Guillermo Raúl Pratta
Full Text Available El objetivo de este trabajo fue evaluar marcadores moleculares y caracteres cuantitativos en un cruzamiento dialélico completo sin recíprocos, entre cinco líneas recombinantes de tomate y sus híbridos. Se obtuvieron perfiles de AFLP ("amplified fragment length polymorphism" y de polipéptidos del pericarpio en cuatro estados de madurez del fruto de 15 genotipos. Se evaluaron, entre otros: peso, acidez titulable, pH, vida poscosecha y firmeza. Se calculó el porcentaje de polimorfismo para los marcadores moleculares y el porcentaje de variabilidad genética para los caracteres cuantitativos en el grupo de líneas recombinantes, el de híbridos y el conjunto de genotipos. Se realizaron análisis de agrupamiento con cada nivel de variación genética. Para AFLP, el porcentaje de polimorfismo varió entre 34 y 54% y, para los perfiles polipeptídicos, entre 40 y 78%. Mayor polimorfismo fue observado en el grupo de híbridos. La variabilidad genética fue de 100% para acidez y 34% para firmeza, con los mayores valores en los parentales. La similitud genética varió entre los genotipos según el nivel de variación genética; pero la consistencia en el agrupamiento de algunas líneas recombinantes y sus híbridos fue conservada, lo que evidenció asociaciones entre los datos moleculares y fenotípicos.
Leneidy Pérez Pelea
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.
Juan Gabriel Correa Medina; Reyes Hernández Díaz
Aplicación de la Informática a el problema de localización de instalaciones desde un aspecto cuantitativo, tomando como base el método de centro de gravedad, utilizando tanto la técnica de la mediana simple como la de distancias euclidianas. Dicho artículo es un extracto de la tesis de grado, Ubicación de Empresas, Enfoque Cuantitativo, cuyo sustentante es el autor del presente artículo. Cabe mencionar que dicha tesis fue auspiciada por el Consejo de Ciencia y Tecno...
Juan Gabriel Correa Medina
Full Text Available Aplicación de la Informática a el problema de localización de instalaciones desde un aspecto cuantitativo, tomando como base el método de centro de gravedad, utilizando tanto la técnica de la mediana simple como la de distancias euclidianas. Dicho artículo es un extracto de la tesis de grado, Ubicación de Empresas, Enfoque Cuantitativo, cuyo sustentante es el autor del presente artículo. Cabe mencionar que dicha tesis fue auspiciada por el Consejo de Ciencia y Tecnología del Estado de Aguascalientes (CONCYTEA
El presente artículo pretende entregar a los investigadores elementos y argumentos útiles sobre los enfoques cualitativo u holístico y cuantitativo o reduccionista de la investigación, demostrando por qué son diferentes y a su vez complementarios e indisociables y forman un todo que ofrece elementos para mejorar la construcción del conocimiento de la realidad social.
Varela, Héctor Hugo
Full Text Available La varianza fenotípica (Vp comprende la varianza genética (Vg, la varianza ambiental general (Veg y la varianza ambiental especial (Ves. Esta última puede estimarse mediante el cálculo de la repetibilidad (r2. Este valor es considerado el límite superior de la heredabilidad (h2 y representa la proporción de la Vg más la Veg con respecto a la Vp (r2= (Vg+Veg/Vp. Esta técnica permite establecer relaciones de parentesco entre grupos a partir de estimadores que maximizan la información genética contenida en los caracteres cuantitativos. Se empleó una muestra constituida por 237 individuos que habitaron durante 4000 años la costa Norte de Chile. Se midieron 6 caracteres métricos en ambos lados del cráneo. Los valores ambientales especiales (es se obtuvieron por regresión. La diferencia entre estos y los valores fenotípicos (p representan los valores genéticos más ambientales generales (g+eg. Un valor r2 promedio de 0.81, indicó que la Ves representa el 19% de la Vp. Se comprobó que la proporción de la componente (g+eg con respecto a p se mantiene estable, reflejando la evolución de un mismo grupo humano. Además, se demuestra una estrecha relación entre los modelos p y (g+eg, lo que sustenta el uso de modelos fenotípicos en la interpretación de la historia evolutiva de un determinado grupo.
Massault, C.; Bovenhuis, H.; Haley, C.S.; Koning, de D.J.
Rapid development of genomics technology is providing new opportunities for genetic studies, including QTL mapping, in many aquaculture species. This paper investigates the strengths and limitations of QTL mapping designs for fish and shellfish under three different controlled breeding schemes. For
MÉNDEZ AGUILAR, REINALDO
El frijol común es originario de México. Es la fuente de proteínas más importante y constituye junto con el maíz la base de la alimentación de los mexicanos con menores ingresos. La sequía es la causa principal en la reducción de la producción de este grano básico seguido por las enfermedades entre las cuales destacan principalmente dos géneros de hongos causantes de pudriciones de la raíz y el tallo: Macrophomina y Fusarium. En la actualidad, con las herramientas de la biología molecular tal...
1. Introducción - 2. Objetivos - 2.1 Objetivos Generales - 2.2 Objetivos Específicos - 3. Materiales - 3.1. Proceso de generación de datos para selección genómica - 3.2. Datos fenotípicos - 3.3. Datos de marcadores moleculares - 4. Metodología - 4.1. Metodología para el análisis de datos fenotípicos - 4.2. Metodología para el análisis de datos moleculares - 4.2.1. Introducción a los marcadores moleculares - 4.2.2. Análisis de los marcadores moleculares - 4.3. Modelos de selección genómica ...
Meuwissen Theo HE
Full Text Available Abstract Two previously described QTL mapping methods, which combine linkage analysis (LA and linkage disequilibrium analysis (LD, were compared for their ability to detect and map multiple QTL. The methods were tested on five different simulated data sets in which the exact QTL positions were known. Every simulated data set contained two QTL, but the distances between these QTL were varied from 15 to 150 cM. The results show that the single QTL mapping method (LDLA gave good results as long as the distance between the QTL was large (> 90 cM. When the distance between the QTL was reduced, the single QTL method had problems positioning the two QTL and tended to position only one QTL, i.e. a "ghost" QTL, in between the two real QTL positions. The multi QTL mapping method (MP-LDLA gave good results for all evaluated distances between the QTL. For the large distances between the QTL (> 90 cM the single QTL method more often positioned the QTL in the correct marker bracket, but considering the broader likelihood peaks of the single point method it could be argued that the multi QTL method was more precise. Since the distances were reduced the multi QTL method was clearly more accurate than the single QTL method. The two methods combine well, and together provide a good tool to position single or multiple QTL in practical situations, where the number of QTL and their positions are unknown.
Full Text Available qtl12.1 Resistance or Tolerance Drought tolerance Plant heigh at maturity SSR C)Int... G. (2007). A Large-Effect QTL for Grain Yield under Reproductive-Stage Drought Stress in Upland Rice. Crop
Josiane Isabela da Silva Rodrigues
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
Varela, Héctor Hugo
Full Text Available En la teoría evolutiva de rasgos cuantitativos el conocimiento de la varianza genética (VG es determinante para hacer inferencias acerca del parentesco. En muchos casos no es posible estimar dicha componente sin la información obtenida a partir de la correlación entre parientes o de experimentos de selección. Por esta razón, en ausencia de datos apropiados es posible lograr una aproximación mediante el análisis de la repetibilidad de caracteres cuantitativos. En este trabajo se estima la proporción de la varianza genética máxima (VGmax o repetibilidad de medidas del cráneo y del esqueleto postcraneal, empleando la información obtenida por la Dra. Silvia Quevedo en el grupo prehistórico de Punta Teatinos (Norte Semiárido de Chile. La VG es igual a la varianza fenotípica (VP menos la varianza ambiental (VE. Esta última se puede particionar en una varianza ambiental especial (VEe y en una varianza ambiental general (VEg. Como la VEe se puede conocer por la medición de caracteres simétricos del lado derecho e izquierdo del individuo, entonces es posible calcular la varianza genética máxima de la siguiente manera, VGmax=VP-VEe. La proporción de la VGmax se obtuvo para siete variables del esqueleto postcraneano en individuos femeninos (n=56, masculinos (n=55, de ambos sexos (n=115 e infantiles (n=66, y para nueve mediciones del cráneo en un único grupo (n=54. Los resultados indican que la proporción media de la VGmax es menor en el cráneo que en el esqueleto postcraneal sugiriendo una distribución diferencial del efecto ambiental desde el punto de vista topográfico. Además, dicha cantidad es mayor en individuos infantiles que en masculinos y femeninos posiblemente por la existencia en aquellos de una mayor influencia del efecto ambiental general confundido con la VGmax.
QTL analyses were performed in tetraploid cotton.An interspecific F2 population consisting of 69 plants,which was developed from the cross between Gossypium hirsutum L.,cv.Handan 208(characterized as high fiber yield) and G.barbadense L.,cv.Pima 90(characterized as excellent fiber quality),was genotyped with SSR,RAPD,SRAP,and REMAP markers.A 1029-locus linkage map was
Fonollosa Guardiet, Juan Bautista; Sallán Leyes, José María; Suñé Torrents, Albert
Esta obra constituye el material básico de estudio de la asignatura Métodos Cuantitativos en Organización Industrial II, de la carrera de segundo ciclo de Ingeniería en Organización Industrial de Terrassa (ETSEIT). En particular, pretende ser la obra de referencia para cursar dicha asignatura de modo semipresencial. En la línea de la obra anterior, se introducen técnicas de métodos cuantitativos para su aplicación en las organizaciones, muy especialmente en las actividades de planificación y ...
Full Text Available qtl12.1 Resistance or Tolerance Drought tolerance Grain yield SSR C)Interval F3 Way...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 ...
Full Text Available qtl12.1 Resistance or Tolerance Drought tolerance Biomass yield SSR C)Interval F3 W.... 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 ...
Full Text Available qtl12.1 Resistance or Tolerance Drought tolerance Flowering delay SSR C)Interval F3...). 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 ...
Full Text Available qtl12.1 Resistance or Tolerance Drought tolerance Harvest index SSR C)Interval F3 W... 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 ...
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. ...
Full Text Available GS3 Morphological trait Seed small grain, CAPS A)Physical BC3F2 Minghui 63 Chuan 7 ...hang, Q. (2006). GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in
LIN Zhong-xu; HE Dao-hua; WANG Hong-mei
@@ QTL analyses were performed in tetraploid cotton.An interspecific F2population consisting of 69 plants,which was developed from the cross between Gossypium hirsutum L.,cv.Handan 208 (characterized as high fiber yield) and G.barbadense L.,cv.Pima 90 (characterized as excellent fiber quality),was genotyped with SSR,RAPD,SRAP,and REMAP markers.A 1029-1ocus linkage map was constructed covering 5472.3 cM with an average distance of 5.32 cM between two markers.
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
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
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
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
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
Full Text Available Physiological trait Source activity spikelet fertility RFLP C)Interval RIL Zhenshan...ison of QTL detection for yield traits using F2 and recombinant inbred lines in rice. Rice Genetics Newsletter 17, 49-51. ...
Full Text Available qPTD-2 Morphological trait Panicle/flower peduncle top diameter RFLP C)Interval DHL...02). QTL analysis of rice peduncle vascular bundle system and panicle traits. Acta Bot Sinica 44, 301-306 ...
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 ...
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 ...
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 ...
Full Text Available , N., Takagi, K., Ichikawa, N., Maruoka, M., and Sano, Y. (2007). A QTL Cluster for Plant Architecture and Its Ecological Significance in Asian Wild Rice. Breeding Science 57, 7-16. ...
Full Text Available gs. TAG Theoretical and Applied Genetics 102, 793-800. http://dx.doi.org/10.1007/s001220000467 ... ... function map: QTL analysis and comparison between QTLs and expressed sequence ta
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.
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.
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...
Carl Henrik Langebaek
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.
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.
Chavarría Orozco, Luis Alberto
El proyecto de investigación está basado teóricamente en un marco de acción de la legislación del impuesto sobre la renta costarricense y de una relación especialmente financiera y contable en cuanto sus elementos medibles del impuesto sobre la renta, llamados Elementos Cuantitativos, para llegar a determinar así la obligación tributaria de un contribuyente, en términos monetarios. El tema que se estudia se relaciona con las Ciencias Administrativas, por tratarse la...
Los modelos cuantitativos para identificación de factores que expliquen el retorno de activos del mercado de valores han venido ganando popularidad en los últimos años ya que a partir de éstos es posible desarrollar estrategias de inversión activas que logren vencer el retorno del mercado. Con el siguiente trabajo se busca determinar los factores que expliquen de manera significativa el retorno de un conjunto de acciones pertenecientes al Mercado Integrado Latinoamericano a través de un model...
Vanessa Padilha Salla
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.
Advances on methods for mapping quantitative trait loci (QTL) are firstly summarized.Then, some new methods, including mapping multiple QTL, fine mapping of QTL, and mapping QTL for dynamic traits, are mainly described. Finally, some future prospects are proposed, including how to dig novel genes in the germplasm resource, map expression QTL (eQTL) by the use of all markers,phenotypes and micro-array data, identify QTL using genetic mating designs and detect viability loci. The purpose is to direct plant geneticists to choose a suitable method in the inheritance analysis of quantitative trait and in search of novel genes in germplasm resource so that more potential genetic information can be uncovered.
Full Text Available Abstract Background Quantitative trait loci (QTL detection on a huge amount of phenotypes, like eQTL detection on transcriptomic data, can be dramatically impaired by the statistical properties of interval mapping methods. One of these major outcomes is the high number of QTL detected at marker locations. The present study aims at identifying and specifying the sources of this bias, in particular in the case of analysis of data issued from outbred populations. Analytical developments were carried out in a backcross situation in order to specify the bias and to propose an algorithm to control it. The outbred population context was studied through simulated data sets in a wide range of situations. The likelihood ratio test was firstly analyzed under the "one QTL" hypothesis in a backcross population. Designs of sib families were then simulated and analyzed using the QTL Map software. On the basis of the theoretical results in backcross, parameters such as the population size, the density of the genetic map, the QTL effect and the true location of the QTL, were taken into account under the "no QTL" and the "one QTL" hypotheses. A combination of two non parametric tests - the Kolmogorov-Smirnov test and the Mann-Whitney-Wilcoxon test - was used in order to identify the parameters that affected the bias and to specify how much they influenced the estimation of QTL location. Results A theoretical expression of the bias of the estimated QTL location was obtained for a backcross type population. We demonstrated a common source of bias under the "no QTL" and the "one QTL" hypotheses and qualified the possible influence of several parameters. Simulation studies confirmed that the bias exists in outbred populations under both the hypotheses of "no QTL" and "one QTL" on a linkage group. The QTL location was systematically closer to marker locations than expected, particularly in the case of low QTL effect, small population size or low density of markers, i
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. ...
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. ...
Full Text Available RIL Nekken-1 IR36 RM5586 RM3916 RM3839 pha Ochiai, K., Uemura, S., Shimizu, A., Okumoto, Y., and Matoh, T. (...2008). Boron toxicity in rice (Oryza sativa L.). I. Quantitative trait locus (QTL) analysis of tolerance to boron toxicity. Theor Appl Genet 117, 125-133. ...
Full Text Available nd Yashima, S. (1998). Identification of QTL for salt tolerance in rice via molecular markers. . Chin. J. Rice Sci. 12, 72-78 ... ...segregated RIL Tesanai 2 CB A RG716 pha Lin, H.X., Yanagihara, S., Zhuang, J.Y., Senboku, T., Zheng, K.L., a
Full Text Available C)Interval RIL IR64 O. rufipogon (Acc 106424) B RG28 RM223 pha Nguyen, B.D., Brar, D.S., Bui, B.C., Nguyen,... T.V., Pham, L.N., and Nguyen, H.T. (2003). Identification and mapping of the QTL for aluminum tolerance int
Full Text Available DHL CT9993-5-10-1-M IR62266-42-6-2 B CDO20 pha Nguyen, T.T., Klueva, N., Chamareck, V., Aarti, A., Magpanta...y, G., Millena, A.C., Pathan, M.S., and Nguyen, H.T. (2004). Saturation mapping of QTL regions and identific
Full Text Available re C)Interval RIL IR64 O. rufipogon (Acc 106424) B RG28 RM223 pha Nguyen, B.D., Brar, D.S., Bui, B.C., Nguye...n, T.V., Pham, L.N., and Nguyen, H.T. (2003). Identification and mapping of the QTL for aluminum tolerance i
Full Text Available Interval DHL CT9993-5-10-1-M IR62266-42-6-2 A RG9 pha Nguyen, T.T., Klueva, N., Chamareck, V., Aarti, A., Ma...gpantay, G., Millena, A.C., Pathan, M.S., and Nguyen, H.T. (2004). Saturation mapping of QTL regions and ide
Full Text Available C)Interval DHL CT9993-5-10-1-M IR62266-42-6-2 A RG9 pha Nguyen, T.T., Klueva, N., Chamareck, V., Aarti, A., ...Magpantay, G., Millena, A.C., Pathan, M.S., and Nguyen, H.T. (2004). Saturation mapping of QTL regions and i
Full Text Available erval DHL CT9993-5-10-1-M IR62266-42-6-2 A RG257 R1261 pha Nguyen, T.T., Klueva, N., Chamareck, V., Aarti, A...., Magpantay, G., Millena, A.C., Pathan, M.S., and Nguyen, H.T. (2004). Saturation mapping of QTL regions an
Full Text Available DHL CT9993-5-10-1-M IR62266-42-6-2 B RG140 pha Nguyen, T.T., Klueva, N., Chamareck, V., Aarti, A., Magpantay..., G., Millena, A.C., Pathan, M.S., and Nguyen, H.T. (2004). Saturation mapping of QTL regions and identifica
Full Text Available al DHL CT9993-5-10-1-M IR62266-42-6-2 A C711 pha Nguyen, T.T., Klueva, N., Chamareck, V., Aarti, A., Magpant...ay, G., Millena, A.C., Pathan, M.S., and Nguyen, H.T. (2004). Saturation mapping of QTL regions and identifi
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. ...
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
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
Full Text Available yashi, H., Hirayama, M., Ohta, H., Nemoto, H., Kato, H., Ando, I., Ohtsubo, K., rsquo, ichi, Yano, M., and Imbe, T. (2007). QTL Detec...tion for Eating Quality Including Glossiness, Stickiness, Taste and Hardness of Cooked Rice. Breeding Science 57, 231-242. ...
Full Text Available yashi, H., Hirayama, M., Ohta, H., Nemoto, H., Kato, H., Ando, I., Ohtsubo, K., rsquo, ichi, Yano, M., and Imbe, T. (2007). QTL Detec...tion for Eating Quality Including Glossiness, Stickiness, Taste and Hardness of Cooked Rice. Breeding Science 57, 231-242. ...
Full Text Available val RIL Bala Azucena B RZ2 G1465 C189 pha Price, A.H., Steele, K.A., Moore, B.J., Barraclough, P.P., and Clark, L.J. (2000). A combin...ed RFLP and AFLP linkage map of upland rice ( Oryza sativa L.) used to identify QTL
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
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
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
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. ...
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. ...
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. ...
Full Text Available qGW3 Morphological trait Seed Grain width Mixture C)Interval F2 98SQ1496 Koshihikari 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. ...
Full Text Available Morphological trait Shoot/Seedling Mesocotyl-length RFLP d)Co-segregated F2 Labelle Black Gora B RZ403 rgn Redofia, E.D., and Mackill, D.J. (1994). Identification and internal mapping of seedling vigor QTL's in rice. Rice Genetics Newsletter 11, 124-126. ...
Full Text Available Morphological trait Seed Grain yield RFLP C)Interval RIL Zhenshan 97B Milyang 46 RG...138 RZ398 pha Zhuang, J.Y., Fan, Y.Y., Wu, J.L., Xia, Y.W., and Zheng, K.L. (2001). Comparison of the detection of QTL for yield trai
Full Text Available Glu6 Physiological trait Eating quality glutelin subunit polypeptides A)Physical OS...JNBa0083F15 pha Xu, J.C., Li, J.Z., Zheng, X.W., Zou, L.X., and Zhu, L.H. (2001). QTL mapping of the root traits in rice seedling. Yi Chuan Xue Bao 28, 433-438. ...
Full Text Available qCR-3 Physiological trait Source activity chlorophyll a/b ratio RFLP C)Interval RIL... Kinmaze DV85 B C25 R518 rgn Hu, M.L., Wang, C.M., Yang, Q.H., Zhai, H.Q., and Wan, J.M. (2004). QTL analysis for trait
Full Text Available Morphological trait Root Maximum Root Length RFLP C)Interval DHL ZYQ8 Jingxi 17 B C...711 G103 pha Xu, J.C., Li, J.Z., Zheng, X.W., Zou, L.X., and Zhu, L.H. (2001). QTL mapping of the root traits in rice seedling. Yi Chuan Xue Bao 28, 433-438. ...
Full Text Available Morphological trait Seed grain yield RFLP C)Interval RIL Zhenshan 97B Milyang 46 RG...138 RZ398 rgn Zhuang, J.Y., Fan, Y.Y., Wu, J.L., Xia, Y.W., and Zheng, K.L. (2000). Comparison of QTL detection for yield trait
Full Text Available qCC-1 Physiological trait Source activity chlorophyll content of leaf RFLP C)Interv...al RIL Kinmaze DV85 B C122 R1012 rgn Hu, M.L., Wang, C.M., Yang, Q.H., Zhai, H.Q., and Wan, J.M. (2004). QTL analysis for trait
Full Text Available Morphological trait Seed 1000-grain weight RFLP C)Interval RIL Zhenshan 97B Milyang...detection of QTL for yield traits in different generations of a rice cross using two mapping approaches. Yi Chuan Xue Bao 28, 458-464. ...
Full Text Available Morphological trait Seed 1000 grain weight RFLP C)Interval F2 Zhenshan 97B Milyang ...46 RG543 RG81 rgn Zhuang, J.Y., Fan, Y.Y., Wu, J.L., Xia, Y.W., and Zheng, K.L. (2000). Comparison of QTL detection for yield trait
Full Text Available siological and agronomic characters on a rice function map: QTL analysis and compar...maru, K., Yano, M., Aoki, N., Ono, K., Hirose, T., Lin, S.Y., Monna, L., Sasaki, T., and Ohsugi, R. (2001). Toward the mapping of phy
Full Text Available Resistance or Tolerance Other soil stress tolerance Plant height (Low N level, Soil... QTL × N-level interaction for plant height in rice (Oriza Sativa L.). Plant and Soil 236, 237-242. http://dx.doi.org/10.1023/A:1012787510201 ...
Full Text Available Resistance or Tolerance Other soil stress tolerance Plant height (High N level, Soi...QTL × N-level interaction for plant height in rice (Oriza Sativa L.). Plant and Soil 236, 237-242. http://dx.doi.org/10.1023/A:1012787510201 ...
Full Text Available Resistance or Tolerance Other soil stress tolerance Plant height (High N level, Soi.... QTL × N-level interaction for plant height in rice (Oriza Sativa L.). Plant and Soil 236, 237-242. http://dx.doi.org/10.1023/A:1012787510201 ...
Full Text Available H.C., McLaren, G., and Khush, G.S. (2003). Identification of QTL for growth- and ...Zheng, K.L., Liu, G.F., Wang, G.C., Sidhu, J.S., Srivantaneeyakul, S., Singh, V.P., Bagali, P.G., Prasanna,
Full Text Available Abstract Background The analysis of expression quantitative trait loci (eQTL is a potentially powerful way to detect transcriptional regulatory relationships at the genomic scale. However, eQTL data sets often go underexploited because legacy QTL methods are used to map the relationship between the expression trait and genotype. Often these methods are inappropriate for complex traits such as gene expression, particularly in the case of epistasis. Results Here we compare legacy QTL mapping methods with several modern multi-locus methods and evaluate their ability to produce eQTL that agree with independent external data in a systematic way. We found that the modern multi-locus methods (Random Forests, sparse partial least squares, lasso, and elastic net clearly outperformed the legacy QTL methods (Haley-Knott regression and composite interval mapping in terms of biological relevance of the mapped eQTL. In particular, we found that our new approach, based on Random Forests, showed superior performance among the multi-locus methods. Conclusions Benchmarks based on the recapitulation of experimental findings provide valuable insight when selecting the appropriate eQTL mapping method. Our battery of tests suggests that Random Forests map eQTL that are more likely to be validated by independent data, when compared to competing multi-locus and legacy eQTL mapping methods.
Daniel R Brooks
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
Mendoza Pérez Cristóbal
Full Text Available En este artículo se hace una revisión teórica sobre la trayectoria teórico-metodológica de la geografía de la población. Se inicia con la discusión sobre el principal objetivo de esta subdisciplina: las variaciones territoriales en la distribución y concentración de la población, en la estructura por edades y sexo y en los eventos sociodemográficos. En segundo lugar, se analiza específicamente el aporte de los métodos cuantitativos y la relevancia de la demografía espacial. Finalmente, se reflexiona sobre el futuro de la geografía de la población, y se propone que esta necesita replantear sus objetivos, ante la evidente complejidad de las sociedades (urbanas del siglo XXI.
Full Text Available ct character Category of object character Character Character Marker Type of marker...ta item Description id ID number of QTL QTL/Gene Name of QTL Major category Major category of quantitative character Category of obje
Giovani Olegario da Silva
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.
Escribano Rocafort, Adrián Gaspar
Una de las premisas adoptadas en la teoría ecológica implica que la variabilidad en la expresión de caracteres funcionales es despreciable entre individuos conespecíficos comparada con la variabilidad existente entre especies. Sin embargo, la evidencia acumulada destaca la variabilidad intraespecífica en el funcionamiento de los ecosistemas y en los procesos de ensamblaje y dinámica de comunidades, especialmente en aquellas dominadas por una o pocas especies. La variabilidad funcional intraes...
Full Text Available OSJNBb0074M06 RMw357 RMw353 C80 C1677 pha Wan, X.Y., Wan, J.M., Jiang, L., Wang, J.K., Zhai, H.Q., Weng, J.F., Wang,... H.L., Lei, C.L., Wang, J.L., Zhang, X., Cheng, Z.J., and Guo, X.P. (2006). QTL analysis for rice gr
Full Text Available Gw2 Morphological trait Seed Grain weight Mixture A)Physical F2 WY3 Fengaizhan-1 AP005004 W024 W004 pha Song, X.J., Huang, W., Shi, M., Zhu, M.Z., and Lin, H.X. (2007). A QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase. Nat Genet 39, 623-630. ...
Full Text Available Morphological trait Root Root / Shoot Ratio of Dry Weight RFLP C)Interval DHL ZYQ8 ...Jingxi 17 B RG653 RG433 pha Xu, J.C., Li, J.Z., Zheng, X.W., Zou, L.X., and Zhu, L.H. (2001). QTL mapping of the root traits in rice seedling. Yi Chuan Xue Bao 28, 433-438. ...
Matejickova, J; Stipkova, M; Sahana, Goutam;
The objective of this study was to find QTL for milk production traits in Czech Fleckvieh cattle on chromosomes 6, 7, 11, 14, and 23 where QTL were previously identified in other dairy cattle populations. Sixteen grandsire families were genotyped for 38 microsatellite markers on the selected...... of milk production in the Czech Fleckvieh cattle....... associated with milk production traits appeared on other studied chromosomes (BTA6, BTA7, BTA11, and BTA23). This first QTL search on five chromosomes in Czech Fleckvieh population showed several suggestive QTL that can be promising for further studies and contribute to better understanding of genetics...
Max F. Rothschild, Zhi-liang Hu, Zhihua Jiang
Full Text Available Over the past 15 years advances in the porcine genetic linkage map and discovery of useful candidate genes have led to valuable gene and trait information being discovered. Early use of exotic breed crosses and now commercial breed crosses for quantitative trait loci (QTL scans and candidate gene analyses have led to 110 publications which have identified 1,675 QTL. Additionally, these studies continue to identify genes associated with economically important traits such as growth rate, leanness, feed intake, meat quality, litter size, and disease resistance. A well developed QTL database called PigQTLdb is now as a valuable tool for summarizing and pinpointing in silico regions of interest to researchers. The commercial pig industry is actively incorporating these markers in marker-assisted selection along with traditional performance information to improve traits of economic performance. The long awaited sequencing efforts are also now beginning to provide sequence available for both comparative genomics and large scale single nucleotide polymorphism (SNP association studies. While these advances are all positive, development of useful new trait families and measurement of new or underlying traits still limits future discoveries. A review of these developments is presented.
Full Text Available Se estudiaron los aspectos morfohistológicos y cuantitativos del ovario de Fulica armillata durante la fase de recrudescencia gonadal. Se utilizaron 5 hembras adultas. El análisis morfohistológico reveló la presencia de numerosos folículos en diferentes estadios de desarrollo y regresión. El epitelio simple de células granulosas caracterizó a los ovocitos primordiales y el pseudoestratificado a los folículos previtelogénicos, ambos tipos foliculares exhibieron un notorio cuerpo de Balbiani. En los folículos vitelogénicos blancos y amarillos (> de 1 mm se evidenció una compleja pared folicular formada por la zona radiada, el epitelio folicular estratificado y las envolturas tecales bien delimitadas, mientras que, en los vitelogénicos amarillos (> de 3 mm fue observado un epitelio simple con células cúbicas muy basófilas. Se identificaron dos tipos de atresia folicular: 1 pared folicular intacta o no bursting, la involución se realiza en el interior del folículo, comprende a la atresia lipoidal (Ovocitos primordiales y lipoglandular (folículos previtelogénicos y vitelogénicos pequeños y 2 atresia por ruptura de la pared o bursting con extrusión del contenido ovoplásmico (folículos vitelogénicos > 1 mm. El análisis cuantitativo reveló una diferencia significativa (p <0,05, entre los folículos en desarrollo (< de 2 mm y los folículos mayores e idéntica diferencia entre lo folículos atrésicos pequeños (lipoidales y lipoglandulares y los folículos bursting. Los procesos de crecimiento y diferenciación (foliculogénesis y vitelogénesis y el de atresia folicular se desarrollan normalmente durante la fase de recrudescencia gonadal, contribuyendo a la homeostasis del ovario de esta ave.
Este estudo teve como objetivos verificar a existência de relações lineares entre caracteres fenológicos, morfológicos e produtivos de cultivares de milho (Zea mays L.) de ciclos precoce e superprecoce e classe transgênica, e identificar quais caracteres possuem elevada correlação e efeitos diretos sobre a produtividade de grãos. Para isso, foram conduzidos seis experimentos com cultivares precoces, superprecoces e transgênicas de milho, nas safras agrícolas 2009-2010 e 2010-2011, na área exp...
When alien DNA inserts into cotton genome in multi-copy manner,several QTL in cotton genome are disrupted,which are called dQTL in this study.Transgenic mutant line is near-isogenic to its recipient which is divergent for the dQTL from remaining QTL.So,a set of data from a transgenic
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.
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
Antonio Alberto Neves de Alcochete
(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.
Álvarez Vázquez, Nelson J.
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
Vallejo Cabrera Franco Alirio
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.
Magda Piedad Valdés Restrepo
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.
Rafael Gustavo Ferreira Morales
Full Text Available Os caracteres morfoagronômicos são tradicionalmente usados na caracterização de cultivares e no estudo da divergência genética, contribuindo na definição de estratégias para o melhoramento genético. Este trabalho teve por objetivo avaliar a divergência genética por meio de caracteres morfoagronômicos de 11 cultivares de morangueiro (Aromas, Camarosa, Camino Real, Campinas, Diamante, Dover, Oso Grande, Sweet Charlie, Toyonoka, Tudla e Ventana, nas condições climáticas da região Centro-Sul do Paraná. Foram analisados 29 caracteres morfoagronômicos relacionados com a planta, folha, flor, fruto e aquênios do morangueiro. As similaridades genéticas foram calculadas por meio de análise multivariada e, os cultivares, agrupados com base na matriz de similaridade genética, usando-se UPGMA. Dentre os 29 caracteres morfoagronômicos avaliados, oito apresentaram diferenças não significativas (p < 0,05. A similaridade média foi de 38%, variando de 19 (aromas e camino real a 62% (Camino Real e Camarosa; Aromas e Sweet Charlie. O dendrograma alocou os cultivares em quatro grupos, contudo, essa divisão não foi coerente com a origem e genealogia dos cultivares. O cultivar Tudla apresenta elevado potencial "per se" para utilização em programas de melhoramento. O cruzamento mais promissor com base nos caracteres morfoagronômicos é entre os cultivares Camarosa e Campinas.
Ruben Eduardo MORA MORENO
Full Text Available La 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.
SHEN Bo; ZHUANG Jie-yun; ZHANG Ke-qin; DAI Wei-min; LU Ye; FU Li-qing; DING Jia-ming; ZHENG Kang-le
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.
GAO Huijiang; YANG Runqing
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.
Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us PGDBj Registered...Policy | Contact Us QTL list - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive ...
Mochón Bezares, Gonzalo
Full Text Available This work offers a quantitative analysis of publicly available thesauri in different European languages in order to check publication trends and their degree of adherence to thesauri construction guidelines. The following parameters were analysed: publisher’s name and location, number of terms, subject coverage, query modes, latest update, level of content in introduction and on-line help. The results reveal the prevalence of thesauri published in Western Europe; English is the most frequently used language; social sciences have the highest number of thesauri among the knowledge areas observed; only one third of the thesauri has a search engine; on average, there is a poor level of content in the introductions and in the on-line help. In conclusion, many publicly available thesauri do not take advantage offered by the Internet for querying their content and should improve their interfaces.
Se realiza un análisis cuantitativo de tesauros de acceso abierto en diversas lenguas europeas para comprobar las tendencias en su edición, así como su grado de adaptación a las directrices de construcción de tesauros. Los parámetros analizados en cada tesauro son el nombre de la institución o persona editora y su ubicación geográfica, el número de términos, las principales materias tratadas, los modos de consulta, la última fecha de actualización, el nivel de contenido de la introducción y la ayuda en línea al usuario. Los resultados indican un predominio de los tesauros editados en Europa Occidental; que el inglés es la lengua más usada; que las ciencias sociales tienen el mayor número de tesauros entre las áreas de conocimiento observadas; que sólo una tercera parte de los tesauros dispone de un motor de búsqueda; que hay un nivel medio de contenido muy bajo en las introducciones; y ausencia de ayuda al usuario en numerosas páginas. En conclusión, gran cantidad de tesauros en acceso abierto no aprovechan las ventajas que
Alessandro Dal'Col Lúcio
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.
Z.K. Li; Y. Sun; L.H. Zhu; D. Dwivedi; Y.M. Gao; T.Q. Zheng; R. Lafitte; J.L. Xu; D. Mackill; B.Y. Fu; J.Domingo
@@ Drought is the most important factor limiting rice yields in the rainfed areas of Asia. To overcome the problem, we developed a new strategy 'designed QTL pyramiding' to more efficiently develop drought tolerant (DT)rice cultivars.
Full Text Available 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 ciudad de La Paz participaron en el estudio. Un cuestionario semi-cuantitativo de frecuencias alimenticias fue aplicado dos veces con un mes de intervalo (Q1 y Q2. Paralelamente, se obtuvieron tres días de registro dietético (3R efectuados por 38 de los estudiantes, para utilizarlos como patrón referencial. Resultados: La mayoría (87% de las preguntas sobre consumo individual de cada ítem de alimentos presentaron niveles entre módicos a sustanciales de concordancia,11 ítems presentaron un nivel regular mientras que sólo 2 ítems presentaron un nivel ligero de concordancia utilizando la estadística kappa. Las cantidades que se obtuvieron de las dos aplicaciones del cuestionario dieron resultados similares (P > 0,05. Las estimaciones de nutrientes obtenidas de Q1, Q2 y 3R no fueron estadísticamente diferentes (P > 0,05. Conclusión: El cuestionario semi-cuantitativo de frecuencias alimenticias es aparentemente confiable y válido para medir el consumo absoluto de alimentos por adolescentes Bolivianos. Se deberá tener cuidado en el futuro para prevenir sobre-estimaciones por este cuestionario particular.
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...
Giovani Olegário da Silva
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.
Karen M Knapp
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
Jesús Basulto Santos
Full Text Available El estudio de la variabilidad en caracteres categóricos rara vez es abordado. A partir de un enfoque menos usado de la variabilidad en variables cuantitativas, el de la disparidad, distinto al de la dispersión que, por ejemplo, proporciona la varianza, se propone la construcción de dos coeficientes de medida de la variabilidad en variables cualitativas o categóricas a los que llamamos coeficientes de disparidad. La sencillez y proximidad de los mismos permiten que sean abordados en un curso introductorio de estadística descriptiva. Ejemplos sencillos son ofrecidos para introducir las medidas y para, también, que el profesor constate la idea que el alumno tiene sobre variabilidad, dispersión y disparidad.The study of variability in categorical characteristics is rarely discussed. From a less used viewpoint of variability in quantitative variables, as it is the one of dissimilarity, which is different from the dispersion that, for example, the variance provides, we propose the construction of two coefficients that measure the variability in qualitative or categorical variables, which we call coefficients of dissimilarity. Simple examples are provided to introduce the measures, so that the teacher can also evaluate the idea students have about variability, dispersion and dissimilarity.
Jesús Basulto Santos
Full Text Available El estudio de la variabilidad en caracteres categóricos rara vez es abordado. A partir de un enfoque menos usado de la variabilidad en variables cuantitativas, el de la disparidad, distinto al de la dispersión que, por ejemplo, proporciona la varianza, se propone la construcción de dos coeficientes de medida de la variabilidad en variables cualitativas o categóricas a los que llamamos coeficientes de disparidad. La sencillez y proximidad de los mismos permiten que sean abordados en un curso introductorio de estadística descriptiva. Ejemplos sencillos son ofrecidos para introducir las medidas y para, también, que el profesor constate la idea que el alumno tiene sobre variabilidad, dispersión y disparidad. The study of variability in categorical characteristics is rarely discussed. From a less used viewpoint of variability in quantitative variables, as it is the one of dissimilarity, which is different from the dispersion that, for example, the variance provides, we propose the construction of two coefficients that measure the variability in qualitative or categorical variables, which we call coefficients of dissimilarity. Simple examples are provided to introduce the measures, so that the teacher can also evaluate the idea students have about variability, dispersion and dissimilarity.
Fa Cui; Anming Ding; Jun Li; Chunhua Zhao; Xingfeng Li; Deshun Feng; Xiuqin Wang; Lin Wang; Jurong Gao; Honggang Wang
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.
Senapathy Senthilvel; Kunnummal Kurungara Vinod; Palaniappan Malarvizhi; Marappa Maheswaran
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.
