Mestrado em Genética e Melhoramento de Plantas (EA)
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Navegando Mestrado em Genética e Melhoramento de Plantas (EA) por Por Orientador "Soares, Thannya Nascimento"
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Item Variabilidade genética quantitativa e molecular em uma coleção de germoplasma de Eugenia dysenterica DC. (Myrtaceae)(Universidade Federal de Goiás, 2012-03-15) Almeida Júnior, Edivaldo Barbosa de; Chaves, Lázaro José; Soares, Thannya Nascimento; http://lattes.cnpq.br/5590256762396056; Soares, Thannya Nascimento; Chaves, Lázaro José; Vasconcellos, Breno de Faria e; Coelho, Alexandre Siqueira GuedesThe cagaiteira (Eugenia dysenterica DC)., is a native species of Cerrado. The plant is known for fruit production, which are used in natura or processed in several ways. It also provides food for the local fauna and, therefore, it conservation is important for maintenance for the communities. In order to maintain the productivity potential of the species, we should invest on plant breeding programs. To support these programs and help the species conservation, it is important to characterize the genetic variability available to breeders, both in germplasm collections and natural populations. This could also help to recommend priority areas to collect and conserve the germplasm. Neutral molecular markers have been used to evaluate the distribution of genetic variability in natural populations. The genetic structure of populations is the result of historical interaction between genetic drift, mutation, and gene flow. To detect the influence of adaptive processes in the genetic differentiation of populations we used 𝑄𝑆𝑇 index. The comparison of 𝑄𝑆𝑇 to the 𝐹𝑆𝑇, for neutral loci, provides values to test hypotheses about the role of natural selection. Therefore, the aim of this study was to characterize the germplasm collection of the cagaiteira from the EA/UFG. We used quantitative traits and microsatellite markers to make inferences about the role of natural selection in the differentiation of the cagaiteira subpopulations of Goiás, Southeast Brazil. Data collected from the quantitative traits were: plant height (AB), height of the first bifurcation (AB), the stem circumference (CC) and mean diameter of the crown projection (DC), leaf length (CL), leaf width (LL), leaf format (FF) and footstalk length (CP). Molecular data were obtained by amplification of eight microsatellite loci. We estimated the following quantitative genetic parameters: heritability and genetic variation coefficient, and the molecular parameters: gene diversity and allelic richness. We compared the probability distributions of the genetic structure parameters for both, quantitative and molecular data (𝑄𝑆𝑇 vs. 𝐹𝑆𝑇). From the quantitative genetic parameters we found modest responses to selection for the traits: AP, CC and DC; and significant responses for CL, LL, FF and CP. It was observed that the samples collected in natural populations are well represented in the germplasm collection, supported by molecular gene diversity. The traits AP, DC and DC are under convergent natural selection, and the traits CL, LL, FF and CP are under divergent natural selection into the cagaiteira subpopulations of Southeast Goiás.Item Análise comparativa de sequências completas de genomas de cloroplasto de Pterodon emarginatus e Pterodon pubescens (Leguminosae)(Universidade Federal de Goiás, 2021-03-11) Freitas, Juliana Borges Pereira Brito; Taquary, Adriana Maria Antunes; http://lattes.cnpq.br/8869318023800691; Soares, Thannya Nascimento; http://lattes.cnpq.br/5590256762396056; Soares, Thannya Nascimento; Coelho, Alexandre Siqueira Guedes; Dias, Renata de OliveiraFREITAS, J. B. P. B. Comparative analysis of complete chloroplast genome sequences of Pterodon emarginatus and P. pubescens (Leguminosae). 2020. Dissertation (Master in Genetics and Plant Breeding) – School of Agronomy, Federal University of Goiás, Goiânia, 2020.¹ The chloroplast is a cellular organelle that has its own genome. Several projects of chloroplast genome sequencing have been developed with species of the legume group, family to which the species Pterodon emarginatus and P. pubescens belong. These two species of the genus Pterodon are native to the Cerrado biome, are popularly known as sucupira branca or faveira, and have potential for medicinal use and lumber. The present work aimed to know and compare the structure and organization of the chloroplastidial genomes of P. emarginatus and P. pubescens, in order to collaborate with the knowledge about the phylogenetic relationships between these species. Sequencing was performed using the Illumina MiSeq platform. The genomes were assembled using a de novo strategy associated with reference genome guided assembly. Annotation of genes and repetitive regions of the genomes was performed. In addition, nucleotide diversity was estimated and phylogenetic relationships of these species with other species of the Leguminosae family, whose chloroplastid genomes are available in databases, were analyzed. These diversity and phylogeny analyses were performed based on the gene sequences of the chloroplastidial genomes. The complete sequence of the chloroplastidial genome of P. emarginatus is 159,823 bp, while that of P. pubescens is 159,818 bp. Both genomes have a quadripartite structure, composed of two inverted regions (IR) with 25,584 bp in both species, separated by a short single copy region (SSC), with 19,359 bp and 19,367 bp, respectively, for P. pubescens and P. emarginatus