Caracterização de recursos genômicos do feijoeiro comum (Phaseolus vulgaris L.) para o desenvolvimento de SSRs e SNPs úteis ao estudo genético e melhoramento da cultura

• Ano de defesa: 2013
• Autor(a) principal: Faria, Bárbara Müller Salomão de
• Orientador(a): Barros, Everaldo Gonçalves de
• Banca de defesa: Novaes, Evandro , Souza, Thiago Lívio Pessoa Oliveira de
• Tipo de documento: Dissertação
• Tipo de acesso: Acesso aberto
• Idioma: por
• Instituição de defesa: Universidade Federal de Viçosa
• Programa de Pós-Graduação: Mestrado em Genética e Melhoramento
• Departamento: Genética animal; Genética molecular e de microrganismos; Genética quantitativa; Genética vegetal; Me
• País: BR
• Palavras-chave em Português: Leguminosas; Genoma; Marcadores moleculares; BAC-end sequences; Diversidade genética; Estrutura populacional
• Palavras-chave em Inglês: Legumes; Genome; Molecular markers; BAC-end sequences; Genetic diversity; Population structure
• Área do conhecimento CNPq: CNPQ::CIENCIAS AGRARIAS::AGRONOMIA::FITOTECNIA::MELHORAMENTO VEGETAL
• Link de acesso: http://locus.ufv.br/handle/123456789/4791

The present work reports results from the research developed at the "International consortium for the sequencing of the genome and transcriptome of the common bean (Phaseolus vulgaris)" (Prosul/CNPq and CYTED) project conducted at Embrapa Rice and Beans (CNPAF) and the Federal University of Viçosa (UFV), which is composed of two distinct subprojects: Sequencing and characterization of the BACs-ends and Identification and development of SNPs markers in common bean . The dissert were structured in two chapters, each derived from their respective subprojects, containing the objectives and the main results presented below: Chapter 1- With the intention of amplifying and deepening the understanding about the P. vulgaris genome structure and composition, the goal of this study was to generate BAC-end sequences (BESs) from one BAC (Bacterial Artificial Chromosome) library and analyze the sequences for the presence of SSRs and genomic annotation. In total, 52,270 BESs were generated and processed equaling 32 Mbp (6.5%) of the P. vulgaris genome, with 39% of GC content. A total of 3,789 BES-SSRs were found, one for every 8.36 kb. Of these, 2,000 SSRs were appropriated for the development of molecular markers, of these 194 were evaluated and 40 were characterized for genetic and operational aspects. Of the 52,270 BESs, approximately, 2% contained sequences that encode transcription factors and 3% contained transposable elements. Through the comparison with the NCBI non-redundant protein database, it was possible to identify putative functions for 24,321 BESs, accounting for 46.53% of the total sequences analyzed. According to Gene Ontology (GO) terms functional categories were assigned to 19,363 BESs involved in biological process (52%), molecular function (65%) and cellular component (22%). This study allowed us to successfully identify BES-SSRs, highly polymorphic, searching for SSRs motifs of tri- to hexanucleotides, adding appropriate genetic features and with the potential to be used in the common bean genetic breeding programs. Additionally, the generated and processed BESs were integrated into the international project of common bean genome sequencing assisting in the composition and assembly of the genome. Chapter 2- The objectives of this study were to evaluate and compare the informativeness of 58 SSRs (24 SSRs-di dinucleotide microsatellites and 34 BES-SSRs tri- to hexanucleotide microsatellites) and 345 SNPs, as suited tools to P. vulgaris breeding programs. A germplasm set of 88 genotypes compounded of 55 breeding material and 33 landraces was evaluated, including eight biparental combinations derived from inter and intra-gene pool crosses. The SSRs-di displayed higher average of alleles/locus (9.916) and gene diversity (72.1%), exhibiting a superior capacity to distinguish the whole group of genotypes. Fourteen SSRs, out of the 58, with a considerable number of private alleles (over 14.93/locus) and high levels of gene diversity (84%), discriminated all 88 genotypes. The polymorphic SNPs, among inter (78.2%) and intra-gene pool (17.7%) combinations, were evaluated concerning their employment in genetic mapping. The approaches utilized to infer the genetic population structure presented correspondent results among all classes of markers, differentiating the genotypes within Andean and Mesoamerican gene pools. The SNPs, however, evidenced a superior (K = 2, FST = 0.895) competence to differentiate between the two gene pools. Furthermore, the SSRs-di distinguished, within Mesoamerican gene pool, the breeding material and the landraces germplasm (K = 3). Despite the high levels of linkage disequilibrium for both SSRs and SNPs, the latter yielded higher levels (84.92%). The linkage disequilibrium levels dropped when Andean and Mesoamerican genotypes were analyzed separately. The SSRs and SNPs distribution in P. vulgaris genome was abundant and random. Concerning the breeding program, SSRs and SNPs genotyping panels are now available, allowing the germplasm origin to be disclosed. In addition, a group of polymorphic SNPs, between several biparental populations, presents itself as an extension of such technology in the development of high-density genetic maps, with a substantial marker overlapping through crosses. This study contributes for the integration of genomic tools within breeding programs, connecting feasible and low cost techniques with efficient/wide genome sampling of the common bean.