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
Giovani Olegário da Silva
Full Text Available O objetivo deste trabalho foi estimar as capacidades de combinação de genitores de batata, em gerações iniciais de seleção. Os experimentos foram realizados em Pelotas e Canoinhas. Foram estudadas 12 famílias, derivadas de dois grupos de genitores, cruzados em esquema dialelo parcial (3 x 4 'Eliza', 'C-1730-7-94' e 'C-1742-8-95'; 'Shepody', 'Asterix', 'White Lady' e 'Caesar'. As famílias foram avaliadas, na geração de plântula e na primeira geração de campo, para caracteres componentes de aparência e rendimento de tubérculos. Os dados foram submetidos às análises de variância e dialélica parcial. No conjunto de caracteres avaliados, verificou-se superioridade de efeitos significativos para a capacidade geral de combinação, em relação à capacidade específica de combinação, indicando predominância de efeitos aditivos dos genes, no controle dos caracteres. Em relação à capacidade geral de combinação, 'White Lady' é o genitor mais destacado positivamente, contribuindo com genes de ação aditiva para a melhoria, tanto dos caracteres que compõem a aparência dos tubérculos, quanto dos caracteres de rendimento. Quanto à capacidade específica de combinação, o cruzamento ('C1730-7-94' x 'White Lady' é o mais indicado para a geração de famílias superiores quanto a caracteres de aparência e a caracteres componentes do rendimento de tubérculos.
Lopes Ângela Celis de Almeida
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.
Loeschcke, Volker; Kristensen, Torsten Nygård; Norry, Fabian M
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...
Lannes Sérgio Dias
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.
Fernando Rohan L
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.
Full Text Available Expression Quantitative Trait Loci (eQTL analysis enables characterisation of functional genetic variation influencing expression levels of individual genes. In outbread populations, including humans, eQTLs are commonly analysed using the conventional linear model, adjusting for relevant covariates, assuming an allelic dosage model and a Gaussian error term. However, gene expression data generally have noise that induces heavy-tailed errors relative to the Gaussian distribution and often include atypical observations, or outliers. Such departures from modelling assumptions can lead to an increased rate of type II errors (false negatives, and to some extent also type I errors (false positives. Careful model checking can reduce the risk of type-I errors but often not type II errors, since it is generally too time-consuming to carefully check all models with a non-significant effect in large-scale and genome-wide studies. Here we propose the application of a robust linear model for eQTL analysis to reduce adverse effects of deviations from the assumption of Gaussian residuals. We present results from a simulation study as well as results from the analysis of real eQTL data sets. Our findings suggest that in many situations robust models have the potential to provide more reliable eQTL results compared to conventional linear models, particularly in respect to reducing type II errors due to non-Gaussian noise. Post-genomic data, such as that generated in genome-wide eQTL studies, are often noisy and frequently contain atypical observations. Robust statistical models have the potential to provide more reliable results and increased statistical power under non-Gaussian conditions. The results presented here suggest that robust models should be considered routinely alongside other commonly used methodologies for eQTL analysis.
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.
Partial resistance to Phytophthora sojae in soybean is controlled by multiple quantitative trait loci (QTL). With traditional QTL mapping approaches, power to detect these QTL, frequently of small effect, can be limited by population size. Joint linkage QTL analysis of nested recombinant inbred li...
YAN Jian-bing; TANG Hua; HUANG Yi-qin; SHI Yong-gang; ZHENG Yong-lian; LI Jian-sheng
Plant height has become one of important agronomic traits with the increase of planting densityrecently and the rapid developments of molecular markers have provided powerful tools to localize importantagronomic QTL at the genomic level. The purposes of this investigation are to map plant height QTL with mo-lecular markers and to analyze their genetic effects in maize. An F2:3 population from an elite combination(Zong3 × 87-1) was utilized for evaluating plant height in two locations, Wuhan and Xiangfan, with a ran-domized complete block design. The mapping population included 266 F2:3 family lines. A genetic linkagemap, containing 150 SSR and 24 RFLP markers, was constructed, spanning a total of 2 531.6 cm with an av-erage interval of 14.5 cm. Totally 10 QTL affecting plant height were mapped on six different chromosomeswith the composite interval mapping. Seven of 10 QTL were detected in two locations. The contributions tophenotypic variations for the single QTL varied between 5.3 and 17.1%. Additive, partial dominance, domi-nance, and overdominance actions existed among all detected QTL affecting plant heights. A large number ofdigenic interactions for plant height were detected by two-way analyses of variance. 107 and 98 two-locus com-binations were found to be significant at a 0.01 probability level in two locations respectively. 23 of them weresimultaneously detected in both locations. They accounted for phenotypic variations of 4.5 -11%. It was no-ticed that a locus, umc1122, had digenic interactive effects with other four different loci for plant height,which distributed on three chromosomes. A few of plant height QTL was involved in significant digenic inter-actions, but most significant interactions occurred between markers that are not adjacent to mapped QTL.These results demonstrated that epistatic interactions might play an equal importance role as the single-locuseffects in determining plant height of maize.
Miguel de Aguilera Moyano
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.
Ben Jemaa, Slim
The aim of this thesis was to map finely female fertility (FF) QTL in the three main French dairy cattle breeds Prim'Holstein, Normande and Montbeliarde. The first step consisted in detecting QTL on 78 families in 12 genomic regions. Six FF QTL were found in Prim'Holstein and two in Normande breeds. In the second step of the study, the QTL on bovine chromosomes BTA01, BTA02, BTA03 and BTA21 were mapped on a sub-sample of 41 families and the confidence interval for BTA01 and BTA03 QTL was redu...
Goddard Mike E
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.
van Kampen Tony A
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.
Full Text Available The main tectonic features of the metasediments in the Ciudad Rodrigo area, in the western part of the Salamanca province, are given in this paper.
The metamorphic rocks –quartzites, conglomerates and slates, as well as some calc-silicates layers– were folded during the Herecynian arogeny, although a pre-Hercynian tectonic phase, without schistosity , is also locally present.
The Hercynian orogeny in the area is characterized by three main tectonic stages which gave place 10 folds trending NW, E and NE respectively. The first one, which produced axial plane schistcsity, was the most important, while the other two , which occasionally originated strain-slip schistosity, are occasionally present. Finally, there are some other tectonic structures, such as kink-bands, and fracturing which are late Hercynian age.
Several granitic intrusions developed simultaneously with the main tectonic phases, especially the first and the second ones.
Se exponen en este trabajo los principales caracteres tectónicos de los metasedimentos situados al O de la provincia de Salamanca, en el área de Ciudad Rodrigo. En términos generales. las rocas que constituyen el área, que corresponden en general a cuarcitas, conglomerados, esquistos y rocas calcosilicatadas, están plegadas por las diversas fases de la orogenia hercínica, además de una fase prehercínica.
Por lo que se refiere a la tectónica hercínica, en el área estudiada se observa la superposición de tres fases principales de deformación, además de otras estructuras debidas a fases posteriores. Las direcciones de los pliegues asociados a cada una de estas fases son respectivamente NO-SE, E-O y NE•SO, resultando de todas ellas la más importante y generalizada la primera, mientras que las otras dos sólo adquieren importancia en áreas localizadas .
En relación con estas tres fases tectónicas, además de una serie de intrusiones graníticas, se
Veerkamp Roel F
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.
Vilkki, Johanna; Dolezal, Marlies A; Sahana, Goutam;
(on BTA3, BTA6, BTA8, BTA19, and BTA27) agreed across the breeds, but no identical associated SNPs were detected. Higher power (imputation to bigger population samples) will be needed to confirm results. On BTA6 the results indicate several QTL within a 5 Mb region. The results provide a basis...
Yousaf HAYAT; Jian YANG; Hai-ming XU; Jun ZHU
A method was proposed for the detection of outliers and influential observations in the framework of a mixed linear model, prior to the quantitative trait locus (QTL) mapping analysis. We investigated the impact of outliers on QTL mapping for complex traits in a mouse BXD population, and observed that the dropping of outliers could provide the evidence of additional QTL and epistatic loci affecting the 1 stBrain-OB and the 2ndBrain-OB in a cross of the abovementioned population. The results could also reveal a remarkable increase in estimating heritabilities of QTL in the absence of outliers. In addition, simulations were conducted to investigate the detection powers and false discovery rates (FDRs) of QTLs in the presence and absence of outliers. The results suggested that the presence of a small proportion of outliers could increase the FDR and hence decrease the detection power of QTLs. A drastic increase could be obtained in the estimates of standard errors for position, additive and additivex environment interaction effects of QTLs in the presence of outliers.
Heuven, Henri C M; Janss, Luc L G
. The locations of the QTLs for separate parameters were very close in some cases and probably caused the genetic correlation observed between ASYM and XMID and SCAL respectively. None of the QTL appeared on chromosome five. Conclusions Repeated observations on individuals were affected by at least nine QTLs...
Melchinger, Albrecht E; Orsini, Elena; Schön, Chris C
In plant breeding, a large number of progenies that will be discarded later in the breeding process must be phenotyped and marker genotyped for conducting QTL analysis. In many cases, phenotypic preselection of lines could be useful. However, in QTL analyses even moderate preselection can have a significant effect on the power of QTL detection and estimation of effects of the target traits. In this study, we provide exact formulas for quantifying the change of allele frequencies within marker classes, expectations of marker contrasts and the variance of the marker contrasts under truncation selection, for the general case of two QTL affecting the target trait and a correlated trait. We focused on homozygous lines derived at random from biparental crosses. The effects of linkage between the marker and the QTL under selection as well as the effect of selection on a correlated trait can be quantified with the given formulas. Theoretical results clearly show that depending on the magnitude of QTL effects, high selection intensities can lead to a dramatic reduction in power of QTL detection and that approximations based on the infinitesimal model deviate substantially from exact solutions. The presented formulas are valuable for choosing appropriate selection intensity when performing QTL mapping experiments on the data on phenotypically preselected traits and enable the calculation and bias correction of the effects of QTL under selection. Application of our theory to experimental data revealed that selection-induced bias of QTL effects can be successfully corrected.
高用明; 朱军; 宋佑胜; 何慈信; 石春海; 邢永忠
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.
Yuqiu; Guo; Xiaohong; Yang; Subhash; Chander; Jianbing; Yan; Jun; Zhang; Tongming; Song; Jiansheng; Li
Oil, protein and starch are key chemical components of maize kernels. A population of 245 recombinant inbred lines(RILs) derived from a cross between a high-oil inbred line, By804, and a regular inbred line, B73, was used to dissect the genetic interrelationships among oil, starch and protein content at the individual QTL level by unconditional and conditional QTL mapping. Combined phenotypic data over two years with a genetic linkage map constructed using 236 markers, nine, five and eight unconditional QTL were detected for oil, protein and starch content, respectively. Some QTL for oil, protein and starch content were clustered in the same genomic regions and the direction of their effects was consistent with the sign of their correlation. In conditional QTL mapping, 37(29/8) unconditional QTL were not detected or showed reduced effects, four QTL demonstrated similar effects under unconditional and conditional QTL mapping, and 17 additional QTL were identified by conditional QTL mapping. These results imply that there is a strong genetic relationship among oil, protein and starch content in maize kernels. The information generated in the present investigation could be helpful in marker-assisted breeding for maize varieties with desirable kernel quality traits.
Full Text Available Molecular markers allowed breeders to Mendelize quantitative trait loci (QTL providing another demonstration that quantitative traits are governed by the same principles as single qualitative genes. This research extends the QTL analysis to two and three QTL and tests our ability to Mendelize an oligogenic trait. In tomato, agricultural yield is determined by the weight of the fruits harvested per unit area and the total soluble solids (% Brix–sugars and acids. The current study explores the segregation of multiple independent yield-related QTL that were identified and mapped using introgression lines (IL of Solanum pennellii in cultivated processing tomato (Solanum lycopersicum. We screened 45 different double and triple IL-QTL combinations for agricultural yield, to identify QTL pyramids that behaved in an additive manner and were suitable substrate for Mendelizing an oligogenic trait. A pyramid of three independent QTL that significantly improved Brix*Yield (BXY - the soluble solids output per unit area compared to M82 was selected. In the progenies of the tri-hybrid we bred using markers a nearly isogenic 'immortalized F2'. While the common mode of QTL-QTL interactions across the 45 IL-QTLs combinations was less than additive, the three QTLs in the selected triple-stack performed in an additive manner which made it an exceptional material for breeding. This study demonstrates that using the phenotypic effect of all 27 possible QTL-alleles combinations it is possible to make reliable predictions about the genotypes that will maximize the yield.
Full Text Available În acest articol autorii şi-au propus scopul să analizeze particularităţile caracterelor specifice vinovăţiei – condiţie a răspunderii juridice civile în ambele ei forme din cadrul dreptului civil, pentru a determina rolul şi importanţa acesteia în aplicarea răspunderii civile şi repararea prejudiciului. Pentru realizarea acestui scop şi determinarea rolului, importanţei şi particularităţilor caracterelor specifice ale vinovăţiei din dreptul civil, autorii au analizat legislaţia în vigoare a Republicii Moldova, a altor state, precum şi doctrina. Ei au caracterizat noţiunea de vinovăţie, caracterele ei specifice, propunând o definiţie proprie, specificul căreia constă în faptul că apare şi ca noţiune de culpă, greşală, prin care se subînţelege atitu-dinea persoanei faţă de fapta săvârşită, toate având un caracter subiectiv. Sunt evidenţiate şi analizate următoarele caractere specifice vinovăţiei civile: intelectiv, volitiv, exterioritiv. Pentru a formula unele concluzii şi recomandări proprii, autorii au analizat în aspect de drept comparat Codul civil al Republicii Moldova, ale altor state cu referire la subiect, precum şi doctrina. În rezultatul cercetărilor efectuate sunt formulate concluzii şi înaintate recomandări, principala fiind că vino-văţia – condiţie a răspunderii juridice civile – este nu doar necesară, dar ar fi bine ca la aplicarea răspunderii juridice civile, la determinarea valorii prejudiciului cauzat să se ţină cont de formele şi de gradele acesteia, aşa ca în dreptul penal.SPECIFIC CHARACTERS GUILT – CONDITION OF LIABILITY CIVIL LEGALIn this article the authors aimed to analyze the peculiarities of specific characters guilt - condition of civil liability in both its forms of civil law to determine the role and importance in the application of liability and compensation. In achieving this goal and determining the role, importance and
N.Manikanda BOOPATHI; Gat SWAPNASHRI; P.KAVITHA; S.SATHISH; R.NITHYA; Wickneswari RATNAM; Arvind KUMAR
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.
Torres Sánchez, Jaime
Full Text Available This article presents results of quantitative analysis done on an unpublished document written by don Fernando de Lovera in Caracas on October 22, 1752, and another attributed to doctor Agustín Marón, Caracas, 1775. This article gives some technical problems stated by calculations, and it presents new tables of values for metrological analysis and corrected tables of food consumption and population.
En este artículo se presentan los resultados del análisis cuantitativo de un documento inédito elaborado por don Fernando de Lovera, en Caracas, el 22 de octubre de 1752, y de otro atribuido al doctor Agustín Marón, fechado en Caracas en 1775. Se examinan algunos problemas técnicos planteados por los cálculos, se presentan nuevas tablas de valores para el examen metrológico y tablas de consumo de alimentos y de población corregidas.
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
Ariosto Ardila Silva
Full Text Available Además de todos los progresos que ha representado el mejoramiento genético animal clásico, este presenta algunas limitaciones como en algunos casos donde el fenotipo no se expresa en el individuo. Con el advenimiento de las enzimas de restricción, del secuenciamiento y de la amplificación del ADN, fue posible el uso de marcadores moleculares asociados con loci de características cuantitativas (QTL, como herramienta que auxilia y perfecciona el mejoramiento genético animal por medio de la selección asistida por marcadores (MAS, lo que aumenta el mérito genético para características de difícil medida, baja heredabilidad y limitadas por el sexo. La raza bovina gyr se caracteriza por su rusticidad y adaptación al trópico, y presenta una buena producción de leche para los países tropicales, por lo que es fundamental en la conformación de la raza gyrholando (5/8holstein y 3/8 gyr. El propósito del presente estudio fue complementar el análisis cuantitativo con la genética molecular, en el mejoramiento genético de la característica porcentaje de sólidos totales en la razagyr en Brasil. Catorce familias (toros gyr con 657 hijas fueron analizadas, siendo el promedio 0,095 % y la desviación estándar 0,1923 del valor genético estimadopara porcentaje de sólidos totales. Al utilizar 27 marcadores microsatélites en el análisis a travésde las 14 familias para porcentaje de sólidos totales en el cromosoma 6, un QTL fue identificado con P< 0,05 y F = 2,34 en la posición 58 cm, próximo al marcador MNB-208 (60,21 cm. Al emplear las familias3 y 4, las más significativas, el mismo QTL fue identificado con P < 0,01 y F = 7,61, pero en la posición 58 cm, próximo al marcador MNB-208.
Alberto Cargnelutti Filho
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%.
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
Willy Schuwarten Júnior
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
Sahana, G; Lund, M S; Andersson-Eklund, L;
A QTL affecting clinical mastitis and/or somatic cell score (SCS) has been reported previously on chromosome 9 from studies in 16 families from the Swedish Red and White (SRB), Finnish Ayrshire (FA) and Danish Red (DR) breeds. In order to refine the QTL location, 67 markers were genotyped over...... mastitis to be mapped to a small interval (BM4208 and INRA084. This QTL showed a pleiotropic effect on SCS in the DR and SRB breeds. Haplotypes associated with variations in mastitis resistance were identified. The haplotypes were predictive in the general population and can be used in marker......-assisted selection. Pleiotropic effects of the mastitis QTL were studied for three milk production traits and eight udder conformation traits. This QTL was also associated with yield traits in DR but not in FA or SRB. No QTL were found for udder conformation traits on chromosome 9...
@@ When alien DNA inserts into cotton genome in multi-copy manner,several QTL in cotton genome are disrupted,which are called dQTL in this study.Transgenic mutant line is near-isogenic to its recipient which is divergent for the dQTL from remaining QTL.So,a set of data from a transgenic QTL mutant line produced by Agrobacterium-mediated transformation,30074,its recipient,their F1 hybrids between them,and three elite lines were analyzed under a modified additive-dominance model with genotype by environment interactions in three different environments to dissect the genetic effects due to dQTL from the whole genome based genetic effects.
Paulo Eduardo Teodoro
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.
Cavanagh, Colin R; Jonas, Elisabeth; Hobbs, Matthew; Thomson, Peter C; Tammen, Imke; Raadsma, Herman W
An (Awassi × Merino) × Merino single-sire backcross family with 165 male offspring was used to map quantitative trait loci (QTL) for body composition traits on a framework map of 189 microsatellite loci across all autosomes. Two cohorts were created from the experimental progeny to represent alternative maturity classes for body composition assessment. Animals were raised under paddock conditions prior to entering the feedlot for a 90-day fattening phase. Body composition traits were derived in vivo at the end of the experiment prior to slaughter at 2 (cohort 1) and 3.5 (cohort 2) years of age, using computed tomography. Image analysis was used to gain accurate predictions for 13 traits describing major fat depots, lean muscle, bone, body proportions and body weight which were used for single- and two-QTL mapping analysis. Using a maximum-likelihood approach, three highly significant (LOD ≥ 3), 15 significant (LOD ≥ 2), and 11 suggestive QTL (1.7 ≤ LOD < 2) were detected on eleven chromosomes. Regression analysis confirmed 28 of these QTL and an additional 17 suggestive (P < 0.1) and two significant (P < 0.05) QTL were identified using this method. QTL with pleiotropic effects for two or more tissues were identified on chromosomes 1, 6, 10, 14, 16 and 23. No tissue-specific QTL were identified.A meta-assembly of ovine QTL for carcass traits from this study and public domain sources was performed and compared with a corresponding bovine meta-assembly. The assembly demonstrated QTL with effects on carcass composition in homologous regions on OAR1, 2, 6 and 21.
Full Text Available The functional consequences of trait associated SNPs are often investigated using expression quantitative trait locus (eQTL mapping. While trait-associated variants may operate in a cell-type specific manner, eQTL datasets for such cell-types may not always be available. We performed a genome-environment interaction (GxE meta-analysis on data from 5,683 samples to infer the cell type specificity of whole blood cis-eQTLs. We demonstrate that this method is able to predict neutrophil and lymphocyte specific cis-eQTLs and replicate these predictions in independent cell-type specific datasets. Finally, we show that SNPs associated with Crohn's disease preferentially affect gene expression within neutrophils, including the archetypal NOD2 locus.
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.
Şığva Hasan Ö
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
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.
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.
AO Yan; HU Zhi-qiu; TANG Zai-xiang; WANG Xue-feng; XU Chen-wu
It's well known that incorporating some existing populations derived from multiple parents may improve QTL mapping and QTL-based breeding programs. However, no general maximum likelihood method has been available for this strategy. Based on the QTL mapping in multiple related populations derived from two parents, a maximum likelihood estimation method was proposed, which can incorporate several populations derived from three or more parents and also can be used to handle different mating designs. Taking a circle design as an example, we conducted simulation studies to study the effect of QTL heritability and sample size upon the proposed method. The results showed that under the same heritability, enhanced power of QTL detection and more precise and accurate estimation of parameters could be obtained when three F2 populations were jointly analyzed, compared with the joint analysis of any two F2 populations. Higher heritability, especially with larger sample sizes, would increase the ability of QTL detection and improve the estimation of parameters. Potential advantages of the method are as follows: firstly, the existing results of QTL mapping in single population can be compared and integrated with each other with the proposed method, therefore the ability of QTL detection and precision of QTL mapping can be improved. Secondly, owing to multiple alleles in multiple parents, the method can exploit gene resource more adequately, which will lay an important genetic groundwork for plant improvement.
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.
Huo, Dongao; Ning, Qiang; Shen, Xiaomeng; Liu, Lei; Zhang, Zuxin
The kernel number is a grain yield component and an important maize breeding goal. Ear length, kernel number per row and ear row number are highly correlated with the kernel number per ear, which eventually determines the ear weight and grain yield. In this study, two sets of F2:3 families developed from two bi-parental crosses sharing one inbred line were used to identify quantitative trait loci (QTL) for four kernel number-related traits: ear length, kernel number per row, ear row number and ear weight. A total of 39 QTLs for the four traits were identified in the two populations. The phenotypic variance explained by a single QTL ranged from 0.4% to 29.5%. Additionally, 14 overlapping QTLs formed 5 QTL clusters on chromosomes 1, 4, 5, 7, and 10. Intriguingly, six QTLs for ear length and kernel number per row overlapped in a region on chromosome 1. This region was designated qEL1.10 and was validated as being simultaneously responsible for ear length, kernel number per row and ear weight in a near isogenic line-derived population, suggesting that qEL1.10 was a pleiotropic QTL with large effects. Furthermore, the performance of hybrids generated by crossing 6 elite inbred lines with two near isogenic lines at qEL1.10 showed the breeding value of qEL1.10 for the improvement of the kernel number and grain yield of maize hybrids. This study provides a basis for further fine mapping, molecular marker-aided breeding and functional studies of kernel number-related traits in maize.
María Soledad Aguilera
Full Text Available Este artículo presenta resultados de una investigación transeccional descriptiva, sobre las metas de aprendizaje que eligen estudiantes secundarios avanzados. Se pretendió conocer y describir las eleccion es motivacionales de alumnos en diferentes situaciones pedagógicas de aula. Los datos se obtuvieron implementando una Encuesta de Relatos Motivacionales, administrada a 126 alumnos de cuatro escuelas públicas de la ciudad de Río Cuarto, Argentina. Los resultados se sistematizaron mediante estadística descriptiva y muestran que: 1 la meta de ‘aprendizaje’ fue elegida principalmente, para describir las acciones más frecuentes orientadas a obtener mejores notas, y para la manera más adecuada de resolver una m ateria especialmente difícil; 2 la meta de ‘no complicarse la vida’ fue seleccionada para caracterizar el mejor modo de enfrentar los aprendizajes, y para describir el propio comportamiento dentro del aula; 3 la meta de la ‘desesperanza aprendida’ fue elegida para describir la historia más frecuente en clases, y para el mejor modo de revolver una asignatura particularmente fácil. Dichas metas aluden a motivos, intereses, razones, creencias y deseos que se proponen los alumnos para orientar su comportamiento dentro del aula, en tanto dicho espacio configura las elecciones que realizan los estudiantes en él. Ellos persiguen diversas metas en función de las condiciones contextuales pedagógicas, optando por distintos modos de relacionarse con las tareas y los contenidos de enseñanza. Por ello, el compromiso, la dedicación y las valoraciones que realizan los alumnos sobre su propio desempeño son altamente situacionales, dependiendo del propósito personal hacia el aprendizaje.
Lin Wang; Fa Cui; Jinping Wang; Li Jun; Anming Ding; Chunhua Zhao; Xingfeng Li; Deshun Feng; Jurong Gao; Honggang Wang
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.
Maria do Socorro Padilha de Oliveira
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.
Wubs, A.M.; Heuvelink, E.; Dieleman, J.A.; Magan, J.J.; Palloix, A.; Eeuwijk, van F.A.
Abstract: QTL for a complex trait like yield tend to be unstable across environments and show QTL by environment interaction. Direct improvement of complex traits by selecting on QTL is therefore difficult. For improvement of complex traits, crop growth models can be useful, as such models can disse
Schurink, A.; Janss, L.L.G.; Heuven, H.C.M.
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
YUE; Genhua; (岳根华); Petra; Beeckmann; Gerhard; Moser; Elisabeth; Müller; Hans; Bartenschlager; Stanislav; Cepica; Jaroslav; Schroffel; Antonin; Stratil; Hermann; Geldermann
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.
van den Berg, Irene; Rodrigue; Fritz, Sebastien
The present availability of sequence data gives new opportunities to narrow down from QTL (quantitative trait locus) regions to causative mutations. Our objective was to decrease the number of candidate causative mutations in a QTL region. For this, a concordance analysis was applied for a leg co...
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...
Full Text Available Systems genetics studies often involve the mapping of numerous regulatory relations between genetic loci and expression traits. These regulatory relations form a bipartite network consisting of genetic loci and expression phenotypes. Modular network organizations may arise from the pleiotropic and polygenic regulation of gene expression. Here we analyzed the expression QTL (eQTL networks derived from expression genetic data of yeast and mouse liver and found 65 and 98 modules respectively. Computer simulation result showed that such modules rarely occurred in randomized networks with the same number of nodes and edges and same degree distribution. We also found significant within-module functional coherence. The analysis of genetic overlaps and the evidences from biomedical literature have linked some eQTL modules to physiological phenotypes. Functional coherence within the eQTL modules and genetic overlaps between the modules and physiological phenotypes suggests that eQTL modules may act as functional units underlying the higher-order phenotypes.
Josiane Isabela da Silva Rodrigues
Full Text Available The objective of this work was to map QTL for agronomic traits in a Brazilian soybean population. For this, 207 F2:3 progenies from the cross CS3035PTA276-1-5-2x UFVS2012 were genotyped and cultivated in Viçosa-MG, using randomized block design with three replications. QTL detection was carried out by linear regression and composite interval mapping. Thirty molecular markers linked to QTL were detected by linear regression for the total of nine agronomic traits. QTL for SWP (seed weight per plant, W100S (weight of 100 seeds, NPP (number of pods per plant, and NSP (number of seeds per plant were detected by composite interval mapping. Four QTL with additive effect are promising for marker-assisted selection (MAS. Particularly, the markers Satt155 and Satt300 could be useful in simultaneous selection for greater SWP, NPP, and NSP.
ZHAO Jing-lan; CHEN Min-sheng; MA Yan-ming; LI Rui-jun; REN Yong-pan; SUN Qing-quan; LI Si-shen
The QTLs for quality traits of Chinese dry noodle(CDN)were mapped based on a population of recombinant inbred lines(RILs)derived from the cross between two Chinese winter wheat varieties,Chuan 35050 and Shannong 483.Sensory quality traits of CDN were tested according to the standard of Ministry of Commerce of P.R.China(SB/T10137-93),and the textural property traits were detected using a texture analyser(TA.XTplus).We have obtained 8 putative QTLs for 6 sensory quality traits and 2 QTLs for textural property of CDN with a single QTL explainning 4.07-75.67% of phenotypic variations on chromosomes 1A,1D,3D,4A,and 6D.A duster of 3 QTLs for palate,elasticity and smoothness of CDN was found near the Glu-D1 locus on chromosome 1D with high contributions.The increasing effect come from Chuan 35050,and the relationship between the QTLs were positive.On chromosome 4A,co-location QTLs for stickiness and total score were detected in the region of Xwmc420-Xswes620-Xswes615.Their contributions were high and the increasing effects come from Shannong 483.A taste QTL QStas.sdau-4A.1 was obtained in Xsrap18-Xswes624c-Xissr25b-Xissr23b on chromosome 4A with the highest contribution of 75.67%.This QTL was a major gene and the increasing effects come from Shannong 483.
Symula, Derek J.; Frazer, Kelly A.; Ueda, Yukihiko; Denefle, Patrice; Stevens, Mary E.; Wang, Zhi-En; Locksley, Richard; Rubin, Edward M.
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.
Curt A McCartney
Full Text Available Fusarium head blight (FHB, caused by Fusarium graminearum, is a very important disease of wheat globally. Damage caused by F. graminearum includes reduced grain yield, reduced grain functional quality, and results in the presence of the trichothecene mycotoxin deoxynivalenol in Fusarium-damaged kernels. The development of FHB resistant wheat cultivars is an important component of integrated management. The objective of this study was to identify QTL for FHB resistance in a recombinant inbred line (RIL population of the spring wheat cross Kenyon/86ISMN 2137. Kenyon is a Canadian spring wheat, while 86ISMN 2137 is an unrelated spring wheat. The RIL population was evaluated for FHB resistance in six FHB nurseries. Nine additive effect QTL for FHB resistance were identified, six from Kenyon and three from 86ISMN 2137. Rht8 and Ppd-D1a co-located with two FHB resistance QTL on chromosome arm 2DS. A major QTL for FHB resistance from Kenyon (QFhb.crc-7D was identified on chromosome 7D. The QTL QFhb.crc-2D.4 from Kenyon mapped to the same region as a FHB resistance QTL from Wuhan-1 on chromosome arm 2DL. This result was unexpected since Kenyon does not share common ancestry with Wuhan-1. Other FHB resistance QTL on chromosomes 4A, 4D, and 5B also mapped to known locations of FHB resistance. Four digenic epistatic interactions were detected for FHB resistance, which involved eight QTL. None of these QTL were significant based upon additive effect QTL analysis. This study provides insight into the genetic basis of native FHB resistance in Canadian spring wheat.
He, Xiaoming; Li, Yuhong; Pandey, Sudhakar; Yandell, Brain S; Pathak, Mamta; Weng, Yiqun
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.
Full Text Available Fusarium head blight (FHB resistant line Soru#1 was hybridized with the German cultivar Naxos to generate 131 recombinant inbred lines for QTL mapping. The population was phenotyped for FHB and associated traits in spray inoculated experiments in El Batán (Mexico, spawn inoculated experiments in Ås (Norway and point inoculated experiments in Nanjing (China, with two field trials at each location. Genotyping was performed with the Illumina iSelect 90K SNP wheat chip, along with a few SSR and STS markers. A major QTL for FHB after spray and spawn inoculation was detected on 2DLc, explaining 15-22% of the phenotypic variation in different experiments. This QTL remained significant after correction for days to heading (DH and plant height (PH, while another QTL for FHB detected at the Vrn-A1 locus on 5AL almost disappeared after correction for DH and PH. Minor QTL were detected on chromosomes 2AS, 2DL, 4AL, 4DS and 5DL. In point inoculated experiments, QTL on 2DS, 3AS, 4AL and 5AL were identified in single environments. The mechanism of resistance of Soru#1 to FHB was mainly of Type I for resistance to initial infection, conditioned by the major QTL on 2DLc and minor ones that often coincided with QTL for DH, PH and anther extrusion (AE. This indicates that phenological and morphological traits and flowering biology play important roles in resistance/escape of FHB. SNPs tightly linked to resistance QTL, particularly 2DLc, could be utilized in breeding programs to facilitate the transfer and selection of those QTL.
Vasconcellos, Renato C. C.; Oraguzie, O. Blessing; Soler, Alvaro; Arkwazee, Haidar; Myers, James R.; Ferreira, Juan J.; Song, Qijian; McClean, Phil; Miklas, Phillip N.
White mold, caused by the fungus Sclerotinia sclerotiorum (Lib.) de Bary, is a major disease that limits common bean production and quality worldwide. The host-pathogen interaction is complex, with partial resistance in the host inherited as a quantitative trait with low to moderate heritability. Our objective was to identify meta-QTL conditioning partial resistance to white mold from individual QTL identified across multiple populations and environments. The physical positions for 37 individual QTL were identified across 14 recombinant inbred bi-parental populations (six new, three re-genotyped, and five from the literature). A meta-QTL analysis of the 37 QTL was conducted using the genetic linkage map of Stampede x Red Hawk population as the reference. The 37 QTL condensed into 17 named loci (12 previously named and five new) of which nine were defined as meta-QTL WM1.1, WM2.2, WM3.1, WM5.4, WM6.2, WM7.1, WM7.4, WM7.5, and WM8.3. The nine meta-QTL had confidence intervals ranging from 0.65 to 9.41 Mb. Candidate genes shown to express under S. sclerotiorum infection in other studies, including cell wall receptor kinase, COI1, ethylene responsive transcription factor, peroxidase, and MYB transcription factor, were found within the confidence interval for five of the meta-QTL. The nine meta-QTL are recommended as potential targets for MAS for partial resistance to white mold in common bean. PMID:28199342
Thirstrup, Janne Pia; Labouriau, Rodrigo; Guldbrandtsen, Bernt
Fur quality in mink (Neovison vison) is a composite trait, consisting of e.g. guard hair length, guard hair thickness and density of wool. A genome wide QTL search was performed to detect QTL for fur quality traits in mink. Here we present the results of QTL analyses for guard hair length, guard...... hair thickness and density of wool. Data from an F2-cross was analysed across fourteen chromosomes using 100 microsatellites as markers with a spacing of approximately 20 cM. The two lines used for the F2-cross were Nordic wild mink and American short nap mink. In total 1,083 animals (21 wild type, 25...... short nap, 103 F1 and 934 F2) were marker typed and recorded for the three presented fur quality traits. For the QTL-analyses a regression analysis implemented in QTL Express software was used. Evidence was found for the existence of QTL for guard hair length, guard hair thickness and density of wool...
Full Text Available Abstract We investigated the joint evolution of neutral and selected genomic regions in three chicken lines selected for immune response and in one control line. We compared the evolution of polymorphism of 21 supposedly neutral microsatellite markers versus 30 microsatellite markers located in seven quantitative trait loci (QTL regions. Divergence of lines was observed by factor analysis. Five supposedly neutral markers and 12 markers in theQTL regions showed Fst values greater than 0.15. However, the non-significant difference (P > 0.05 between matrices of genetic distances based on genotypes at supposedly neutral markers on the one hand, and at markers in QTL regions, on the other hand, showed that none of the markers in the QTL regions were influenced by selection. A supposedly neutral marker and a marker located in the QTL region on chromosome 14 showed temporal variations in allele frequencies that could not be explained by drift only. Finally, to confirm thatmarkers located inQTL regions on chromosomes 1, 7 and 14were under the influence of selection, simulations were performed using haplotype dropping along the existing pedigree. In the zone located on chromosome 14, the simulation results confirmed that selection had an effect on the evolution of polymorphism of markers within the zone.
Lam Mary K
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.
Tur Mongé, Inma 1985-
La cartogra a gen etica dels trets quantitatius d'expressi o (eQTL) esdev e un gran repte degut a la naturalesa multivariant d'alta dimensionalitat dels trets continus d'expressi o g enica i els genotips discrets dels experiments de gen omica gen etica. A m es de l'heterogene tat de l'expressi o produ da pels factors de confusi o i altres fonts de variabilitat no desitjada, els efectes indirectes s'estenen per tots els gens com a resultat de perturbacions gen etiques, molecul...
Raul Sampaio de Almeida Prado and Marcilio Dias Silveira da Mota
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.
Aurinelza Batista Teixeira Condé
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.
Borràs Català, Vicent; LÓPEZ-ROLDÁN, Pedro
Son casi innumerables las reflexiones que se han hecho en el campo de la metodología de las ciencias sociales, sobre la dicotomía, real o inexistente, entre las perspectivas de análisis cuantitativo y cualitativo, mientras que han sido menos abundantes los trabajos teóricos, aunque van siendo más frecuentes los empíricos, que han tratado de compatibilizar y/o complementar ambas perspectivas. En muchos casos los trabajos cualitativos cubren solamente los primeros pasos de la investigación soci...
Borràs Català, Vicent; López, Pedro; Lozares Colina, Carlos
Son casi innumerables las reflexiones que se han hecho en el campo de la metodología de las ciencias sociales, sobre la dicotomía, real o inexistente, entre las perspectivas de análisis cuantitativo y cualitativo, mientras que han sido menos abundantes los trabajos teóricos, aunque van siendo más abundantes los empíricos, que han tratado de compatibilizar y/o complementar ambas perspectivas. En muchos casos los trabajos cualitativos cubren solamente los primeros pasos de la investigación soci...
Cesar Augusto Ayala Diago
Full Text Available 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.
Jeffrey A Fawcett
Full Text Available Genes involved in the transition from wild to cultivated crop species should be of great agronomic importance. Population genomic approaches utilizing genome resequencing data have been recently applied for this purpose, although it only reports a large list of candidate genes with no biological information. Here, by resequencing more than 30 genomes altogether of wild rice Oryza rufipogon and cultivated rice O. sativa, we identified a number of regions with clear footprints of selection during the domestication process. We then focused on identifying candidate domestication genes in these regions by utilizing the wealth of QTL information in rice. We were able to identify a number of interesting candidates such as transcription factors that should control key domestication traits such as shattering, awn length, and seed dormancy. Other candidates include those that might have been related to the improvement of grain quality and those that might have been involved in the local adaptation to dry conditions and colder environments. Our study shows that population genomic approaches and QTL mapping information can be used together to identify genes that might be of agronomic importance.
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.