and a long single copy region (LSC), with 89,291 bp in P. pubescens and 89,288 bp in P. emarginatus. A total of 127 genes were predicted in the chloroplast genome in both species, among which, 109 single copy genes and 18 duplicated genes in the inverted regions. A total of 143 microsatellite regions were identified in P. emarginatus and 141 in P. pubescens. The gene content was similar to that of other chloroplastidial genomes of legume species, with an emphasis on similarity with Dipteryx alata and Styphnolobium japonicum, with few exceptions of gene losses and gains. Nucleotide diversity estimates of gene regions were 0.062 in LSC, 0.076 in SSC, and 0.036 in IR. Phylogenetic analysis demonstrated the proximity between the genera Pterodon and Dipteryx, both from the clade Dipterygeae as well as the close relationship between the clades ADA and Cladrastis. The genetic information obtained on the chloroplastidial genomes of P. emarginatus and P. pubescens in this study reinforces the similarity and evolutionary proximity between these species. These results may contribute to other studies, such as molecular systematics and population genetics and phylogeography.Item Tamanho genômico e marcadores microssatélites para Pterodon pubescens e Pterodon emarginatus (Leguminosae)(Universidade Federal de Goiás, 2018-08-31) Melo, Priscila Zei; Novaes, Carolina Ribeiro Diniz Boaventura; http://lattes.cnpq.br/5640015140973531; Antunes, Adriana Maria; http://lattes.cnpq.br/8869318023800691; Soares, Thannya Nascimento; http://lattes.cnpq.br/5590256762396056; Soares, Thannya Nascimento; Telles, Mariana Pires de Campos; Rodrigues, Flávia MeloPterodonpubescensBenth (Leguminosae) is popularly known as sucupira-branca or faveiro, widely distributed in the Cerrado, widely used as a medicinal plant and in civil construction. Microsatellite markers are valuable tools for accessing the genetic variability of plants and their population genetic structure, due to characteristics such as the polymorphic nature, co- dominant inheritance and abundance in the genome.Thus, the objective of this work was to estimate the genomic size, to assemble the partial genome, to develop microsatellite markers for the P. pubescens species and to test the transferability of these markers to P. emarginatus. The size of the P. pubescensgenome obtained by floxo cytometry to verify how much of the genome was sequenced. The DNA of an individual of the P. pubescens species was sequenced according to the Nextera DNA (Illumina) protocol and the sequences assembled with the Dipspades software. The identification of perfect microsatellite regions and primer design were performed using the QDD software. Pairs of primers designed were tested for the amplification efficiency and identification of polymorphic locos in P. pubescens and P. emarginatusspecies. Pairs of primers were chosen to be fluorescently labeled for the evaluation of polymorphism and genetic variability of the locos, using 24 individuals of P. pubescens and 24 of P. emarginatus. The estimated haploid size of the genome of P. pubescens was 0,725 pg, which corresponds to 117 Mpb. Mounting the genome of P. pubescens resulted in a total of 711 Mb, so the assembled sequences represent 16,4% of the genome of the species. In these sequences 6,090 microsatellite regions were detected, with the number of tandem repeats ranging from 5 to 30 times. Thus, it was possible to design 17.546 pairs of primers for microsatellite regions. Of these, 30 primer pairs were synthesized for the amplification tests. Of the 30 pairs of primers tested in P.pubescens27 presented a good pattern of amplification product and 26 locos were polymorphic.In P.emarginatus 26 pairs of primers were successfully transferred and all locos were polymorphic. Thus it was possible to evaluate a population of P. pubescens and another of P. emarginatus with two systems of multipliex composed by 10 locos. The mean number of alleles per locus for P. pubescens and P. emarginatus was 7,1 and 7,7 respectively. The expected mean heterozygosity was 0,684 and 0,646, and the mean heterozygosity observed was 0,662 and 0,578, respectively for P. pubescens and P. emarginatus. There was a significant deviation of the HWE (p <0.05) locos Pem 21 and Pem 22 in P. pubescens and Pem 22 and Pem 26 and Pem 24.It was foundevidence of linkage imbalance in the locos (Pem 21 / Pem 22, Pem 15 / Pem 21, Pem 23 / Pem 22, Pem 21 / Pem23 and Pem 10/22) for P. pubescens, while in P. emarginatus in the locos (Pem 21 / Pem 22, Pem 21 / Pem23, Pem 15/21, Pem 23 / Pem 22, Pem 10 / Pem 22). The combined probability of identity of P. pubescens and P. emarginatus was (I) 7,9 x 10-10 and 1.4 x 10-6 respectively and paternity exclusion probability was 0,999 for the two species. The available microsatellite markers are a promising tool for future population genetic studies for the species, besides the possibility of being transferred to species of the same family.Item Diversidade e estrutura genética em populações naturais de Pterodon emarginatus Vogel (leguminosae)(Universidade Federal de Goiás, 2017-09-22) Pinto, Marcos Vinícius Pereira; Soares, Thannya Nascimento; http://lattes.cnpq.br/5590256762396056; Soares, Thannya Nascimento; Telles, Mariana Pires de Campos; Mansano, Vidal de FreitasGenetic diversity is a fundamental component for the survival of any species over evolutionary time, because it is the repertoire of possible responses to environmental pressures, which are dynamic and constant. Knowledge of the magnitude and structuring patterns of this