparted a favorable increase in the trait value. Conclusions The present data represents a first report on whole-genome mapping of proline accumulation and leaf wilting in barley. The detected QTL are linked to new alleles from both cultivated and wild accessions which bring out an initial insight on the genetic inheritance of PC and WS. These QTL alleles are fixed in the isogenic background of Scarlett, which will allow for positional cloning of underlying genes and to develop drought resilient barley cultivars.

  4. Variation and inheritance of iron reductase activity in the roots of common bean (Phaseolus vulgaris L. and association with seed iron accumulation QTL

    Directory of Open Access Journals (Sweden)

    Fernandez Andrea C

    2010-10-01

    Full Text Available Abstract Background Iron deficiency anemia is a global problem which often affects women and children of developing countries. Strategy I plants, such as common bean (Phaseolus vulgaris L. take up iron through a process that involves an iron reduction mechanism in their roots; this reduction is required to convert ferric iron to ferrous iron. Root absorbed iron is critical for the iron nutrition of the plant, and for the delivery of iron to the shoot and ultimately the seeds. The objectives of this study were to determine the variability and inheritance for iron reductase activity in a range of genotypes and in a low × high seed iron cross (DOR364 × G19833, to identify quantitative trait loci (QTL for this trait, and to assess possible associations with seed iron levels. Results The experiments were carried out with hydroponically grown plants provided different amounts of iron varying between 0 and 20 μM Fe(III-EDDHA. The parents, DOR364 and G19833, plus 13 other cultivated or wild beans, were found to differ in iron reductase activity. Based on these initial experiments, two growth conditions (iron limited and iron sufficient were selected as treatments for evaluating the DOR364 × G19833 recombinant inbred lines. A single major QTL was found for iron reductase activity under iron-limited conditions (1 μM Fe on linkage group b02 and another major QTL was found under iron sufficient conditions (15 μM Fe on linkage group b11. Associations between the b11 QTL were found with several QTL for seed iron. Conclusions Genes conditioning iron reductase activity in iron sufficient bean plants appear to be associated with genes contributing to seed iron accumulation. Markers for bean iron reductase (FRO homologues were found with in silico mapping based on common bean synteny with soybean and Medicago truncatula on b06 and b07; however, neither locus aligned with the QTL for iron reductase activity. In summary, the QTL for iron reductase activity

  5. 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...

  6. 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...

  7. QTL Analysis of Forage Quantity and Quality-Related Traits of Barley

    Directory of Open Access Journals (Sweden)

    M Naghavi

    2009-04-01

    Full Text Available In order to map the genomic regions affecting barley forage quantity and quality, two experiments were conducted with 72 doubled haploid lines and their two parents (‘Steptoe’ and ‘Morex’, at the Research Farms of the Faculty of Crop and Animal Sciences, University College of Agriculture and Natural Resources, University of Tehran and Agriculture and Natural Resources Research Station of Sistan, in 2007. The experiments were arranged in a randomized complete block design with two replications. Each plot consisted of six rows that were 3m in length and spaced 25cm apart. QTL analysis was conducted by Composite interval mapping (CIM method separately for each trait in each location. The main effect of genotype was high significant for all the studied traits. Transgressive segregation in both directions (positive and negative was observed for all the studied traits. There was a negative relationship between forage qualityrelated with quantity-related traits. Thirty-three QTLs controlling different studied traits were identified. Phenotypic variance explained by these QTLs varies from 7.07 to 39.04%. Highest LOD scores were obtained for the leaf to stem ratio on chromosome 2H. QTLs of forage quality (total digestible nutrient, dry organic matter digestibility, leaf to stem ratio, seed to forage ratio and number of tiller per plant and quantity (plant height, forage wet and dry matter indexes were found on chromosomes 1H, 2H, 3H, 4H, 5H, 6H and 7H. Most of mapped QTLs appear to be fairly stable between locations and can become candidates for marker-assisted selection.