Jia, Jun-Zhong; Tian, Li-Ping; Xue, Lin; Wei, Yi-Nong
Two hundred and six F2:3 families from the cross between TD22 and HT-1-1-1-1 were used for dynamic QTL research of tomato soluble solid content and correlative traits, and correlation analysis of soluble solid content (SSC) with fruit weight (FW), fruit shape index (FSI), soluble sugar, vitamin C (VC), and organic acid at three different development stages. The results showed that there were differences in QTL loci for soluble solid content during the three stages of tomato fruit development. Four and eight QTLs were detected in green ripe stage and red ripe stage, respectively. These QTLs showed dynamic changes, and two markers LEaat006 and Tomato|TC162363 were detected in two stages, which might be useful in molecular-marker assisted selection (MAS). The result also showed that there was extremely significant difference in SSC at the three different stages, and its main correlative traits were different at different stages. Soluble solid content was positively correlated with soluble sugar, but negatively correlated with FW at green ripe stage; SSC was positively correlated with soluble sugar and organic acid at yellow ripe stage; SSC was positively correlated with soluble sugar and organic acid, but negatively correlated with fruit weight at red ripe stage. Based on correlation analysis of these traits, linear regression model was constructed. Non-tested varieties were used to test the fitness, and the result showed that it is well fitted, and the fitness is above 95%.
Full Text Available Biomass yield of rice (Oryza sativa L. is an important breeding target, yet it is not easy to improve because the trait is complex and phenotyping is laborious. Using progeny derived from a cross between two high-yielding Japanese cultivars, we evaluated whether quantitative trait locus (QTL-based selection can improve biomass yield. As a measure of biomass yield, we used plant weight (aboveground parts only, which included grain weight and stem and leaf weight. We measured these and related traits in recombinant inbred lines. Phenotypic values for these traits showed a continuous distribution with transgressive segregation, suggesting that selection can affect plant weight in the progeny. Four significant QTLs were mapped for plant weight, three for grain weight, and five for stem and leaf weight (at α = 0.05; some of them overlapped. Multiple regression analysis showed that about 43% of the phenotypic variance of plant weight was significantly explained (P < 0.0001 by six of the QTLs. From F2 plants derived from the same parental cross as the recombinant inbred lines, we divergently selected lines that carried alleles with positive or negative additive effects at these QTLs, and performed successive selfing. In the resulting F6 lines and parents, plant weight significantly differed among the genotypes (at α = 0.05. These results demonstrate that QTL-based selection is effective in improving rice biomass yield.
XU Jichen; WANG Jiulin; LING Zhongzhuan; ZHU Lihuang
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.
Thomson Peter C
Full Text Available Abstract An (Awassi × Merino × Merino single-sire backcross family with 165 male offspring was used to map quantitative trait loci (QTL for body composition traits on a framework map of 189 microsatellite loci across all autosomes. Two cohorts were created from the experimental progeny to represent alternative maturity classes for body composition assessment. Animals were raised under paddock conditions prior to entering the feedlot for a 90-day fattening phase. Body composition traits were derived in vivo at the end of the experiment prior to slaughter at 2 (cohort 1 and 3.5 (cohort 2 years of age, using computed tomography. Image analysis was used to gain accurate predictions for 13 traits describing major fat depots, lean muscle, bone, body proportions and body weight which were used for single- and two-QTL mapping analysis. Using a maximum-likelihood approach, three highly significant (LOD ≥ 3, 15 significant (LOD ≥ 2, and 11 suggestive QTL (1.7 ≤ LOD P P A meta-assembly of ovine QTL for carcass traits from this study and public domain sources was performed and compared with a corresponding bovine meta-assembly. The assembly demonstrated QTL with effects on carcass composition in homologous regions on OAR1, 2, 6 and 21.
Full Text Available Quantitative Trait Loci (QTL mapping is a powerful technique for dissecting the genetic basis of traits and species differences. Established tomato mapping populations between domesticated tomato (Solanum lycopersicum and its more distant interfertile relatives typically follow a near isogenic line (NIL design, such as the S. pennellii Introgression Line (IL population, with a single wild introgression per line in an otherwise domesticated genetic background. Here, we report on a new advanced backcross QTL mapping resource for tomato, derived from a cross between the M82 tomato cultivar and S. pennellii. This so-called Backcrossed Inbred Line (BIL population is comprised of a mix of BC2 and BC3 lines, with domesticated tomato as the recurrent parent. The BIL population is complementary to the existing S. pennellii IL population, with which it shares parents. Using the BILs, we mapped traits for leaf complexity, leaflet shape, and flowering time. We demonstrate the utility of the BILs for fine-mapping QTL, particularly QTL initially mapped in the ILs, by fine-mapping several QTL to single or few candidate genes. Moreover, we confirm the value of a backcrossed population with multiple introgressions per line, such as the BILs, for epistatic QTL mapping. Our work was further enabled by the development of our own statistical inference and visualization tools, namely a heterogeneous hidden Markov model for genotyping the lines, and by using state-of-the-art sparse regression techniques for QTL mapping.
Roennberg-Waestljung, Ann Christin; Bertholdsson, Nils-Ove; Glynn, Carolyn; Weih, Martin; Aahman, Inger [SLU, Uppsala (Sweden). Dept. of Plant Biology and Forest Genetics
Quantitative trait loci (QTL) for growth traits, water use efficiency and tolerance/resistance against metals and herbivores have been identified. A hybrid F2 population originating from a cross between a Salix dasyclados-clone (SW901290) and a S. viminalis-clone ('Jorunn') was used for the different studies in this project. The growth response was analyzed in a greenhouse experiment with two water treatments, normal and drought. In addition, three field experiments with contrasting soils and climates were established. QTL specific for each treatment or field environment but also QTL stable over the treatments or field environments were detected. Each QTL explained from 8 to 29 % of the phenotypic variation depending on trait, treatment or field environment. Clusters of QTL for different traits were mapped indicating a common genetic base or tightly-linked QTL. Stable QTL identified for dryweight can be useful tools for early selection in Salix. In a separate greenhouse experiment, with a subset of ten genotypes from the F2 population, we show that genotype is more important than irrigation treatment for production of phenolic substances as well as for resistance to herbivory by P vulgatissima.
The relative superiority in selection response of two basic marker-assisted selection strategies, marker-as- sisted BLUP (MBLUP) and two-stage selection, in comparison to standard BLUP was investigated using stochastic simulation of a closed nucleus herd. In marker-assisted BLUP the marker information and the phenotypic information were utilized simultaneously for selecting parental animals, whereas in two-stage selection they were utilized separately in two stages. Different heritabilities and QTL sizes were considered in the simulation. The QTL was assumed to be referred only via flanking markers, which were incompletely linked to the QTL. It was shown that both MBLUP and two-stage selection increased the QTL response but decreased the polygenic response. When the heritability was low or the QTL effect was large MBLUP was superior to standard BLUP by up to 5% with respect to total genetic response. While the two-stage selection did not show any superiority although it gave extremely large increase in QTL response due to a rapid increase in favorable QTL allele frequency. The relative responses of MAS were stark associated with the generations of selection. The superiority or inferiority of MAS was large in the early generations and became small or vanished in the later generations.
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.
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.
Hanocq, E; Niarquin, M; Heumez, E; Rousset, M; Le Gouis, J
Earliness, an adaptative trait and factor of variation for agronomic characters, is a major trait in plant breeding. Its constituent traits, photoperiod sensitivity (PS), vernalization requirement (VR) and intrinsic earliness (IE), are largely under independent genetic controls. Mapping of major genes and quantitative trait loci (QTL) controlling these components is in progress. Most of the studies focusing on earliness considered it as a whole or through one (or two) of its components. The purpose of this study was to detect and map QTL for the three traits together through an experimental design combining field trials and controlled growth conditions. QTL were mapped in a population of F(7) recombinant inbred lines derived by single-seed descent from a cross between two French varieties, 'Renan' and 'Recital'. A map was previously constructed, based on 194 lines and 254 markers, covering about 77% of the genome. Globally, 13 QTL with a LOD>2.5 were detected, of which four control PS, five control VR and four control IE. Two major photoperiod sensitive QTL, together explaining more than 31% of the phenotypic variation, were mapped on chromosomes 2B and 2D, at the same position as the two major genes Ppd-B1 and Ppd-D1. One major VR QTL explaining (depending on the year) 21.8-39.6% of the phenotypic variation was mapped on 5A. Among the other QTL, two QTL of PS and VR not referenced so far were detected on 5A and 6D, respectively. A VR QTL already detected on 2B in a connected population was confirmed.
Suchocki, T; Szyda, J; Zhang, Q
In statistical models, a quantitative trait locus (QTL) effect has been incorporated either as a fixed or as a random term, but, up to now, it has been mainly considered as a time-independent variable. However, for traits recorded repeatedly, it is very interesting to investigate the variation of QTL over time. The major goal of this study was to estimate the position and effect of QTL for milk, fat, protein yields and for somatic cell score based on test day records, while testing whether the effects are constant or variable throughout lactation. The analysed data consisted of 23 paternal half-sib families (716 daughters of 23 sires) of Chinese Holstein-Friesian cattle genotyped at 14 microsatellites located in the area of the casein loci on BTA6. A sequence of three models was used: (i) a lactation model, (ii) a random regression model with a QTL constant in time and (iii) a random regression model with a QTL variable in time. The results showed that, for each production trait, at least one significant QTL exists. For milk and protein yields, the QTL effect was variable in time, while for fat yield, each of the three models resulted in a significant QTL effect. When a QTL is incorporated into a model as a constant over time, its effect is averaged over lactation stages and may, thereby, be difficult or even impossible to be detected. Our results showed that, in such a situation, only a longitudinal model is able to identify loci significantly influencing trait variation.
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.
Full Text Available Abstract Background Numerous QTL mapping resource populations are available in livestock species. Usually they are analysed separately, although the same founder breeds are often used. The aim of the present study was to show the strength of analysing F2-crosses jointly in pig breeding when the founder breeds of several F2-crosses are the same. Methods Three porcine F2-crosses were generated from three founder breeds (i.e. Meishan, Pietrain and wild boar. The crosses were analysed jointly, using a flexible genetic model that estimated an additive QTL effect for each founder breed allele and a dominant QTL effect for each combination of alleles derived from different founder breeds. The following traits were analysed: daily gain, back fat and carcass weight. Substantial phenotypic variation was observed within and between crosses. Multiple QTL, multiple QTL alleles and imprinting effects were considered. The results were compared to those obtained when each cross was analysed separately. Results For daily gain, back fat and carcass weight, 13, 15 and 16 QTL were found, respectively. For back fat, daily gain and carcass weight, respectively three, four, and five loci showed significant imprinting effects. The number of QTL mapped was much higher than when each design was analysed individually. Additionally, the test statistic plot along the chromosomes was much sharper leading to smaller QTL confidence intervals. In many cases, three QTL alleles were observed. Conclusions The present study showed the strength of analysing three connected F2-crosses jointly. In this experiment, statistical power was high because of the reduced number of estimated parameters and the large number of individuals. The applied model was flexible and was computationally fast.
Liu, Peng; Wang, Le; Wan, Zi Yi; Ye, Bao Qing; Huang, Shuqing; Wong, Sek-Man; Yue, Gen Hua
Viral nervous necrosis disease (VNN), caused by nervous necrosis virus (NNV), leads to mass mortality in mariculture. However, phenotypic selection for resistance against VNN is very difficult. To facilitate marker-assisted selection (MAS) for resistance against VNN and understanding of the genetic architecture underlying the resistance against this disease, we mapped quantitative trait loci (QTL) for resistance against VNN in Asian seabass. We challenged fingerlings at 37 days post-hatching (dph), from a single back-cross family, with NNV at a concentration of 9 × 10(6) TCID50/ml for 2 h. Daily mortalities were recorded and collected. A panel of 330 mortalities and 190 surviving fingerlings was genotyped using 149 microsatellites with 145 successfully mapped markers covering 24 linkage groups (LGs). Analysis of QTL for both resistance against VNN and survival time was conducted using interval mapping. Five significant QTL located in four LGs and eight suggestive QTL in seven LGs were identified for resistance. Another five significant QTL in three LGs and five suggestive QTL in three LGs were detected for survival time. One significant QTL, spanning 3 cM in LG20, was identified for both resistance and survival time. These QTL explained 2.2-4.1% of the phenotypic variance for resistance and 2.2-3.3% of the phenotypic variance for survival time, respectively. Our results suggest that VNN resistance in Asian seabass is controlled by many loci with small effects. Our data provide information for fine mapping of QTL and identification of candidate genes for a better understanding of the mechanism of disease resistance.
Rolleri, Cristina H.
. 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.
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.
Truntzler, M; Barrière, Y; Sawkins, M C; Lespinasse, D; Betran, J; Charcosset, A; Moreau, L
A meta-analysis of quantitative trait loci (QTL) associated with plant digestibility and cell wall composition in maize was carried out using results from 11 different mapping experiments. Statistical methods implemented in "MetaQTL" software were used to build a consensus map, project QTL positions and perform meta-analysis. Fifty-nine QTL for traits associated with digestibility and 150 QTL for traits associated with cell wall composition were included in the analysis. We identified 26 and 42 metaQTL for digestibility and cell wall composition traits, respectively. Fifteen metaQTL with confidence interval (CI) smaller than 10 cM were identified. As expected from trait correlations, 42% of metaQTL for digestibility displayed overlapping CIs with metaQTL for cell wall composition traits. Coincidences were particularly strong on chromosomes 1 and 3. In a second step, 356 genes selected from the MAIZEWALL database as candidates for the cell wall biosynthesis pathway were positioned on our consensus map. Colocalizations between candidate genes and metaQTL positions appeared globally significant based on χ(2) tests. This study contributed in identifying key chromosomal regions involved in silage quality and potentially associated genes for most of these regions. These genes deserve further investigation, in particular through association mapping.
Katou, Taku; Namise, Masahiro; Kitagaki, Hiroshi; Akao, Takeshi; Shimoi, Hitoshi
A haploid sake yeast strain derived from the commercial diploid sake yeast strain Kyokai no. 7 showed better characteristics for sake brewing compared to the haploid laboratory yeast strain X2180-1B, including higher production of ethanol and aromatic components. A hybrid of these two strains showed intermediate characteristics in most cases. After sporulation of the hybrid strain, we obtained 100 haploid segregants of the hybrid. Small-scale sake brewing tests of these segregants showed a smooth continuous distribution of the sake brewing characteristics, suggesting that these traits are determined by multiple quantitative trait loci (QTLs). To examine these sake brewing characteristics at the genomic level, we performed QTL analysis of sake brewing characteristics using 142 DNA markers that showed heterogeneity between the two parental strains. As a result, we identified 25 significant QTLs involved in the specification of sake brewing characteristics such as ethanol fermentation and the production of aromatic components.
Inès Ben Sadok
Full Text Available One of the challenge fruit growers are facing is to balance between tree production and vegetative growth from year to year. To investigate the existence of genetic determinism for reproductive behaviour in olive tree, we studied an olive segregating population derived from a cross between 'Olivière' and 'Arbequina' cultivars. Our strategy was based on (i an annual assessment of individual trees yield, and (ii a decomposition of adult growth units at the crown periphery into quantitative variables related to both flowering and fruiting process in relation to their growth and branching. Genetic models, including the year, genotype effects and their interactions, were built with variance function and correlation structure of residuals when necessary. Among the progeny, trees were either 'ON' or 'OFF' for a given year and patterns of regular vs. irregular bearing were revealed. Genotype effect was significant on yield but not for flowering traits at growth unit (GU scale, whereas the interaction between genotype and year was significant for both traits. A strong genetic effect was found for all fruiting traits without interaction with the year. Based on the new constructed genetic map, QTLs with small effects were detected, revealing multigenic control of the studied traits. Many were associated to alleles from 'Arbequina'. Genetic correlations were found between Yield and Fruit set at GU scale suggesting a common genetic control, even though QTL co-localisations were in spe`cific years only. Most QTL were associated to flowering traits in specific years, even though reproductive traits at GU scale did not capture the bearing status of the trees in a given year. Results were also interpreted with respect to ontogenetic changes of growth and branching, and an alternative sampling strategy was proposed for capturing tree fruiting behaviour. Regular bearing progenies were identified and could constitute innovative material for selection programs.
Full Text Available Expression Quantitative Trait Locus (eQTL analysis is a powerful tool to study the biological mechanisms linking the genotype with gene expression. Such analyses can identify genomic locations where genotypic variants influence the expression of genes, both in close proximity to the variant (cis-eQTL, and on other chromosomes (trans-eQTL. Many traditional eQTL methods are based on a linear regression model. In this study, we propose a novel method by which to identify eQTL associations with information theory and machine learning approaches. Mutual Information (MI is used to describe the association between genetic marker and gene expression. MI can detect both linear and non-linear associations. What's more, it can capture the heterogeneity of the population. Advanced feature selection methods, Maximum Relevance Minimum Redundancy (mRMR and Incremental Feature Selection (IFS, were applied to optimize the selection of the affected genes by the genetic marker. When we applied our method to a study of apoE-deficient mice, it was found that the cis-acting eQTLs are stronger than trans-acting eQTLs but there are more trans-acting eQTLs than cis-acting eQTLs. We compared our results (mRMR.eQTL with R/qtl, and MatrixEQTL (modelLINEAR and modelANOVA. In female mice, 67.9% of mRMR.eQTL results can be confirmed by at least two other methods while only 14.4% of R/qtl result can be confirmed by at least two other methods. In male mice, 74.1% of mRMR.eQTL results can be confirmed by at least two other methods while only 18.2% of R/qtl result can be confirmed by at least two other methods. Our methods provide a new way to identify the association between genetic markers and gene expression. Our software is available from supporting information.
Shuaidong Hu; Thomas Lübberstedt; Guangwu Zhao; Michael Lee
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...
Francisco Eduardo Torres
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.
Jun-Qiang Ding; Jin-Liang Ma; Chun-Rong Zhang; Hua-Fang Dong; Zhang-Ying Xi; Zong-Liang Xia; Jian-Yu Wu
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.
Huang, Yung-Fen; Bertrand, Yves; Guiraud, Jean-Luc; Vialet, Sandrine; Launay, Amandine; Cheynier, Véronique; Terrier, Nancy; This, Patrice
Expression quantitative locus (eQTL) mapping was proposed as a valuable approach to dissect the genetic basis of transcript variation, one of the prime causes of natural phenotypic variation. Few eQTL studies have been performed on woody species due to the difficulty in sample homogenisation. Based on previous knowledge on berry colour formation, we performed eQTL mapping in field experimentation of grapevine with appropriate sampling criteria. The transcript level of VvUFGT, a key enzyme for anthocyanin synthesis was measured by real-time qRT-PCR in grape berry on a 191-individual pseudo-F1 progeny, derived from a cross between Syrah and Grenache cultivars. Two eQTLs were identified: one, explaining 20%, of genotypic variance and co-locating with VvUFGT itself (cis-eQTL), was principally due to the contrast between Grenache alleles; the other, explaining 35% of genotypic variance, was a trans-eQTL due to Syrah allelic contrast and co-located with VvMYBAs, transcription factors known to activate the expression of VvUFGT. This study assessed and validated the feasibility of eQTL mapping approach in grapevine and offered insights and new hypotheses on grape skin colour formation.
Full Text Available Abstract Individual loci of economic importance (QTL can be detected by comparing the inheritance of a trait and the inheritance of loci with alleles readily identifiable by laboratory methods (genetic markers. Data on allele segregation at the individual level are costly and alternatives have been proposed that make use of allele frequencies among progeny, rather than individual genotypes. Among the factors that may affect the power of the set up, the most important are those intrinsic to the QTL: the additive effect of the QTL, and its dominance, and distance between markers and QTL. Other factors are relative to the choice of animals and markers, such as the frequency of the QTL and marker alleles among dams and sires. Data collection may affect the detection power through the size of half-sib families, selection rate within families, and the technical error incurred when estimating genetic frequencies. We present results for a sensitivity analysis for QTL detection using pools of DNA from selected half-sibs. Simulations showed that conclusive detection may be achieved with families of at least 500 half-sibs if sires are chosen on the criteria that most of their marker alleles are either both missing, or one is fixed, among dams.
LI Jia-qi; ZHANG Hao; LIU Xiao-hong; GAO Ping; WANG Chong; WU Qiu-hao; ZHANG Xi-quan; CHEN Yao-sheng
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.
Xiangling L(U); Xinhai LI; Chuanxiao XIE; Zhuanfang HAO; Hailian JI; Liyu SHI; Shihuang ZHANG
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.
Xiaoqian; Wang; Yunlong; Pang; Jian; Zhang; Qiang; Zhang; Yonghong; Tao; Bo; Feng; Tianqing; Zheng; Jianlong; Xu; Zhikang; Li
QTLs for quantitative traits are influenced by genetic background(GB) and environment.Identification of QTL with GB independency and environmental stability is prerequisite for effective marker-assisted selection(MAS). In this study, QTLs and QTL × environment interactions affecting grain yield per plant(GY) and its component traits, filled grain number per panicle(FGN), panicle number per plant(PN) and 1000-grain weight(TGW) across six environments were dissected using two sets of reciprocal introgression lines(ILs) derived from the cross Lemont × Teqing and SNP genotypic data. ANOVA indicated that the differences among genotypes and environments within each set of ILs were highly significant for all traits. A total of 72 distinct QTLs for GY and its component traits including 15 for GY, 25 for FGN, 18 for PN, and 29 for TGW were detected over the six environments. Most QTLs(87.4%) showed significant QTL × environment interactions(QEIs) and appeared to be more or less environment-specific. Among 72 QTLs, 15(20.8%) QTLs and 12(16.7%) QEIs were commonly identified in both backgrounds, indicating QTL especially QEI for yield and its component traits had strong GB effects. Four QTL regions affecting GY and its component traits, including S1269707–S4288071, S16661497–S17511092, and S35861863–S36341768 on chromosome 3, and S4134205–S7643153 on chromosome 5, were detected in both backgrounds and coincided with cloned genes for yield-related traits. These regions can be the targeted in rice breeding for high yield potential through MAS. Application of QTL main effects and their environmental interaction effects in MAS was discussed in detail.
Felipe Bermudez Pereira
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.
Full Text Available Estudiamos los esqueletos teñidos y transparentados como también secos de veinticuatro especies pertenecientes a los principales clados de Liolaemus (grupos L. kingii - L. archeforus, L. lineomaculatus, L. chiliensis, L. signifer, L. boulengeri y L. wiegmannii de acuerdo con la taxonomía de Etheridge, 1995. Pudimos describir variación en la morfología, proporciones y otras carácterísticas que pueden definirse como caracteres. Los caracteres descriptos en este estudio incluyen variación en los cartílagos de las costillas preesternales, procesos de la cintura pélvica, laringe, anillos traqueales y aparato hioideo, variación en la morfología de huesos craneales y poscraneales. Se describe un total de 35 caracteres (uno autoapomórfico que representan diecisiete continuos (morfométricos o no, nueve binarios polimórficos, seis binarios no polimórficos, dos multiestado polimórficos y un multiestado no polimórfico. Se encontró un alto grado de congruencia de la información brindada por los caracteres encontrados en el esqueleto con los principales grupos de especies aceptados actualmente en la literatura. We studied claired and stained and dry skeletons of twenty four species belonging to the main clades of Liolaemus (L. kingii- L. archeforus, L. lineomaculatus, L. chiliensis, L. signifer, L. boulengeri and L. wiegmannii groups, according to the taxonomy of Etheridge, 1995. We were able to describe variation in the morphology, measurement ratios and other features that could be defined as characters. Characters described in this study include variation on cartilages of presternal ribs, pelvic processes, larynx, tracheal rings and hyoid apparatus, variation on the morphology of cranial and postcranial bones. The total number of characters described here is thirty five (one autapomorphic that represent seventeen continuos (morphometric or not, nine binary polymorphic, six binary not polymorphic, two multistate polymorphic and one
Alves, Silfran Rog?rio Marialva
A presente pesquisa teve como objetivos avaliar o pot?ncial da espectroscopia no infravermelho pr?ximo (NIR) para distinguir esp?cies do g?nero Capsicum, avaliar a viabilidade de cruzamento entre subamostras de Capsicum chinense Jacq. com Capsicum annuum L. e analisar a variabilidade gen?tica a partir de par?metros gen?ticos para os caracteres: germina??o e vigor de sementes de germoplasma de C. chinense Jacq.. Para o estudo da discrimina??o de esp?cies de Capsicum com espec...
Wim E. Crusio
Full Text Available In this study we identified a quantitative trait locus (QTL on mouse Chromosome 7 associated with locomotor activity and rearing post morphine treatment. This QTL was revealed after correcting for the effects of another QTL peak on Chromosome 10 using composite interval mapping. The positional candidate genes are Syt9 and Ppfibp2. Several other genes within the interval are linked to neural processes, locomotor activity, and the defensive response to harmful stimuli.
Wim E. Crusio
Full Text Available In this study we identified a quantitative trait locus (QTL on mouse Chromosome 7 associated with locomotor activity and rearing post morphine treatment. This QTL was revealed after correcting for the effects of another QTL peak on Chromosome 10 using composite interval mapping. The positional candidate genes are Syt9 and Ppfibp2. Several other genes within the interval are linked to neural processes, locomotor activity, and the defensive response to harmful stimuli.
González López, Óscar R.
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.
Full Text Available BACKGROUND: Improved genetic resolution and availability of sequenced genomes have made positional cloning of moderate-effect QTL realistic in several systems, emphasizing the need for precise and accurate derivation of positional confidence intervals (CIs for QTL. Support interval (SI methods based on the shape of the QTL likelihood curve have proven adequate for standard interval mapping, but have not been shown to be appropriate for use with composite interval mapping (CIM, which is one of the most commonly used QTL mapping methods. RESULTS: Based on a non-parametric confidence interval (NPCI method designed for use with the Haley-Knott regression method for mapping QTL, a CIM-specific method (CIM-NPCI was developed to appropriately account for the selection of background markers during analysis of bootstrap-resampled data sets. Coverage probabilities and interval widths resulting from use of the NPCI, SI, and CIM-NPCI methods were compared in a series of simulations analyzed via CIM, wherein four genetic effects were simulated in chromosomal regions with distinct marker densities while heritability was fixed at 0.6 for a population of 200 isolines. CIM-NPCIs consistently capture the simulated QTL across these conditions while slightly narrower SIs and NPCIs fail at unacceptably high rates, especially in genomic regions where marker density is high, which is increasingly common for real studies. The effects of a known CIM bias toward locating QTL peaks at markers were also investigated for each marker density case. Evaluation of sub-simulations that varied according to the positions of simulated effects relative to the nearest markers showed that the CIM-NPCI method overcomes this bias, offering an explanation for the improved coverage probabilities when marker densities are high. CONCLUSIONS: Extensive simulation studies herein demonstrate that the QTL confidence interval methods typically used to positionally evaluate CIM results can be
Full Text Available Abstract Background Linkage mapping is used to identify genomic regions affecting the expression of complex traits. However, when experimental crosses such as F2 populations or backcrosses are used to map regions containing a Quantitative Trait Locus (QTL, the size of the regions identified remains quite large, i.e. 10 or more Mb. Thus, other experimental strategies are needed to refine the QTL locations. Advanced Intercross Lines (AIL are produced by repeated intercrossing of F2 animals and successive generations, which decrease linkage disequilibrium in a controlled manner. Although this approach is seen as promising, both to replicate QTL analyses and fine-map QTL, only a few AIL datasets, all originating from inbred founders, have been reported in the literature. Methods We have produced a nine-generation AIL pedigree (n = 1529 from two outbred chicken lines divergently selected for body weight at eight weeks of age. All animals were weighed at eight weeks of age and genotyped for SNP located in nine genomic regions where significant or suggestive QTL had previously been detected in the F2 population. In parallel, we have developed a novel strategy to analyse the data that uses both genotype and pedigree information of all AIL individuals to replicate the detection of and fine-map QTL affecting juvenile body weight. Results Five of the nine QTL detected with the original F2 population were confirmed and fine-mapped with the AIL, while for the remaining four, only suggestive evidence of their existence was obtained. All original QTL were confirmed as a single locus, except for one, which split into two linked QTL. Conclusions Our results indicate that many of the QTL, which are genome-wide significant or suggestive in the analyses of large intercross populations, are true effects that can be replicated and fine-mapped using AIL. Key factors for success are the use of large populations and powerful statistical tools. Moreover, we believe that
Parés Casanova, Pere-Miquel
Full Text Available ResumenSe estudiaron las relaciones fenéticas entre ocho razas o tipos ovinosturcos y uno de francés a fin de evaluar las variables más discriminantes en la distinción racial. Para ello se compuso una matriz de caracteres morfológicos (7 variables y caracteres referidos al vellón (4 variables, siendo sometidas a un análisis de agrupación de K-medias. Nuestros resultados sugieren que cuatro características del vellón -peso del vellón sucio, longitud de la mecha, diámetro de las fibras, y porcentaje de fibras meduladas- ya permiten una diferenciación clara entre grupos.SummaryTo evaluate which are the best discriminant variables to distinguishovine breeds, phenetic relationships among eight turkish and onefrench breeds or types were studied. A matrix of 7 morphological and4 wool characters were analyzed by a K-means test. Results suggestthat four fleece traits alone –total wool weight, staple length, fiberdiameter and percentage of medullated fibers- permit a glimpse ofdifferentiation among sheep breeds.
Miyakawa, Misato O; Mikheyev, Alexander S
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 diversity of CSD
Richard S. Fletcher
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.
Julian K Christians
Full Text Available Infections caused by the fungus Aspergillus are a major cause of morbidity and mortality in immunocompromised populations. To identify genes required for virulence that could be used as targets for novel treatments, we mapped quantitative trait loci (QTL affecting virulence in the progeny of a cross between two strains of A. nidulans (FGSC strains A4 and A91. We genotyped 61 progeny at 739 single nucleotide polymorphisms (SNP spread throughout the genome, and constructed a linkage map that was largely consistent with the genomic sequence, with the exception of one potential inversion of ∼527 kb on Chromosome V. The estimated genome size was 3705 cM and the average intermarker spacing was 5.0 cM. The average ratio of physical distance to genetic distance was 8.1 kb/cM, which is similar to previous estimates, and variation in recombination rate was significantly positively correlated with GC content, a pattern seen in other taxa. To map QTL affecting virulence, we measured the ability of each progeny strain to kill model hosts, larvae of the wax moth Galleria mellonella. We detected three QTL affecting in vivo virulence that were distinct from QTL affecting in vitro growth, and mapped the virulence QTL to regions containing 7-24 genes, excluding genes with no sequence variation between the parental strains and genes with only synonymous SNPs. None of the genes in our QTL target regions have been previously associated with virulence in Aspergillus, and almost half of these genes are currently annotated as "hypothetical". This study is the first to map QTL affecting the virulence of a fungal pathogen in an animal host, and our results illustrate the power of this approach to identify a short list of unknown genes for further investigation.
Whitney, Kenneth D.; Broman, Karl W.; Kane, Nolan C.; Hovick, Stephen M.; Randell, Rebecca A.; Rieseberg, Loren H.
The wild North American sunflowers Helianthus annuus and H. debilis are participants in one of the earliest identified examples of adaptive trait introgression, and the exchange is hypothesized to have triggered a range expansion in H. annuus. However, the genetic basis of the adaptive exchange has not been examined. Here, we combine quantitative trait locus (QTL) mapping with field measurements of fitness to identify candidate H. debilis QTL alleles likely to have introgressed into H. annuus to form the natural hybrid lineage H. a. texanus. Two 500-individual BC1 mapping populations were grown in central Texas, genotyped for 384 SNP markers, and then phenotyped in the field for two fitness and 22 herbivore resistance, ecophysiological, phenological, and architectural traits. We identified a total of 110 QTL, including at least one QTL for 22 of the 24 traits. Over 75% of traits exhibited at least one H. debilis QTL allele that would shift the trait in the direction of the wild hybrid H. a. texanus. We identified three chromosomal regions where H. debilis alleles increased both female and male components of fitness; these regions are expected to be strongly favored in the wild. QTL for a number of other ecophysiological, phenological, and architectural traits co-localized with these three regions and are candidates for the actual traits driving adaptive shifts. G × E interactions played a modest role, with 17% of the QTL showing potentially divergent phenotypic effects between the two field sites. The candidate adaptive chromosomal regions identified here serve as explicit hypotheses for how the genetic architecture of the hybrid lineage came into existence. PMID:25522096
Francisco Cervantes Ortiz; Gabino García de los Santos; Aquiles Carballo Carballo; David Bergvinson; J. Luis Crossa; Mariano Mendoza Elos; Ernesto Moreno Martínez
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...
Roberto Fritsche-Neto; Glauco Vieira Miranda; Rodrigo Oliveira DeLima; Leandro Vagno de Souza; Jaeveson da Silva
O objetivo deste trabalho foi identificar os efeitos genéticos que controlam a herança de caracteres associados à eficiência de utilização do fósforo (EUP) em milho e determinar as relações entre esses caracteres. Foi realizado um dialelo entre seis cultivares de milho do qual foram obtidas 15 combinações híbridas. Estas cultivares foram avaliadas em alta e baixa disponibilidade de fósforo, em casa de vegetação e campo. Foram medidas a resposta das plantas à disponibilidade de fósforo (RU) e ...
Jongjoo, Kim; Davis, Scott K; Taylor, Jeremy F
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.
CHEN Liang; LOU Qiao-jun; SUN Zong-xiu; XING Yong-zhong; YU Xin-qiao; LUO Li-jun
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.
An F2 population derived from the cross between Jiucaiqing (japonica) and IR36 (indica) was used to analyze the inheritance of salt tolerance in rice by genetic model of major-genes plus polygenes, and to map the corresponding QTLs by SSR molecular markers. Rice plants of P1, P2, F1 and F2 at 5- to 6- leaf stage were treated under 140 mmol/L NaCl for 10 days. Three indices representing the ability of salt tolerance of rice seedlings were measured, including salt tolerance rating (STR), Na+/K+ ratio in roots and dry matter weight of shoots (DWS). STR, Na+/K+ and DWS were all controlled by two major genes with modification by polygenes. Heritability of these traits from major genes was 17.8, 53.3 and 52.3%, respectively. The linkage map constructed by 62 SSR molecular markers covered a total length of about 1 142 cM. There were three QTLs detected for STR located on chromosome 1, 5 and 9, two QTLs for DWS on chromosomes 8 and 9, and two QTLs for Na+/K+ on chromosomes 2 and 6, one on each chromosome respectively. Single QTL accounted for 6.7 to 19.3% of phenotypic variation. Identification method of salt tolerance in rice and breeding of rice varieties with salt tolerance based on molecular markers assisted selection had been discussed.
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.
CHEN Qing-shan; ZHANG Zhong-chen; LIU Chun-yan; XIN Da-wei; QIU Hong-mei; SHAN Da-peng; SHAN Cai-yun; HU Guo-hua
Soybean is a main crop, and most agronomic traits of soybean are quantitative; therefore, there is very important studying and applying value to locating these traits. A F2:10 RIL population containing 154 lines, derived from the cross between Charleston as female and Dongnong 594 as male parent, were used in this experiment. A genetic linkage map was constructed with 164 SSR primers, which were screened with the two parents and amplified on the 154 lines. 12 agronomic traits different between the two parents were investigated, and QTLs of all the traits were analyzed using the software Windows QTL Cartographer V2.0. The agronomic traits included quality traits: protein content, oil content, and content of protein and oil; yield traits: pods per plant, seed weight per plant, arnd 100 seeds weight; and other agronomic traits: plant height, days to maturity, branches, nod number in main stem, average leaf length, and average leaf width. The results showed that 68 QTLs in total were found for the 12 agronomic traits. The number of QTLs per trait varied from 3 for the average leaf width to 11 for 100 seeds weight and plant height, and was 5.8 on average. Good accordance was seen in many QTLs between the results of this study and the results obtained by other similar studies; therefore, these QTLs may be valuable for molecular marker assistant selection in soybean. In this study, 68 major QTLs of 12 important traits of soybean were analyzed.
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/16 h, 18°C/8 h and optimum temperature (28°C/24 h between the parental lines. Only three QTL were identified for controlling optimum-temperature germination rate. Six QTL controlling low-temperature germination rate were detected on chromosome 4, 5, 6, 7 and 9, and contribution rate of single QTL explained between 3.39%~11.29%. In addition, six QTL controlling low-temperature primary root length were detected in chromosome 4, 5, 6, and 9, and the contribution rate of single QTL explained between 3.96%~8.41%. Four pairs of QTL were located at the same chromosome position and together controlled germination rate and primary root length under low temperature condition. The nearest markers apart from the corresponding QTL (only 0.01 cM were umc1303 (265.1 cM on chromosome 4, umc1 (246.4 cM on chromosome 5, umc62 (459.1 cM on chromosome 6, bnl14.28a (477.4 cM on chromosome 9, respectively. A total of 3155 candidate genes were extracted from nine separate intervals based on the Maize Genetics and Genomics Database (http://www.maizegdb.org. Five candidate genes were selected for analysis as candidates putatively affecting seed germination and seedling growth at low temperature. The results provided a basis for further fine mapping, molecular marker assisted breeding and functional study of cold-tolerance at the stage of seed germination in maize.
Hu, Shuaidong; Lübberstedt, Thomas; Zhao, Guangwu; Lee, Michael
Low temperature is the primary factor to affect maize sowing in early spring. It is, therefore, vital for maize breeding programs to improve tolerance to low temperatures at seed germination stage. However, little is known about maize QTL involved in low-temperature germination ability. 243 lines of the intermated B73×Mo17 (IBM) Syn4 recombinant inbred line (RIL) population was used for QTL analysis of low-temperature germination ability. There were significant differences in germination-related traits under both conditions of low temperature (12°C/16 h, 18°C/8 h) and optimum temperature (28°C/24 h) between the parental lines. Only three QTL were identified for controlling optimum-temperature germination rate. Six QTL controlling low-temperature germination rate were detected on chromosome 4, 5, 6, 7 and 9, and contribution rate of single QTL explained between 3.39%~11.29%. In addition, six QTL controlling low-temperature primary root length were detected in chromosome 4, 5, 6, and 9, and the contribution rate of single QTL explained between 3.96%~8.41%. Four pairs of QTL were located at the same chromosome position and together controlled germination rate and primary root length under low temperature condition. The nearest markers apart from the corresponding QTL (only 0.01 cM) were umc1303 (265.1 cM) on chromosome 4, umc1 (246.4 cM) on chromosome 5, umc62 (459.1 cM) on chromosome 6, bnl14.28a (477.4 cM) on chromosome 9, respectively. A total of 3155 candidate genes were extracted from nine separate intervals based on the Maize Genetics and Genomics Database (http://www.maizegdb.org). Five candidate genes were selected for analysis as candidates putatively affecting seed germination and seedling growth at low temperature. The results provided a basis for further fine mapping, molecular marker assisted breeding and functional study of cold-tolerance at the stage of seed germination in maize.
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.
