Diversidad genética en seis poblaciones de tilapia roja, usando microsatelites como marcadores genéticos

Objetivo. Determinar y evaluar la diversidad genética de seis poblaciones de tilapia roja híbrida, con el propósito de evaluar el potencial beneficio de un futuro programa de mejoramiento adelantado en el Centro de Investigación para la Acuicultura (CENIACUA), Colombia. Materiales y métodos. Fueron genotipados un total de 300 individuos utilizando un grupo de 5 microsatélites fluorescentes. Las muestras se tomaron en 6 fincas diferentes en 4 departamentos de Colombia, representando una amplia variabilidad genética. Resultados. El número medio de alelos por locus por población fue de 8.367. La población 5 tuvo el número más alto de alelos por locus: 9.6, seguida de la población 4 con 9.4, población 2 con 9.2, población 3 con 8.0, población 1 con 7.2 y población 6 con 6,8 alelos. Los análisis de distribución de la variación genética fueron de (17.32%) entre las poblaciones mientras que dentro de las poblaciones fue de (28.55%), y entre los individuos fue de (54.12%). Los índices de diversidad estándar mostraron que la población 4 fue la más variable (media He=0.837) seguida de la población 1 (media He=0.728), población 3 (media He=0.721), población 5 (media He=0.705), población 2 (media He=0.690) y población 6 (media He=0.586). Todas las poblaciones mostraron desviaciones significativas de equilibrio de Hardy–Weinberg, debido principalmente a la falta de heterocigotos. Las frecuencias genotípicas de los locis UNH 106 de la población 5 y loci UNH 172 de la población 6 estuvieron en equilibrio de Hardy-Weinberg. Conclusiones. La distancia Fst evidenció que las muestras estan diferenciadas geneticamente y es posible usar esas poblaciones para el programa de mejorameinto genético, sin embargo, es recomendable introducir otros individuos

Diversidade genética de acessos cultivados e espécies silvestres de seringueira por meio de marcadores EST‑SSR

O objetivo deste trabalho foi avaliar a eficiência de marcadores EST‑SSR na determinação da diversidade genética de genótipos de seringueira e verificar a transferibilidade destes marcadores para espécies silvestres de Hevea. Foram utilizados 45 acessos de seringueira (H. brasiliensis) do Instituto Agronômico e seis espécies silvestres. As informações fornecidas pela distância genética de Roger modificada foram usadas para analisar os dados de EST‑SSR. O agrupamento UPGMA dividiu as amostras em dois grandes grupos com alta diferenciação genética, enquanto o programa Structure distribuiu os 51 clones em oito grupos. Foi possível traçar um paralelo entre ambos os métodos de agrupamento. Os 30 EST‑SSRs polimórficos mostraram de dois a dez alelos e foram eficientes em amplificar as seis espécies silvestres. Microssatélites funcionais EST‑SSR são eficientes na avaliação da diversidade genética entre clones de seringueira e podem ser usados para traduzir diferenças genéticas entre cultivares e para gerar perfis genéticos de materiais próximos. Os acessos do Instituto Agronômico apresentam elevada diversidade genética. Os marcadores EST‑SSR, desenvolvidos para Hevea brasilensis, apresentam transferabilidade e são capazes de amplificar outras espécies de Hevea.The objective of this work was to evaluate the efficiency of EST‑SSR markers in the assessment of the genetic diversity of rubber tree genotypes (Hevea brasiliensis) and to verify the transferability of these markers for wild species of Hevea. Forty‑five rubber tree accessions from the Instituto Agronômico (Campinas, SP, Brazil) and six wild species were used. Information provided by modified Roger’s genetic distance were used to analyze EST‑SSR data. UPGMA clustering divided the samples into two major groups with high genetic differentiation, while the software Structure distributed the 51 clones into eight groups. A parallel could be established between both clustering analyses. The 30 polymorphic EST‑SSRs showed from two to ten alleles and were efficient in amplifying the six wild species. Functional EST‑SSR microsatellites are efficient in evaluating the genetic diversity among rubber tree clones and can be used to translate the genetic differences among cultivars and to fingerprint closely related materials. The accessions from the Instituto Agronômico show high genetic diversity. The EST‑SSR markers, developed from Hevea brasiliensis, show transferability and are able to amplify other species of Hevea

Linkage and mapping of quantitative trait loci associated with angular leaf spot and powdery mildew resistance in common beans

Angular leaf spot (ALS) and powdery mildew (PWM) are two important fungi diseases causing significant yield losses in common beans. In this study, a new genetic linkage map was constructed using single sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs), in a segregating population derived from the AND 277 x SEA 5 cross, with 105 recombinant inbred lines. Phenotypic evaluations were performed in the greenhouse to identify quantitative trait loci (QTLs) associated with resistance by means of the composite interval mapping analysis. Four QTLs were identified for ALS resistance. The QTL ALS11AS, linked on the SNP BAR 5054, mapped on chromosome Pv11, showed the greatest effect (R2 = 26.5%) on ALS phenotypic variance. For PWM resistance, two QTLs were detected, PWM2AS and PWM11AS, on Pv2 and Pv11, explaining 7% and 66% of the phenotypic variation, respectively. Both QTLs on Pv11 were mapped on the same genomic region, suggesting that it is a pleiotropic region. The present study resulted in the identification of new markers closely linked to ALS and PWM QTLs, which can be used for marker-assisted selection, fine mapping and positional cloning