  8. 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.

  9. Correlações fenotípicas entre tamanho de grãos e outros caracteres em topocruzamentos de soja tipo alimento com tipo grão

    Directory of Open Access Journals (Sweden)

    YOKOMIZO GILBERTO KEN-ITI

    2000-01-01

    Full Text Available Este trabalho foi conduzido para avaliar a correlação fenotípica entre vários caracteres em topocruzamentos entre soja tipo alimento e soja tipo grão (Doko e FT-2. Valores de interesse para facilitar a seleção foram obtidos nas correlações entre peso de cem sementes (tamanho de sementes e dias para atingir a maturidade, e entre tamanho de sementes e largura visual da vagem. Na correlação entre produtividade de grãos e tamanho de sementes somente os topocruzamentos com Doko foram significativos. As estimativas de correlações em plantas individuais tenderam a confirmar aquelas obtidas em médias de parcelas. Os valores de correlação foram diferentes entre os tipos (grão, broto/"natto" e hortaliça de soja envolvidos, o que sugere a adoção de estratégias de seleção distintas. O estudo de correlações para cada topocruzamento é importante, pois podem ocorrer diferenças no desempenho das plantas como foi observado nos resultados obtidos.

  10. Expressão de caracteres de tubérculos em função do tamanho de recipiente usado no cultivo de batata na geração de plântulas Expression of tuber traits as a function of pot size used to grow potato seedlings

    Directory of Open Access Journals (Sweden)

    Mario Alvaro Aloisio Verissimo

    2012-12-01

    Full Text Available No melhoramento genético de batata, para alguns caracteres, é possível eliminar genótipos inferiores já nas gerações iniciais, o que permite reduzir o número de genótipos avaliados a campo, proporcionando redução de custos. O objetivo deste trabalho foi verificar a influência do tamanho de vaso na expressão de caracteres de tubérculo, em famílias de batata, na geração de plântula. Em casa de vegetação, dez famílias de batata foram avaliadas em dois tamanhos de recipientes, vaso grande (1 L e vaso pequeno (250 ml. Os caracteres de tubérculos avaliados foram: cor, aspereza, profundidade de olho, sobrancelha, formato, uniformidade de formato, apontamento, curvatura, achatamento, aparência geral, massa por planta, massa média e número de tubérculos. O vaso grande proporciona maior expressão da variação genética para os caracteres profundidade de olho, sobrancelha, curvatura, achatamento, aparência geral e todos os componentes de rendimento. As maiores médias de produção de tubérculos em número, tamanho e massa foram obtidas no vaso grande, enquanto o maior coeficiente de variação genético para os caracteres formato, uniformidade de formato e apontamento de tubérculo foi obtido no vaso pequeno.In potato breeding, the exclusion of inferior genotypes by selection in early generations provides more versatility and cost reduction. The objective of this study was to evaluate the influence of pot size on the expression of tuber traits in potato families grown as seedling generation. Ten potato families were planted in two pot sizes, large (1 L and small (250 ml, in the greenhouse. The following tuber traits were evaluated: color, roughness, depth of eye, eyebrow, shape, uniformity of shape, pointing, curvature, flattening, tuber general appearance, total mass per plant, average tuber weight and number of tubers. The larger pot provided greater expression of genetic variation for the depth of eye, eyebrow, curvature

  11. 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...

  12. QTL dissection of Lag phase in wine fermentation reveals a new translocation responsible for Saccharomyces cerevisiae adaptation to sulfite.