Gregersen, V R; Sørensen, K K; Christensen, O F; Busch, M E; Vingborg, R K K; Velander, I H; Lund, M S; Bendixen, C
Pleuropneumonia is a major problem in pig production. At the time of slaughter, chronic pleuritis (CP) developed from pleuropneumonia is a common finding, and breeding for a reduced incidence of CP using marker-assisted selection (MAS) would be advantageous. Before applying MAS, quantitative trait loci (QTL) or markers associated with the prevalence of CP should be identified. In this study, 7470 pigs from crosses between 12 Danish Duroc boars and 604 sows (Danish Landrace × Danish Large White) were evaluated for CP located on the dorso-caudal part of the lungs. Quantitative trait loci were identified within boar families using both a Binomial logistic regression method and a chi-square test of association. Significant QTL for CP were detected on Sus scrofa chromosomes (SSC) 2, 8, 12, 13, 14 and 18 using both methods. One QTL on SSC 8 was also detected across families. For the QTL identified 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 part of the lungs.
Bink, Marco C A M; Totir, L Radu; ter Braak, Cajo J F; Winkler, Christopher R; Boer, Martin P; Smith, Oscar S
The common assumption in quantitative trait locus (QTL) linkage mapping studies that parents of multiple connected populations are unrelated is unrealistic for many plant breeding programs. We remove this assumption and propose a Bayesian approach that clusters the alleles of the parents of the current mapping populations from locus-specific identity by descent (IBD) matrices that capture ancestral marker and pedigree information. Moreover, we demonstrate how the parental IBD data can be incorporated into a QTL linkage analysis framework by using two approaches: a Threshold IBD model (TIBD) and a Latent Ancestral Allele Model (LAAM). The TIBD and LAAM models are empirically tested via numerical simulation based on the structure of a commercial maize breeding program. The simulations included a pilot dataset with closely linked QTL on a single linkage group and 100 replicated datasets with five linkage groups harboring four unlinked QTL. The simulation results show that including parental IBD data (similarly for TIBD and LAAM) significantly improves the power and particularly accuracy of QTL mapping, e.g., position, effect size and individuals' genotype probability without significantly increasing computational demand.
Nissenbaum, Jonathan; Shpigler, Hagai; Pisanté, Anne; DelCanho, Sonia; Minert, Anne; Seltzer, Ze'ev; Devor, Marshall; Darvasi, Ariel
We aimed to locate a chronic pain-associated QTL in the rat (Rattus norvegicus) based on previous findings of a QTL (pain1) on chromosome 15 of the mouse (Mus musculus). The work was based on rat selection lines HA (high autotomy) and LA (low autotomy) which show a contrasting pain phenotype in response to nerve injury in the neuroma model of neuropathic pain. An F(2) segregating population was generated from HA and LA animals. Phenotyped F(2) rats were genotyped on chromosome 7 and chromosome 2, regions that share a partial homology with mouse chromosome 15. Our interval mapping analysis revealed a LOD score value of 3.63 (corresponding to p=0.005 after correcting for multiple testing using permutations) on rat chromosome 2, which is suggestive of the presence of a QTL affecting the predisposition to neuropathic pain. This QTL was mapped to the 14-26cM interval of chromosome 2. Interestingly, this region is syntenic to mouse chromosome 13, rather than to the region of mouse chromosome 15 that contains pain1. This chromosomal position indicates that it is possibly a new QTL, and hence we name it pain2. Further work is needed to replicate and to uncover the underlying gene(s) in both species.
Miles, L G; Isberg, S R; Thomson, P C; Glenn, T C; Lance, S L; Dalzell, P; Moran, C
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.
Snoek, L Basten; Van der Velde, K Joeri; Arends, Danny; Li, Yang; Beyer, Antje; Elvin, Mark; Fisher, Jasmin; Hajnal, Alex; Hengartner, Michael O; Poulin, Gino B; Rodriguez, Miriam; Schmid, Tobias; Schrimpf, Sabine; Xue, Feng; Jansen, Ritsert C; Kammenga, Jan E; Swertz, Morris A
Here, we present WormQTL (http://www.wormqtl.org), an easily accessible database enabling search, comparative analysis and meta-analysis of all data on variation in Caenorhabditis spp. Over the past decade, Caenorhabditis elegans has become instrumental for molecular quantitative genetics and the systems biology of natural variation. These efforts have resulted in a valuable amount of phenotypic, high-throughput molecular and genotypic data across different developmental worm stages and environments in hundreds of C. elegans strains. WormQTL provides a workbench of analysis tools for genotype-phenotype linkage and association mapping based on but not limited to R/qtl (http://www.rqtl.org). All data can be uploaded and downloaded using simple delimited text or Excel formats and are accessible via a public web user interface for biologists and R statistic and web service interfaces for bioinformaticians, based on open source MOLGENIS and xQTL workbench software. WormQTL welcomes data submissions from other worm researchers.
Merchuk-Ovnat, Lianne; Barak, Vered; Fahima, Tzion; Ordon, Frank; Lidzbarsky, Gabriel A.; Krugman, Tamar; Saranga, Yehoshua
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
ZHONG Ming; WANG Ling-qiang; YuAN De-jun; LUO Li-jun; Xu Cai-guo; HE Yu-qing
The phenotypes of protein and amino acid contents were measured in an F9 recombinant inbred line population derived from a cross between Zhenshan 97B and Delong 208.A total of 48 and 64 QTLs were identified in 2004 and 2005,respectively.The contribution of each QTL to the phenotypic variation ranged from 4.0％ to 43.7％.Most QTLs co-localized,forming 29 QTL clusters on the chromosomes with three major ones detected in both years,which were mapped on chromosomes 1,7 and 9,respectively.The two QTL clusters for amino acid content,qAa1 and qAa7,influenced almost all the traits with the allele from Zhenshan 97B,and the third QTL cluster for amino acid content,qAa9,increased the lysine content with the allele from Delong 208.A wide coincidence was found between the QTL detected under this study and the loci involved in amino acid metabolism pathways in nitrogen assimilation and transport,or protein biosynthesis.The results would facilitate the identification of candidate genes and could be used in marker-assisted selection for the favorable allele in rice quality improvement.
Merchuk-Ovnat, Lianne; Barak, Vered; Fahima, Tzion; Ordon, Frank; Lidzbarsky, Gabriel A; Krugman, Tamar; Saranga, Yehoshua
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.
Firdaus, Syarifin; van Heusden, Adriaan W; Hidayati, Nurul; Supena, Ence Darmo Jaya; Mumm, Roland; de Vos, Ric C H; Visser, Richard G F; Vosman, Ben
Solanum galapagense is closely related to the cultivated tomato and can show a very good resistance towards whitefly. A segregating population resulting from a cross between the cultivated tomato and a whitefly resistant S. galapagense was created and used for mapping whitefly resistance and related traits, which made it possible to study the genetic basis of the resistance. Quantitative trait loci (QTL) for adult survival co-localized with type IV trichome characteristics (presence, density, gland longevity and gland size). A major QTL (Wf-1) was found for adult survival and trichome characters on Chromosome 2. This QTL explained 54.1 % of the variation in adult survival and 81.5 % of the occurrence of type IV trichomes. A minor QTL (Wf-2) for adult survival and trichome characters was identified on Chromosome 9. The major QTL was confirmed in F3 populations. Comprehensive metabolomics, based on GCMS profiling, revealed that 16 metabolites segregating in the F2 mapping population were associated with Wf-1 and/or Wf-2. Analysis of the 10 most resistant and susceptible F2 genotypes by LCMS showed that several acyl sugars were present in significantly higher concentration in the whitefly resistant genotypes, suggesting a role for these components in the resistance as well. Our results show that whitefly resistance in S. galapagense seems to inherit relatively simple compared to whitefly resistance from other sources and this offers great prospects for resistance breeding as well as elucidating the underlying molecular mechanism(s) of the resistance.
Torres Sánchez, Jaime
Full Text Available Se examinan algunos caracteres de la actividad de trabajo y del régimen alimenticio de los peones de un grupo de hatos del Alto Apure, cuyo propietario era el presidente de Venezuela, Juan Vicente Gómez. La construcción de la ración media permite sostener que presentaba un adecuado nivel calórico y que su calidad nutricional podría haber estado reducida a los mínimos exigibles para la manutención del nivel de actividad en el trabajo del llano. Es posible que las características del funcionamiento económico de los hatos estudiados presionaran los costos de alimentación.
La monotonía de la dieta podría haber sido garantía de equilibrio nutricional, al combinarse con actividades personales de caza y pesca, de tal modo que la estacionalidad en el empleo de la mano de obra aparece como una condición de supervivencia.
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
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.
Lawrenson, K.; Li, Q.; Kar, S.; Seo, J.H.; Tyrer, J.; Spindler, T.J.; Lee, J. van der; Chen, Y; Karst, A.; Drapkin, R.; Aben, K.K.H.; Anton-Culver, H.; Antonenkova, N.; Baker, H.; Bandera, E.V.; Bean, Y.; Beckmann, M.W.; Berchuck, A.; Bisogna, M.; Bjorge, L.; Bogdanova, N.; Brinton, L.A.; Brooks-Wilson, A.; Bruinsma, F.; Butzow, R.; Campbell, I.G.; Carty, K.; Chang-Claude, J.; Chenevix-Trench, G.; Chen, A; Chen, Z.; Cook, L.S.; Cramer, D.W; Cunningham, J.M.; Cybulski, C.; Dansonka-Mieszkowska, A.; Dennis, J.; Dicks, E.; Doherty, J.A.; Dork, T.; Bois, A. du; Durst, M.; Eccles, D.; Easton, D.T.; Edwards, R.P.; Eilber, U.; Ekici, A.B.; Fasching, P.A.; Fridley, B.L.; Gao, Y.T.; Gentry-Maharaj, A.; Giles, G.G.; Glasspool, R.; Goode, E.L.; Goodman, M.T.; Grownwald, J.; Harrington, P.; Harter, P.; Hasmad, H.N.; Hein, A.; Heitz, F.; Hildebrandt, M.A.; Hillemanns, P.; Hogdall, E.; Hogdall, C.; Hosono, S.; Iversen, E.S.; Jakubowska, A.; James, P.; Jensen, A.; Ji, B.T.; Karlan, B.Y.; Kjaer, S. Kruger; Kelemen, L.E.; Kellar, M.; Kelley, J.L.; Kiemeney, L.A.; Krakstad, C.; Kupryjanczyk, J.; Lambrechts, D.; Lambrechts, S.; Le, N.D.; Lee, A.W.; Lele, S.; Leminen, A.; Lester, J.; Levine, D.A.; Liang, D.; Lissowska, J.; Lu, K.; Lubinski, J.; Lundvall, L.; Massuger, L.F.; Matsuo, K.; McGuire, V.; McLaughlin, J.R.; Nevanlinna, H.; McNeish, I.; Menon, U.; Modugno, F.
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 associat
Li, Chengqi; Wang, Xiaoyun; Dong, Na; Zhao, Haihong; Xia, Zhe; Wang, Rui; Converse, Richard L; Wang, Qinglian
Making use of the markers linked closely to QTL for early-maturing traits for MAS (Marker-assisted selection) is an effective method for the simultaneous improvement of early maturity and other properties in cotton. In this study, two F2 populations and their F2:3 families were generated from the two upland cotton (Gossypium hirsutum L.) crosses, Baimian2 × TM-1 and Baimian2 × CIR12. QTL for early-maturing traits were analyzed using F2:3 families. A total of 54 QTL (31 suggestive and 23 significant) were detected. Fourteen significant QTL had the LOD scores not only > 3 but also exceeding permutation threshold. At least four common QTL, qBP-17 for bud period (BP), qGP-17a/qGP-17b (qGP-17) for growth period (GP), qYPBF-17a/qYPBF-17b (qYPBF-17) for yield percentage before frost (YPBF) and qHFFBN-17 for height of first fruiting branch node (HFFBN), were found in both populations. These common QTL should be reliable and could be used for MAS to facilitate early maturity. The common QTL, qBP-17, had a LOD score not only > 3 but also exceeding permutation threshold, explaining 12.6% of the phenotypic variation. This QTL should be considered preferentially in MAS. Early-maturing traits of cotton are primarily controlled by dominant and over-dominant effects.
Norgard, Elizabeth A; Jarvis, Joseph P; Roseman, Charles C; Maxwell, Taylor J; Kenney-Hunt, Jane P; Samocha, Kaitlin E; Pletscher, L Susan; Wang, Bing; Fawcett, Gloria L; Leatherwood, Christopher J; Wolf, Jason B; Cheverud, James M
Quantitative trait locus (QTL) mapping techniques are frequently used to identify genomic regions associated with variation in phenotypes of interest. However, the F(2) intercross and congenic strain populations usually employed have limited genetic resolution resulting in relatively large confidence intervals that greatly inhibit functional confirmation of statistical results. Here we use the increased resolution of the combined F(9) and F(10) generations (n = 1455) of the LG,SM advanced intercross to fine-map previously identified QTL associated with the lengths of the humerus, ulna, femur, and tibia. We detected 81 QTL affecting long-bone lengths. Of these, 49 were previously identified in the combined F(2)-F(3) population of this intercross, while 32 represent novel contributors to trait variance. Pleiotropy analysis suggests that most QTL affect three to four long bones or serially homologous limb segments. We also identified 72 epistatic interactions involving 38 QTL and 88 novel regions. This analysis shows that using later generations of an advanced intercross greatly facilitates fine-mapping of confidence intervals, resolving three F(2)-F(3) QTL into multiple linked loci and narrowing confidence intervals of other loci, as well as allowing identification of additional QTL. Further characterization of the biological bases of these QTL will help provide a better understanding of the genetics of small variations in long-bone length.
Bin Wang; Zhanhui Zhang; Zhiyuan Fu; Zonghua Liu; Yanmin Hu; Jihua Tang
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.
Jouffe, Vincent; Rowe, Suzanne; Liaubet, Laurence
a case study where we explore ways to integrate QTL data and microarray data for the pig, which has only a partial genome sequence. We outline various procedures to localize differentially expressed genes on the pig genome and link this with information on published QTL. The starting point is a set...... of 237 differentially expressed cDNA clones in adrenal tissue from two pig breeds, before and after treatment with adrenocorticotropic hormone (ACTH) 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 provide a case study where we explore ways to integrate QTL data and microarray data for the pig, which has only a partial genome sequence. We outline various procedures to localize differentially expressed genes on the pig genome and link...
Liang Tong; Weijun Ma; Haidong Liu; Chaofeng Yuan; Ying Zhou
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.
Ren, Zhimin; Qiu, Anli; Zhang, Aiqi; Huang, Lijun; Rao, Shuquan
Schizophrenia is a devastating mental disorder, with heritability as high as 80%. Although genome-wide association studies have identified multiple promising risk variants of schizophrenia, they could only explain a small portion of the disease heritability, and other variants with low to moderate effect remain to be identified. Abelson helper integration site 1 (AHI1) is highly expressed in mammals throughout the developing brain, with lower expression continuing into adulthood. Besides, previous evidence suggested that AHI1 expression was changed in schizophrenia patients. Furthermore, association signal between AHI1 variants and schizophrenia has been reported in several European samples. In the present study, we first analyzed two expression quantitative trait loci (eQTL) datasets in healthy individuals and investigated the associations of eQTL of AHI1 with schizophrenia in independent European samples. We observed that a cis-eQTL of AHI1, rs11154801, showed significant association with AHI1 expression in both datasets (PEuropean populations.
Ding, J.; Ma, J.; Chen, J.; Ai, T.; Li, Z.; Tian, Z.; Wu, S.; Chen, W.; Wu, J.
Barren tip on corn ear is an important agronomic trait in maize, which is highly associated with grain yield. Understanding the genetic basis of tip-barrenness may help to reduce the ear tip-barrenness in breeding programs. In this study, ear tip-barrenness was evaluated in two environments in a F2:3 population, and it showed significant genotypic variation for ear tip-barrenness in both environments. Using mixed-model composite interval mapping method, three additive effects quantitative trait loci (QTL) for ear tip-barrenness were mapped on chromosomes 2, 3 and 6, respectively. They explained 16.6% of the phenotypic variation, and no significant QTL × Environment interactions and digenic interactions were detected. The results indicated that additive effect was the main genetic basis for ear tip-barrenness in maize. This is the first report of QTL mapped for ear tip-barrenness in maize. (Author)
Mignon-Grasteau, Sandrine; Chantry-Darmon, Céline; Boscher, Marie-Yvonne; Sellier, Nadine; Chabault-Dhuit, Marie; Le Bihan-Duval, Elisabeth; Narcy, Agnès
Skeletal integrity in meat-type chickens is affected by many factors including rapid growth rate, nutrition and genetics. To investigate the genetic basis of bone and mineral metabolism, a QTL detection study was conducted in an intercross between two lines of meat-type chickens divergently selected for their high (D +) or low (D -) digestive efficiency. Tibia size (length, diameter, volume) and ash content were determined at 3 weeks of age as well as phosphorus (P) retention and plasma concentration. Heritability of these traits and their genetic correlations with digestive efficiency were estimated. A QTL mapping study was performed using 3379 SNP markers. Tibia size, weight, ash content and breaking strength were highly heritable (0.42 to 0.61). Relative tibia diameter and volume as well as P retention were strongly and positively genetically correlated with digestive efficiency (0.57 to 0.80). A total of 35 QTL were identified (9 for tibia weight, 13 for tibia size, 5 for bone strength, 5 for bone mineralization, 2 for plasma P concentration and 1 for P retention). Six QTL were genome-wide significant, and 3 QTL for tibia relative volume, weight and ash weight on chromosome 6 were fixed, the positive allele coming from the D-line. For two QTL for ash content on chromosome 18 and relative tibia length on chromosome 26, the confidence intervals were small enough to identify potential candidate genes. These findings support the evidence of multiple genetic loci controlling bone and mineral metabolism. The identification of candidate genes may provide new perspectives in the understanding of bone regulation, even beyond avian species.
Kelly, Scott A; Nehrenberg, Derrick L; Hua, Kunjie; Garland, Theodore; Pomp, Daniel
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 voluntary exercise, body composition, and changes in body composition as a result of exercise. Using brain tissue in a subset of the G4 (n = 244), we have also previously reported expression QTL (eQTL) colocalizing with the QTL for the higher-level phenotypes. Here, we examined the transcriptional landscape of hind limb muscle tissue via global mRNA expression profiles. Correlations revealed an ∼1,168% increase in significant relationships between muscle transcript expression levels and the same exercise and body composition phenotypes examined previously in the brain. The exercise trait most often significantly correlated with gene expression in the brain was running duration while in the muscle it was maximum running speed. This difference may indicate that time spent engaging in exercise behavior may be more influenced by central (neurobiological) mechanisms, while intensity of exercise may be largely controlled by peripheral mechanisms. Additionally, we used subsets of cis-acting eQTL, colocalizing with QTL, to identify candidate genes based on both positional and functional evidence. We discuss three plausible candidate genes (Insig2, Prcp, Sparc) and their potential regulatory role.
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
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.
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.
Full Text Available Abstract Background Ostrinia nubilalis (ECB and Sesamia nonagrioides (MCB are two maize stem borers which cause important losses in temperate maize production, but QTL analyses for corn borer resistance were mostly restricted to ECB resistance and maize materials genetically related (mapping populations derived from B73. Therefore, the objective of this work was to identify and characterize QTLs for MCB resistance and agronomic traits in a RILs population derived from European flint inbreds. Results Three QTLs were detected for stalk tunnel length at bins 1.02, 3.05 and 8.05 which explained 7.5% of the RILs genotypic variance. The QTL at bin 3.05 was co-located to a QTL related to plant height and grain humidity and the QTL at bin 8.05 was located near a QTL related to yield. Conclusions Our results, when compared with results from other authors, suggest the presence of genes involved in cell wall biosynthesis or fortification with effects on resistance to different corn borer species and digestibility for dairy cattle. Particularly, we proposed five candidate genes related to cell wall characteristics which could explain the QTL for stalk tunnelling in the region 3.05. However, the small proportion of genotypic variance explained by the QTLs suggest that there are also many other genes of small effect regulating MCB resistance and we conclude that MAS seems not promising for this trait. Two QTLs detected for stalk tunnelling overlap with QTLs for agronomic traits, indicating the presence of pleitropism or linkage between genes affecting resistance and agronomic traits.
Ikhide G. Imumorin
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.
Rumph Janice M
Full Text Available Abstract Background A variety of analysis approaches have been applied to detect quantitative trait loci (QTL in experimental populations. The initial genome scan of our Duroc x Pietrain F2 resource population included 510 F2 animals genotyped with 124 microsatellite markers and analyzed using a line-cross model. For the second scan, 20 additional markers on 9 chromosomes were genotyped for 954 F2 animals and 20 markers used in the first scan were genotyped for 444 additional F2 animals. Three least-squares Mendelian models for QTL analysis were applied for the second scan: a line-cross model, a half-sib model, and a combined line-cross and half-sib model. Results In total, 26 QTL using the line-cross model, 12 QTL using the half-sib model and 3 additional QTL using the combined line-cross and half-sib model were detected for growth traits with a 5% false discovery rate (FDR significance level. In the line-cross analysis, highly significant QTL for fat deposition at 10-, 13-, 16-, 19-, and 22-wk of age were detected on SSC6. In the half-sib analysis, a QTL for loin muscle area at 19-wk of age was detected on SSC7 and QTL for 10th-rib backfat at 19- and 22-wk of age were detected on SSC15. Conclusions Additional markers and animals contributed to reduce the confidence intervals and increase the test statistics for QTL detection. Different models allowed detection of new QTL which indicated differing frequencies for alternative alleles in parental breeds.
Wright, F.A. [Univ. of California, San Diego, CA (United States)]|[Univ. of Texas, El Paso, TX (United States)
Kruglyak and Lander provide an important synthesis of methods for (IBD) sib-pair linkage mapping, with an emphasis on the use of complete multipoint inheritance information for each sib pair. These procedures are implemented in the computer program MAPMAKER/SIBS, which performs interval mapping for dichotomous and quantitative traits. The authors present three methods for mapping quantitative trait loci (QTLs): a variant of the commonly used Haseman-Elston regression approach, a maximum-likelihood procedure involving variance components, and a rank-based nonparametric procedure. These approaches and related work use the magnitude of the difference in the sibling phenotype values for each sib pair as the observation for analysis. Linkage is detected if siblings sharing more alleles IBD have similar phenotypes (i.e., a small difference in the phenotype values), while siblings sharing fewer alleles IBD have less similar phenotypes. Such techniques have been used to detect linkage for a number of quantitative traits. However, the exclusive reliance on the phenotypic differences may be due in large part to historical inertia. A likelihood argument is presented here to show that, under certain classical assumptions, the phenotypic differences do not contain the full likelihood information for QTL mapping. Furthermore, considerable gains in power to detect linkage can be achieved with an expanded likelihood model. The development here is related to previous work, which incorporates the full set of phenotypic data using likelihood and robust quasi-likelihood methods. The purpose of this letter is not to endorse a particular approach but to spur research in alternative and perhaps more powerful linkage tests. 17 refs.
B. Emma Huang
Full Text Available dlmap is a software package capable of mapping quantitative trait loci (QTL in a variety of genetic studies. Unlike most other QTL mapping packages, dlmap is built on a linear mixed model platform, and thus can simultaneously handle multiple sources of genetic and environmental variation. Furthermore, it can accommodate both experimental crosses and association mapping populations within a versatile modeling framework. The software implements a mapping algorithm with separate detection and localization stages in a user-friendly manner. It accepts data in various common formats, has a flexible modeling environment, and summarizes results both graphically and numerically.
Conti José Henrique; Minami Keigo; Tavares Flavio Cesar Almeida
Caracteres morfológicos (forma dos dentes, ângulo da base e razão entre o comprimento e a largura do folíolo, cor da folha, posição da inflorescência em relação à folhagem e tamanho do cálice em relação ao fruto), agronômicos (grau de proteção da inflorescência pelas folhas, presença de "pescoço" no fruto, produção, número e peso médio de frutos, teor de sólidos solúveis, pH, textura e cor externa e interna) e moleculares foram estudados em cultivares do morangueiro, para verificar se os dado...
Moeses Andrigo Danner
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
Hudsonkléio da Costa Silva
A cana-de-açúcar (Saccharum spp.) apresenta-se como uma cultura de grande importância social e econômica para o Brasil. Os programas de melhoramento genético vêm contribuindo para o aumento da produtividade nas áreas canavieiras do país, graças à substituição e renovação dos canaviais, esse incremento atingiu aumentos de trinta por cento nas três últimas décadas. No entanto, a eficácia dos programas de melhoramento de cana-de-açúcar depende da repetibilidade espacial e temporal dos caracteres...
Magda Piedad Valdés Restrepo
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.
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.
Gemma Maria Santiago Alonso
Full Text Available Con este artículo se ha querido delimitar y describir una de las áreas más problemáticas del aprendizaje del español para estudiantes eslovenos: la adquisición del artículo. A partir de un análisis cuantitativo de errores se ha podido observar y analizar qué tipo de errores presentaban en sus producciones escritas, cuáles eran las áreas más problemáticas, en qué estructuras aparecían y por qué se producían. Las implicaciones didácticas derivadas de esta investigación nos obligan a reflexionar sobre la metodología y los materiales utilizados en el aula para la enseñanza del artículo, ya que tanto los errores analizados, las estrategias utilizadas, como el problema de fosilización de dichos errores subrayan claramente insuficiencias didácticas y metodológicas. Esto nos lleva a la necesidad de crear materiales específicos para los aprendices eslovenos que cuenten con una metodología de enseñanza en consonancia con las necesidades y características de nuestros aprendices.
José Miguel Rodríguez-Antón
Full Text Available El objetivo del presente trabajo consiste en proponer un modelo cuantitativo objetivo de competitividad de los países como destinos turísticos. Este modelo, basado en el propuesto por el World Economic Forum, está compuesto exclusivamente por indicadores extraídos de bases de datos y de estadísticas elaboradas por instituciones públicas o privadas. Para determinar los pesos que cada uno de los pilares y variables que lo integran, se distribuyó un cuestionario a una muestra formada por 186 profesionales del sector turismo, especialistas del sector turismo y profesores universitarios, que dio lugar a un modelo lineal de competitividad turística, el cual fue aplicado a los 28 países que integran la Unión Europea, resultando que Alemania es el país con mayor competitividad turística, seguido por Italia, Reino Unido, Francia y España.
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.
Mario Alvaro Aloisio Verissimo
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.
B. P. Mallikarjuna Swamy; K. Kaladhar; G. Ashok Reddy; B. C. Viraktamath; N. Sarla
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.
Yuling Li; Yanzhao Wang; Mengguan Wei; Xuehui Li; Jiafeng Fu
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.
Norry, Fabian M.; Scannapieco, Alejandra C.; Sambucetti, Pablo;
The thermotolerance effect of heat hardening (also called short-term acclimation), knockdown resistance to high temperature (KRHT) with and without heat hardening and chill-coma recovery (CCR) are important phenotypes of thermal adaptation in insects and other organisms. Drosophila melanogaster......-hardened and nonhardened RIL. Composite interval mapping revealed a more complex genetic architecture for KRHT without heat-hardening than for KRHT in heat-hardened insects. Five quantitative trait loci (QTL) were found for KRHT, but only two of them were significant after heat hardening. KRHT and CCR showed trade...... decreased by heat hardening. We discuss candidate loci for each QTL. One HHE-QTL was found in the region of small heat-shock protein genes. However, HHE-QTL explained only a small fraction of the phenotypic variance. Most heat-resistance QTL did not colocalize with CCR-QTL. Large-effect QTL for CCR and KRHT...
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.
ENDANG TRI MARGAWATI
Full Text Available Four half-sib families (n = 382 consisting predominantly of ITT x Merino x Merino backcross progeny, including some F2 progeny were used to analyze QTL for two production traits (Birth weight = BW1 and Body weight at 360 days = BW360. The study exploited differences in weight performance between the Merino and ITT sheep. A total of 141 informative microsatellite markers were used in a genome-wide scan covering the 26 autosomal sheep chromosomes. QTL analysis was conducted online using QTL Express. This study reports the effect of QTL for birth weight on Chromosomes 5 (p < 0.05 at 112cM (0cM-128cM. Location of candidate genes for birth weight was predicted at the region of flanking markers MCM527-BMS1247. A QTL for BW360 days existed on Chromosome 18 (p < 0.01 at 104cM (25.0-125cM. Location of candidate genes related to production traits for body weight 360 days was predicted at the segment of flanking markers of CSSM018-TMR1. Only the QTL on Chromosome 18 retained significance (p < 0.01 under experiment-wide significance testing. This QTL region is being examined for candidate genes by investigating to the homologous human chromosomal segments.
Thirstrup, Janne Pia; Anistoroaei, Razvan Marian; Guldbrandtsen, Bernt;
, 3, 4, 6, 11, and 13, for guard hair length on chromosomes 2, 3, and 6 and for wool density on chromosome 6, 7, and 13. Similar locations of QTL for guard hair length and guard hair thickness on chromosomes 2, 3, and 6 suggest that these traits are in part under the influence of the same genes...
Demetrashvili, Nino; Van den Heuvel, Edwin R; Wit, Ernst C
Background: Many QTL studies have two common features: (1) often there is missing marker information, (2) among many markers involved in the biological process only a few are causal. In statistics, the second issue falls under the headings "sparsity" and "causal inference". The goal of this work is
Klein, Melinda A; Grusak, Michael A
Legume seeds have the potential to provide a significant portion of essential micronutrients to the human diet. To identify the genetic basis for seed nutrient density, quantitative trait locus (QTL) analysis was conducted with the Miyakojima MG-20 x Gifu B-129 recombinant inbred population from the model legume Lotus japonicus. This population was grown to seed under greenhouse conditions in 2006 and 2007. Phenotypic data were collected for seed calcium (Ca), copper (Cu), iron (Fe), potassium (K), magnesium (Mg), manganese (Mn), phosphorus (P), sulfur (S), and zinc (Zn) concentrations and content. Data for physical seed traits (average seed mass and seed-pod allocation values) were also collected. Based on these phenotypic data, QTL analyses identified 103 QTL linked to 55 different molecular markers. Transgressive segregation, identified within this recombinant inbred population for both seed nutrient and physical traits, suggests new allelic combinations are available for agronomic trait improvement. QTL co-localization was also seen, suggesting that common transport processes might contribute to seed nutrient loading. Identification of loci involved in seed mineral density can be an important first step in identifying the genetic factors and, consequently, the physiological processes involved in mineral distribution to developing seeds. Longer term research efforts will focus on facilitating agronomic breeding efforts through ortholog identification in related crop legumes.
Heuven, H.C.M.; van Wijk, R.H.J.; Dibbits, B.; van Kampen, T.A.; Knol, E.F.
Genet Sel Evol. 2009 Jan 5;41:4. Mapping carcass and meat quality QTL on Sus Scrofa chromosome 2 in commercial finishing pigs. Heuven HC, van Wijk RH, Dibbits B, van Kampen TA, Knol EF, Bovenhuis H. Animal Breeding and Genomics Centre, Wageningen University, Wageningen, The Netherlands. h.c.m.heuven
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…
Bink, M.C.A.M.; Radu Totir, L.; Braak, ter C.J.F.; Winkler, C.R.; Boer, M.P.; Smith, O.S.
The common assumption in quantitative trait locus (QTL) linkage mapping studies that parents of multiple connected populations are unrelated is unrealistic for many plant breeding programs. We remove this assumption and propose a Bayesian approach that clusters the alleles of the parents of the curr
Klasen, J R; Piepho, H-P; Stich, B
A major goal of today's biology is to understand the genetic basis of quantitative traits. This can be achieved by statistical methods that evaluate the association between molecular marker variation and phenotypic variation in different types of mapping populations. The objective of this work was to evaluate the statistical power of quantitative trait loci (QTL) detection of various multi-parental mating designs, as well as to assess the reasons for the observed differences. Our study was based on an empirical data of 20 Arabidopsis thaliana accessions, which have been selected to capture the maximum genetic diversity. The examined mating designs differed strongly with respect to the statistical power to detect QTL. We observed the highest power to detect QTL for the diallel cross with random mating design. The results of our study suggested that performing sibling mating within subpopulations of joint-linkage mapping populations has the potential to considerably increase the power for QTL detection. Our results, however, revealed that using designs in which more than two parental alleles segregate in each subpopulation increases the power even more. PMID:22334115
Siwek-Gapinska, M.Z.; Cornelissen, S.J.B.; Nieuwland, M.G.B.; Buitenhuis, A.J.; Bovenhuis, H.; Crooijmans, R.P.M.A.; Groenen, M.A.M.; Vries Reilingh, de G.; Parmentier, H.K.; Poel, van der J.J.
The aim of this study is to detect quantitative trait loci (QTL) involved in the regulation of the primary and the secondary immune response to sheep red blood cells (SRBC) in a resource population using microsatellite DNA markers. The F2 resource population originates from a cross of two divergentl
Han Zhang; Jiansheng Chen; Ruyu Li; Zhiying Deng; Kunpu Zhang; Bin Liu; Jichun Tian
Spike number per m~2(SN),kernel number per spike(KNPS) and thousand-kernel weight(TKW)are the three main components determining wheat(Triticum aestivum L.) yield.To evaluate the relationships among them a doubled haploid(DH) population consisting of 168 lines grown at three locations for three years was analyzed by unconditional and conditional QTL mapping.Thirty-three unconditional QTL and fifty-nine conditional QTL were detected.Among them,two QTL(QSN-DH-2B and QSN-DH-3A-1.1) improved SN,with no effect on KNPS.QKNPS-DH-2B-2.1 improved KNPS,with no effect on SN.QKNPS-DH-1A-1.1,QKNPS-DH-2D-1.1and QKNPS-DH-6A improved KNPS,with no effect on SN or TKW.QKNPS-DH-6B was associated with increased SN and TKW.In addition,QTKW-DH-4B,QTKW-DH-5B and QTKW-DH-7B increased TKW without decreasing KNPS.These results provide useful information for marker assisted selection(MAS) and improvement in wheat yield.
Schejbel, B; Jensen, L B; Asp, T;
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...
Calenge, F.; Drouet, D.; Weg, van de W.E.; Brisset, M.N.; Paulin, J.P.; Durel, C.E.
Fire blight, caused by the bacterial pathogen Erwinia amylovora, is one of the most destructive diseases of apple (Malus x domestica). In order to analyse the genetic determinism of resistance to fire blight in apple, a quantitative trait analysis (QTL) approach was used. A F1 progeny of 164 individ
Seasonal flowering of strawberry is described as remontant and non-remontant. The genetic basis of this trait is important for breeding. This study was conducted to validate the existence of a major QTL for remontancy and weeks of flowering in F. × ananassa on LG IV, to determine if the level of flo...
Full Text Available Understanding several modes of duplication contributing on the present genome structure is getting an attention because it could be related to numerous agronomically important traits. Since soybean serves as a rich protein source for animal feeds and human consumption, breeding efforts in soybean have been directed toward enhancing seed protein content. The publicly available soybean sequences and its genomically featured elements facilitate comprehending of quantitative trait loci (QTL for seed protein content in concordance with homeologous regions in soybean genome. Although parts of chromosome (Chr 20 and Chr 10 showed synteny, QTLs for seed protein content present only on Chr 20. Using comparative analysis of gene contents in recently duplicated genomic regions harboring QTL for protein/oil content on Chrs 20 and 10, a total of 27 genes are present in duplicated regions of both chromosomes. Notably, 4 tandem duplicates of the putative homeobox protein 22 (HB22 are present only on Chr 20 and this Medicago truncatula homolog expressed in endosperm at seed filling stage. These tandem duplicates could contribute on the protein/oil QTL of Chr 20. Our study suggests that non-shared gene contents within the duplicated genomic regions might lead to absence/presence of QTL related to protein/oil content.
Massault, C.; Hellemans, J.; Louro, B.; Batargias, C.; Houdt, van I.S.; Canario, A.; Volckaert, F.A.M.; Bovenhuis, H.; Haley, C.S.; Koning, de D.J.
Natural mating and mass spawning in the European sea bass (Dicentrarchus labrax L., Moronidae, Teleostei) complicate genetic studies and the implementation of selective breeding schemes. We utilized a two-step experimental design for detecting QTL in mass-spawning species: 2122 offspring from natura
Fruit size and shape are important determinants of market class and value in cucumber; however, underlying mechanisms regulating size and shape have not been identified. To gain insight into possible factors regulating cucumber fruit growth, we used a combined QTL and transcriptome approach to exami...
Full Text Available The genetic basis of variation in complex traits remains poorly understood, and few genes underlying variation have been identified. Previous work identified a quantitative trait locus (QTL responsible for much of the response to selection on growth in mice, effecting a change in body mass of approximately 20%. By fine-mapping, we have resolved the location of this QTL to a 660-kb region containing only two genes of known function, Gpc3 and Gpc4, and two other putative genes of unknown function. There are no non-synonymous polymorphisms in any of these genes, indicating that the QTL affects gene regulation. Mice carrying the high-growth QTL allele have approximately 15% lower Gpc3 mRNA expression in kidney and liver, whereas expression differences at Gpc4 are non-significant. Expression profiles of the two other genes within the region are inconsistent with a factor responsible for a general effect on growth. Polymorphisms in the 3' untranslated region of Gpc3 are strong candidates for the causal sequence variation. Gpc3 loss-of-function mutations in humans and mice cause overgrowth and developmental abnormalities. However, no deleterious side-effects were detected in our mice, indicating that genes involved in Mendelian diseases also contribute to complex trait variation. Furthermore, these findings show that small changes in gene expression can have substantial phenotypic effects.
Snoek, L. Basten; Van der Velde, K. Joeri; Arends, Danny; Li, Yang; Beyer, Antje; Elvin, Mark; Fisher, Jasmin; Hajnal, Alex; Hengartner, Michael O.; Poulin, Gino B.; Rodriguez, Miriam; Schmid, Tobias; Schrimpf, Sabine; Xue, Feng; Jansen, Ritsert C.; Kammenga, Jan E.; Swertz, Morris A.
Here, we present WormQTL (http://www.wormqtl.org), an easily accessible database enabling search, comparative analysis and meta-analysis of all data on variation in Caenorhabditis spp. Over the past decade, Caenorhabditis elegans has become instrumental for molecular quantitative genetics and the sy
CONG YANG; LEI ZHANG; AIMIN JIA; TINGZHAO RONG
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
Full Text Available In the context of genetics and breeding research on multiple phenotypic traits, reconstructing the directional or causal structure between phenotypic traits is a prerequisite for quantifying the effects of genetic interventions on the traits. Current approaches mainly exploit the genetic effects at quantitative trait loci (QTLs to learn about causal relationships among phenotypic traits. A requirement for using these approaches is that at least one unique QTL has been identified for each trait studied. However, in practice, especially for molecular phenotypes such as metabolites, this prerequisite is often not met due to limited sample sizes, high noise levels and small QTL effects. Here, we present a novel heuristic search algorithm called the QTL+phenotype supervised orientation (QPSO algorithm to infer causal directions for edges in undirected phenotype networks. The two main advantages of this algorithm are: first, it does not require QTLs for each and every trait; second, it takes into account associated phenotypic interactions in addition to detected QTLs when orienting undirected edges between traits. We evaluate and compare the performance of QPSO with another state-of-the-art approach, the QTL-directed dependency graph (QDG algorithm. Simulation results show that our method has broader applicability and leads to more accurate overall orientations. We also illustrate our method with a real-life example involving 24 metabolites and a few major QTLs measured on an association panel of 93 tomato cultivars. Matlab source code implementing the proposed algorithm is freely available upon request.
