Titre:	Decifrando a diversidade e estrutura genética de coleções de germoplasma de Zea Mays L. por meio da alelotipagem de SNPs
Auteur(s):	Alcântara, Bianca de Sousa
Orientador(es)::	Grattapaglia, Dario
Assunto::	Milho SNPs Alelotipagem Germoplasma Diversidade genética
Date de publication:	3-mar-2026
Data de defesa::	27-fév-2025
Référence bibliographique:	ALCÂNTARA, Bianca de Sousa. Decifrando a diversidade e estrutura genética de coleções de germoplasma de Zea Mays L. por meio da alelotipagem de SNPs. 2025. 147 f., il. Dissertação (Mestrado em Biologia Molecular) — Universidade de Brasília, Brasília, 2025.
Abstract:	The Brazilian Maize Germplasm Bank (Maize BAG) has over 4.000 accessions preserved in its base collection. This BAG also has the Brazilian Maize Core Collection, a representative sample of the base collection, and a collection of accessions classified as indigenous landraces and/or originating from indigenous lands. Although over 80% of the BAG accessions have been characterized according to morphological descriptors of the maize plant, to date, little is known about the genome-wide molecular diversity effectively preserved in these collections. Knowledge of the diversity, common ancestry and genetic structure of a germplasm collection at the molecular level is important information to validate and complement phenotypic and origin information in the design of conservation and use strategies for genetic resources and targeted improvement. One of the challenges of genomic analysis of germplasm collections composed of large numbers of genetically heterogeneous accessions (populations or non-inbred varieties) is how to deal with the genetic variation existing within the accessions. Genotyping several individuals per accession makes the effort time-consuming and expensive. Accession allelotyping, on the other hand, estimating the allele frequencies of a pooled sample of individuals of an accession, represents an elegant alternative for high-precision and low-cost genetic analysis. A set of 3.526 SNPs distributed in the maize genome, interrogated on the EMBRAPA 65kMultispecies chip, was used in this genetic study. To evaluate the accuracy of the method, three pool assembly treatments were evaluated for four different accessions, comparing the allele frequency estimates obtained by the normalized allele intensity ratio of the two alleles at the SNP in pools of 16 plants, in three replicates, with the estimate of the same plants genotyped individually. Three methods were tested: (1). Equimolar pool of individually extracted DNA and concentration measured by spectrophotometry in “Nanodrop” equipment; (2). Same as (1), but DNA measured by fluorimetry with “picogreen”; 3. DNA extraction from a consolidated sample (pool or bulk) of leaf tissues of the various plants, weighed to the nearest 0.1 gram. The allele frequencies estimated from the allelotyping of DNA prepared with method (3) of bulk leaf extraction, showed the lowest root mean square deviation (6.3%) and the highest correlation (0.984) with the allele frequencies estimated from individual plants. Using this method, DNA pools from 24 plants of each of the 293 accessions of the Brazilian Maize Core Collection and 188 accessions of the indigenous maize collection were allelotyped. A set of 64 biological replicates was also allelotyped for evaluation of reproducibility assessed by Wright's genetic differentiation estimate. Accurate estimates of allele frequencies were obtained with negligeable sampling error estimated by a mean 𝐹𝑆𝑇 among replicates of 0.0038. Genetic distance and structure analyses were performed for the 481 accessions together with data from the same allelotyped SNPs obtained from the literature for maize and Teosinte accessions conserved by the international center CIMMYT (Centro Internacional de Mejoramiento de Maíz y Trigo) representative of tropical, subtropical and temperate germplasm. The core and indigenous collections showed moderate genetic differentiation, with an average 𝐹𝑆𝑇 of 0.136 revealing a pattern of population structure in which accessions from the core collection overlapped with accessions of indigenous origin and CIMMYT germplasm. However, the indigenous collection showed greater genetic differentiation between accessions (𝐹𝑆𝑇 = 0.140) compared to the core collection (𝐹𝑆𝑇 = 0.109), which suggests the need to update the composition of the latter including more indigenous accessions and thus expand the genetic diversity represented in the available germplasm of the species. Clustering by k-means detected seven groups, that contained variable proportions of core and indigenous accessions. Patterns of genetic structure based on genetic distance, as defined by SNP data, were found to partially overlap with classifications of the germplasm accessions used in the establishment of the collections, such as maize grain types, domestication level and origin of the collected material. However, some important discrepancies were also detected where such classifications did not match what the DNA data showed. These results indicate that the unbiased genomic information derived from SNP data provides important additional and alternative information that more precisely reflects the ancestral origin of the germplasm accessions. We propose that the genomic data generated in this work be promptly integrated with the available passport data of the studied accessions to arrive at a more accurate representation of the maize germplasm conserved in the two collections.
metadata.dc.description.unidade:	Instituto de Ciências Biológicas (IB) Departamento de Biologia Celular (IB CEL)
Description:	Dissertação (mestrado)—Universidade de Brasília, Instituto de Ciências Biológicas, Departamento de Biologia Celular, Programa de Pós-Graduação em Biologia Molecular, 2025.
metadata.dc.description.ppg:	Programa de Pós-Graduação em Biologia Molecular
Licença::	A concessão da licença deste item refere-se ao termo de autorização impresso assinado pelo autor com as seguintes condições: Na qualidade de titular dos direitos de autor da publicação, autorizo a Universidade de Brasília e o IBICT a disponibilizar por meio dos sites www.unb.br, www.ibict.br, www.ndltd.org sem ressarcimento dos direitos autorais, de acordo com a Lei nº 9610/98, o texto integral da obra supracitada, conforme permissões assinaladas, para fins de leitura, impressão e/ou download, a título de divulgação da produção científica brasileira, a partir desta data.
Agência financiadora:	Conselho Nacional de Desenvolvimento Científico, Tecnológico (CNPq) e Fundação de Apoio à Pesquisa do Distrito Federal (FAP/DF).
Collection(s) :	Teses, dissertações e produtos pós-doutorado

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