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    Adrien Zimmer

    Full Text Available Quantitative genetics and QTL mapping are efficient strategies for deciphering the genetic polymorphisms that explain the phenotypic differences of individuals within the same species. Since a decade, this approach has been applied to eukaryotic microbes such as Saccharomyces cerevisiae in order to find natural genetic variations conferring adaptation of individuals to their environment. In this work, a QTL responsible for lag phase duration in the alcoholic fermentation of grape juice was dissected by reciprocal hemizygosity analysis. After invalidating the effect of some candidate genes, a chromosomal translocation affecting the lag phase was brought to light using de novo assembly of parental genomes. This newly described translocation (XV-t-XVI involves the promoter region of ADH1 and the gene SSU1 and confers an increased expression of the sulfite pump during the first hours of alcoholic fermentation. This translocation constitutes another adaptation route of wine yeast to sulfites in addition to the translocation VIII-t-XVI previously described. A population survey of both translocation forms in a panel of domesticated yeast strains suggests that the translocation XV-t-XVI has been empirically selected by human activity.

  13. Ancestral QTL alleles from wild emmer wheat improve grain yield, biomass and photosynthesis across enviroinments in modern wheat.

    Science.gov (United States)

    Merchuk-Ovnat, Lianne; Fahima, Tzion; Krugman, Tamar; Saranga, Yehoshua

    2016-10-01

    Wild emmer wheat (Triticum turgidum ssp. dicoccoides) is considered a promising source for improving drought resistance in domesticated wheat. Nevertheless, wild germplasm has not been widely used in wheat breeding for abiotic stress resilience. In the current study, a near isogenic line NIL-7A-B-2, introgressed with a drought-related QTL from wild emmer wheat on chromosome 7A, and its recurrent parent, bread wheat cv. BarNir, were investigated under four environments across 2 years-water-limited and well-watered conditions in a rain-protected screen-house (Year 1) and two commercial open field plots under ample precipitation (Year 2). NIL-7A-B-2 exhibited an advantage over BarNir in grain yield and biomass production under most environments. Further physiological analyses suggested that enhanced photosynthetic capacity and photochemistry combined with higher flag leaf area are among the factors underlying the improved productivity of NIL-7A-B-2. These were coupled with improved sink capacity in NIL-7A-B-2, manifested by greater yield components than its parental line. This study provides further support for our previous findings that introgression of wild emmer QTL alleles, using marker assisted selection, can enhance grain yield and biomass production across environments in domesticated wheat, thereby enriching the modern gene pool with essential diversity for the improvement of yield and drought resistance. PMID:27593460

  14. Identification and validation of quantitative trait loci (QTL for canine hip dysplasia (CHD in German Shepherd Dogs.

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    Lena Fels

    Full Text Available Canine hip dysplasia (CHD is the most common hereditary skeletal disorder in dogs. To identify common alleles associated with CHD, we genotyped 96 German Shepherd Dogs affected by mild, moderate and severe CHD and 96 breed, sex, age and birth year matched controls using the Affymetrix canine high density SNP chip. A mixed linear model analysis identified five SNPs associated with CHD scores on dog chromosomes (CFA 19, 24, 26 and 34. These five SNPs were validated in a by sex, age, birth year and coancestry stratified sample of 843 German Shepherd Dogs including 277 unaffected dogs and 566 CHD-affected dogs. Mean coancestry coefficients among and within cases and controls were <0.1%. Genotype effects of these SNPs explained 20-32% of the phenotypic variance of CHD in German Shepherd Dogs employed for validation. Genome-wide significance in the validation data set could be shown for each one CHD-associated SNP on CFA24, 26 and 34. These SNPs are located within or in close proximity of genes involved in bone formation and related through a joint network. The present study validated positional candidate genes within two previously known quantitative trait loci (QTL and a novel QTL for CHD in German Shepherd Dogs.