Quantitative trait loci identified for root traits associated with drought resistance in common bean

Common bean has a high sensitivity to drought stress, particularly during reproductive development which reduces its yield. In this study we aimed to: (i) evaluate differences in shoot and root response of a mapping population of 107 recombinant inbred lines (RILs) of SEA 5 × AND 277 cross under drought stress, and (ii) identify the QTLs associated with improved plant performance under water stress treatment. Phenotyping was performed under greenhouse conditions where the plants were grown using rhizotrons under well-watered and water-stress conditions. Four QTLs were identified that are related to improved performance under water stress and three of them were related specifically to roots and these are located on chromosomes Pv1 and Pv6. Root superficial area trait explained 32.6% of the variance and may contribute to greater water uptake and improved adaptation of common bean under water stress conditions

Development of DArT platform and quantitative trait loci identification associated to drought tolerance in common bean (Phaseolus vulgaris L.)

Orientadores: Luciana Lasry Benchimol Reis, Matthew Ward BlairTese (doutorado) - Universidade Estadual de Campinas, Instituto de BiologiaResumo: O feijão comum (Phaseolus vulgaris L.) é uma cultura importante economicamente tanto para o consumo nacional como para a exportação. A seca é um dos principais estresses abióticos em todo o mundo e afeta cerca de 60% da área de cultivo de feijão. O avanço nas tecnologias de marcadores moleculares oferecem poderosos métodos para examinar as relações entre as características, gerando um grande volume de informações potencialmente úteis para assessorar os programas de melhoramento. O presente projeto teve como objetivo o desenvolvimento da Plataforma DArT para feijão comum junto à empresa DArT Pty Ltd, e o mapeamento destes marcadores juntamente com microssatélites e SNPs na população AND 277 x SEA 5 proveniente do CIAT (Colômbia), a fim de localizar os QTLs associados à tolerância à seca. O genitor SEA 5 é uma linhagem avançada do BAT 477, é tolerante à seca e de origem Mesoamericano e o genitor AND 277 é um genótipo resistente à mancha angular e antracnose e de origem Andina. Um total de 4.468 marcadores DArTs, 288 marcadores SNPs e 180 marcadores microssatélites polimórficos foram identificados na população e utilizados na genotipagem para construir um mapa genético saturado. A fenotipagem das 105 linhagens endogâmicas recombinantes (RILs) na geração F8 mais os dois genitores foi realizada avaliando 18 características associadas à tolerância a seca utilizando um delineamento inteiramente casualizado com quatro repetições, aplicando um estresse terminal na fase vegetativa V3/V4. Dois mapas foram construídos, um integrando 80 SSR e 251 SNPs e outro com cinco SSR, 91 SNPs e 4.468 DArTs. A identificação dos QTLs foi realizada através da análise de mapeamento por intervalo composto (CIM) para o mapa SSR - SNPs e mapeamento de precisão (SML) para o mapa SSR-SNPs-DArT. Um total de 12 QTLs foram identificados para o tratamento não irrigado e 29 QTLs para o tratamento irrigado pela análise CIM. Para as análises SML, 23 QTLs foram identificados para o tratamento não irrigado e 11 QTLs para o irrigado. QTLs de maior efeito foram encontrados para clorofila, biomassa fresca do caule e da folha, Massa seco da folia, temperatura da folha, número de vagens, número de sementes, massa de sementes, dias para florescimento, massa seca das vagens e produtividade nos dois tratamentos. Todos os QTLs detectados sob condições de seca apresentaram o alelo do genitor SEA 5. Este estudo é importante para o melhoramento genético não só para entender melhor a herança genética de uma característica tão complexa como a tolerância à seca, bem como para encontrar ferramentas moleculares a serem utilizados para a seleção assistida por marcadoresAbstract: Common bean (Phaseolus vulgaris L.) is the most important food legume for consumption and for exportation. Drought is one of the main abiotic stresses in the world and affects about 60% of bean growing area across the world. The advance in technologies of molecular markers provide a powerful method to examine the relationships between traits, generating large amount of potentially useful information to assist the breeding programs. The objective of this project was the development of DArT platform for common beans with DArT Pty Ltd and the mapping of these markers with microsatellites and SNPs in the population AND 277 x SEA 5 from CIAT (Colombia), in order to locate the QTLs associated with drought tolerance. The SEA 5 parent is a drought tolerant advanced line (Mesoamerican) and the AND 277 is resistant to the angular leaf spot and antracnose (Andean). A total of 4.468 DArT markers, 288 SNP and 180 SSR polymorphic markers were identified in the population and used in genotyping to constructed a saturated genetic map. Phenotyping of 105 recombinant inbred lines (RILs) in F8 generation plus the genitors were performed evaluating 18 traits associated with drought tolerance using a completely randomized design with four replicates, applying terminal stress at vegetative phase V3/V4. Two maps were constructed, one integrating 80 SSR and 251 SNPs and another with five SSR, 91 SNPs and 4,468 DArTs. The identification of QTL analysis was performed by composite interval mapping (CIM) for the SSR - SNPs map and the precision mapping (SML) to map DArT-SSR-SNPs. A total of 12 QTLs were identified for the non-irrigated treatment and 29 QTLs for the irrigated treatment by CIM analysis. For SML analysis, 23 QTLs were identified for the non-irrigated and 11 QTLs for irrigated treatment. QTLs of major effect was found for chlorophyll, fresh biomass of stem and leaf dry weight, leaf temperature, number of pods, number of seeds, seed weight, days to flowering, dry weight of pods and yield in both treatments. All QTLs detected under dry conditions showed the allele of parent SEA 5. This study is important for genetic improvement not only to better understand the genetic inheritance of a trait as complex as drought tolerance, as well as to find molecular tools to be used for marker assisted selectionDoutoradoGenetica Vegetal e MelhoramentoDoutor em Genetica e Biologia Molecula

