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 desequilibrium study in Phaseolus vulgaris L. to perform associative mapping of biotic and abiotic traits

Orientador: Luciana Lasry Benchimol ReisTese (doutorado) - Universidade Estadual de Campinas, Instituto de BiologiaResumo: O resumo poderá ser visualizado no texto completo da tese digitalAbstract: The abstract is available with the full electronic documentDoutoradoGenetica Vegetal e MelhoramentoDoutora em Genética e Biologia Molecula

Genetic diversity in cultivated carioca common beans based on molecular marker analysis

A wide array of molecular markers has been used to investigate the genetic diversity among common bean species. However, the best combination of markers for studying such diversity among common bean cultivars has yet to be determined. Few reports have examined the genetic diversity of the carioca bean, commercially one of the most important common beans in Brazil. In this study, we examined the usefulness of two molecular marker systems (simple sequence repeats – SSRs and amplified fragment length polymorphisms – AFLPs) for assessing the genetic diversity of carioca beans. The amount of information provided by Roger’s modified genetic distance was used to analyze SSR data and Jaccards similarity coefficient was used for AFLP data. Seventy SSRs were polymorphic and 20 AFLP primer combinations produced 635 polymorphic bands. Molecular analysis showed that carioca genotypes were quite diverse. AFLPs revealed greater genetic differentiation and variation within the carioca genotypes (Gst = 98% and Fst = 0.83, respectively) than SSRs and provided better resolution for clustering the carioca genotypes. SSRs and AFLPs were both suitable for assessing the genetic diversity of Brazilian carioca genotypes since the number of markers used in each system provided a low coefficient of variation. However, fingerprint profiles were generated faster with AFLPs, making them a better choice for assessing genetic diversity in the carioca germplasm

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

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.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.1087109

Genome-Wide Association Studies of Anthracnose and Angular Leaf Spot Resistance in Common Bean (Phaseolus vulgaris L.).

The common bean (Phaseolus vulgaris L.) is the world's most important legume for human consumption. Anthracnose (ANT; Colletotrichum lindemuthianum) and angular leaf spot (ALS; Pseudocercospora griseola) are complex diseases that cause major yield losses in common bean. Depending on the cultivar and environmental conditions, anthracnose and angular leaf spot infections can reduce crop yield drastically. This study aimed to estimate linkage disequilibrium levels and identify quantitative resistance loci (QRL) controlling resistance to both ANT and ALS diseases of 180 accessions of common bean using genome-wide association analysis. A randomized complete block design with four replicates was performed for the ANT and ALS experiments, with four plants per genotype in each replicate. Association mapping analyses were performed for ANT and ALS using a mixed linear model approach implemented in TASSEL. A total of 17 and 11 significant statistically associations involving SSRs were detected for ANT and ALS resistance loci, respectively. Using SNPs, 21 and 17 significant statistically associations were obtained for ANT and angular ALS, respectively, providing more associations with this marker. The SSR-IAC167 and PvM95 markers, both located on chromosome Pv03, and the SNP scaffold00021_89379, were associated with both diseases. The other markers were distributed across the entire common bean genome, with chromosomes Pv03 and Pv08 showing the greatest number of loci associated with ANT resistance. The chromosome Pv04 was the most saturated one, with six markers associated with ALS resistance. The telomeric region of this chromosome showed four markers located between approximately 2.5 Mb and 4.4 Mb. Our results demonstrate the great potential of genome-wide association studies to identify QRLs related to ANT and ALS in common bean. The results indicate a quantitative and complex inheritance pattern for both diseases in common bean. Our findings will contribute to more effective screening of elite germplasm to find resistance alleles for marker-assisted selection in breeding programs

Developing A Common Bean Core Collection Suitable For Association Mapping Studies.

Because of the continuous introduction of germplasm from abroad, some collections have a high number of accessions, making it difficult to explore the genetic variability present in a germplasm bank for conservation and breeding purposes. Therefore, the aim of this study was to quantify and analyze the structure of genetic variability among 500 common bean accessions to construct a core collection. A total of 58 SSRs were used for this purpose. The polymorphism information content (PIC) in the 180 common bean accessions selected to compose the core collection ranged from 0.17 to 0.86, and the discriminatory power (DP) ranged from 0.21 to 0.90. The 500 accessions were clustered into 15 distinct groups and the 180 accessions into four distinct groups in the Structure analysis. According to analysis of molecular variance, the most divergent accessions comprised 97.2% of the observed genetic variability present within the base collection, confirming the efficiency of the selection criterion. The 180 selected accessions will be used for association mapping in future studies and could be potentially used by breeders to direct new crosses and generate elite cultivars that meet current and future global market needs.3867-7

Associations between SSR and SNP marker loci and Anthracnose (race 4) severity determined by unified mixed linear models (MLM).

<p>Associations between SSR and SNP marker loci and Anthracnose (race 4) severity determined by unified mixed linear models (MLM).</p