diversity allows to understand how environmental and microevolutionary factors have interacted over time and shaped the populations. Microsatellite markers have been the most used molecular tool in recent decades for mapping studies of diversity and genetic structure due to its high degree of polymorphism, genomic abundance and codominant nature. For native species these markers rarely are available, however, the regions flanking the microsatellites are usually conserved among evolutionarily close species, which allows the transfer of these markers. Pterodon emarginatus Vogel, popularly known as Sucupira branca, is a tree plant belonging to the legume family. This species is widely used for medicinal purposes because of the broad properties of its secondary compounds. In addition, it provides rigid wood of interest for construction and is also used as an ornamental species. Despite the substantial number of studies directed to the medicinal potential, little is known about the genetic diversity present in this species. Therefore, the objectives of the work were to transfer to P. emarginatus microsatellite markers developed for Dipteryx alata and to access the diversity and genetic structure in natural populations of P. emarginatus. For this, the cross-amplification of 25 primers were tested and 12 natural populations were genotyped for 6 loci. Of the 25 primers tested, 2 (8%) showed good amplification and polymorphism pattern. The set of markers used revealed a total of 45 alleles for the 12 populations evaluated, with a mean of 7.667 per locus. This value ranged from 4 (DaE12) to 22 (PVESTBR067). Populations showed intermediate levels of genetic diversity (He = 0.555) and greater variability within populations than among populations. Small but significant levels of inbreeding were detected due to both the mating system and the population subdivision (f = 0.07; Fst = 0.073). These results support that the species presents a mixed mating system, being preferentially allogama. The pattern of divergence among populations was moderately structured in space (Mantel = 0.440, p <0.002) indicating a profile of large continuous populations with significant levels of gene flow over distances up to approximately 400 km.Item Diversidade e estrutura genética de Pterodon emarginatus vogel (leguminosae) no cerrado(Universidade Federal de Goiás, 2020-06-29) Sousa, Daniel Ferreira de; Soares, Thannya Nascimento; http://lattes.cnpq.br/5590256762396056; Soares, Thannya Nascimento; Chaves, Lázaro José; Rocha, Dulce Maria Sucena daPterodon emarginatus Vogel, popularly known as white sucupira, has characteristics that allow its exploitation as a timber, ornamental and medicinal resource. Knowing the genetic variability in natural populations of a plant genetic resource is important for defining strategies for its use and conservation. The present study had as objective to know the genetic diversity of natural populations of P. emarginatus in the Brazilian cerrado, for use and conservation purposes. 302 individuals were collected, from 13 Brazilian cerrado populations. These individuals were analyzed using 10 microsatellite markers. The detection of the genotypes was performed using the ABI-3500 genetic analyzer (Applied Biosystems). The quality of the loci was evaluated based on estimates of probability of identity and probability of exclusion of paternity, in the Identity4 program. The analyzes of diversity and genetic population structure were performed in the GDA programs and by the hierfstat package, in environment R. The cluster analysis was performed by the Bayesian method, using the STRUCUTRE program. The genetic divergence (pairwise FST) and the Mantel test were estimated, using the hierfstat and Vegan packages in environment R. The presence of genetic discontinuity was verified with the application of the Monmonier algorithm. The identification of priority populations for conservation was performed by the Greedy algorithm, in an R environment. The battery of loci proved to be adequate for the analysis of individual discrimination and for population genetic studies, since the probability of identity was low (PI = 2, 4109 x 10-11) and the exclusion of paternity was high (Q = 0.9999). An average of 15.9 alleles were identified per locus. The observed heterozygosity (0.521) was less than the expected heterozygosity (0.654). The populations exhibited a significant population genetic structure (θp = 0.104), with the presence of inbreeding due to the reproductive system (f = 0.207). The inbreeding of the population group was also high and significant (F = 0.290). Six groups were detected by Bayesian analysis. No relationship was detected between genetic and geographical distance. The populations of Araguaçu TO and Porangatu GO showed genetic discontinuity with four other populations. It was not possible to establish a minimum number of priority populations for conservation, as there is a need to conserve all of them (13) in order to sample all the alleles identified in the present study. This study reveals that the natural populations of P. emarginatus have high genetic diversity, but this diversity .is structured among populations and that there is inbreeding within populations due to the reproductive system. In addition, the genetic divergence is not explained by the geographical distance and the populations have a low redundancy of allelic richness. Such results imply the need for a greater sampling effort, both of individuals and populations, in works aimed at the conservation and use of the species.