Genetic diversity of six populations of red hybrid tilapia, using microsatellites genetic markers

Objective. To determine and evaluate the genetic diversity of six populations of red hybrid tilapia, with the purpose to assess the potential benefit of a future breeding program conducted at the Research Center for Aquaculture (Ceniacua), Colombia. Material and methods. A total of 300 individuals, representing a wide genetic variability, were genotyped using a fluorescent microsatellite marker set of 5 gene-based SSRs in 6 different farms belonging to 4 States of Colombia. Results. The result showed that the mean number of alleles per locus per population was 8.367. The population 5 had the highest mean number of alleles with 9.6 alleles, followed by population 4 with 9.4 alleles, population 2 with 9.2, population 3 with 8.0, population 1 with 7.2 and population 6 with 6.8 alleles. The analysis of the distribution of genetic variation was (17.32%) among population, while among individuals within populations was (28.55%) and within individuals was high (54.12%). The standard diversity indices showed that population 4 was the more variable (mean He=0.837) followed by population 1 (mean He=0.728), population 3 (mean He=0.721), population 5 (mean He=0.705), population 2 (mean He=0.690), population 6 (mean He=0.586). Highly significant deviations from Hardy¿Weinberg, exhibited all of the populations, mostly due to deficits of heterozygotes. Genotype frequencies at loci UNH 106 of population 5 and loci UNH 172 of population 6 were Hardy-Weinberg equilibrium (HWE). Conclusions. The results of this study, contribute to the genetic breeding program of Tilapia, conduced by the Research Center for Aquaculture. The Fst distance showed that the samples are differentiated genetically and it is possible to use at the beginning of the genetic program. However, it is recommended to introduce others individuals to the crossbreeding program.Objetivo. Determinar y evaluar la diversidad genética de seis poblaciones de tilapia roja híbrida, con el propósito de evaluar el potencial beneficio de un futuro programa de mejoramiento adelantado en el Centro de Investigación para la Acuicultura (CENIACUA), Colombia. Materiales y métodos. Fueron genotipados un total de 300 individuos utilizando un grupo de 5 microsatélites fluorescentes. Las muestras se tomaron en 6 fincas diferentes en 4 departamentos de Colombia, representando una amplia variabilidad genética. Resultados. El número medio de alelos por locus por población fue de 8.367. La población 5 tuvo el número más alto de alelos por locus: 9.6, seguida de la población 4 con 9.4, población 2 con 9.2, población 3 con 8.0, población 1 con 7.2 y población 6 con 6,8 alelos. Los análisis de distribución de la variación genética fueron de (17.32%) entre las poblaciones mientras que dentro de las poblaciones fue de (28.55%), y entre los individuos fue de (54.12%). Los índices de diversidad estándar mostraron que la población 4 fue la más variable (media He=0.837) seguida de la población 1 (media He=0.728), población 3 (media He=0.721), población 5 (media He=0.705), población 2 (media He=0.690) y población 6 (media He=0.586). Todas las poblaciones mostraron desviaciones significativas de equilibrio de Hardy�Weinberg, debido principalmente a la falta de heterocigotos. Las frecuencias genotípicas de los locis UNH 106 de la población 5 y loci UNH 172 de la población 6 estuvieron en equilibrio de Hardy-Weinberg. Conclusiones. La distancia Fst evidenció que las muestras estan diferenciadas geneticamente y es posible usar esas poblaciones para el programa de mejorameinto genético, sin embargo, es recomendable introducir otros individuos