Su, C F; Wang, W; Gong, S L; Zuo, J H; Li, S J
The accuracy of quantitative trait loci (QTLs) identified using different sample sizes and marker densities was evaluated in different genetic models. Model I assumed one additive QTL; Model II assumed three additive QTLs plus one pair of epistatic QTLs; and Model III assumed two additive QTLs with opposite genetic effects plus two pairs of epistatic QTLs. Recombinant inbred lines (RILs) (50-1500 samples) were simulated according to the Models to study the influence of different sample sizes under different genetic models on QTL mapping accuracy. RILs with 10-100 target chromosome markers were simulated according to Models I and II to evaluate the influence of marker density on QTL mapping accuracy. Different marker densities did not significantly influence accurate estimation of genetic effects with simple additive models, but influenced QTL mapping accuracy in the additive and epistatic models. The optimum marker density was approximately 20 markers when the recombination fraction between two adjacent markers was 0.056 in the additive and epistatic models. A sample size of 150 was sufficient for detecting simple additive QTLs. Thus, a sample size of approximately 450 is needed to detect QTLs with additive and epistatic models. Sample size must be approximately 750 to detect QTLs with additive, epistatic, and combined effects between QTLs. The sample size should be increased to >750 if the genetic models of the data set become more complicated than Model III. Our results provide a theoretical basis for marker-assisted selection breeding and molecular design breeding.
Imumorin, I.G.; Kim, B.; Li, Y.; Koning, de D.J.; Arendonk, van J.A.M.; Donato, S.
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
Full Text Available Abstract Background Quantitative trait loci (QTL analyses in pig have revealed numerous individual QTL affecting growth, carcass composition, reproduction and meat quality, indicating a complex genetic architecture. In general, statistical QTL models consider only additive and dominance effects and identification of epistatic effects in livestock is not yet widespread. The aim of this study was to identify and characterize epistatic effects between common and novel QTL regions for carcass composition and meat quality traits in pig. Methods Five hundred and eighty five F2 pigs from a Duroc × Pietrain resource population were genotyped using 131 genetic markers (microsatellites and SNP spread over the 18 pig autosomes. Phenotypic information for 26 carcass composition and meat quality traits was available for all F2 animals. Linkage analysis was performed in a two-step procedure using a maximum likelihood approach implemented in the QxPak program. Results A number of interacting QTL was observed for different traits, leading to the identification of a variety of networks among chromosomal regions throughout the porcine genome. We distinguished 17 epistatic QTL pairs for carcass composition and 39 for meat quality traits. These interacting QTL pairs explained up to 8% of the phenotypic variance. Conclusions Our findings demonstrate the significance of epistasis in pigs. We have revealed evidence for epistatic relationships between different chromosomal regions, confirmed known QTL loci and connected regions reported in other studies. Considering interactions between loci allowed us to identify several novel QTL and trait-specific relationships of loci within and across chromosomes.
Savall-Alemany,Francisco; Domènech-Blanco,Josep Lluís; Martínez-Torregrosa,Joaquín
La introducción de la física cuántica en el bachillerato se limita en gran medida al estudio de los espectros de los gases y el efecto fotoeléctrico, obviando la gran cantidad de aplicaciones cotidianas que esta tiene. La construcción y calibrado de un espectroscopio cuantitativo nos permite trabajar con modelos cuánticos más allá de las experiencias que sirvieron para establecerlos.
Full Text Available Eggplant, pepper and tomato are the most exploited berry-producing vegetables within the Solanaceae family. Their genomes differ in size, but each has 12 chromosomes which have undergone rearrangements causing a redistribution of loci. The genome sequences of all three species are available but differ in coverage, assembly quality and percentage of anchorage.Determining their syntenic relationship and QTL orthology will contribute to exploit genomic resources and genetic data for key agronomic traits.The syntenic analysis between tomato and pepper based on the alignment of 34,727 tomato CDS to the pepper genome sequence, identified 19,734 unique hits. The resulting synteny map confirmed the 14 inversions and 10 translocations previously documented, but also highlighted 3 new translocations and 4 major new inversions. Furthermore, each of the 12 chromosomes exhibited a number of rearrangements involving small regions of 0.5-0.7 Mbp.Due to high fragmentation of the publicly available eggplant genome sequence, physical localization of most eggplant QTL was not possible, thus, we compared the organization of the eggplant genetic map with the genome sequence of both tomato and pepper. The eggplant/tomato syntenic map confirmed all the 10 translocations but only 9 of the 14 known inversions; on the other hand, a newly detected inversion was recognized while another one was not confirmed. The eggplant/pepper syntenic map confirmed 10 translocations and 8 inversions already detected and suggested a putative new translocation.In order to perform the assessment of eggplant and pepper QTL orthology, the eggplant and pepper sequence-based markers located in their respective genetic map were aligned onto the pepper genome. GBrowse in pepper was used as reference platform for QTL positioning. A set of 151 pepper QTL were located as well as 212 eggplant QTL, including 76 major QTL (PVE ≥ 10% affecting key agronomic traits. Most were confirmed to cluster in
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
Zhang, Zhanhui; Liu, Zonghua; Hu, Yanmin; Li, Weihua; Fu, Zhiyuan; Ding, Dong; Li, Haochuan; Qiao, Mengmeng; Tang, Jihua
Kernel size and weight are important determinants of grain yield in maize. In this study, multivariate conditional and unconditional quantitative trait loci (QTL), and digenic epistatic analyses were utilized in order to elucidate the genetic basis for these kernel-related traits. Five kernel-related traits, including kernel weight (KW), volume (KV), length (KL), thickness (KT), and width (KWI), were collected from an immortalized F2 (IF2) maize population comprising of 243 crosses performed at two separate locations over a span of two years. A total of 54 unconditional main QTL for these five kernel-related traits were identified, many of which were clustered in chromosomal bins 6.04-6.06, 7.02-7.03, and 10.06-10.07. In addition, qKL3, qKWI6, qKV10a, qKV10b, qKW10a, and qKW7a were detected across multiple environments. Sixteen main QTL were identified for KW conditioned on the other four kernel traits (KL, KWI, KT, and KV). Thirteen main QTL were identified for KV conditioned on three kernel-shape traits. Conditional mapping analysis revealed that KWI and KV had the strongest influence on KW at the individual QTL level, followed by KT, and then KL; KV was mostly strongly influenced by KT, followed by KWI, and was least impacted by KL. Digenic epistatic analysis identified 18 digenic interactions involving 34 loci over the entire genome. However, only a small proportion of them were identical to the main QTL we detected. Additionally, conditional digenic epistatic analysis revealed that the digenic epistasis for KW and KV were entirely determined by their constituent traits. The main QTL identified in this study for determining kernel-related traits with high broad-sense heritability may play important roles during kernel development. Furthermore, digenic interactions were shown to exert relatively large effects on KL (the highest AA and DD effects were 4.6% and 6.7%, respectively) and KT (the highest AA effects were 4.3%).
Full Text Available Abstract Background Common bean (Phaseolus vulgaris L. is the most important grain legume for human diet worldwide and the angular leaf spot (ALS is one of the most devastating diseases of this crop, leading to yield losses as high as 80%. In an attempt to breed resistant cultivars, it is important to first understand the inheritance mode of resistance and to develop tools that could be used in assisted breeding. Therefore, the aim of this study was to identify quantitative trait loci (QTL controlling resistance to ALS under natural infection conditions in the field and under inoculated conditions in the greenhouse. Results QTL analyses were made using phenotypic data from 346 recombinant inbreed lines from the IAC-UNA x CAL 143 cross, gathered in three experiments, two of which were conducted in the field in different seasons and one in the greenhouse. Joint composite interval mapping analysis of QTL x environment interaction was performed. In all, seven QTLs were mapped on five linkage groups. Most of them, with the exception of two, were significant in all experiments. Among these, ALS10.1DG,UC presented major effects (R2 between 16% - 22%. This QTL was found linked to the GATS11b marker of linkage group B10, which was consistently amplified across a set of common bean lines and was associated with the resistance. Four new QTLs were identified. Between them the ALS5.2 showed an important effect (9.4% under inoculated conditions in the greenhouse. ALS4.2 was another major QTL, under natural infection in the field, explaining 10.8% of the variability for resistance reaction. The other QTLs showed minor effects on resistance. Conclusions The results indicated a quantitative inheritance pattern of ALS resistance in the common bean line CAL 143. QTL x environment interactions were observed. Moreover, the major QTL identified on linkage group B10 could be important for bean breeding, as it was stable in all the environments. Thereby, the GATS11b
徐礼羿; 谭礼强; 王丽鸳; 齐桂年; 成浩; 韦康
In order to provide a basis for breeding tea plants with anthracnose resistance, 170 F1 plants, derived from LJ43♀×BHZ♂, were used to constructed a linkage map by SSR markers. Field observation and indoor test were carried out in 2014. The data of phenotypic characters were used for QTL mapping and analysis by the method of MQM mapping. A pathogen was isolated from a diseased leaf of the F1 plants, and its gene sequence of ITS had 99%similarity with Colletotrichum sp. based on NCBI BLAST. The plants grown in open field were more easy to be infected by the pathogen than those grown in rooms. Eight QTLs were detected in six different linkage groups by QTL analysis. The LOD and PVE of individual QTLs ranged from 2.53 to 6.80 and 5.6% to 13.8%, respectively. A main QTL with LOD 6.80 and PVE 13.8% was detected in LG10.%以茶树 SSR 遗传连锁图谱为基础，选取龙井43为母本，白毫早为父本的170株 F1遗传群体为试验材料，于2014年对该群体分别进行了茶树炭疽病抗性性状的田间观测和室内侵染试验，并采用复合区间作图法对该性状进行 QTL 定位与分析。结果显示：从 F1群体病叶上分离纯化出一种茶树炭疽病病菌 HZ-1，经NCBI BLAST 比对，其 ITS 基因序列与炭疽菌（Colletotrichum sp.）的亲缘关系最近，序列相似度为99%。对F1群体的炭疽病抗性表型分析发现，田间环境下的感病单株的占比（41%）高于室内环境（24%）。QTL 分析显示，在6个不同的遗传连锁群（Linkage group，LG）上共检测到8个 QTLs，单个 QTL 的 LOD 阈值变幅为2.53~6.80，单个 QTL 的表型变异贡献率的变幅为5.6%~13.8%。LG10存在1个控制茶树炭疽病抗性性状的主效 QTL，LOD 值6.80，表型变异贡献率13.8%。
YAN Jianbing; TANG Hua; HUANG Yiqin; SHI Yonggang; LI Jiansheng; ZHENG Yonglian
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.
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.
Sallé, G; Jacquiet, P; Gruner, L; Cortet, J; Sauvé, C; Prévot, F; Grisez, C; Bergeaud, J P; Schibler, L; Tircazes, A; François, D; Pery, C; Bouvier, F; Thouly, J C; Brunel, J C; Legarra, A; Elsen, J M; Bouix, J; Rupp, R; Moreno, C R
Gastrointestinal nematodes are one of the main health issues in sheep breeding. To identify loci affecting the resistance to Haemonchus contortus, a genome scan was carried out using 1,275 Romane × Martinik Black Belly backcross lambs. The entire population was challenged with Haemonchus contortus in 2 consecutive experimental infections, and fecal egg counts (FEC) and packed cell volumes were measured. A subgroup of 332 lambs with extreme FEC was necropsied to determine the total worm burden, length of female worms, sex ratio in the worm population, abomasal pH, and serum and mucosal G immunoglobulins (IgG) responses. Pepsinogen concentration was measured in another subset of 229 lambs. For QTL detection, 160 microsatellite markers were used as well as the Illumina OvineSNP50 BeadChip that provided 42,469 SNP markers after quality control. Linkage, association, and joint linkage and association analyses were performed with the QTLMAP software. Linkage disequilibrium (LD) was estimated within each pure breed, and association analyses were carried out either considering or not the breed origin of the haplotypes. Four QTL regions on sheep chromosomes (OAR)5, 12, 13, and 21 were identified as key players among many other QTL with small to moderate effects. A QTL on OAR21 affecting pepsinogen concentration exactly matched the pepsinogen (PGA5) locus. A 10-Mbp region affecting FEC after the 1st and 2nd infections was found on OAR12. The SNP markers outperformed microsatellites in the linkage analysis. Taking advantage of the LD helped to refine the locations of the QTL mapped on OAR5 and 13.
Wei, Qing-Zhen; Fu, Wen-Yuan; Wang, Yun-Zhu; Qin, Xiao-Dong; Wang, Jing; Li, Ji; Lou, Qun-Feng; Chen, Jin-Feng
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.
Helen Cristina de Arruda Rodrigues
Full Text Available Um dos grandes desafios atuais da pesquisa agrícola é a produção de cultivares melhoradas de mamoneira, com estabilidade genética, alta qualidade e potencial produtivo. Objetivou-se, no presente trabalho, estimar as correlações genotípica, fenotípica e de ambiente entre caracteres de mamona para facilitar a caracterização dos acessos. Foram avaliados em Lavras, MG, no delineamento de blocos casualizados com três repetições, quinze acessos de mamona. Os caracteres avaliados foram altura da planta, altura do caule, número de internódios, diâmetro do caule, número de cachos, estande final e peso de 100 sementes. Observou-se que houve correlação fenotípica positiva do número de internódios e altura do caule, altura do caule e altura da planta, altura da planta e diâmetro do caule e por fim entre diâmetro do caule e peso de 100 sementes. Houve também correlação ambiental positiva entre as correlações altura de caule e altura de planta, altura de planta e diâmetro do caule, altura da planta e estande final e diâmetro do caule e número de cachos, concluindo que as correlações estimadas possibilitaram conhecer as associações entre os caracteres, fornecendo importantes informações para o estabelecimento de um plano de melhoramento genético da mamona, a partir dos acessos avaliados.One of the great current challenges of agricultural research is the production of improved castor bean cultivars, with genetic stability, high quality and high yielding potential. The objective this work was to estimate genotypic, phenotypic and environmental correlations among traits of the castor bean plant to make the characterization of the accessions easy. They were evaluated in Lavras, MG, Brazil, in a randomized block design with three replicates, fifteen castor bean accessions. The traits evaluated were: plant height, stem height, number of nodes, stem diameter, final number of clusters, stand and 100-seed weight. It was observed
Maricelma Simiano Jung
Full Text Available O maracujazeiro-doce, Passiflora alata Curtis, é uma planta frutífera que vem despertando interesse econômico principalmente para o consumo in natura. Contudo, precisam ser superados alguns entraves tecnológicos em relação ao seu cultivo, tais como a ausência de cultivares que apresentem frutos com alto rendimento de polpa, resistência mecânica e elevado teor de sólidos solúveis totais. Nesse sentido, este trabalho teve por objetivo estimar a herdabilidade (h² e o ganho genético esperado com a seleção, para os caracteres peso do fruto, peso da polpa, espessura da casca, sólidos solúveis totais e rendimento de polpa em maracujazeiro-doce, por meio da avaliação de 36 cruzamentos envolvendo seis genitores femininos e seis masculinos. Os resultados obtidos evidenciaram uma ampla variação na magnitude dos valores da h² entre os cruzamentos e a predominância de efeitos gênicos de aditividade no controle genético dos caracteres. Assim, é necessário levar em consideração o grande efeito do fator cruzamento na estimativa da h², bem como a realização da seleção direta na maioria das progênies avaliadas em razão de que os efeitos aditivos predominaram no controle da maioria dos caracteres estudados.The sweet passion fruit, Passiflora alata Curtis, is a fruit tree that has been gaining economic importance because their fruits can be consumed in natura due to its unique flavor. However, some technologic obstacles need to be overcome in order to allow plantation in large scale, such as the absence of cultivars producing fruits with high pulp output, mechanic resistance in its skin, and high levels of soluble solids. In this context, this work was carried out to estimate the inheritability (h² and the genetic gain as expected selection response for the traits: weigh of the fruit, weight of the pulp, thickness of the skin, Brix degree and pulp output. To achieve the goals, it was used F1 progenies from 36 crosses involving
WANG Yi; YAO Ji; ZHANG Zhengfeng; ZHENG Yonglian
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.
JIANG Feng; ZHAO Jun; ZHOU Lei; GUO WangZhen; ZHANG TianZhen
Verticillium wilt is s destructive disease with international consequences for cotton production. Breeding broad-spectrum resistant cultivars is considered to be one of the most effective means for reducing crop losses. A resistant cotton cultivar, 60182, was crossed with a susceptible cultivar, Junmian 1, to identify markers for Verticillium resistance genes and validate the mode of its inheritance. Genetic segregation analysis for Verticillium wilt resistance was evaluated based upon infected leaf percentage in the seedling stage using major gene-polygene mixed inheritance models and joint analysis of P_1, P_2, F_1, B_1, B_2 and F_2 populations obtained from the cultivar cross. We found that resistance of upland cotton cultivar 60182 to isolates BP2, VD8 and T9, and their isoconcentration mixture was controlled by two major genes with additive-dominance-epistatic effects, and the inheritance of the major gene was dominant. Furthermore, a genetic linkage map was constructed using F_2 segregating population and resistance phenotypic data were obtained using F_(2:3) families inoculated with different isolates and detected in different developmental stages. The genetic linkage map with 139 loci was comprised of 31 linkage groups covering 1165 cM, with an average distance of 8.38 cM between two markers, or 25.89% of the cotton genome length. From 60182, we found 4 QTL on chromosome D7 and 4 QTL on D9 for BP2, 5 QTL on D7 and 9 QTL on D9 for VD8, 4 QTL on D7 and 5 QTL on D9 for T9 and 3 QTL on D7 and 7 QTL on D7 for mixed pathogens. The QTL mapping results revealed that QTL clusters with high contribution rates were screened simultaneously on chromosomes D9 and D7 by multiple interval mapping (CIM), whether from resistance phenotypic data from different developmental stages or for different isolates. The result is consistent with the genetic model of two major genes in 60182 and suggests broad-spectrum resistance to both defoliating isolates of V. dahliae and
Lin, Grace; Chua, Elaine; Orban, Laszlo; Yue, Gen Hua
In aquaculture, growth and sex are economically important traits. To accelerate genetic improvement in increasing growth in salt-tolerant tilapia, we conducted QTL mapping for growth traits and sex with an F2 family, including 522 offspring and two parents. We used 144 polymorphic microsatellites evenly covering the genome of tilapia to genotype the family. QTL analyses were carried out using interval mapping for all individuals, males and females in the family, respectively. Using all individuals, three suggestive QTL for body weight, body length and body thickness respectively were detected in LG20, LG22 and LG12 and explained 2.4% to 3.1% of phenotypic variance (PV). When considering only males, five QTL for body weight were detected on five LGs, and explained 4.1 to 6.3% of PV. Using only females from the F2 family, three QTL for body weight were detected on LG1, LG6 and LG8, and explained 7.9–14.3% of PV. The QTL for body weight in males and females were located in different LGs, suggesting that in salt-tolerant tilapia, different set of genes ‘switches’ control the growth in males and females. QTL for sex were mapped on LG1 and LG22, indicating multigene sex determination in the salt-tolerant tilapia. This study provides new insights on the locations and effects of QTL for growth traits and sex, and sets the foundation for fine mapping for future marker-assisted selection for growth and sex in salt-tolerant tilapia aquaculture. PMID:27870905
Muchero, Wellington; Ehlers, Jeffrey D; Close, Timothy J; Roberts, Philip A
Cowpea is an important crop for subsistence farmers in arid regions of Africa, Asia, and South America. Efforts to develop cultivars with improved productivity under drought conditions are constrained by lack of molecular markers associated with drought tolerance. Here, we report the mapping of 12 quantitative trait loci (QTL) associated with seedling drought tolerance and maturity in a cowpea recombinant inbred (RIL) population. One hundred and twenty-seven F(8) RILs developed from a cross between IT93K503-1 and CB46 were screened with 62 EcoR1 and Mse1 primer combinations to generate 306 amplified fragment length polymorphisms for use in genetic linkage mapping. The same population was phenotyped for maintenance of stem greenness (stg) and recovery dry weight (rdw) after drought stress in six greenhouse experiments. In field experiments conducted over 3 years, visual ratings and dry weights were used to phenotype drought stress-induced premature senescence in the RIL population. Kruskall-Wallis and multiple-QTL model mapping analysis were used to identify QTL associated with drought response phenotypes. Observed QTL were highly reproducible between stg and rdw under greenhouse conditions. Field studies confirmed all ten drought-response QTL observed under greenhouse conditions. Regions harboring drought-related QTL were observed on linkage groups 1, 2, 3, 5, 6, 7, 9, and 10 accounting for between 4.7 and 24.2% of the phenotypic variance (R(2)). Further, two QTL for maturity (R(2) = 14.4-28.9% and R(2) = 11.7-25.2%) mapped on linkage groups 7 and 8 separately from drought-related QTL. These results provide a platform for identification of genetic determinants of seedling drought tolerance in cowpea.
Giovani Olegario da Silva
Full Text Available O objetivo do presente trabalho foi verificar os ganhos esperados com a seleção correlacionada na geração de plântula, para caracteres componentes do rendimento e aparência geral de tubérculos de batata. Foram avaliadas duas populações em casa de vegetação nos cultivos de outono e primavera de 2004. Estimaram-se os ganhos esperados com a seleção direta e ganhos esperados por meio da seleção de caracteres correlacionados geneticamente. Verificou-se que para alguns caracteres os ganhos correlacionados esperados podem ser obtidos na geração de plântula, sendo uma boa opção quando favoreceram caracteres com menores herdabilidades. A curvatura de tubérculo foi o caráter que proporcionou maiores ganhos correlacionados esperados para aparência geral de tubérculo.The objective of the present research was to estimate the expected gains with correlated selection for tuber yield and general appearance component traits at the seedling stage in potato. Two populations were evaluated at seedling stage (i.e. plantlets obtained from true seeds cultivated in glasshouse in the Fall and Spring seasons of 2004. Expected gains and gains obtained from selection of genetically correlated traits were estimated in the two experiments. For some traits the expected correlated gains could be obtained at the seedling generation, being, therefore an alternative to increase selection efficiency, especially with traits of low heritability. The tuber curvature was the trait that provided the largest expected correlated gains for general tuber appearance.
Sun, Y D; Liang, Y; Wu, J M; Li, Y Z; Cui, X; Qin, L
Fruit lycopene content and total soluble solid content are important factors determining fruit quality of tomatoes; however, the dynamic quantitative trait loci (QTL) controlling lycopene and soluble solid content have not been well studied. We mapped the chromosomal regions controlling these traits in different periods in F(2:3) families derived from a cross between the domestic and wild tomato species Solanum lycopersicum and S. pimpinellifolium. Fifteen QTLs for lycopene and soluble solid content and other related traits analyzed at three different fruit ripening stages were detected with a composite interval mapping method. These QTLs explained 7-33% of the individual phenotypic variation. QTLs detected in the color-changing period were different from those detected in the other two periods. On chromosome 1, the soluble solid content QTL was located in the same region during the color-changing and full-ripe periods. On chromosome 4, the same QTL for lycopene content was found during the color-changing and full-ripe periods. The QTL for lycopene content on chromosome 4 co-located with the QTL for soluble solid content during the full-ripe period. Co-location of lycopene content QTL and soluble solid content QTLs may be due to pleiotropic effects of a single gene or a cluster of genes via physiological relationships among traits. On chromosome 9, the same two QTLs for lycopene content at two different fruit ripening periods may reflect genes controlling lycopene content that are always expressed in tomato fruit development.
Bin Wang; Zhanhui Zhang; Zhiyuan Fu; Zonghua Liu; Yanmin Hu; Jihua Tang
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℃ 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（28QTL） 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 qVI4 b and qGE3 a 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.
Zeevaert-Wiechers, L. [Universidad Nacional Autonoma de Mexico, Mexico, D.F. (Mexico)
apoyan sobre ellos. De ahi la necesidad de conocer los parametros cuantitativos que rigen el comportamiento estatico y dinamico de este tipo de suelos en relacion con los cambios ambientales de humedad. La investigacion basica es importante y necesaria en mecanica de suelos e ingenieria de cimentaciones, y debera efectuarse en los diferentes tipos de suelos que se encuentran en la naturaleza. Se muestran las curvas de compresibilidad de sedimentos eolicos finos, asi como curva de colapsos por hidratacion de suelo tipo loessial. Se presenta una figura de la relacion de colapsos, de esfuerzos y finalmente se da una tabla de los elementos.
María de los Angeles Bacigalupe
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
Agenor Martinho Correa
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
Diego Sebastián Crescentino
Full Text Available El presente artículo reflexiona sobre las transformaciones de la normativa migratoria argentina entre 2004-2014. Se analizan los preceptos legales dictados con posterioridad a la promulgación de la Ley de Migraciones N.25.871/04, observando la presencia de caracteres culturales en las mismas, y el fomento de principios de interculturalidad en la sociedad argentina. Además, se examina si se ha contemplado una alternativa a la representación de una identidad nacional homogénea instituida a partir de la demarcación del Estado Moderno.Por otra parte, se pone a consideración la estructura orgánica de la institución estatal responsable de la cultura a nivel nacional, comprobando la incorporación de los principios multiculturalistas en sus objetivos. Para concluir, se verifican las tareas pendientes para el cumplimiento de la ley; y se indaga sobre la pertinencia de estas políticas para la interpretación de la realidad cultural argentina.
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.
Haggard, J Erron; Johnson, Emily B; St Clair, Dina A
When the allele of a wild species at a quantitative trait locus (QTL) conferring a desirable trait is introduced into cultivated species, undesirable effects on other traits may occur. These negative phenotypic effects may result from the presence of wild alleles at other closely linked loci that are transferred along with the desired QTL allele (i.e., linkage drag) and/or from pleiotropic effects of the desired allele. Previously, a QTL for resistance to Phytophthora infestans on chromosome 5 of Solanum habrochaites was mapped and introgressed into cultivated tomato (S. lycopersicum). Near-isogenic lines (NILs) were generated and used for fine-mapping of this resistance QTL, which revealed coincident or linked QTL with undesirable effects on yield, maturity, fruit size, and plant architecture traits. Subsequent higher-resolution mapping with chromosome 5 sub-NILs revealed the presence of multiple P. infestans resistance QTL within this 12.3 cM region. In our present study, these sub-NILs were also evaluated for 17 horticultural traits, including yield, maturity, fruit size and shape, fruit quality, and plant architecture traits in replicated field experiments over the course of two years. Each previously detected single horticultural trait QTL fractionated into two or more QTL. A total of 41 QTL were detected across all traits, with ∼30% exhibiting significant QTL × environment interactions. Colocation of QTL for multiple traits suggests either pleiotropy or tightly linked genes control these traits. The complex genetic architecture of horticultural and P. infestans resistance trait QTL within this S. habrochaites region of chromosome 5 presents challenges and opportunities for breeding efforts in cultivated tomato.
Schejbel, Britt; Jensen, Louise Friis Bach; Xing, Yongzhong;
as well as by artificial pathogen inoculations using a detached leaf assessment. The broad sense heritability values for the field, detached leaf and combined assays were 0.42, 0.56, and 0.64, respectively, indicating a good potential for selection for crown rust resistance. A total of six QTLs were......Crown rust is an economically devastating disease of perennial ryegrass. Both artificial crown rust inoculations, with the possibility of several selection cycles in one year, as well as marker-assisted selection can be used for more efficient breeding of new resistant cultivars. The objective...... of this study was to map quantitative trait loci (QTL) for response to crown rust infection in perennial ryegrass. In order to identify relevant markers for response to crown rust infection, QTL mapping was performed on a ryegrass mapping population which was evaluated for resistance in the field for two years...
van den Berg, Irene; Guldbrandtsen, Bernt; Hozé, C;
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......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...
Antanaviciute, L; Šurbanovski, N; Harrison, N; McLeary, K J; Simpson, D W; Wilson, F; Sargent, D J; Harrison, R J
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.
Xu, K; Riaz, S; Roncoroni, N C; Jin, Y; Hu, R; Zhou, R; Walker, M A
Resistance to the dagger nematode Xiphinema index has been an important objective in grape rootstock breeding programs. This nematode not only causes severe feeding damage to the root system, but it also vectors grapevine fanleaf virus (GFLV), the causal agent of fanleaf degeneration and one of the most severe viral diseases of grape. The established screening procedures for dagger nematode resistance are time consuming and can produce inconsistent results. A fast and reliable greenhouse-based system for screening resistance to X. index that is suitable for genetic studies and capable of evaluating breeding populations is needed. In this report, the dynamics of nematode numbers, gall formation, and root weight loss were investigated using a variety of soil mixes and pot sizes over a 52-week period. Results indicated that the number of galls formed was correlated with the size of the nematode population and with the degree of root weight loss. After inoculation with 100 nematodes, gall formation could be reliably evaluated in 4-8 weeks in most plant growth conditions and results were obtained 6 months more rapidly than past evaluation methods. This modified X. index resistance screening method was successfully applied to 185 of the 188 F(1) progeny from a cross of D8909-15 x F8909-17 (the 9621 population), which segregates for a form of X. index resistance originally derived from Vitis arizonica. Quantitative trait loci (QTL) analysis was carried out on both parental genetic maps of 255 markers using MapQTL 4.0. Results revealed that X. index resistance is controlled by a major QTL, designated Xiphinema index Resistance 1 (XiR1), near marker VMC5a10 on chromosome 19. The XiR1 QTL was supported by a LOD score of 36.9 and explained 59.9% of the resistance variance in the mapping population.
Kelly, Scott A; Nehrenberg, Derrick L.; Hua, Kunjie; Garland, Theodore; Pomp, Daniel
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...
Full Text Available Studies of the relationship between DNA variation and gene expression variation, often referred to as "expression quantitative trait loci (eQTL mapping", have been conducted in many species and resulted in many significant findings. Because of the large number of genes and genetic markers in such analyses, it is extremely challenging to discover how a small number of eQTLs interact with each other to affect mRNA expression levels for a set of co-regulated genes. We present a Bayesian method to facilitate the task, in which co-expressed genes mapped to a common set of markers are treated as a module characterized by latent indicator variables. A Markov chain Monte Carlo algorithm is designed to search simultaneously for the module genes and their linked markers. We show by simulations that this method is more powerful for detecting true eQTLs and their target genes than traditional QTL mapping methods. We applied the procedure to a data set consisting of gene expression and genotypes for 112 segregants of S. cerevisiae. Our method identified modules containing genes mapped to previously reported eQTL hot spots, and dissected these large eQTL hot spots into several modules corresponding to possibly different biological functions or primary and secondary responses to regulatory perturbations. In addition, we identified nine modules associated with pairs of eQTLs, of which two have been previously reported. We demonstrated that one of the novel modules containing many daughter-cell expressed genes is regulated by AMN1 and BPH1. In conclusion, the Bayesian partition method which simultaneously considers all traits and all markers is more powerful for detecting both pleiotropic and epistatic effects based on both simulated and empirical data.
Full Text Available Abstract Background We have recently identified a number of Quantitative Trait Loci (QTL contributing to the 2-fold muscle weight difference between the LG/J and SM/J mouse strains and refined their confidence intervals. To facilitate nomination of the candidate genes responsible for these differences we examined the transcriptome of the tibialis anterior (TA muscle of each strain by RNA-Seq. Results 13,726 genes were expressed in mouse skeletal muscle. Intersection of a set of 1061 differentially expressed transcripts with a mouse muscle Bayesian Network identified a coherent set of differentially expressed genes that we term the LG/J and SM/J Regulatory Network (LSRN. The integration of the QTL, transcriptome and the network analyses identified eight key drivers of the LSRN (Kdr, Plbd1, Mgp, Fah, Prss23, 2310014F06Rik, Grtp1, Stk10 residing within five QTL regions, which were either polymorphic or differentially expressed between the two strains and are strong candidates for quantitative trait genes (QTGs underlying muscle mass. The insight gained from network analysis including the ability to make testable predictions is illustrated by annotating the LSRN with knowledge-based signatures and showing that the SM/J state of the network corresponds to a more oxidative state. We validated this prediction by NADH tetrazolium reductase staining in the TA muscle revealing higher oxidative potential of the SM/J compared to the LG/J strain (p Conclusion Thus, integration of fine resolution QTL mapping, RNA-Seq transcriptome information and mouse muscle Bayesian Network analysis provides a novel and unbiased strategy for nomination of muscle QTGs.
Xiang Yu; Han Wang; Weili Zhong; Jinjuan Bai; Pinglin Liu; Yuke He
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...
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.
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.
Beatty Mary; Luck Stanley; Holloway Beth; Rafalski J-Antoni; Li Bailin
Abstract Background Expression QTL analyses have shed light on transcriptional regulation in numerous species of plants, animals, and yeasts. These microarray-based analyses identify regulators of gene expression as either cis-acting factors that regulate proximal genes, or trans-acting factors that function through a variety of mechanisms to affect transcript abundance of unlinked genes. Results A hydroponics-based genetical genomics study in roots of a Zea mays IBM2 Syn10 double haploid pop...
Holloway, Beth; Luck, Stanley; Beatty, Mary; Rafalski, J-Antoni; Li, Bailin
Background Expression QTL analyses have shed light on transcriptional regulation in numerous species of plants, animals, and yeasts. These microarray-based analyses identify regulators of gene expression as either cis-acting factors that regulate proximal genes, or trans-acting factors that function through a variety of mechanisms to affect transcript abundance of unlinked genes. Results A hydroponics-based genetical genomics study in roots of a Zea mays IBM2 Syn10 double haploid population i...
John Goodstal, F; Kohler, Glenn R; Randall, Leslie B; Bloom, Arnold J; St Clair, Dina A
Many plants of tropical or subtropical origin, such as tomato, suffer damage under chilling temperatures (under 10 degrees C but above 0 degrees C). An earlier study identified several quantitative trait loci (QTLs) for shoot turgor maintenance (stm) under root chilling in an interspecific backcross population derived from crossing chilling-susceptible cultivated tomato (Lycopersicon esculentum) and chilling-tolerant wild L. hirsutum. The QTL with the greatest phenotypic effect on stm was located in a 28 cM region on chromosome 9 (designated stm 9), and enhanced chilling-tolerance was conferred by the presence of the Lycopersicon hirsutum allele at this QTL. Here, near-isogenic lines (NILs) were used to verify the effect of stm 9, and recombinant sub-NILs were used to fine map its position. Replicated experiments were performed with NILs and sub-NILs in a refrigerated hydroponic tank in the greenhouse. Sub-NIL data was analyzed using least square means separations, marker-genotype mean t-tests, and composite interval mapping. A dominant QTL controlling shoot turgor maintenance under root chilling was confirmed on chromosome 9 using both NILs and sub-NILs. Furthermore, sub-NILs permitted localization of stm 9 to a 2.7 cM interval within the original 28 cM QTL region. If the presence of the L. hirsutum allele at stm 9 also confers chilling-tolerance in L. esculentum plants grown under field conditions, it has the potential to expand the geographic areas in which cultivated tomato can be grown for commercial production.
Ordas, Bernardo; Malvar, Rosa A; Santiago, Rogelio; Sandoya, German; Romay, Maria C; Butron, Ana
The Mediterranean corn borer or pink stem borer (MCB, Sesamia nonagrioides Lefebvre) causes important yield losses as a consequence of stalk tunneling and direct kernel damage. B73 and Mo17 are the source of the most commercial valuable maize inbred lines in temperate zones, while the intermated B73 x Mo17 (IBM) population is an invaluable source for QTL identification. However, no or few experiments have been carried out to detect QTL for corn borer resistance in the B73 x Mo17 population. The objective of this work was to locate QTL for resistance to stem tunneling and kernel damage by MCB in the IBM population. We detected a QTL for kernel damage at bin 8.05, although the effect was small and two QTL for stalk tunneling at bins 1.06 and 9.04 in which the additive effects were 4 cm, approximately. The two QTL detected for MCB resistance were close to other QTL consistently found for European corn borer (ECB, Ostrinia nubilalis Hübner) resistance, indicating mechanisms of resistance common to both pests or gene clusters controlling resistance to different plagues. The precise mapping achieved with the IBM population will facilitate the QTL pyramiding and the positional cloning of the detected QTL.
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.
González-Prendes, Rayner; Quintanilla, Raquel; Cánovas, Angela; Manunza, Arianna; Figueiredo Cardoso, Tainã; Jordana, Jordi; Noguera, José Luis; Pena, Ramona N.; Amills, Marcel
Meat quality traits have an increasing importance in the pig industry because of their strong impact on consumer acceptance. Herewith, we have combined phenotypic and microarray expression data to map loci with potential effects on five meat quality traits recorded in the longissimus dorsi (LD) and gluteus medius (GM) muscles of 350 Duroc pigs, i.e. pH at 24 hours post-mortem (pH24), electric conductivity (CE) and muscle redness (a*), lightness (L*) and yellowness (b*). We have found significant genome-wide associations for CE of LD on SSC4 (~104 Mb), SSC5 (~15 Mb) and SSC13 (~137 Mb), while several additional regions were significantly associated with meat quality traits at the chromosome-wide level. There was a low positional concordance between the associations found for LD and GM traits, a feature that reflects the existence of differences in the genetic determinism of meat quality phenotypes in these two muscles. The performance of an eQTL search for SNPs mapping to the regions associated with meat quality traits demonstrated that the GM a* SSC3 and pH24 SSC17 QTL display positional concordance with cis-eQTL regulating the expression of several genes with a potential role on muscle metabolism. PMID:28054563
Full Text Available Abstract Background Understanding the genetic basis of heritable spinal curvature would benefit medicine and aquaculture. Heritable spinal curvature among otherwise healthy children (i.e. Idiopathic Scoliosis and Scheuermann kyphosis accounts for more than 80% of all spinal curvatures and imposes a substantial healthcare cost through bracing, hospitalizations, surgery, and chronic back pain. In aquaculture, the prevalence of heritable spinal curvature can reach as high as 80% of a stock, and thus imposes a substantial cost through production losses. The genetic basis of heritable spinal curvature is unknown and so the objective of this work is to identify quantitative trait loci (QTL affecting heritable spinal curvature in the curveback guppy. Prior work with curveback has demonstrated phenotypic parallels to human idiopathic-type scoliosis, suggesting shared biological pathways for the deformity. Results A major effect QTL that acts in a recessive manner and accounts for curve susceptibility was detected in an initial mapping cross on LG 14. In a second cross, we confirmed this susceptibility locus and fine mapped it to a 5 cM region that explains 82.6% of the total phenotypic variance. Conclusions We identify a major QTL that controls susceptibility to curvature. This locus contains over 100 genes, including MTNR1B, a candidate gene for human idiopathic scoliosis. The identification of genes associated with heritable spinal curvature in the curveback guppy has the potential to elucidate the biological basis of spinal curvature among humans and economically important teleosts.