  15. Prospect of the QTL-qSB-9Tq utilized in molecular breeding program of japonica rice against sheath blight

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    The major QTL-qSB-9Tq conferring partial resistance to rice (Oryza sativa L.) sheath blight (Rhizoctonia solani Kühn) has been verified on chromosome 9 of the indica rice cultivar, Teqing. In this study, the prospect of this QTL utilized in molecular breeding program of japonica rice for sheath blight resistance was investigated. Most of the japonica rice cultivars showed lower level of sheath blight resistance than the indica rice cultivars. At the corresponding site of qSB-9Tq, nine typical japonica rice culfivars from different ecological regions or countries proved to possess the susceptible allele(s). Introgression of qSB-9Tq into these cultivars enhanced their resistance level by decreasing sheath blight score of 1.0 (0.5-1.3), which indicated that qSB-9Tq had a large potential in strengthening the resistance of japonica rice to sheath blight. The use of the three molecular markers, which were polymorphic between Teqing and many japonica rice cultivars, promotes the application of qSB-9Tq in a concrete molecular breeding program.

  16. High-resolution physical mapping and construction of a porcine contig spanning the intramuscular fat content QTL.

    Science.gov (United States)

    Sato, S; Hasebe, H; Sato, S; Asahi, Y; Hayashi, T; Kobayashi, E; Sugimoto, Y

    2006-04-01

    We previously mapped a locus for porcine intramuscular fat content (IMF) by linkage analysis to a 17.1-cM chromosome interval on Sus scrofa chromosome 7 (SSC7) flanked by microsatellite markers SW1083 and SW581. In this study, we identified 34 microsatellite markers and 14 STSs from the 17.1-cM IMF quantitative trait loci (QTL) region corresponding to HSA14q and aligned those loci using the INRA-University of Minnesota porcine radiation hybrid (IMpRH) panel. We then constructed a 5.2-Mb porcine bacterial artificial chromosome (BAC) contig of this region that was aligned using the RH panel. Finally, the IMF QTL was fine-mapped to 12.6 cM between SJ169 and MM70 at the 0.1% chromosome-wise significance level by genotyping the previously studied F2 resource family with 17 additional microsatellites. We also demonstrated that the SJ169-MM70 interval spans approximately 3.0 Mb and contains at least 12 genes: GALC, GPR65, KCNK10, SPATA7, PTPN21, FLJ11806, EML5, TTC8, CHES1, CAP2P1, CHORDC2P and C14orf143. PMID:16573525

  17. Identification and validation of quantitative trait loci (QTL) for canine hip dysplasia (CHD) in German Shepherd Dogs.

    Science.gov (United States)

    Fels, Lena; Distl, Ottmar

    2014-01-01

    Canine hip dysplasia (CHD) is the most common hereditary skeletal disorder in dogs. To identify common alleles associated with CHD, we genotyped 96 German Shepherd Dogs affected by mild, moderate and severe CHD and 96 breed, sex, age and birth year matched controls using the Affymetrix canine high density SNP chip. A mixed linear model analysis identified five SNPs associated with CHD scores on dog chromosomes (CFA) 19, 24, 26 and 34. These five SNPs were validated in a by sex, age, birth year and coancestry stratified sample of 843 German Shepherd Dogs including 277 unaffected dogs and 566 CHD-affected dogs. Mean coancestry coefficients among and within cases and controls were Dogs employed for validation. Genome-wide significance in the validation data set could be shown for each one CHD-associated SNP on CFA24, 26 and 34. These SNPs are located within or in close proximity of genes involved in bone formation and related through a joint network. The present study validated positional candidate genes within two previously known quantitative trait loci (QTL) and a novel QTL for CHD in German Shepherd Dogs. PMID:24802516

  18. Advanced Backcross QTL Analysis for the Whole Plant Growth Duration Salt Tolerance in Rice (Oryza sativa L.)

    Institute of Scientific and Technical Information of China (English)

    CHAI Lu; LI Zhi-kang; ZHANG Jian; PAN Xiao-biao; ZHANG Fan; ZHENG Tian-qing; ZHAO Xiu-qing; WANG Wen-sheng; Ali Jauhar; XU Jian-long