Kuroda, Yosuke; Kaga, Akito; Tomooka, Norihiko; Yano, Hiroshi; Takada, Yoshitake; Kato, Shin; Vaughan, Duncan
The objective of this study was to identify quantitative trait loci (QTL) affecting fitness of hybrids between wild soybean (Glycine soja) and cultivated soybean (Glycine max). Seed dormancy and seed number, both of which are important for fitness, were evaluated by testing artificial hybrids of G. soja × G. max in a multiple-site field trial. Generally, the fitness of the F1 hybrids and hybrid derivatives from self-pollination was lower than that of G. soja due to loss of seed dormancy, whereas the fitness of hybrid derivatives with higher proportions of G. soja genetic background was comparable with that of G. soja. These differences were genetically dissected into QTL for each population. Three QTLs for seed dormancy and one QTL for total seed number were detected in the F2 progenies of two diverse cross combinations. At those four QTLs, the G. max alleles reduced seed number and severely reduced seed survival during the winter, suggesting that major genes acquired during soybean adaptation to cultivation have a selective disadvantage in natural habitats. In progenies with a higher proportion of G. soja genetic background, the genetic effects of the G. max alleles were not expressed as phenotypes because the G. soja alleles were dominant over the G. max alleles. Considering the highly inbreeding nature of these species, most hybrid derivatives would disappear quickly in early self-pollinating generations in natural habitats because of the low fitness of plants carrying G. max alleles.
Hu, Xiaoxiang; Gao, Yu; Feng, Chungang; Liu, Qiuyue; Wang, Xiaobo; Du, Zhuo; Wang, Qingsong; Li, Ning
Rapid progress in farm animal breeding has been made in the last few decades. Advanced technologies for genomic analysis in molecular genetics have led to the identification of genes or markers associated with genes that affect economic traits. Molecular markers, large-insert libraries and RH panels have been used to build the genetic linkage maps, physical maps and comparative maps in different farm animals. Moreover, EST sequencing, genome sequencing and SNPs maps are helping us to understand how genomes function in various organisms and further areas will be studied by DNA microarray technologies and proteomics methods. Because most economically important traits in farm animals are controlled by multiple genes and the environment, the main goal of genome research in farm animals is to map and characterize genes determining QTL. There are two main strategies to identify trait loci, candidate gene association tests and genome scan approaches. In recent years, some new concepts, such as RNAi, miRNA and eQTL, have been introduced into farm animal research, especially for QTL mapping and finding QTN. Several genes that influence important traits have already been identified or are close to being identified, and some of them have been applied in farm animal breeding programs by marker-assisted selection.
Yang Xiang; Yumei Li; Zaiming Liu; Zhenqiu Sun
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.
Xiang, Yang; Li, Yumei; Liu, Zaiming; Sun, Zhenqiu
An entropy-based statistic T(PE) has been proposed for genomic association study for disease-susceptibility locus. The statistic T(PE) may be directly adopted and/or extended to quantitative-trait locus (QTL) mapping for quantitative traits. In this article, the statistic T(PE) 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 T(PE) 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 T(PE) for genetic association study.
Controversias epistemológicas y metodológicas entre el paradigma cualitativo y cuantitativo en psicología/ epistemological and methodological controversies between the qualitative and quantitative paradigm in psychology
Cuenya, Lucas; Ruetti, Eliana
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...
Castanho, Roberto Barboza; FACIP - UFU, Ituiutaba
A partir do desenvolvimento do projeto intitulado “Análisis Espacial de la Salud�? del Programa de Estudios Geográficos (PROEG), projeto esse coordenado pelo Professor Doutor Gustavo Daniel Buzai, resultou o livro “Métodos cuantitativos em Geografía de la Salud�?, publicado em 2007, com o apoio do “Departamento de Ciencias Sociales�? da “Universidad Nacional de Luján�? (Argentina), o qual expõe aos leitores, uma série de artigos sobre Geografia da Saúde, técnicas cartográficas, SIG, bem como ...
Luis Germán Cordero Muñoz; Cecilia Montes Jave; José Enrique Velásquez Hurtado; Yuleika Rodríguez Calviño; Walter Eduardo Vigo Valdez; Ángel Martín Rosas-Aguirre
Objetivos. Evaluar cinco elementos importantes de la calidad de atención (espacio físico, equipamiento, personal, tiempo para la atención, y consejería) en servicios de crecimiento y desarrollo (CRED) de 18 establecimientos de salud (EE. SS.) en nueve regiones con altos índices de pobreza en Perú. Materiales y métodos. Estudio cuali-cuantitativo realizado en Amazonas, Apurímac, Ayacucho, Cajamarca, Cusco, Huánuco, Huancavelica, Puno y Ucayali, que incluyó la observación directa (OD) durante l...
Como continuacion de una linea de investigación que hemos venido desarrollando los últimos años, en este trabajo nos planteamos analizar los y las protagonistas en las series de animación emitidas especificamente para el público infantil. Partimos de un análisis cuantitativo de la programación de los tres canales en abierto que tienen como objetivo el público infantil. A partir de los resultados, elegimos tres series representativas, una de cada canal y hacemos un análisis cualitativo de los ...
Souza Alessandra A.
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.
Full Text Available 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
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
Fan, B; Glenn, K L; Geiger, B; Mileham, A; Rothschild, M F
Previous studies have uncovered several significant quantitative trait loci (QTL) relevant to meat colour traits mapped at the end of SSC17 in the pig. Furthermore, results released from the porcine genome sequencing project have identified genes underlying the entire QTL regions and can further contribute to mining the region for likely causative genes. Ten protein coding genes or novel transcripts located within the QTL regions were screened for single nucleotide polymorphisms (SNPs). Linkage mapping and association studies were carried out in the ISU Berkshire x Yorkshire (B x Y) pig resource family. The total length of the new SSC17 linkage map was 126.6 cM and additional markers including endothelin 3 (EDN3) and phosphatase and actin regulator 3 (PHACTR3) genes were assigned at positions 119.4 cM and 122.9 cM, respectively. A new QTL peak was noted at approximately 120 cM, close to the EDN3 gene, and for some colour traits QTL exceeded the 5% chromosome-wise significance threshold. The association analyses in the B x Y family showed that the EDN3 BslI and PHACTR3 PstI polymorphisms were strongly associated with the subjective colour score and objective colour reflectance measures in the loin, as well as average drip loss percentage and pH value. The RNPC1 DpnII and CTCFL HpyCH4III polymorphisms were associated with some meat colour traits. No significant association between CBLN4, TFAP2C, and four novel transcripts and meat colour traits were detected. The association analyses conducted in one commercial pig line found that both EDN3 BslI and PHACTR3 PstI polymorphisms were associated with meat colour reflectance traits such as centre loin hue angle and Minolta Lightness score. The present findings suggested that the EDN3 and PHACTR3 genes might have potential effects on meat colour in pigs, and molecular mechanisms of their functions are worth exploring.
Boer, Martin P; Wright, Deanne; Feng, Lizhi; Podlich, Dean W; Luo, Lang; Cooper, Mark; van Eeuwijk, Fred A
Complex quantitative traits of plants as measured on collections of genotypes across multiple environments are the outcome of processes that depend in intricate ways on genotype and environment simultaneously. For a better understanding of the genetic architecture of such traits as observed across environments, genotype-by-environment interaction should be modeled with statistical models that use explicit information on genotypes and environments. The modeling approach we propose explains genotype-by-environment interaction by differential quantitative trait locus (QTL) expression in relation to environmental variables. We analyzed grain yield and grain moisture for an experimental data set composed of 976 F(5) maize testcross progenies evaluated across 12 environments in the U.S. corn belt during 1994 and 1995. The strategy we used was based on mixed models and started with a phenotypic analysis of multi-environment data, modeling genotype-by-environment interactions and associated genetic correlations between environments, while taking into account intraenvironmental error structures. The phenotypic mixed models were then extended to QTL models via the incorporation of marker information as genotypic covariables. A majority of the detected QTL showed significant QTL-by-environment interactions (QEI). The QEI were further analyzed by including environmental covariates into the mixed model. Most QEI could be understood as differential QTL expression conditional on longitude or year, both consequences of temperature differences during critical stages of the growth.
B P Mallikarjuna Swamy
Full Text Available BACKGROUND: Rice (Oryza sativa L. is a highly drought sensitive crop, and most semi dwarf rice varieties suffer severe yield losses from reproductive stage drought stress. The genetic complexity of drought tolerance has deterred the identification of agronomically relevant quantitative trait loci (QTL that can be deployed to improve rice yield under drought in rice. Convergent evidence from physiological characterization, genetic mapping, and multi-location field evaluation was used to address this challenge. METHODOLOGY/PRINCIPAL FINDINGS: Two pairs of backcross inbred lines (BILs from a cross between drought-tolerant donor Aday Sel and high-yielding but drought-susceptible rice variety IR64 were produced. From six BC4F3 mapping populations produced by crossing the +QTL BILs with the -QTL BILs and IR64, four major-effect QTL--one each on chromosomes 2, 4, 9, and 10--were identified. Meta-analysis of transcriptome data from the +QTL/-QTL BILs identified differentially expressed genes (DEGs significantly associated with QTL on chromosomes 2, 4, 9, and 10. Physiological characterization of BILs showed increased water uptake ability under drought. The enrichment of DEGs associated with root traits points to differential regulation of root development and function as contributing to drought tolerance in these BILs. BC4F3-derived lines with the QTL conferred yield advantages of 528 to 1875 kg ha⁻¹ over IR64 under reproductive-stage drought stress in the targeted ecosystems of South Asia. CONCLUSIONS/SIGNIFICANCE: Given the importance of rice in daily food consumption and the popularity of IR64, the BC4F3 lines with multiple QTL could provide higher livelihood security to farmers in drought-prone environments. Candidate genes were shortlisted for further characterization to confirm their role in drought tolerance. Differential yield advantages of different combinations of the four QTL reported here indicate that future research should include
Taxonomic value of foliar characters in Dahlstedtia Malme: Leguminosae, Papilionoideae, Millettieae Valor taxonômico de caracteres foliares em Dahlstedtia Malme: Leguminosae, Papilionoideae, Millettieae
Simone de Pádua Teixeira
Full Text Available Dahlstedtia Malme (Leguminosae is a neotropical genus, native to the Brazilian Atlantic Forest, and comprises two species, D. pinnata (Benth. Malme and D. pentaphylla (Taub. Burk., although it has been considered a monotypic genus by some authors. Leaf anatomy was compared to verify the presence of anatomical characters to help delimit species. Foliar primordium, leaflet, petiolule, petiole and pulvinus were collected from cultivated plants (Campinas, SP, Brazil and from natural populations (Picinguaba, Ubatuba and Caraguatatuba, SP, Brazil - D. pinnata; Antonina, PR, Brazil - D. pentaphylla. Studies on leaflet surface assessment (Scanning Electron Microscopy, as well as histology and venation analyses were carried out of dehydrated, fresh and fixed material from two species. Leaflet material was macerated for stomatal counts. Histological sections, obtained by free-hand cut or microtome, were stained with Toluidine Blue, Safranin/Alcian Blue, Ferric Chloride, Acid Phloroglucin. Secretory cavities are present in the lamina, petiolule, petiole, pulvinus and leaf primordium in D. pentaphylla, but not in D. pinnata, and can be considered an important character for species diagnosis. Other leaf characters were uninformative in delimiting Dahlstedtia species. There is cambial activity in the petiolule, petiole and pulvinus. This study, associated with other available data, supports the recognition of two species in Dahlstedtia.Dahlstedtia Malme (Leguminosae é um gênero neotropical, com duas espécies reconhecidas, D. pinnata (Benth. Malme e D. pentaphylla (Taub. Burk., embora tenha sido considerado monotípico por alguns autores. Seus representantes ocorrem na Floresta Atlântica, nos Estados do Sul e Sudeste do Brasil. Neste trabalho, realizamos um estudo comparativo da anatomia foliar, para verificar a presença de caracteres que possam auxiliar a identificação das espécies. Primórdio foliar, lâmina foliar, peciólulo, pecíolo e pulvino
Cleusa Adriane Menegassi Bianchi Krüger
Full Text Available O objetivo deste trabalho foi estimar a herdabilidade e avaliar a correlação fenotípica entre caracteres de canola (Brassica napus relacionados à produtividade de grãos e à arquitetura de plantas. Foram realizados três experimentos, com espaçamento entre linhas de 0,20, 0,40 e 0,60 m. Durante dois anos de cultivo (2008 e 2009, os genótipos 'Hyola 432' e 'Hyola 61' foram avaliados em quatro densidades de plantio (20, 40, 60 e 80 plantas por metro quadrado, em cada experimento. Empregou-se o delineamento de blocos ao acaso, em arranjo fatorial 2x2x4 (anos x genótipos x densidades, com quatro repetições. Foram avaliados componentes ligados à produção (produtividade de grãos por área e por planta, número de síliquas por planta, número de grãos por síliqua e por planta, e massa de síliqua e à morfologia da canola (comprimento de síliqua, número de ramos secundários, altura de inserção do ramo secundário, comprimento de ramo e número de ramos terciários. A produtividade de grãos por área e por planta apresenta maior herdabilidade no menor espaçamento entre linhas. O número de síliquas e o de grãos por planta são os componentes de produção com maior correlação direta e positiva com a produtividade de grãos.
He, Xinyao; Skinnes, Helge; Oliver, Rebekah E; Jackson, Eric W; Bjørnstad, Asmund
Mycotoxins caused by Fusarium spp. is a major concern on food and feed safety in oats, although Fusarium head blight (FHB) is often less apparent than in other small grain cereals. Breeding resistant cultivars is an economic and environment-friendly way to reduce toxin content, either by the identification of resistance QTL or phenotypic evaluation. Both are little explored in oats. A recombinant-inbred line population, Hurdal × Z595-7 (HZ595, with 184 lines), was used for QTL mapping and was phenotyped for 3 years. Spawn inoculation was applied and deoxynivalenol (DON) content, FHB severity, days to heading and maturity (DH and DM), and plant height (PH) were measured. The population was genotyped with DArTs, AFLPs, SSRs and selected SNPs, and a linkage map of 1,132 cM was constructed, covering all 21 oat chromosomes. A QTL for DON on chromosome 17A/7C, tentatively designated as Qdon.umb-17A/7C, was detected in all experiments using composite interval mapping, with phenotypic effects of 12.2–26.6 %. In addition, QTL for DON were also found on chromosomes 5C, 9D, 13A, 14D and unknown_3, while a QTL for FHB was found on 11A. Several of the DON/FHB QTL coincided with those for DH, DM and/or PH. A half-sib population of HZ595, Hurdal × Z615-4 (HZ615, with 91 lines), was phenotyped in 2011 for validation of QTL found in HZ595, and Qdon.umb-17A/7C was again localized with a phenotypic effect of 12.4 %. Three SNPs closely linked to Qdon.umb-17A/7C were identified in both populations, and one each for QTL on 5C, 11A and 13A were identified in HZ595. These SNPs, together with those yet to be identified, could be useful in marker-assisted selection to pyramiding resistance QTL.
Thirstrup, Janne Pia; Anistoroaei, Razvan Marian; Guldbrandtsen, Bernt;
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 (F design). In the parental generation, Nordic Brown mink were crossed reciprocally with Ameri......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 (F design). In the parental generation, Nordic Brown mink were crossed reciprocally...... correlations and heritabilities were estimated using the average information-restricted maximum-likelihood method. Evidence was found for QTL affecting fur quality traits on nine autosomes. QTL were detected for guard hair thickness on chromosomes 1, 2, 3, 6 and 13; for guard hair length on chromosomes 2, 3...... and 6; for wool density on chromosomes 6 and 13; for surface on chromosomes 7, 12 and 13; for quality on chromosomes 6, 7, 11 and 13; and for skin length on chromosomes 7 and 9. Proximity of locations of QTL for guard hair length, guard hair thickness and for wool density and quality suggests that some...
Sahana, G; Guldbrandtsen, B; Thomsen, B; Lund, M S
A genome-wide association study of 2098 progeny-tested Nordic Holstein bulls genotyped for 36 387 SNPs on 29 autosomes was conducted to confirm and fine-map quantitative trait loci (QTL) for mastitis traits identified earlier using linkage analysis with sparse microsatellite markers in the same population. We used linear mixed model analysis where a polygenic genetic effect was fitted as a random effect and single SNPs were successively included as fixed effects in the model. We detected 143 SNP-by-trait significant associations (P mastitis-related traits. Among them, 21 SNP-by-trait combinations exceeded the genome-wide significant threshold. For 12 chromosomes, both the present association study and the previous linkage study detected QTL, and of these, six were in the same chromosomal locations. Strong associations of SNPs with mastitis traits were observed on bovine autosomes 6, 13, 14 and 20. Possible candidate genes for these QTL were identified. Identification of SNPs in linkage disequilibrium with QTL will enable marker-based selection for mastitis resistance. The candidate genes identified should be further studied to detect candidate polymorphisms underlying these QTL.
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
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 illustrating the polygenic nature of these traits. QTLs for multiple traits co-localized and we identified eight hotspots for quantitative trait loci (QTL) of seed weight, seed germination, and root and shoot lengths. A QTL hotspot for seed germination on A02 mapped at the B. rapa Flowering Locus C (BrFLC2). Another hotspot on A05 with salt stress specific QTLs co-located with the B. rapa Fatty acid desaturase 2 (BrFAD2) locus. Epistatic interactions were observed between QTL hotspots for seed germination on A02 and A10 and with a salt tolerance QTL on A05. These results contribute to the understanding of the genetics of seed quality and seeding vigor in B. rapa and can offer tools for Brassica breeding.
Haley Christopher S
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.
Zhang, Dan; Zhang, Hengyou; Chu, Shanshan; Li, Hongyan; Chi, Yingjun; Triebwasser-Freese, Daniella; Lv, Haiyan; Yu, Deyue
Soybean is a high phosphorus (P) demand species that is sensitive to low-P stress. Although many quantitative trait loci (QTL) for P efficiency have been identified in soybean, but few of these have been cloned and agriculturally applied mainly due to various limitations on identifying suitable P efficiency candidate genes. Here, we combined QTL mapping, transcriptome profiling, and plant transformation to identify candidate genes underlying QTLs associated with low-P tolerance and response mechanisms to low-P stress in soybean. By performing QTL linkage mapping using 152 recombinant inbred lines (RILs) that were derived from a cross between a P-efficient variety, Nannong 94-156, and P-sensitive Bogao, we identified four major QTLs underlying P efficiency. Within these four QTL regions, 34/81 candidate genes in roots/leaves were identified using comparative transcriptome analysis between two transgressive RILs, low-P tolerant genotype B20 and sensitive B18. A total of 22 phosphatase family genes were up-regulated significantly under low-P condition in B20. Overexpression of an acid phosphatase candidate gene, GmACP2, in soybean hairy roots increased P efficiency by 15.43-24.54 % compared with that in controls. Our results suggest that integrating QTL mapping and transcriptome profiling could be useful for rapidly identifying candidate genes underlying complex traits, and phosphatase-encoding genes, such as GmACP2, play important roles involving in low-P stress tolerance in soybean.
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.
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
Liu, Feng; Sun, Fei; Xia, Jun Hong; Li, Jian; Fu, Gui Hong; Lin, Grace; Tu, Rong Jian; Wan, Zi Yi; Quek, Delia; Yue, Gen Hua
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 growth traits was identified in the sex-determining locus in LG1, explaining 71.7%, 67.2% and 64.9% of the phenotypic variation (PV) of body weight, total length and standard length, respectively. In addition, a candidate gene GHR2 in a QTL was significantly associated with body weight, explaining 13.1% of PV. Real-time qPCR revealed that different genotypes at the GHR2 locus influenced the IGF-1 expression level. The markers located in the major QTL for growth traits could be used in marker-assisted selection of tilapia. The associations between GHR2 variants and growth traits suggest that the GHR2 gene should be an important gene that explains the difference in growth among tilapia species.
Eloi R Verrier
Full Text Available Health control is a major issue in animal breeding and a better knowledge of the genetic bases of resistance to diseases is needed in farm animals including fish. The detection of quantitative trait loci (QTL will help uncovering the genetic architecture of important traits and understanding the mechanisms involved in resistance to pathogens. We report here the detection of QTL for resistance to Viral Haemorrhagic Septicaemia Virus (VHSV, a major threat for European aquaculture industry. Two induced mitogynogenetic doubled haploid F2 rainbow trout (Oncorhynchus mykiss families were used. These families combined the genome of susceptible and resistant F0 breeders and contained only fully homozygous individuals. For phenotyping, fish survival after an immersion challenge with the virus was recorded, as well as in vitro virus replication on fin explants. A bidirectional selective genotyping strategy identified seven QTL associated to survival. One of those QTL was significant at the genome-wide level and largely explained both survival and viral replication in fin explants in the different families of the design (up to 65% and 49% of phenotypic variance explained respectively. These results evidence the key role of innate defence in resistance to the virus and pave the way for the identification of the gene(s responsible for resistance. The identification of a major QTL also opens appealing perspectives for selective breeding of fish with improved resistance.
Verrier, Eloi R; Dorson, Michel; Mauger, Stéphane; Torhy, Corinne; Ciobotaru, Céline; Hervet, Caroline; Dechamp, Nicolas; Genet, Carine; Boudinot, Pierre; Quillet, Edwige
Health control is a major issue in animal breeding and a better knowledge of the genetic bases of resistance to diseases is needed in farm animals including fish. The detection of quantitative trait loci (QTL) will help uncovering the genetic architecture of important traits and understanding the mechanisms involved in resistance to pathogens. We report here the detection of QTL for resistance to Viral Haemorrhagic Septicaemia Virus (VHSV), a major threat for European aquaculture industry. Two induced mitogynogenetic doubled haploid F2 rainbow trout (Oncorhynchus mykiss) families were used. These families combined the genome of susceptible and resistant F0 breeders and contained only fully homozygous individuals. For phenotyping, fish survival after an immersion challenge with the virus was recorded, as well as in vitro virus replication on fin explants. A bidirectional selective genotyping strategy identified seven QTL associated to survival. One of those QTL was significant at the genome-wide level and largely explained both survival and viral replication in fin explants in the different families of the design (up to 65% and 49% of phenotypic variance explained respectively). These results evidence the key role of innate defence in resistance to the virus and pave the way for the identification of the gene(s) responsible for resistance. The identification of a major QTL also opens appealing perspectives for selective breeding of fish with improved resistance.
Liu, Peng; Wang, Le; Wong, Sek-Man; Yue, Gen Hua
Asian seabass has suffered from viral nervous necrosis (VNN) disease. Our previous study has mapped quantitative trait loci (QTL) for resistance to VNN disease. To fine map these QTL and identify causative genes, we identified 6425 single nucleotide polymorphisms (SNPs) from 85 dead and 94 surviving individuals. Combined with 155 microsatellites, we constructed a genetic map consisting of 24 linkage groups (LGs) containing 3000 markers, with an average interval of 1.27 cM. We mapped one significant and three suggestive QTL with phenotypic variation explained (PVE) of 8.3 to 11.0%, two significant and two suggestive QTL with PVE of 7.8 to 10.9%, for resistance in three LGs and survival time in four LGs, respectively. Further analysis one QTL with the largest effect identified protocadherin alpha-C 2-like (Pcdhac2) as the possible candidate gene. Association study in 43 families with 1127 individuals revealed a 6 bp insertion-deletion was significantly associated with disease resistance. qRT-PCR showed the expression of Pcdhac2 was significantly induced in the brain, muscle and skin after nervous necrosis virus (NNV) infection. Our results could facilitate marker-assisted selection (MAS) for resistance to NNV in Asian seabass and set up the basis for functional analysis of the potential causative gene for resistance.
Lawrenson, Kate; Li, Qiyuan; Kar, Siddhartha
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...
Calus, M.P.L.; Meuwissen, T.H.E.; Windig, J.J.; Knol, E.F.; Schrooten, C.; Vereijken, A.L.J.; Veerkamp, R.F.
The aim of this paper was to compare the effect of haplotype definition on the precision of QTL-mapping and on the accuracy of predicted genomic breeding values. In a multiple QTL model using identity-by-descent (IBD) probabilities between haplotypes, various haplotype definitions were tested i.e. i
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
Maria do Socorro Padilha de Oliveira
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
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.
Chao; Lv; Yanxia; Song; Lifeng; Gao; Qin; Yao; Ronghua; Zhou; Rugen; Xu; Jizeng; Jia
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.
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
Full Text Available BACKGROUND: An understanding of the genetic determinism of photoperiod response of flowering is a prerequisite for the successful exchange of germplasm across different latitudes. In order to contribute to resolve the genetic basis of photoperiod sensitivity in maize, a set of 201 recombinant inbred lines (RIL, derived from a temperate and tropical inbred line cross were evaluated in 5 field trials spread in short- and long-day environments. METHODOLOGY/PRINCIPAL FINDINGS: Firstly, QTL analyses for flowering time and photoperiod sensitivity in maize were conducted in individual photoperiod environments separately, and then, the total genetic effect was partitioned into additive effect (A and additive-by-environment interaction effect (AE by using a mixed-model-based composite interval mapping (MCIM method. CONCLUSIONS/SIGNIFICANCE: Seven putative QTL were found associated with DPS thermal time based on the data estimated in individual environments. Nine putative QTL were found associated with DPS thermal time across environments and six of them showed significant QTL×enviroment (QE interactions. Three QTL for photoperiod sensitivity were identified on chromosome 4, 9 and 10, which had the similar position to QTL for DPS thermal time in the two long-day environment. The major photoperiod sensitive loci qDPS10 responded to both short and long-day photoperiod environments and had opposite effects in different photoperiod environment. The QTL qDPS3, which had the greatest additive effect exclusively in the short-day environment, were photoperiod independent and should be classified in autonomous promotion pathway.
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.
LUO Li-li; ZHANG Ying-xin; CHEN Dai-bo; ZHAN Xiao-deng; SHEN Xi-hong; CHENG Shi-hua; CAO Li-yong
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.
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
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.
He, Xin; Fuller, Chris K; Song, Yi; Meng, Qingying; Zhang, Bin; Yang, Xia; Li, Hao
Genetic mapping of complex diseases to date depends on variations inside or close to the genes that perturb their activities. A strong body of evidence suggests that changes in gene expression play a key role in complex diseases and that numerous loci perturb gene expression in trans. The information in trans variants, however, has largely been ignored in the current analysis paradigm. Here we present a statistical framework for genetic mapping by utilizing collective information in both cis and trans variants. We reason that for a disease-associated gene, any genetic variation that perturbs its expression is also likely to influence the disease risk. Thus, the expression quantitative trait loci (eQTL) of the gene, which constitute a unique "genetic signature," should overlap significantly with the set of loci associated with the disease. We translate this idea into a computational algorithm (named Sherlock) to search for gene-disease associations from GWASs, taking advantage of independent eQTL data. Application of this strategy to Crohn disease and type 2 diabetes predicts a number of genes with possible disease roles, including several predictions supported by solid experimental evidence. Importantly, predicted genes are often implicated by multiple trans eQTL with moderate associations. These genes are far from any GWAS association signals and thus cannot be identified from the GWAS alone. Our approach allows analysis of association data from a new perspective and is applicable to any complex phenotype. It is readily generalizable to molecular traits other than gene expression, such as metabolites, noncoding RNAs, and epigenetic modifications.
Lionikas, A; Cheng, R; Lim, J E; Palmer, A A; Blizard, D A
Genetic variation plays a substantial role in variation in strength, but the underlying mechanisms remain poorly understood. The objective of the present study was to examine the mechanisms underlying variation in muscle mass, a predictor of strength, between LG/J and SM/J strains, which are the inbred progeny of mice selected, respectively, for high and low body weight. We measured weight of five hindlimb muscles in LG/J and SM/J males and females, in F(1) and F(2) intercrosses, and in an advanced intercross (AI), F(34), between the two. F(2) mice were genotyped using 162 SNPs throughout the genome; F(34) mice were genotyped at 3,015 SNPs. A twofold difference in muscle mass between the LG/J and SM/J mouse strains was observed. Integrated genome-wide association analysis in the combined population of F(2) and AI identified 22 quantitative trait loci (QTL; genome-wide P LG/J allele conferred greater muscle weight in all cases. The 1.5-LOD QTL support intervals ranged between 0.3 and 13.4 Mb (median 3.7 Mb) restricting the list of candidates to between 5 and 97 genes. Selection for body weight segregated the alleles affecting skeletal muscle, the most abundant tissue in the body. Combination of analyses in an F(2) and AI was an effective strategy to detect and refine the QTL in a genome-wide manner. The achieved resolution facilitates further elucidation of the underlying genetic mechanisms affecting muscle mass.
Niedziela, A; Bednarek, P T; Labudda, M; Mańkowski, D R; Anioł, A
Triticale (x Triticosecale Wittmack) is a relatively new cereal crop. In Poland, triticale is grown on 12 % of arable land ( http://www.stat.gov.pl ). There is an increasing interest in its cultivation due to lowered production costs and increased adaptation to adverse environmental conditions. However, it has an insufficient tolerance to the presence of aluminum ions (Al(3+)) in the soil. The number of genes controlling aluminum tolerance in triticale and their chromosomal location is not known. Two F2 mapping biparental populations (MP1 and MP15) segregating for aluminum (Al) tolerance were tested with AFLP, SSR, DArT, and specific PCR markers. Genetic mapping enabled the construction of linkage groups representing chromosomes 7R, 5R and 2B. Obtained linkage groups were common for both mapping populations and mostly included the same markers. Composite interval mapping (CIM) allowed identification of a single QTL that mapped to the 7R chromosome and explained 25 % (MP1) and 36 % (MP15) of phenotypic variation. The B1, B26 and Xscm150 markers were 0.04 cM and 0.02 cM from the maximum of the LOD function in the MP1 and MP15, respectively and were highly associated with aluminum tolerance as indicated by Kruskal-Wallis nonparametric test. Moreover, the molecular markers B1, B26, Xrems1162 and Xscm92, previously associated with the Alt4 locus that encoded an aluminum-activated malate transporter (ScALMT1) that was involved in Al tolerance in rye (Secale cereale) also mapped within QTL. Biochemical analysis of plants represented MP1 and MP15 mapping populations confirmed that the QTL located on 7R chromosome in both mapping populations is responsible for Al tolerance.
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
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.
Pérez-Doria, Alveiro; Bejarano,Eduar Elías; Sierra,Diana; Vélez,Iván Darío
En Colombia están registradas 143 especies de Lutzomyia França, pero menos del 7% de éstas se encuentran incriminadas como vectores de Leishmania spp. Debido a la alta semejanza morfológica de algunas especies vectoras con otras no vectoras, se necesitan caracteres taxonómicos alternativos para identificar correctamente los flebotomíneos de cada zona geográfica del país. Con este objetivo, en el presente trabajo se secuenció el extremo 3’ del gen mitocondrial que codifica para la proteína cit...
Meta-analysis for heritability estimates of vegetative and reproductive traits of Coffea arabica L.Meta-análise para estimativas de herdabilidade de caracteres vegetativos e reprodutivos de Coffea arabica L.
Danielle Pereira Baliza
Full Text Available The compilation of informations resulting from independent studies has been difficulted in almost all scientific fields, mainly due to the great number of scientific papers published in recent years. As a result, summarizing information became a need. In this context, a meta-analysis was conducted with the objective of summarizing the estimates for the heritability for vegetative and reproductive traits of coffee (Coffea arabica L.. Heritability estimates were appraised regarding the following traits: average height of plant, average diameter of the canopy, vegetative vigor, production of processed coffee, yield and rust. The data regarding the heritability estimates are from scientific articles published in national and international journals, congress annals, PhD thesis and Master dissertations. The technique of meta-analysis summarized the estimates heritability from different studies and made possible to conclude that all of the appraised traits are highly inherited, reflecting the great genetic variety of coffee plants, and that is possible to reach satisfactory genetic gains in improvement programs in which those traits are evaluated. A compilação de informações advindas de estudos independentes tem sido dificultada em quase todos os campos da ciência, devido principalmente, ao grande número de trabalhos científicos publicados nos últimos anos. Assim, sumarizar informações tornou-se uma necessidade. Neste contexto, uma meta-análise foi conduzida com o objetivo de sistematizar as estimativas para a herdabilidade de caracteres vegetativos e reprodutivos de cafeeiros (Coffea arabica L.. Foram avaliadas as estimativas de herdabilidade referentes aos seguintes caracteres: altura média da planta, diâmetro médio da copa, vigor vegetativo, produção de café beneficiado, rendimento e resistência a ferrugem. Os dados referentes às estimativas de herdabilidade são provenientes de artigos científicos publicados em revistas
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.
Fernández Ana I
Full Text Available Abstract Background The traditional strategy to map QTL is to use linkage analysis employing a limited number of markers. These analyses report wide QTL confidence intervals, making very difficult to identify the gene and polymorphisms underlying the QTL effects. The arrival of genome-wide panels of SNPs makes available thousands of markers increasing the information content and therefore the likelihood of detecting and fine mapping QTL regions. The aims of the current study are to confirm previous QTL regions for growth and body composition traits in different generations of an Iberian x Landrace intercross (IBMAP and especially identify new ones with narrow confidence intervals by employing the PorcineSNP60 BeadChip in linkage analyses. Results Three generations (F3, Backcross 1 and Backcross 2 of the IBMAP and their related animals were genotyped with PorcineSNP60 BeadChip. A total of 8,417 SNPs equidistantly distributed across autosomes were selected after filtering by quality, position and frequency to perform the QTL scan. The joint and separate analyses of the different IBMAP generations allowed confirming QTL regions previously identified in chromosomes 4 and 6 as well as new ones mainly for backfat thickness in chromosomes 4, 5, 11, 14 and 17 and shoulder weight in chromosomes 1, 2, 9 and 13; and many other to the chromosome-wide signification level. In addition, most of the detected QTLs displayed narrow confidence intervals, making easier the selection of positional candidate genes. Conclusions The use of higher density of markers has allowed to confirm results obtained in previous QTL scans carried out with microsatellites. Moreover several new QTL regions have been now identified in regions probably not covered by markers in previous scans, most of these QTLs displayed narrow confidence intervals. Finally, prominent putative biological and positional candidate genes underlying those QTL effects are listed based on recent porcine
In durum wheat, two major QTL for grain yield (Qyld.idw-2B and Qyld.idw-3B) and related traits were identified in a recombinant population derived from Kofa and Svevo (Maccaferri et al. 2008). To further investigate the genetic and physiological basis of allelic variation for this important trait, the fine mapping of Qyld.idw-2B e Qyld.idw-3B was done during the PhD. In this regard, new molecular markers were added to increase the map resolution in the target interval. For Qyld.idw-2B ...
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...
Full Text Available Ormosia arborea (Vell. Harms e Ormosia fastigiata Tul. são espécies similares em muitos caracteres morfológicos, o que resulta em dificuldade na sua identificação, tanto em campo quanto em material herborizado. Neste estudo foram descritas as características morfológicas das sementes e morfoanatômicas das plântulas e plantas jovens de O. arborea e O. fastigiata, coletadas em restinga e em mata ciliar, respectivamente. Sementes e plântulas foram processadas segundo técnicas usuais. As sementes de O. arborea são mais pesadas e têm germinação hipógea criptocotiledonar. O caule contém tricomas tectores esparsos e grande quantidade de lenticelas e, na raiz, nodulações. A folha apresenta parênquima paliçádico de células mais curtas, com base mais larga e presença de pigmentos vacuolares, espaços intercelulares conspícuos no parênquima esponjoso, tricomas tectores restritos à nervura principal e células epidérmicas da face adaxial maiores que as da face abaxial. A germinação de O. fastigiata é fanerocotiledonar, e a plântula possui muitos tricomas ao longo do caule e lenticelas restritas à região basal deste. As folhas apresentam tricomas tectores em todas as nervuras, com parênquima paliçádico de células tipicamente alongadas e parênquima esponjoso com espaços intercelulares reduzidos. Tais características são consistentes para separar as plântulas e sementes dessas espécies, que têm a mesma denominação popular e contribuem com informações úteis para o meio produtivo.
EDUARDO JAVIER ARANCIBIA VASQUEZ
Com o advento da tecnologia digital nas comunicações móveis, passa a ser de grande importância a caracterização em faixa larga do ambiente. O canal rádio móvel é descrito como um sistema linear variante no tempo e através de técnicas apropriadas determina-se a sua função de transferência. As duas técnicas de sondagem mais conhecidas são estudadas e implementadas para medir a resposta impulsiva em algumas regioões da cidade do Rio de Janeiro. Esta cidade apresen...
Leduc, Magalie S; Lyons, Malcolm; Darvishi, Katayoon; Walsh, Kenneth; Sheehan, Susan; Amend, Sarah; Cox, Allison; Orho-Melander, Marju; Kathiresan, Sekar; Paigen, Beverly; Korstanje, Ron
Genome-wide association (GWA) studies represent a powerful strategy for identifying susceptibility genes for complex diseases in human populations but results must be confirmed and replicated. Because of the close homology between mouse and human genomes, the mouse can be used to add evidence to genes suggested by human studies. We used the mouse quantitative trait loci (QTL) map to interpret results from a GWA study for genes associated with plasma HDL cholesterol levels. We first positioned single nucleotide polymorphisms (SNPs) from a human GWA study on the genomic map for mouse HDL QTL. We then used mouse bioinformatics, sequencing, and expression studies to add evidence for one well-known HDL gene (Abca1) and three newly identified genes (Galnt2, Wwox, and Cdh13), thus supporting the results of the human study. For GWA peaks that occur in human haplotype blocks with multiple genes, we examined the homologous regions in the mouse to prioritize the genes using expression, sequencing, and bioinformatics from the mouse model, showing that some genes were unlikely candidates and adding evidence for candidate genes Mvk and Mmab in one haplotype block and Fads1 and Fads2 in the second haplotype block. Our study highlights the value of mouse genetics for evaluating genes found in human GWA studies.
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.
Howard, Thomas; Rejab, Nur Ardiyana; Griffiths, Simon; Leigh, Fiona; Leverington-Waite, Michelle; Simmonds, James; Uauy, Cristobal; Trafford, Kay
Starch within the endosperm of most species of the Triticeae has a unique bimodal granule morphology comprising large lenticular A-type granules and smaller near-spherical B-type granules. However, a few wild wheat species (Aegilops) are known to lack B-granules. Ae. peregrina and a synthetic tetraploid Aegilops with the same genome composition (SU) were found to differ in B-granule number. The synthetic tetraploid had normal A- and B-type starch granules whilst Ae. peregrina had only A-granules because the B-granules failed to initiate. A population segregating for B-granule number was generated by crossing these two accessions and was used to study the genetic basis of B-granule initiation. A combination of Bulked Segregant Analysis and QTL mapping identified a major QTL located on the short arm of chromosome 4S that accounted for 44.4% of the phenotypic variation. The lack of B-granules in polyploid Aegilops with diverse genomes suggests that the B-granule locus has been lost several times independently during the evolution of the Triticeae. It is proposed that the B-granule locus is susceptible to silencing during polyploidization and a model is presented to explain the observed data based on the assumption that the initiation of B-granules is controlled by a single major locus per haploid genome. PMID:21227932
The cucumber lines, S94 (Northern China open-field type, powdery mildew (PM) susceptible) and S06 (European greenhouse type, PM resistant), and their F6:7 populations were used to investigate PM re-sistance under seedling spray inoculation in 2005/Autumn and 2006/Spring. QTL analysis was under-taken based on a constructed molecular linkage map of the corresponding F6 population using com-posite interval mapping. A total of four QTLs (pm1.1, pm2.1, pm4.1 and pm6.1) for PM resistance were identified and located on LG 1, 2, 4 and 6, respectively, explaining 5.2%-21.0% of the phenotypic variation. Three consistent QTLs (pm1.1, pm2.1 and pm4.1) were detected under the two test conditions. The QTL pm6.1 was only identified in 2005/Autumn. The total phenotypic variation explained by the QTLs was 52.0% and 42.0% in 2005/Autumn and 2006/Spring, respectively. Anchor markers tightly linked to those loci (<5 cM) could lay a basis for both molecular marker-assisted breeding and map-based gene cloning of the PM-resistance gene in cucumber.
DENG Zhi-ying; ZHAO Liang; LIU Bin; ZHANG Kun-pu; CHEN Jian-sheng; QU Hou-lan; SUN Cai-ling; ZHANG Yong-xiang; TIAN Ji-chun
To evaluate the possible genetic interrelationships between lfour components and the sedimentation volume (SD), a doubled haploid (DH) population comprising 168 lines were used to identify the conditional quantitative trait loci (QTLs) for SD in three environments. Ten additive QTLs and 15 pairs of epistatic QTLs were detected for SD through unconditional and conditional QTL mapping. Three major additive QTLs were detected for SD conditioned on the seven quality traits. Two additive QTLs were found to be independent of these traits. Three additive QTLs were suppressed by three of the seven traits because of non-detection in unconditional mapping.Three pairs of epistatic QTLs were completely affected by the seven traits because of detection in unconditional mapping but no-detection in conditional mapping. Twelve pairs of epistatic QTLs were detected in conditional mapping. Our results indicated that conditional mapping could contribute to a better understanding of the interdependence of different and closely correlated traits at the QTL molecular level, especially some minor QTLs were found. The conditional mapping approach provides new insights that will make it possible to avoid the disadvantages of different traits by breeding through molecular design.
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
Leite, D C; Pinheiro, J B; Campos, J B; Di Mauro, A O; Unêda-Trevisoli, S H
The present study was undertaken to detect and map the quantitative trait loci (QTL) related to soybean oil content. We used 244 progenies derived from a bi-parental cross of the Lineage 69 (from Universidade Estadual Paulista "Júlio de Mesquita Filho"/Faculdade de Ciências Agrárias e Veterinárias - Breeding Program) and Tucunaré cultivar. A total of 358 simple sequence repeat (SSR; microsatellite) markers were used to investigate the polymorphism between the parental lines, and for the polymorphic lines all the F2 individuals were tested. Evaluation of the oil content and phenotype was performed with the aid of a Tango equipment by near infra-red reflectance spectroscopy, using single F2 seeds and F2:3 progenies, in triplicate. The data were analyzed by QTL Cartographer program for 56 SSR polymorphic markers. Two oil-content related QTLs were detected on K and H linkage groups. The total phenotypic variation explained by QTLs ranged from 7.8 to 46.75% for oil content. New QTLs were identified for the oil content in addition to those previously identified in other studies. The results reported in this study show that regions different from those already known could be involved in the genetic control of soybean oil content.
Marco Vinicio Sánchez C.
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.
Sérgio Luiz Rodrigues Donato
Full Text Available Os caracteres observados em áreas experimentais têm natureza fenotípica e suas correlações são estimadas visando mensurar alterações em um caráter quando se altera outro relacionado. Objetivou-se com este trabalho, quantificar a relação entre os caracteres da planta e do cacho observados na época do florescimento e da colheita de 13 genótipos (variedades e híbridos de bananeira (Musa spp., em dois ciclos de produção, em Guanambi, Bahia. Foram utilizadas as variedades Prata anã, Pacovan (AAB, Grande naine e Nanicão (AAA, e os híbridos PA42-44, PV42-85, PV42-142, PV42-68 e ST12-31 (AAAB e Ambrosia, Calipso, Bucaneiro e FHIA02 (AAAA, selecionados na Embrapa Mandioca e Fruticultura. Consideraram-se os caracteres: altura da planta; perímetro do pseudocaule; número de folhas vivas no florescimento e na colheita; número de dias do plantio ao florescimento e à colheita; intervalo florescimento à colheita; peso do cacho, da ráquis e da pencas; comprimento e diâmetro do engaço; número de pencas e de frutos; peso da segunda penca; peso, comprimento e diâmetro do fruto e espessura da casca. As correlações entre o peso do cacho e os demais caracteres estudados, variaram entre genótipos e ciclos. As associações entre o peso do cacho e os caracteres da planta, de forma geral foram não-significativas, e entre o peso do cacho e os caracteres do cacho significativas e positivas para a maioria dos genótipos, nos ciclos avaliados. As correlações entre os caracteres envolvendo todos os genótipos ao longo dos dois ciclos foram predominantemente positivas e não- significativas, entretanto, as associações entre os caracteres do cacho foram em maioria significativas, positivas e com valores expressivos.The characters observed in a experimental areas has phenotypic nature and their correlations are estimated with the purpose to verify alterations in one character when is altered another. The objectives of this work were to
Taís Cristina Bastos Soares
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
Variabilidad en caracteres morfológicos relacionados con la implantación de Desmanthus virgatus (L.) Willd. y Desmanthus paspalaceus (Lindm.) Burkart Variability in morphological traits related with the establishment of Desmanthus virgatus (L.) Willd y Desmanthus paspalaceus (Lindm.) Burkart
J.M. Zabala; J. Giavedoni; P.A. Tomas; E.A. Budini
En la actualidad, una prioridad para mejorar la producción ganadera en el centro-norte de Argentina es la búsqueda de leguminosas forrajeras adaptadas a la región.Este trabajo tuvo como objetivos: a) analizar la variabilidad de caracteres morfológicos relacionados con el crecimiento inicial en poblaciones de dos especies de forrajeras nativas, Desmanthus virgatus y D. paspalaceus, y b) evaluar la implantación a campo en dos ambientes. Se encontró variación en los caracteres relacionados con e...
Giovani O da Silva
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
Lauro Saraiva Lessa
Full Text Available O estudo de correlação tem como propósito mensurar a alteração em um caráter quando se altera outro. Neste trabalho, objetivou-se estimar correlações fenotípicas entre o número de frutos por cacho e 22 caracteres avaliados em híbridos diploides (AA de bananeira. No experimento, conduzido na Embrapa Mandioca e Fruticultura, em blocos casualizados com quatro repetições, foram avaliados 11 híbridos diploides (AA de bananeira. Os caracteres avaliados foram: altura de plantas, diâmetro do pseudocaule, número de filhos, número de folhas na floração, período do plantio ao florescimento, presença de pólen, peso do cacho e da ráquis, sigatoka-amarela no florescimento, número de folhas na colheita, Sigatoka-amarela na colheita do cacho, número de dias do florescimento à colheita, comprimento e diâmetro do engaço, peso da segunda penca, número de pencas e de frutos por cacho, fragilidade do pedicelo, comprimento e diâmetro do fruto e comprimento do pedicelo, além de presença de semente. Após a tabulação, procederam-se a estudos de correlação entre o número de frutos e os demais caracteres da planta. Essas correlações variaram entre os genótipos, sendo assim, observado que as associações entre o número de frutos e os caracteres vegetativos da planta foram, de forma geral, não significativas. Já as relações entre o número de frutos por cacho e os outros caracteres produtivos foram, predominantemente, significativas.The objective of the present study was to estimate the phenotypic correlations between the number of fruits per bunch and 22 characters evaluated in banana (AA diploid hybrids. The experiment was carried out at Embrapa Cassava and Fruits in randomized blocks with four repetitions and 11 (AA banana diploid hybrids were evaluated. The following characteristics were evaluated: plant height, pseudostem diameter, number of suckers, number of leaves during flowering, plant cycle until emission of the
Lívia M de Souza
Full Text Available Genotypic, phenotypic and environmental correlations were estimated for all possible pairs among eleven characters of tomatoes. Fifteen treatments including five parents and ten hybrids of Instituto Agronômico (IAC tomato breeding program were evaluated using a randomized complete block experimental design, with tree replications in Itatiba, São Paulo state, Brazil, during 2005/2006. The following traits were evaluated: fruit yield per plant (FP, fruit number per plant (FN, average fruit weight (FW, cluster number per plant (CN, fruit number per cluster (FC, number of locules per fruit (NL, fruit length (FL, fruit width (WI, fruit wall thickness (FT, total soluble solids (SS, and total titratable acidity (TA. The genotypic (rG, phenotypic (rF and environmental correlations (rA for two pairs of plant traits were estimated using the Genes© program. High similarity was found among the estimates of genotypic and phenotypic correlations. Positive and high phenotypic and genotypic correlations were observed between FP and the traits FN, FW and FT, and these associations contributed for yield increasing. FW and FT contributed to yield increase and should be considered together as primary yield components in tomato. Positive values of the genotypic and phenotypic correlations revealed that FP influenced FN with high direct effect and significant positive correlation. These traits may be included as the main selection criteria for tomato yield improvement.Correlações fenotípica, genotípica e ambiental foram estimadas entre todos os possíveis pares de onze caracteres de tomate de mesa. Quinze tratamentos, incluindo cinco parentais e dez híbridos do programa de melhoramento de tomate do Instituto Agronômico (IAC foram testados no delineamento em blocos casualizados completos, em Itatiba-SP, em 2005/2006. Os seguintes caracteres foram avaliados: produção (FP, número (FN e peso médio do fruto (FW, número de pencas por planta (CN, número de
Marilene Leão Alves Bovi
Full Text Available Estudaram-se caracteres vegetativos da planta e do palmito de açaizeiros (Euterpe oleracea Mart cultivados na Estação Experimental de Ubatuba, litoral norte do Estado de São Paulo, Brasil, com o objetivo principal de identificar caracteres não-destrutíveis que possam ser utilizados na seleção de plantas superiores no programa de melhoramento genético dessa palmeira. Entre os dez caracteres estudados, o número de perfilhos, o peso bruto do palmito e os pesos do resíduo basal e do palmito mostraram maior variabilidade (CV acima de 40%. Menor variabilidade foi encontrada para os caracteres número de folhas e circunferência da planta-mãe (CV entre 14 e 18%. O peso, os diâmetros e o comprimento do palmito mostraram-se positivamente correlacionados com a circunferência da planta. Correlação negativa foi evidenciada entre peso bruto do palmito e número de perfilhos e entre esta última variável e o peso do resíduo basal. O número de folhas mostrou correlação parcial significativa apenas com o diâmetro médio do palmito e com o peso do palmito bruto. Entre os caracteres vegetativos não-destrutíveis avaliados, a circunferência da planta foi o que mais contribuiu para a variação apresentada pelo palmito bruto e liquído (peso, diâmetro e comprimento, sendo responsável por mais de 65% da variação do peso bruto, 35% do peso líquido e em tomo de 50% de seu diâmetro. Constitui-se, assim, em um caráter útil, além de não-destrutível e facilmente mensurável, para orientar a seleção de plantas superiores de açaizeiro num programa de melhoramento genético de palmeiras desta espécie.Three vegetative characters and palmito yield components of assai palms (Euterpe oleracea Mart. were studied in an experiment at Ubatuba, State of São Paulo, Brazil, in order to identify non-destructive traits that could be used to estimate yield in superior material evaluation and selection. Partial correlation coefficients showed
Tortereau, F.; Gilbert, H.; Heuven, H.C.M.; Bidanel, J-P.; Groenen, M.A.M.; Riquet, J.
Genet Sel Evol. 2010 Nov 25;42(1):42. [Epub ahead of print] Combining two Meishan F2 crosses improves the detection of QTL on pig chromosomes 2, 4 and 6. Tortereau F, Gilbert H, Heuven HC, Bidanel JP, Groenen MA, Riquet J. Abstract ABSTRACT: BACKGROUND: In pig, a number of experiments have been set
Alfalfa (Medicago sativa L.) is an internationally significant forage crop. Forage yield, lodging resistance and spring vigor are important agronomic traits conditioned by quantitative genetic and environmental effects. The objective of this study was to identify quantitative trait loci (QTL) and mo...
Jie Xu; Tingzhao Rong; Yaxi Liu; Jian Liu; Moju Cao; Jing Wang; Hai Lan; Yunbi Xu; Yanli Lu; Guangtang Pan
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.
Rodrigues, P.C.; Malosetti, M.; Gauch, H.G.
Genotype-by-environment (G × E) interaction (GEI) and quantitative trait locus (QTL)-by-environment interaction (QEI) are common phenomena in multiple-environment trials and represent a major challenge to breeders. The additive main effects and multiplicative interaction (AMMI) model is a widely use
Fruit quality traits and dayneutrality are two major foci of several strawberry breeding programs. The identification of quantitative trait loci (QTL) and molecular markers linked to these traits could improve breeding efficiency. In this work, an F1 population derived from the cross ‘Delmarvel’ × ...
Thibodeau, S. N.; French, A. J.; McDonnell, S. K.; Cheville, J.; Middha, S.; Tillmans, L.; Riska, S.; Baheti, S.; Larson, M. C.; Fogarty, Z.; Zhang, Y.; Larson, N.; Nair, A.; O'Brien, D.; Wang, L.; Schaid, D J.
Multiple studies have identified loci associated with the risk of developing prostate cancer but the associated genes are not well studied. Here we create a normal prostate tissue-specific eQTL data set and apply this data set to previously identified prostate cancer (PrCa)-risk SNPs in an effort to identify candidate target genes. The eQTL data set is constructed by the genotyping and RNA sequencing of 471 samples. We focus on 146 PrCa-risk SNPs, including all SNPs in linkage disequilibrium with each risk SNP, resulting in 100 unique risk intervals. We analyse cis-acting associations where the transcript is located within 2 Mb (±1 Mb) of the risk SNP interval. Of all SNP–gene combinations tested, 41.7% of SNPs demonstrate a significant eQTL signal after adjustment for sample histology and 14 expression principal component covariates. Of the 100 PrCa-risk intervals, 51 have a significant eQTL signal and these are associated with 88 genes. This study provides a rich resource to study biological mechanisms underlying genetic risk to PrCa. PMID:26611117
Genetic background plays a dominant role in mammary gland development and breast cancer (BrCa). Despite this, the role of genetics is only partially understood. This study used strain-dependent variation in an inbred mouse mapping panel, to identify quantitative trait loci (QTL) underlying structura...
Marker-assisted selection (MAS) may help mitigate some of the current challenges regarding the genetic improvement of cotton fiber quality, such as low genetic diversity and the negative association between fiber quality and lint yield. A multitude of quantitative trait loci (QTL) for fiber length a...
Background Genome wide association studies are now widely used in the livestock sector to estimate the association among single nucleotide polymorphisms (SNPs) distributed across the whole genome and one or more trait. As computational power increases, the use of machine learning techniques to analyze large genome wide datasets becomes possible. Methods The objective of this study was to identify SNPs associated with the three traits simulated in the 16th MAS-QTL workshop dataset using the Random Forest (RF) approach. The approach was applied to single and multiple trait estimated breeding values, and on yield deviations and to compare them with the results of the GRAMMAR-CG method. Results The two QTL mapping methods used, GRAMMAR-CG and RF, were successful in identifying the main QTLs for trait 1 on chromosomes 1 and 4, for trait 2 on chromosomes 1, 4 and 5 and for trait 3 on chromosomes 1, 2 and 3. Conclusions The results of the RF approach were confirmed by the GRAMMAR-CG method and validated by the effective QTL position, even if their approach to unravel cryptic genetic structure is different. Furthermore, both methods showed complementary findings. However, when the variance explained by the QTL is low, they both failed to detect significant associations. PMID:25519518
DeWoody, J.; Viger, M.; Lakatos, F.; Tuba, K.; Taylor, G.; Smulders, M.J.M.
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 gard
Basal stalk rot (BSR) caused by the ascomycete fungus Sclerotinia sclerotiorum (Lib.) de Bary is a serious disease of sunflower (Helianthus annuus L.) in the cool and humid production areas of the world. Quantitative trait loci (QTL) for BSR resistance were identified in a sunflower recombinant inbr...
Corominas, J.; Marchesi, J.A.; Puig-Oliveras, A.; Revilla, M.; Estelle, J.; Alves, E.; Folch, J.M.; Ballester, M.
BACKGROUND: In previous studies on an Iberian x Landrace cross, we have provided evidence that supported the porcine ELOVL6 gene as the major causative gene of the QTL on pig chromosome 8 for palmitic and palmitoleic acid contents in muscle and backfat. The single nucleotide polymorphism (SNP) ELOVL
Lerceteau-Köhler, E; Moing, A; Guérin, G; Renaud, C; Petit, A; Rothan, C; Denoyes, Béatrice
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.
Zhao, Jianyi; Becker, Heiko C; Zhang, Dongqing; Zhang, Yaofeng; Ecke, Wolfgang
Oil content in rapeseed (Brassica napus L.) is generally regarded as a character with high heritability that is negatively correlated with protein content and influenced by plant developmental and yield related traits. To evaluate possible genetic interrelationships between these traits and oil content, QTL for oil content were mapped using data on oil content and on oil content conditioned on the putatively interrelated traits. Phenotypic data were evaluated in a segregating doubled haploid population of 282 lines derived from the F(1) of a cross between the old German cultivar Sollux and the Chinese cultivar Gaoyou. The material was tested at four locations, two each in Germany and in China. QTLMapper version 1.0 was used for mapping unconditional and conditional QTL with additive (a) and locus pairs with additive x additive epistatic (aa) effects. Clear evidence was found for a strong genetic relationship between oil and protein content. Six QTL and nine epistatic locus pairs were found, which had pleiotropic effects on both traits. Nevertheless, two QTL were also identified, which control oil content independent from protein content and which could be used in practical breeding programs to increase oil content without affecting seed protein content. In addition, six additional QTL with small effects were only identified in the conditional mapping. Some evidence was apparent for a genetic interrelationship between oil content and the number of seeds per silique but no evidence was found for a genetic relationship between oil content and flowering time, grain filling period or single seed weight. The results indicate that for closely correlated traits conditional QTL mapping can be used to dissect the genetic interrelationship between two traits at the level of individual QTL. Furthermore, conditional QTL mapping can reveal additional QTL with small effects that are undetectable in unconditional mapping.
Valeria Rosado Pinheiro
Full Text Available O objetivo deste trabalho foi avaliar eficiência de modelos de regressão aleatória (MRA para detectar locus de características quantitativas (QTL para características de crescimento, em suínos. Utilizou-se uma população divergente F2 Piau x Comercial. A eficiência da metodologia proposta na detecção de QTL foi comparada à da metodologia tradicional de regressão por intervalo de mapeamento. Para tanto, utilizaram-se MRA com efeitos aleatórios poligênicos, de ambiente permanente e de QTL, tendo-se utilizado o enfoque de matriz de covariância "identical‑by‑descent" associada aos efeitos de QTL. Testou-se a significância dos efeitos de QTL mediante a razão de verossimilhanças, tendo-se considerado o modelo como completo quando houve efeito de QTL, ou nulo, quando não. A comparação entre os modelos foi feita nas posições dos marcadores (seis marcadores microssatélites e nas intermediárias, entre os marcadores. O MRA detectou QTL significativo na posição 65 cM do cromossomo 7 e, portanto, foi mais eficiente que a metodologia tradicional, que não detectou QTL significativo em nenhum dos fenótipos avaliados. A metodologia proposta possibilitou a detecção de QTL com efeito sobre toda a trajetória de crescimento, dentro da amplitude de idade considerada (do nascimento aos 150 dias.
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
@@ 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
Full Text Available The pearl oyster, Pinctada fucata (P. fucata, is one of the marine bivalves that is predominantly cultured for pearl production. To obtain more genetic information for breeding purposes, we constructed a high-density linkage map of P. fucata and identified quantitative trait loci (QTL for growth-related traits. One F1 family, which included the two parents, 48 largest progeny and 50 smallest progeny, was sampled to construct a linkage map using restriction site-associated DNA sequencing (RAD-Seq. With low coverage data, 1956.53 million clean reads and 86,342 candidate RAD loci were generated. A total of 1373 segregating SNPs were used to construct a sex-average linkage map. This spanned 1091.81 centimorgans (cM, with 14 linkage groups and an average marker interval of 1.41 cM. The genetic linkage map coverage, Coa, was 97.24%. Thirty-nine QTL-peak loci, for seven growth-related traits, were identified using the single-marker analysis, nonparametric mapping Kruskal-Wallis (KW test. Parameters included three for shell height, six for shell length, five for shell width, four for hinge length, 11 for total weight, eight for soft tissue weight and two for shell weight. The QTL peak loci for shell height, shell length and shell weight were all located in linkage group 6. The genotype frequencies of most QTL peak loci showed significant differences between the large subpopulation and the small subpopulation (P<0.05. These results highlight the effectiveness of RAD-Seq as a tool for generation of QTL-targeted and genome-wide marker data in the non-model animal, P. fucata, and its possible utility in marker-assisted selection (MAS.
Zaidi, Pervez Haider; Rashid, Zerka; Vinayan, Madhumal Thayil; Almeida, Gustavo Dias; Phagna, Ramesh Kumar; Babu, Raman
Waterlogging is an important abiotic stress constraint that causes significant yield losses in maize grown throughout south and south-east Asia due to erratic rainfall patterns. The most economic option to offset the damage caused by waterlogging is to genetically incorporate tolerance in cultivars that are grown widely in the target agro-ecologies. We assessed the genetic variation in a population of recombinant inbred lines (RILs) derived from crossing a waterlogging tolerant line (CAWL-46-3-1) to an elite but sensitive line (CML311-2-1-3) and observed significant range of variation for grain yield (GY) under waterlogging stress along with a number of other secondary traits such as brace roots (BR), chlorophyll content (SPAD), % stem and root lodging (S&RL) among the RILs. Significant positive correlation of GY with BR and SPAD and negative correlation with S&RL indicated the potential use of these secondary traits in selection indices under waterlogged conditions. RILs were genotyped with 331 polymorphic single nucleotide polymorphism (SNP) markers using KASP (Kompetitive Allele Specific PCR) Platform. QTL mapping revealed five QTL on chromosomes 1, 3, 5, 7 and 10, which together explained approximately 30% of phenotypic variance for GY based on evaluation of RIL families under waterlogged conditions, with effects ranging from 520 to 640 kg/ha for individual genomic regions. 13 QTL were identified for various secondary traits associated with waterlogging tolerance, each individually explaining from 3 to 14% of phenotypic variance. Of the 22 candidate genes with known functional domains identified within the physical intervals delimited by the flanking markers of the QTL influencing GY and other secondary traits, six have previously been demonstrated to be associated with anaerobic responses in either maize or other model species. A pair of flanking SNP markers has been identified for each of the QTL and high throughput marker assays were developed to facilitate
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
Full Text Available QTL IciMapping 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.
Lei; Meng; Huihui; Li; Luyan; Zhang; Jiankang; Wang
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.
Lei Meng; Huihui Li; Luyan Zhang; Jiankang Wang
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.
Tuyen, D D; Lal, S K; Xu, D H
Salt-affected soils are generally classified into two main categories, sodic (alkaline) and saline. Our previous studies showed that the wild soybean accession JWS156-1 (Glycine soja) from the Kinki area of Japan was tolerant to NaCl salt, and the quantitative trait locus (QTL) for NaCl salt tolerance was located on soybean linkage group N (chromosome 3). Further investigation revealed that the wild soybean accession JWS156-1 also had a higher tolerance to alkaline salt stress. In the present study, an F(6) recombinant inbred line mapping population (n = 112) and an F(2) population (n = 149) derived from crosses between a cultivated soybean cultivar Jackson and JWS156-1 were used to identify QTL for alkaline salt tolerance in soybean. Evaluation of soybean alkaline salt tolerance was carried out based on salt tolerance rating (STR) and leaf chlorophyll content (SPAD value) after treatment with 180 mM NaHCO(3) for about 3 weeks under greenhouse conditions. In both populations, a significant QTL for alkaline salt tolerance was detected on the molecular linkage group D2 (chromosome 17), which accounted for 50.2 and 13.0% of the total variation for STR in the F(6) and the F(2) populations, respectively. The wild soybean contributed to the tolerance allele in the progenies. Our results suggest that QTL for alkaline salt tolerance is different from the QTL for NaCl salt tolerance found previously in this wild soybean genotype. The DNA markers closely associated with the QTLs might be useful for marker-assisted selection to pyramid tolerance genes in soybean for both alkaline and saline stresses.
Full Text Available We have performed a metabolite quantitative trait locus (mQTL study of the (1H nuclear magnetic resonance spectroscopy ((1H NMR metabolome in humans, building on recent targeted knowledge of genetic drivers of metabolic regulation. Urine and plasma samples were collected from two cohorts of individuals of European descent, with one cohort comprised of female twins donating samples longitudinally. Sample metabolite concentrations were quantified by (1H NMR and tested for association with genome-wide single-nucleotide polymorphisms (SNPs. Four metabolites' concentrations exhibited significant, replicable association with SNP variation (8.6×10(-11
QTL associations. The study's longitudinal twin design allowed detailed variance-components analysis of the sources of population variation in metabolite levels. The mQTLs explained 40%-64% of biological population variation in the corresponding metabolites' concentrations. These effect sizes are stronger than those reported in a recent, targeted mQTL study of metabolites in serum using the targeted-metabolomics Biocrates platform. By re-analysing our plasma samples using the Biocrates platform, we replicated the mQTL findings of the previous study and discovered a previously uncharacterized yet substantial familial component of variation in metabolite levels in addition to the heritability contribution from
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
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.
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
R. J. C. Cantet
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
Rodolphe, F.; Lefort, M. (INRA Centre de Recherches de Jouy en Josas (France))
A statistical method is presented for detecting quantitative trait loci (QTLs), based on the linear model. Unlike methods able to detect a few well separated QTLs and to estimate their effects and positions, this method considers the genome as a whole and enables the detection of chromosomal segments involved in the differences between two homozygous lines, and their backcross, doubled haploid, or F[sub 2] progenies, for a quantitative trait. Genetic markers must be codominant, but missing markers are accepted, provided they are missing independently from the experiment. Asymptotic properties, which are of practical use, are developed. This method does not rely on strong genetic hypotheses, and thus does not permit any precise genetic analysis of the trait under study, but it does assess which regions of the genome are involved, whatever the complexity of the genetic determinism (number, effects and interactions among QTLs). Simultaneous use of several methods, including this one, should lead to better efficiency in QTL detection.
Czembor, Pawel C; Arseniuk, Edward; Czaplicki, Andrzej; Song, Qijiang; Cregan, Perry B; Ueng, Peter P
Stagonospora nodorum blotch is an important foliar and glume disease in cereals. Inheritance of resistance in wheat appears to be quantitative. To date, breeding of partially resistant cultivars has been the only effective way to combat this pathogen. The partial resistance components, namely length of incubation period, disease severity, and length of latent period, were evaluated on a population of doubled haploids derived from a cross between the partially resistant Triticum aestivum 'Liwilla' and susceptible Triticum aestivum 'Begra'. Experiments were conducted in a controlled environment and the fifth leaf was examined. Molecular analyses were based on bulked segregant analyses using 240 microsatellite markers. Four QTLs were significantly associated with partial resistance components and were located on chromosomes 2B, 3B, 5B, and 5D. The percentage of phenotypic variance explained by a single QTL ranged from 14 to 21% for incubation period, from 16 to 37% for disease severity, and from 13 to 28% for latent period,
Kadri, Naveen Kumar; Guldbrandtsen, Bernt; Lund, Mogens Sandø;
but not the former situation, undesirable genetic correlation could potentially be broken by selecting animals that have favorable variants for both traits. First, we performed a within-breed association study using a haplotype-based method in Danish Holstein cattle (HOL). Next, we analyzed Nordic Red dairy cattle...... (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...... nucleotide polymorphisms (SNP) on BTA20. Data were combined, phased, and clustered into haplotype states, followed by within- and across-breed haplotype-based association analyses using a linear mixed model. Association signals for both CM and MY peaked in the 26 to 40 Mb region on BTA20 in HOL. Single...
Bert, P-F; Jouan, I; Tourvieille de Labrouhe, D; Serre, F; Philippon, J; Nicolas, P; Vear, F
Seed weight and oil content are important properties of cultivated sunflower under complex genetic and environmental control, and associated with morphological and developmental characteristics such as plant height or flowering dates. Using a genetic map with 290 markers for a cross between two inbred sunflower lines and 2 years of observations on F3 families, QTL controlling seed weight, oil content, plant height, plant lodging, flowering dates, maturity dates and delay from flowering to maturity were detected. QTL detected were compared between the F2 and F3 generations and between the 2 years of testing for the F3 families in 1997 and 1999. Some of the QTL controlling seed weight overlapped with those controlling oil content. Several other co-localisations of QTL controlling developmental or morphological characteristics were observed and the relationships between the traits were also shown by correlation analyses. The relationships between all these traits and with resistance to Sclerotinia sclerotiorum and Diaporthe helianthi are discussed.
Full Text Available The inheritance of resistance to white tip disease (WTDR in rice (Oryza sativa L. was analyzed with an artificial inoculation test in a segregating population derived from the cross between Tetep, a highly resistant variety that was identified in a previous study, and a susceptible cultivar. Three resistance-associated traits, including the number of Aphelenchoides besseyi (A. besseyi individuals in 100 grains (NA, the loss rate of panicle weight (LRPW and the loss rate of the total grains per panicle (LRGPP were analyzed for the detection of the quantitative trait locus (QTL in the population after construction of a genetic map. Six QTLs distributed on chromosomes 3, 5 and 9 were mapped. qNA3 and qNA9, conferring reproduction number of A. besseyi in the panicle, accounted for 16.91% and 12.54% of the total phenotypic variance, respectively. qDRPW5a and qDRPW5b, associated with yield loss, were located at two adjacent marker intervals on chromosome 5 and explained 14.15% and 14.59% of the total phenotypic variation and possessed LOD values of 3.40 and 3.39, respectively. qDRPW9 was considered as a minor QTL and only explained 1.02% of the phenotypic variation. qLRGPP5 contributed to the loss in the number of grains and explained 10.91% of the phenotypic variation. This study provides useful information for the breeding of resistant cultivars against white tip disease in rice.
Winter, Shawn M J; Shelp, Barry J; Anderson, Terry R; Welacky, Tom W; Rajcan, Istvan
Soybean cyst nematode (Heterodera glycines Ichinohe; SCN) is the primary disease responsible for yield loss of soybean [Glycine max (L.) Merr.]. Resistant cultivars are an effective management tool; however, the sources currently available have common resistant genes. Glycine soja Sieb. and Zucc., the wild ancestor of domesticated soybean, represents a diverse germplasm pool with known SCN resistance. The objectives of this research were to: (1) determine the genetic variation and inheritance of SCN resistance in a G. max ('S08-80') x G. soja (PI464925B) F (4:5) recombinant inbred line (RIL) population; and (2) identify and evaluate quantitative trait loci (QTL) associated with SCN resistance. Transgressive segregation for resistance was observed, although neither parent was resistant to the Chatham and Ruthven SCN isolates. Broad sense heritability was 0.81 for the Ruthven and 0.91 for the Chatham isolate. Root dry weight was a significant covariate that influenced cyst counts. One RIL [female index (FI) = 5.2 +/- 1.11] was identified as resistant to the Chatham isolate (FI soja, were identified on linkage groups I, K, and O, and individually explained 8, 7 and 5% (LOD = 2.1-2.7) of the total phenotypic variation, respectively. Significant epistatic interactions were found between pairs of SSR markers that individually may or may not have been associated with SCN resistance, which explained between 10 and 15% of the total phenotypic variation. Best-fit regression models explained 21 and 31% of the total phenotypic variation in the RIL population to the Chatham and Ruthven isolates, respectively. The results of this study help to improve the understanding of the genetic control of SCN resistance in soybean caused by minor genes resulting in horizontal resistance. The incorporation of the novel resistance QTL from G. soja could increase the durability of SCN-resistance in soybean cultivars, especially if major gene resistance breaks down.
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.
Qu, Yan-Chun; Deng, Chang-Yan; Xiong, Yuan-Zhu; Zheng, Rong; Yu, Li; Su, Yu-Hong; Liu, Gui-Lan
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.
Full Text Available The timing of flowering initiation is a fundamental trait for the adaptation of annual plants to different environments. Large amounts of intraspecific quantitative variation have been described for it among natural accessions of many species, but the molecular and evolutionary mechanisms underlying this genetic variation are mainly being determined in the model plant Arabidopsis thaliana. To find novel A. thaliana flowering QTL, we developed introgression lines from the Japanese accession Fuk, which was selected based on the substantial transgression observed in an F(2 population with the reference strain Ler. Analysis of an early flowering line carrying a single Fuk introgression identified Flowering Arabidopsis QTL1 (FAQ1. We fine-mapped FAQ1 in an 11 kb genomic region containing the MADS transcription factor gene SHORT VEGETATIVE PHASE (SVP. Complementation of the early flowering phenotype of FAQ1-Fuk with a SVP-Ler transgen demonstrated that FAQ1 is SVP. We further proved by directed mutagenesis and transgenesis that a single amino acid substitution in SVP causes the loss-of-function and early flowering of Fuk allele. Analysis of a worldwide collection of accessions detected FAQ1/SVP-Fuk allele only in Asia, with the highest frequency appearing in Japan, where we could also detect a potential ancestral genotype of FAQ1/SVP-Fuk. In addition, we evaluated allelic and epistatic interactions of SVP natural alleles by analysing more than one hundred transgenic lines carrying Ler or Fuk SVP alleles in five genetic backgrounds. Quantitative analyses of these lines showed that FAQ1/SVP effects vary from large to small depending on the genetic background. These results support that the flowering repressor SVP has been recently selected in A. thaliana as a target for early flowering, and evidence the relevance of genetic interactions for the intraspecific evolution of FAQ1/SVP and flowering time.
Analiza G. Tagle
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
Full Text Available 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.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.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 report that the wheat
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
Zhou, Tao; Liu, Shikai; Geng, Xin; Jin, Yulin; Jiang, Chen; Bao, Lisui; Yao, Jun; Zhang, Yu; Zhang, Jiaren; Sun, Luyang; Wang, Xiaozhu; Li, Ning; Tan, Suxu; Liu, Zhanjiang
Disease problems cause major economic losses for the aquaculture industries. In catfish, enteric septicemia of catfish (ESC), caused by the bacterial pathogen Edwardsiella ictaluri, is the leading disease problem, causing tens of millions of dollars of annual economic losses. In this study, we conducted a genome-wide association study to determine quantitative trait loci (QTL) for resistance against ESC using an interspecific hybrid system. Five hundred fish were used in the analysis and 192 phenotypic extremes were used for genotyping with the catfish 250K SNP arrays. A genomic region on linkage group (LG) 1 was found significantly associated with ESC disease resistance. In addition, two suggestively associated QTL for ESC resistance were identified on LG 12 and LG 16. The nlrc3 duplicates were identified within all the three QTL, suggesting their importance in association with the QTL. Within the significant QTL on LG 1, 16 genes with known functions in immunity were identified. Of particular interest is the nck1 gene nearby the most significantly associated SNP. Nck1 was known to function as an adaptor to facilitating the pathogenesis of enteropathogenic Escherichia coli (EPEC) in humans. E. ictaluri and EPEC pathogens belong to the same bacterial family and share many common characteristics. The fact that nck1 is mapped in the QTL and that it was significantly upregulated in channel catfish intestine after ESC challenge suggested its candidacy of being involved in resistance/susceptibility of ESC.
Hanocq, E; Laperche, A; Jaminon, O; Lainé, A-L; Le Gouis, J
Earliness is one of the most important adaptation traits in plant breeding. Our purpose was to identify the genome regions of bread wheat involved in the control of earliness and its three components: photoperiod sensitivity (PS), vernalization requirement (VR) and intrinsic earliness (IE). A QTL meta-analysis was carried out to examine the replicability of QTL across 13 independent studies and to propose meta-QTL (MQTL). Initial QTL were projected on a recent consensus map (2004). Quality criteria were proposed to assess the reliability of this projection. These criteria were based on the distances between markers in the QTL regions. Chromosomes of groups 2 and 5 had a greater incidence on earliness control as they carry the known, major genes Ppd and Vrn. Other chromosome regions played an intermediate role in earliness control: 4A [heading date (HD) Meta-QTL], 4B (HD MQTL), 2B (VR MQTL) and 5B (IE MQTL). Markers at this four MQTL should prove helpful in marker-assisted selection, to better control earliness.
Quantitative trait locus (QTL) mapping is frequently used in evolutionary studies to understand the genetic architecture of continuously varying traits. The majority of studies have been conducted in specially created crosses, in which genetic differences between parental lines are identified by linkage analysis. Detecting QTL segregating within populations is more problematic, especially in wild populations, because these populations typically have complicated and unbalanced multigenerational pedigrees. However, QTL mapping can still be conducted in such populations using a variance components mixed model approach, and the advent of appropriate statistical frameworks and better genotyping methods mean that the approach is gaining popularity. In this study it is shown that all studies described to date report evidence of QTL of major effect on trait variation, but that these findings are probably caused by inflated estimates of QTL effect sizes due to the Beavis effect. Using simulations I show that even the most powerful studies conducted to date are likely to give misleading descriptions of the genetic architecture of a trait. I show that an interpretation of a mapping study of beak color in the zebra finch (Taeniopygia guttata), that suggested genetic variation was determined by a small number of loci of large effect, which are possibly maintained by antagonistic pleiotropy, is likely to be incorrect. More generally, recommendations are made to how QTL mapping can be combined with other approaches to provide more accurate descriptions of a trait's genetic architecture.