    2014-01-01

    Salinity is a major factor limiting rice yield in coastal areas of Asia. To facilitate breeding salt tolerant rice varieties, the whole-plant growth duration salt tolerance (ST) was genetically dissected by phenotyping two sets of BC2F5 introgression lines (ILs) for four yield traits under severe natural salt stress and non-stress ifled conditions using SSR markers and the methods of advanced backcross QTL (AB-QTL) analysis and selective introgression. Many QTLs affecting four yield traits under salt stress and non-stress conditions were identiifed, most (>90%) of which were clustered in 13 genomic regions of the rice genome and involved in complex epistasis. Most QTLs affecting yield traits were differentially expressed under salt stress and non-stress conditions. Our results suggested that genetics complementarily provides an adequate explanation for the hidden genetic diversity for ST observed in both IL populations. Some promising Huanghuazhan (HHZ) ILs with favorable donor alleles at multiple QTLs and signiifcantly improved yield traits under salt stress and non-stress conditions were identiifed, providing excellent materials and relevant genetic information for improving rice ST by marker-assisted selection (MAS) or genome selection.

  19. QTL mapping of fruit rot resistance to the plant pathogen Phytophthora capsici in a recombinant inbred line Capsicum annuum population.

    Science.gov (United States)

    Naegele, R P; Ashrafi, H; Hill, T A; Chin-Wo, S Reyes; Van Deynze, A E; Hausbeck, M K

    2014-05-01

    Phytophthora capsici is an important pepper (Capsicum annuum) pathogen causing fruit and root rot, and foliar blight in field and greenhouse production. Previously, an F6 recombinant inbred line population was evaluated for fruit rot susceptibility. Continuous variation among lines and partial and isolate-specific resistance were found. In this study, Phytophthora fruit rot resistance was mapped in the same F6 population between Criollo del Morelos 334 (CM334), a landrace from Mexico, and 'Early Jalapeno' using a high-density genetic map. Isolate-specific resistance was mapped independently in 63 of the lines evaluated and the two parents. Heritability of the resistance for each isolate at 3 and 5 days postinoculation (dpi) was high (h(2) = 0.63 to 0.68 and 0.74 to 0.83, respectively). Significant additive and epistatic quantitative trait loci (QTL) were identified for resistance to isolates OP97 and 13709 (3 and 5 dpi) and 12889 (3 dpi only). Mapping of fruit traits showed potential linkage with few disease resistance QTL. The partial fruit rot resistance from CM334 suggests that this may not be an ideal source for fruit rot resistance in pepper. PMID:24168044

  20. Three-locus and four-locus QTL interactions influence mouse insulin-like growth factor-I.

    Science.gov (United States)

    Hanlon, Philip; Lorenz, William Andrew; Shao, Zhihong; Harper, James M; Galecki, Andrzej T; Miller, Richard A; Burke, David T

    2006-06-16

    A previous analysis of serum insulin-like growth factor I (IGF-I) levels in a mouse population (n = 961) derived from a cross of (BALB/cJ x C57BL/6J) F1 females and (C3H/HeJ x DBA/2J) F1 males documented quantitative trait loci (QTL) on chromosomes 1, 10, and 17. We employed a newly developed, random walk-based method to search for three- and four-way allelic combinations that might influence IGF-I levels through nonadditive (conditional or epistatic) interactions among 185 genotyped biallelic loci and with significance defined by experiment-wide permutation (P genetic interactions. In two cases, the four-allele combinations were associated with animals having high levels of IGF-I, and, in the third case, a four-allele combination was associated with animals having low IGF-I levels. The multiple-locus genome scan algorithm revealed new IGF-I QTL on chromosomes 2, 4, 5, 7, 8, and 12 that had not been detected in the single-locus genome search and showed that levels of this hormone can be regulated by complex, nonadditive interactions among multiple loci. The analysis method can detect multilocus interactions in a genome scan experiment and may provide new ways to explore the genetic architecture of complex physiological phenotypes. PMID:16782841