Caroline Moor Wagner
Este trabalho está inserido no programa de melhoramento genético de Capsicum da Embrapa Hortaliças. Teve como principal objetivo investigar a base genética e a variabilidade de uma população segregante de Capsicum em relação à pungência e a alguns caracteres do fruto para, fornecer informações úteis ao programa. Os genótipos utilizados compreenderam dois genitores homozigóticos contrastantes para o caráter principal, a pungência, bem como as respectivas gerações F1, RC11 e progênies F4.3...
MOTA, J. H.; YURI, J. E.; RESENDE, G. M. de.; De Souza, R. J.
Caracteres morfológicos (altura da planta, largura da folha, número de folhas e ângulo de folhas), físico-químicos (sólidos solúveis, acidez total titulável e pH), produtivos (produção comercial e massa média de bulbos) e molecular (por meio de marcadores moleculares RAPD) foram estudados em alho (Allium sativum L.). Doze cultivares, seis seminobre (Gigante Curitibanos, Gigante Roxo, Gigante Roxão, Gravatá, Amarante e Cateto Roxo) e seis nobre (Caçador, Chonan, Contestado 12, Caçador 30, Caça...
Full Text Available O objetivo deste trabalho foi identificar os efeitos genéticos que controlam a herança de caracteres associados à eficiência de utilização do fósforo (EUP em milho e determinar as relações entre esses caracteres. Foi realizado um dialelo entre seis cultivares de milho do qual foram obtidas 15 combinações híbridas. Estas cultivares foram avaliadas em alta e baixa disponibilidade de fósforo, em casa de vegetação e campo. Foram medidas a resposta das plantas à disponibilidade de fósforo (RU e as características associadas às eficiências de utilização e translocação do nutriente. As combinações híbridas apresentaram interação significativa com a disponibilidade de P, para os caracteres massa de matéria seca da planta (MSP, teor de P na planta (PAP e razão entre as massas de matéria seca da parte aérea e da raiz (RMS. A interação entre capacidade geral de combinação e RU foi significativa para PAP e RMS e, entre capacidade específica de combinação e RU, para MSP e PAP. As EUP em baixa e alta disponibilidade do nutriente estiveram correlacionadas entre si e com RU. A EUP em baixa disponibilidade de P não se correlacionou com a produtividade de grãos. Contudo, sob alta disponibilidade do nutriente, esses parâmetros se correlacionaram. Os efeitos não aditivos têm maior importância para caracteres relacionados à EUP, de modo que a seleção deve ser realizada nas combinações híbridas.The objective of this work was to determine the genetic effects that control the inheritance of characters associated with the phosphorus utilization efficiency (PUE in maize, and to determine the relationship among them. A diallel between six maize cultivars was performed and 15 hybrid combinations were obtained from it. These cultivars were evaluated in high and low phosphorus availability in the greenhouse and field. Plant response to nutrient availability (RU and traits associated to utilization and translocation
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
Nilson César Corrêa Padilha
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
Ulisses Andrade Santana
Full Text Available O objetivo deste trabalho foi determinar as capacidades geral e específica de combinação, os parâmetros genéticos e a correlação entre caracteres morfoagronômicos, em acessos de pinhão-manso (Jatropha curcas. Utilizou-se o delineamento experimental de blocos ao acaso, com três repetições. Foram avaliados os caracteres: PR, produção de sementes; AP, altura de planta; NRS, número de ramos secundários; NFF, número de flores femininas; DC, diâmetro de colo; P100, massa de 100 sementes; AR, altura de ramificação; e DCO, diâmetro de copa. A capacidade geral de combinação foi significativa para PR, NRS, DC, P100 e AR, enquanto a capacidade específica foi significativa apenas para NFF e NRS. As estimativas de herdabilidade foram superiores a 70%, em NRS, NFF, DC e AR. Observou-se correlações genotípicas positivas entre NRS e DC (0,942, NRS e AP (0,762, NRS e DCO (0,798, NRS e PR (0,759, DC e AP (0,738, DC e DCO (0,844, DC e PR (0,802, e DCO e PR (0,742; e negativas entre NRS e AR (-0,665, e DC e AR (-0,687. O NFF explicou mais de 50% da variação dos híbridos de pinhão-manso. A capacidade geral de combinação é preponderante na maioria das características avaliadas.
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.
Sahana, Goutam; Guldbrandtsen, Bernt; Thomsen, Bo;
A genome-wide association study of 2098 progeny-tested Nordic Holstein bulls genotyped for 36 387 SNPs on 29 autosomes was conducted to confirm and fine-map quantitative trait loci (QTL) for mastitis traits identified earlier using linkage analysis with sparse microsatellite markers in the same...... population. We used linear mixed model analysis where a polygenic genetic effect was fitted as a random effect and single SNPs were successively included as fixed effects in the model. We detected 143 SNP-by-trait significant associations (P mastitis-related traits....... Among them, 21 SNP-by-trait combinations exceeded the genome-wide significant threshold. For 12 chromosomes, both the present association study and the previous linkage study detected QTL, and of these, six were in the same chromosomal locations. Strong associations of SNPs with mastitis traits were...
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.
Yun, Lan; Larson, Steve R; Mott, Ivan W; Jensen, Kevin B; Staub, Jack E
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).
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......
Muhammad Azeem Asad
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.
Lu, A T-H; Yoon, J; Geschwind, D H; Cantor, R M
Autism Spectrum Disorder (ASD) has a heterogeneous etiology that is genetically complex. It is defined by deficits in communication and social skills and the presence of restricted and repetitive behaviors. Genetic analyses of heritable quantitative traits that correlate with ASD may reduce heterogeneity. With this in mind, deficits in nonverbal communication (NVC) were quantified based on items from the Autism Diagnostic Interview Revised. Our previous analysis of 228 families from the Autism Genetics Research Exchange (AGRE) repository reported 5 potential quantitative trait loci (QTL). Here we report an NVC QTL replication study in an independent sample of 213 AGRE families. One QTL was replicated (PNVC with a P-value of 0.001. Three associated haplotype blocks were intronic to the Nerve Growth Factor (NGF) gene (P=0.001, 0.001, 0.002), and one was intronic to KCND3 (P=0.001). Individual haplotypes within the associated blocks drove the associations (0.003, 0.0004 and 0.0002) for NGF and 0.0001 for KCND3. Using the same methods, these genes were tested for association with NVC in an independent sample of 1517 families from an Autism Genome Project (AGP). NVC was associated with a haplotype in an adjacent NGF block (P=0.0005) and one 46 kb away from the associated block in KCND3 (0.008). These analyses illustrate the value of QTL and targeted association studies for genetically complex disorders such as ASD. NGF is a promising risk gene for NVC deficits.
Muhammad; Azeem; Asad; Bin; Bai; Caixia; Lan; Jun; Yan; Xianchun; Xia; Yong; Zhang; Zhonghu; He
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.
Full Text Available Abstract Background Teat number is an important fertility trait for pig production, reflecting the mothering ability of sows. It is also a discrete and often canalized trait presenting bilateral symmetry with minor differences between the two sides, providing a potential power to evaluate fluctuating asymmetry and developmental instability. The knowledge of its genetic control is still limited. In this study, a genome-wide scan was performed with 183 microsatellites covering the pig genome to identify quantitative trait loci (QTL for three traits related to teat number including the total teat number (TTN, the teat number at the left (LTN and right (RTN sides in a large scale White Duroc × Erhualian resource population. Results A sex-average linkage map with a total length of 2350.3 cM and an average marker interval of 12.84 cM was constructed. Eleven genome-wide significant QTL for TTN were detected on 8 autosomes including pig chromosomes (SSC 1, 3, 4, 5, 6, 7, 8 and 12. Six suggestive QTL for this trait were detected on SSC6, 9, 13, 14 and 16. Eight chromosomal regions each on SSC1, 3, 4, 5, 6, 7, 8 and 12 showed significant associations with LTN. These regions were also evidenced as significant QTL for RTN except for those on SSC6 and SSC8. The most significant QTL for the 3 traits were all located on SSC7. Erhualian alleles at most of the identified QTL had positive additive effects except for three QTL on SSC1 and SSC7, at which White Duroc alleles increased teat numbers. On SSC1, 6, 9, 13 and 16, significant dominance effects were observed on TTN, and predominant imprinting effect on TTN was only detected on SSC12. Conclusion The results not only confirmed the QTL regions from previous experiments, but also identified five new QTL for the total teat number in swine. Minor differences between the QTL regions responsible for LTN and RTN were validated. Further fine mapping should be focused on consistently identified regions with small
Casas Guillén, Mercedes
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.
Marullo, Philippe; Aigle, Michel; Bely, Marina; Masneuf-Pomarède, Isabelle; Durrens, Pascal; Dubourdieu, Denis; Yvert, Gaël
Natural Saccharomyces cerevisiae yeast strains exhibit very large genotypic and phenotypic diversity. However, the link between phenotype variation and genetic determinism is still difficult to identify, especially in wild populations. Using genome hybridization on DNA microarrays, it is now possible to identify single-feature polymorphisms among divergent yeast strains. This tool offers the possibility of applying quantitative genetics to wild yeast strains. In this instance, we studied the genetic basis for variations in acetic acid production using progeny derived from two strains from grape must isolates. The trait was quantified during alcoholic fermentation of the two strains and 108 segregants derived from their crossing. A genetic map of 2212 markers was generated using oligonucleotide microarrays, and a major quantitative trait locus (QTL) was mapped with high significance. Further investigations showed that this QTL was due to a nonsynonymous single-nucleotide polymorphism that targeted the catalytic core of asparaginase type I (ASP1) and abolished its activity. This QTL was only effective when asparagine was used as a major nitrogen source. Our results link nitrogen assimilation and CO(2) production rate to acetic acid production, as well as, on a broader scale, illustrating the specific problem of quantitative genetics when working with nonlaboratory microorganisms.
Beraldi, Dario; McRae, Allan F; Gratten, Jacob; Pilkington, Jill G; Slate, Jon; Visscher, Peter M; Pemberton, Josephine M
A genome-wide scan was performed to detect quantitative trait loci (QTL) for resistance to gastrointestinal parasites and ectoparasitic keds segregating in the free-living Soay sheep population on St. Kilda (UK). The mapping panel consisted of a single pedigree of 882 individuals of which 588 were genotyped. The Soay linkage map used for the scans comprised 251 markers covering the whole genome at average spacing of 15cM. The traits here investigated were the strongyle faecal egg count (FEC), the coccidia faecal oocyst count (FOC) and a count of keds (Melophagus ovinus). QTL mapping was performed by means of variance component analysis so that the genetic parameters of the study traits were also estimated and compared with previous studies in Soay and domestic sheep. Strongyle FEC and coccidia FOC showed moderate heritability (h(2)=0.26 and 0.22, respectively) in lambs but low heritability in adults (h(2)scans were performed for the traits with moderate heritability and two genomic regions reached the level of suggestive linkage for coccidia FOC in lambs (logarithm of the odds=2.68 and 2.21 on chromosomes 3 and X, respectively). We believe this is the first study to report a QTL search for parasite resistance in a free-living animal population and therefore may represent a useful reference for similar studies aimed at understanding the genetics of host-parasite co-evolution in the wild.
Thongjuea, Supat; Ruanjaichon, Vinitchan; Bruskiewich, Richard; Vanavichit, Apichart
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.
We propose a novel statistical framework for integrating the result from molecular quantitative trait loci (QTL) mapping into genome-wide genetic association analysis of complex traits, with the primary objectives of quantitatively assessing the enrichment of the molecular QTLs in complex trait-associated genetic variants and the colocalizations of the two types of association signals. We introduce a natural Bayesian hierarchical model that treats the latent association status of molecular QTLs as SNP-level annotations for candidate SNPs of complex traits. We detail a computational procedure to seamlessly perform enrichment, fine-mapping and colocalization analyses, which is a distinct feature compared to the existing colocalization analysis procedures in the literature. The proposed approach is computationally efficient and requires only summary-level statistics. We evaluate and demonstrate the proposed computational approach through extensive simulation studies and analyses of blood lipid data and the whole blood eQTL data from the GTEx project. In addition, a useful utility from our proposed method enables the computation of expected colocalization signals using simple characteristics of the association data. Using this utility, we further illustrate the importance of enrichment analysis on the ability to discover colocalized signals and the potential limitations of currently available molecular QTL data. The software pipeline that implements the proposed computation procedures, enloc, is freely available at https://github.com/xqwen/integrative. PMID:28278150
Bidanel Jean P
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.
Salinas, María; Capel, Carmen; Alba, Juan Manuel; Mora, Blanca; Cuartero, Jesús; Fernández-Muñoz, Rafael; Lozano, Rafael; Capel, Juan
A novel source of resistance to two-spotted spider mite (Tetranychus urticae Koch) was found in Solanum pimpinellifolium L. accession TO-937 and thereby a potential source of desirable traits that could be introduced into new tomato varieties. This resistance was found to be controlled by a major locus modulated by minor loci of unknown location in the genome of this wild tomato. We first applied a bulked segregant analysis (BSA) approach in an F(4) population as a method for rapidly identifying a genomic region of 17 cM on chromosome 2, flanked by two simple sequence repeat markers, harboring Rtu2.1, one of the major QTL involved in the spider mite resistance. A population of 169 recombinant inbred lines was also evaluated for spider mite infestation and a highly saturated genetic map was developed from this population. QTL mapping corroborated that chromosome 2 harbored the Rtu2.1 QTL in the same region that our previous BSA findings pointed out, but an even more robust QTL was found in the telomeric region of this chromosome. This QTL, we termed Rtu2.2, had a LOD score of 15.43 and accounted for more than 30% of the variance of two-spotted spider mite resistance. Several candidate genes involved in trichome formation, synthesis of trichomes exudates and plant defense signaling have been sequenced. However, either the lack of polymorphisms between the parental lines or their map position, away from the QTL, led to their rejection as candidate genes responsible for the two-spotted spider mite resistance. The Rtu2 QTL not only serve as a valuable target for marker-assisted selection of new spider mite-resistant tomato varieties, but also as a starting point for a better understanding of the molecular genetic functions underlying the resistance to this pest.
Eskandari, Mehrzad; Cober, Elroy R; Rajcan, Istvan
Soybean seed is a major source of oil for human consumption worldwide and the main renewable feedstock for biodiesel production in North America. Increasing seed oil concentration in soybean [Glycine max (L.) Merrill] with no or minimal impact on protein concentration could be accelerated by exploiting quantitative trait loci (QTL) or gene-specific markers. Oil concentration in soybean is a polygenic trait regulated by many genes with mostly small effects and which is negatively associated with protein concentration. The objectives of this study were to discover and validate oil QTL in two recombinant inbred line (RIL) populations derived from crosses between three moderately high-oil soybean cultivars, OAC Wallace, OAC Glencoe, and RCAT Angora. The RIL populations were grown across several environments over 2 years in Ontario, Canada. In a population of 203 F(3:6) RILs from a cross of OAC Wallace and OAC Glencoe, a total of 11 genomic regions on nine different chromosomes were identified as associated with oil concentration using multiple QTL mapping and single-factor ANOVA. The percentage of the phenotypic variation accounted for by each QTL ranged from 4 to 11 %. Of the five QTL that were tested in a population of 211 F(3:5) RILs from the cross RCAT Angora × OAC Wallace, a "trait-based" bidirectional selective genotyping analysis validated four QTL (80 %). In addition, a total of seven two-way epistatic interactions were identified for oil concentration in this study. The QTL and epistatic interactions identified in this study could be used in marker-assisted introgression aimed at pyramiding high-oil alleles in soybean cultivars to increase oil concentration for biodiesel as well as edible oil applications.
Bartlett, Christopher W; Cheong, Soo Yeon; Hou, Liping; Paquette, Jesse; Lum, Pek Yee; Jäger, Günter; Battke, Florian; Vehlow, Corinna; Heinrich, Julian; Nieselt, Kay; Sakai, Ryo; Aerts, Jan; Ray, William C
In 2011, the IEEE VisWeek conferences inaugurated a symposium on Biological Data Visualization. Like other domain-oriented Vis symposia, this symposium's purpose was to explore the unique characteristics and requirements of visualization within the domain, and to enhance both the Visualization and Bio/Life-Sciences communities by pushing Biological data sets and domain understanding into the Visualization community, and well-informed Visualization solutions back to the Biological community. Amongst several other activities, the BioVis symposium created a data analysis and visualization contest. Unlike many contests in other venues, where the purpose is primarily to allow entrants to demonstrate tour-de-force programming skills on sample problems with known solutions, the BioVis contest was intended to whet the participants' appetites for a tremendously challenging biological domain, and simultaneously produce viable tools for a biological grand challenge domain with no extant solutions. For this purpose expression Quantitative Trait Locus (eQTL) data analysis was selected. In the BioVis 2011 contest, we provided contestants with a synthetic eQTL data set containing real biological variation, as well as a spiked-in gene expression interaction network influenced by single nucleotide polymorphism (SNP) DNA variation and a hypothetical disease model. Contestants were asked to elucidate the pattern of SNPs and interactions that predicted an individual's disease state. 9 teams competed in the contest using a mixture of methods, some analytical and others through visual exploratory methods. Independent panels of visualization and biological experts judged entries. Awards were given for each panel's favorite entry, and an overall best entry agreed upon by both panels. Three special mention awards were given for particularly innovative and useful aspects of those entries. And further recognition was given to entries that correctly answered a bonus question about how a
Wu, Haibin; He, Xiaoli; Gong, Hao; Luo, Shaobo; Li, Mingzhu; Chen, Junqiu; Zhang, Changyuan; Yu, Ting; Huang, Wangping; Luo, Jianning
The hybrids between Luffa acutangula (L.) Roxb. and L.cylindrica (L.) Roem. have strong heterosis effects. However, some reproductive isolation traits hindered their normal hybridization and fructification, which was mainly caused by the flowering time and hybrid pollen sterility. In order to study the genetic basis of two interspecific reproductive isolation traits, we constructed a genetic linkage map using an F2 population derived from a cross between S1174 [L. acutangula (L.) Roxb.] and 93075 [L. cylindrica (L.) Roem.]. The map spans 1436.12 CentiMorgans (cM), with an average of 8.11 cM among markers, and consists of 177 EST-SSR markers distributed in 14 linkage groups (LG) with an average of 102.58 cM per LG. Meanwhile, we conducted colinearity analysis between the sequences of EST-SSR markers and the genomic sequences of cucumber, melon and watermelon. On the basis of genetic linkage map, we conducted QTL mapping of two reproductive isolation traits in sponge gourd, which were the flowering time and hybrid male sterility. Two putative QTLs associated with flowering time (FT) were both detected on LG 1. The accumulated contribution of these two QTLs explained 38.07% of the total phenotypic variance (PV), and each QTL explained 15.36 and 22.71% of the PV respectively. Four QTLs for pollen fertility (PF) were identified on LG 1 (qPF1.1 and qPF1.2), LG 3 (qPF3) and LG 7 (qPF7), respectively. The percentage of PF explained by these QTLs varied from 2.91 to 16.79%, and all together the four QTLs accounted for 39.98% of the total PV. Our newly developed EST-SSR markers and linkage map are very useful for gene mapping, comparative genomics and molecular marker-assisted breeding. These QTLs for interspecific reproductive isolation will also contribute to the cloning of genes relating to interspecific reproductive isolation and the utilization of interspecific heterosis in sponge gourd in further studies. PMID:27458467
Zhang, Song; Wang, Ye; Zhang, Sheng-Ping; Gu, Xing-Fang
Mechanized harvesting of cucumbers offers significant advantages compared to manual labor as both shortages and costs of labor increase. However the efficient use of machines depends on breeding plants with longer peduncles, but the genetic and molecular basis of fruit peduncle development in cucumber is not well understood. In this study, F2 populations were developed from a cross between two inbred lines, 1101 with a long peduncle and 1694 with a short peduncle. These were grown at two field sites, Hainan, with a tropical marine climate, in December 2014, and Beijing, with a warm temperate climate, in May 2015. Electron microscope examination of the pith cells in the peduncles of the two parental lines showed that line 1101 had significantly greater numbers of smaller cells compared to line 1694. The inheritance of cucumber fruit peduncle length (FPL) was investigated by the mixed major gene and polygene inheritance model. Genetic analysis indicated that FPL in cucumber is quantitatively inherited and controlled by one additive major gene and additive-dominant polygenes (D-2 model). A total of 1460 pairs of SSR (simple sequence repeat) primers were analyzed to identify quantitative trait loci (QTLs). Two similar genetic maps with 78 SSR markers which covered 720.6 cM in seven linkage groups were constructed based on two F2 populations. QTL analysis from the data collected at the two field sites showed that there are two minor QTLs on chromosome 1, named qfpl1.1 and qfpl1.2, and one major QTL on chromosome 6, named qfpl6.1. The marker UW021226, which was the closest one to qfpl6.1, had an accuracy rate of 79.0% when tested against plants selected from populations of the two parents. The results from this study provide insights into the inheritance and molecular mechanism of the variation of FPL in cucumber, and further research will be carried out to fine map qfpl6.1 to develop more accurate markers for MAS breeding. PMID:27936210
In 2011, the IEEE VisWeek conferences inaugurated a symposium on Biological Data Visualization. Like other domain-oriented Vis symposia, this symposium's purpose was to explore the unique characteristics and requirements of visualization within the domain, and to enhance both the Visualization and Bio/Life-Sciences communities by pushing Biological data sets and domain understanding into the Visualization community, and well-informed Visualization solutions back to the Biological community. Amongst several other activities, the BioVis symposium created a data analysis and visualization contest. Unlike many contests in other venues, where the purpose is primarily to allow entrants to demonstrate tour-de-force programming skills on sample problems with known solutions, the BioVis contest was intended to whet the participants' appetites for a tremendously challenging biological domain, and simultaneously produce viable tools for a biological grand challenge domain with no extant solutions. For this purpose expression Quantitative Trait Locus (eQTL) data analysis was selected. In the BioVis 2011 contest, we provided contestants with a synthetic eQTL data set containing real biological variation, as well as a spiked-in gene expression interaction network influenced by single nucleotide polymorphism (SNP) DNA variation and a hypothetical disease model. Contestants were asked to elucidate the pattern of SNPs and interactions that predicted an individual's disease state. 9 teams competed in the contest using a mixture of methods, some analytical and others through visual exploratory methods. Independent panels of visualization and biological experts judged entries. Awards were given for each panel's favorite entry, and an overall best entry agreed upon by both panels. Three special mention awards were given for particularly innovative and useful aspects of those entries. And further recognition was given to entries that correctly answered a bonus question about how a
Meirmans Patrick G
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
Houston Ross D
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
LIU Qiang-ming; JIANG Jian-hua; NIU Fu-an; HE Ying-jun; HONG De-lin
QTL mapping for seven quality traits was conducted by using 254 recombinant inbred lines (RIL) derived from a japonica-japonica rice cross of Xiushui 791C Bao.The seven traits investigated were grain length (GL),grain length to width ratio (LWR),chalk grain rate (CGR),chalkiness degree (CD),gelatinization temperature (GT),amylose content (AC) and gel consistency (GC) of head rice.Three mapping methods employed were composite interval mapping in QTLMapper 2.0 software based on mixed linear model (MCIM),inclusive composite interval mapping in QTL IciMapping 3.0 software based on stepwise regression linear model (ICIM) and multiple interval mapping with regression forward selection in Windows QTL Cartographer 2.5 based on multiple regression analysis (MIMR).Results showed that five QTLs with additive effect (A-QTLs) were detected by all the three methods simultaneously,two by two methods simultaneously,and 23 by only one method.Five A-QTLs were detected by MCIM,nine by ICIM and 28 by MIMR.The contribution rates of single A-QTL ranged from 0.89％ to 38.07％.All the QTLs with epistatic effect (E-QTLs) detected by MIMR were not detected by the other two methods.Fourteen pairs of E-QTLs were detected by both MCIM and ICIM,and 142 pairs of E-QTLs were detected by only one method.Twenty-five pairs of E-QTLs were detected by MCIM,141 pairs by ICIM and four pairs by MIMR.The contribution rates of single pair of E-QTL were from 2.60％ to 23.78％.In the Xiu-Bao RIL population,epistatic effect played a major role in the variation of GL and CD,and additive effect was the dominant in the variation of LWR,while both epistatic effect and additive effect had equal importance in the variation of CGR,AC,GT and GC.QTLs detected by two or more methods simultaneously were highly reliable,and could be applied to improve the quality traits in japonica hybrid rice.
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
Jairo Vidal Vieira
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
McCallum, John; Pither-Joyce, Meeghan; Shaw, Martin; Kenel, Fernand; Davis, Sheree; Butler, Ruth; Scheffer, John; Jakse, Jernej; Havey, Michael J
Onion exhibits wide genetic and environmental variation in bioactive organosulfur compounds that impart pungency and health benefits. A PCR-based molecular marker map that included candidate genes for sulfur assimilation was used to identify genomic regions affecting pungency in the cross 'W202A' x 'Texas Grano 438'. Linkage mapping revealed that genes encoding plastidic ferredoxin-sulfite reductase (SiR) and plastidic ATP sulfurylase (ATPS) are closely linked (1-2 cM) on chromosome 3. Inbred F(3) families derived from the F(2 )population used to construct the genetic map were grown in replicated trials in two environments and bulb pungency was evaluated as pyruvic acid or lachrymatory factor. Broad-sense heritability of pungency was estimated to be 0.78-0.80. QTL analysis revealed significant associations of both pungency and bulb soluble solids content with marker intervals on chromosomes 3 and 5, which have previously been reported to condition pleiotropic effects on bulb carbohydrate composition. Highly significant associations (LOD 3.7-8.7) were observed between ATPS and SiR Loci and bulb pungency but not with bulb solids content. This association was confirmed in two larger, independently derived F(2) families from the same cross. Single-locus models suggested that the partially dominant locus associated with these candidate genes controls 30-50% of genetic variation in pungency in these pedigrees. These markers may provide a practical means to select for lower pungency without correlated selection for lowered solids.
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
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.
JIN Meng-yang; LI Jia-na; FU Fu-you; ZHANG Zheng-sheng; ZHANG Xue-kun; LIU Lie-zhao
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.
Fountain, Toby; Ravinet, Mark; Naylor, Richard; Reinhardt, Klaus; Butlin, Roger K.
The rapid evolution of insecticide resistance remains one of the biggest challenges in the control of medically and economically important pests. Insects have evolved a diverse range of mechanisms to reduce the efficacy of the commonly used classes of insecticides, and finding the genetic basis of resistance is a major aid to management. In a previously unstudied population, we performed an F2 resistance mapping cross for the common bed bug, Cimex lectularius, for which insecticide resistance is increasingly widespread. Using 334 SNP markers obtained through RAD-sequencing, we constructed the first linkage map for the species, consisting of 14 putative linkage groups (LG), with a length of 407 cM and an average marker spacing of 1.3 cM. The linkage map was used to reassemble the recently published reference genome, facilitating refinement and validation of the current genome assembly. We detected a major QTL on LG12 associated with insecticide resistance, occurring in close proximity (1.2 Mb) to a carboxylesterase encoding candidate gene for pyrethroid resistance. This provides another example of this candidate gene playing a major role in determining survival in a bed bug population following pesticide resistance evolution. The recent availability of the bed bug genome, complete with a full list of potential candidate genes related to insecticide resistance, in addition to the linkage map generated here, provides an excellent resource for future research on the development and spread of insecticide resistance in this resurging pest species. PMID:27733453
Full Text Available The rapid evolution of insecticide resistance remains one of the biggest challenges in the control of medically and economically important pests. Insects have evolved a diverse range of mechanisms to reduce the efficacy of the commonly used classes of insecticides, and finding the genetic basis of resistance is a major aid to management. In a previously unstudied population, we performed an F2 resistance mapping cross for the common bed bug, Cimex lectularius, for which insecticide resistance is increasingly widespread. Using 334 SNP markers obtained through RAD-sequencing, we constructed the first linkage map for the species, consisting of 14 putative linkage groups (LG, with a length of 407 cM and an average marker spacing of 1.3 cM. The linkage map was used to reassemble the recently published reference genome, facilitating refinement and validation of the current genome assembly. We detected a major QTL on LG12 associated with insecticide resistance, occurring in close proximity (1.2 Mb to a carboxylesterase encoding candidate gene for pyrethroid resistance. This provides another example of this candidate gene playing a major role in determining survival in a bed bug population following pesticide resistance evolution. The recent availability of the bed bug genome, complete with a full list of potential candidate genes related to insecticide resistance, in addition to the linkage map generated here, provides an excellent resource for future research on the development and spread of insecticide resistance in this resurging pest species.
Yesudas, C R; Sharma, H; Lightfoot, D A
Soybean [Glycine max (L.) Merr.] was one of the most important legume crops in the world in 2010. Japanese beetles (JB; Popillia japonica, Newman) in the US were an introduced and potentially damaging insect pest for soybean. JBs are likely to spread across the US if global warming occurs. Resistance to JB in soybean was previously reported only in plant introductions. The aims here were to identify loci underlying resistance to JB herbivory in recombinant inbred lines (RILs) derived from the cross of Essex x Forrest cultivars (EF94) and to correlate those with loci with factors that confer insect resistance in soybean cultivars. The RIL population was used to map 413 markers, 238 satellite markers and 177 other DNA markers. Field data were from two environments over 2 years. Pest severity (PS) measured defoliation on a 0-9 scale. Pest incidence (PI) was the percentage of plants within each RIL with beetles on them. Antibiosis and antixenosis data were from feeding assays with detached leaves in petri plates. Five QTL were detected for the mean PS field trait (16% root knot nematode (LG F) but not other major loci underlying resistance to nematode or insect pests (LGs G, H and M).
YAN Xing-ying; QU Cun-min; LI Jia-na; CHEN Li; LIU Lie-zhao
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.
de Jong, Simone; van Eijk, Kristel R; Zeegers, Dave W L H; Strengman, Eric; Janson, Esther; Veldink, Jan H; van den Berg, Leonard H; Cahn, Wiepke; Kahn, René S; Boks, Marco P M; Ophoff, Roel A
There is genetic evidence that schizophrenia is a polygenic disorder with a large number of loci of small effect on disease susceptibility. Genome-wide association studies (GWASs) of schizophrenia have had limited success, with the best finding at the MHC locus at chromosome 6p. A recent effort of the Psychiatric GWAS consortium (PGC) yielded five novel loci for schizophrenia. In this study, we aim to highlight additional schizophrenia susceptibility loci from the PGC study by combining the top association findings from the discovery stage (9394 schizophrenia cases and 12 462 controls) with expression QTLs (eQTLs) and differential gene expression in whole blood of schizophrenia patients and controls. We examined the 6192 single-nucleotide polymorphisms (SNPs) with significance threshold at Pschizophrenia cases and controls (n=202). After correction for multiple testing, the eQTL analysis yielded 40 significant cis-acting effects of the SNPs. Seven of these transcripts show differential expression between cases and controls. Of these, the effect of three genes (RNF5, TRIM26 and HLA-DRB3) coincided with the direction expected from meta-analysis findings and were all located within the MHC region. Our results identify new genes of interest and highlight again the involvement of the MHC region in schizophrenia susceptibility.
Suthram, Silpa; Beyer, Andreas; Karp, Richard M; Eldar, Yonina; Ideker, Trey
Analysis of expression quantitative trait loci (eQTLs) is an emerging technique in which individuals are genotyped across a panel of genetic markers and, simultaneously, phenotyped using DNA microarrays. Because of the spacing of markers and linkage disequilibrium, each marker may be near many genes making it difficult to finely map which of these genes are the causal factors responsible for the observed changes in the downstream expression. To address this challenge, we present an efficient method for prioritizing candidate genes at a locus. This approach, called 'eQTL electrical diagrams' (eQED), integrates eQTLs with protein interaction networks by modeling the two data sets as a wiring diagram of current sources and resistors. eQED achieved a 79% accuracy in recovering a reference set of regulator-target pairs in yeast, which is significantly higher than the performance of three competing methods. eQED also annotates 368 protein-protein interactions with their directionality of information flow with an accuracy of approximately 75%.
Full Text Available 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.
Yu, Xiang; Wang, Han; Zhong, Weili; Bai, Jinjuan; Liu, Pinglin; He, Yuke
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.
HU Song-ping; YANG Hua; ZOU Gui-hua; LIU Hong-yan; LIU Guo-lan; MEI Han-wei; CAI Run; LI Ming-shou; LUO Li-jun
By using a set of recombinant inbred line (RIL) population involving in 195 lines derived from a cross of Zhenshan 97B (lowland variety) and IRAT109 (upland variety), the correlation analysis between coleoptile length (CL) and drought resistance index (DRI) and their QTL identification were conducted. There existed a significantly positive relationship between CL and DRI with the correlation coefficient of 0.2206** under water stress conditions. Under normal and water stress conditions, a total of eleven and four QTLs for CL and DRI, respectively, were detected on chromosomes 1, 2, 4, 5, 6, 7, 9, 11 and 12 by using a linkage map including 213SSR markers, which explained 4.84% to 22.65% of phenotypic variance. Chromosomes 1 and 9 possessing the QTLs for DRI harbored simultaneously QTLs for CL, and qCL9 shared the same chromosome location with qDRI9 (RM160-RM215). Comparing the QTLs related to drought resistance in other studies, QTLs for CL and DRI were located in the same or adjacent marker interval as those related to root traits, such as number, dry weight, depth, and length of root. Moreover, sixteen and three pairs of epistatic loci for CL and DRI were found, which accounted for 56.17% and 11.93% of the total variation in CL and DRI, respectively.
Ebrahimi, A; Maury, P; Berger, M; Calmon, A; Grieu, P; Sarrafi, A
The purpose of this study was to identify genomic regions controlling seed protein content, kernel and hull weights, and seed density in water-stress conditions in sunflower (Helianthus annuus L.). The experiments consisted of a split-plot design (water treatment and recombinant inbred lines) with three blocks in two environments (greenhouse and field). High significant variation was observed between genotypes for all traits as well as for water treatment x genotype interaction. Several specific and nonspecific QTLs were detected for all traits under well-watered and water-stress conditions. Two SSR markers, ORS671_2 and HA2714, linked to protein content were identified that have no interaction with water treatments in greenhouse conditions. We also detected the E35M60_4 marker associated with kernel weight that had no interaction with water treatments. A specific QTL for protein content was detected with important phenotypic variance (17%) under water-stress conditions. Overlapping QTLs for protein content and seed density were identified in linkage group 15. This region probably has a peliotropic effect on protein content and seed density. QTLs for protein content colocated with grain weight traits were also identified.
Liu, Haiying; Quampah, Alfred; Chen, Jinhong; Li, Jinrong; Huang, Zhuangrong; He, Qiuling; Shi, Chunhai; Zhu, Shuijin
Amino acid is an important nutrient resource for both human and animals. Using a set of 188 RILs population derived from an elite hybrid cross of upland cotton cultivars 'HS46' × 'MARCABUCAG8US-1-88' and their immortal F2 (IF2) with reciprocal backcrosses BC1F1 and BC2F1 (BC) populations in two environments, the QTLs located on the embryo genome and maternal plant genome for nine amino acids of cottonseed were studied across environments. The QTL Network-CL-2.0-seed software was used to analyze the QTLs and their genetic effects for nine amino acids. A total of 56 QTLs for nine amino acids were detected in both populations, with many having over 5% of phenotypic variation. Ten of the total QTLs could be simultaneously found in the IF2 and BC populations. For most QTLs, the genetic effects from embryo genome were more important than those from maternal plant genome for the performance of nine amino acids. Significant embryo additive main effects and maternal additive main effect with their environment interaction effects from many QTLs were also found in present experiment. Some QTLs with larger phenotypic variation were important for improving the amino-acid contents in cottonseeds.
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.
JIANG Gong-hao; XU Cai-guo; LI Xiang-hua; HE Yu-qing
Main-effect QTL, epistatic effects and their interactions with environment are important genetic components of quantitative traits. In this study, we analyzed the QTL, epistatic effects and QTL by environment interactions (QE) underlying plant height and heading date, using a doubled-haploid (DH) population consisting of 190 lines from the cross between an indica parent Zhenshan 97 and a japonica parent Wuyujing 2, and tested in two-year replicated field trials. A genetic linkage map with 179 SSR (simple sequence repeat) marker loci was constructed. A mixed linear model approach was applied to detect QTL, digenic interactions and QEs for the two traits. In total, 20 main-effect QTLs, 9 digenic interactions involving 18 loci, and 5 QTL by environment interactions were found to be responsible for the two traits. No interactions were detected between the digenic interaction and environment. The amounts of variations explained by QTLs of main effect were 53.9% for plant height and 57.8% for heading date, larger than that explained by epistasis and QEs. However,the epistasis and QE interactions sometimes accounted for a significant part of phenotypic variation and should not be disregarded.
Calus, Mario P L; Meuwissen, Theo H E; Windig, Jack J; Knol, Egbert F; Schrooten, Chris; Vereijken, Addie L J; Veerkamp, Roel F
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.
Arms, Erin M; Bloom, Arnold J; St Clair, Dina A
QTL stm9 controlling rapid-onset water stress tolerance in S. habrochaites was high-resolution mapped to a chromosome 9 region that contains genes associated with abiotic stress tolerances. Wild tomato (Solanum habrochaites) exhibits tolerance to abiotic stresses, including drought and chilling. Root chilling (6 °C) induces rapid-onset water stress by impeding water movement from roots to shoots. S. habrochaites responds to such changes by closing stomata and maintaining shoot turgor, while cultivated tomato (S. lycopersicum) fails to close stomata and wilts. This response (shoot turgor maintenance under root chilling) is controlled by a major QTL (designated stm9) on chromosome 9, which was previously fine-mapped to a 2.7-cM region. Recombinant sub-near-isogenic lines for chromosome 9 were marker-selected, phenotyped for shoot turgor maintenance under root chilling in two sets of replicated experiments (Fall and Spring), and the data were used to high-resolution map QTL stm9 to a 0.32-cM region. QTL mapping revealed a single QTL that was coincident for both the Spring and Fall datasets, suggesting that the gene or genes contributing to shoot turgor maintenance under root chilling reside within the marker interval H9-T1673. In the S. lycopersicum reference genome sequence, this chromosome 9 region is gene-rich and contains representatives of gene families that have been associated with abiotic stress tolerance.
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.
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
Douglas André Mallmann Schmidt
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
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.