Mestrado em Genética e Melhoramento de Plantas (EA)
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Item Avaliação da tecnologia Oxford Nanopore para análise de identidade genética de clones de cana-de-açúcar (Saccharum spp.)(Universidade Federal de Goiás, 2020-03-31) Borges, Sâmella de Souza; Bandeira, Ludmila Ferreira; http://lattes.cnpq.br/5329718658913234; Coelho, Alexandre Siqueira Guedes; http://lattes.cnpq.br/0840926305216925; Coelho, Alexandre Siqueira Guedes; Novaes, Evandro; Borba, Tereza Cristina de Oliveira; Taquary, Adriana Maria Antunes; Vianello, Rosana PereiraBrazil is currently the world's largest producer of sugarcane, which is the raw material for two important products for the Brazilian economy: sugar and ethanol. Aiming both to assess the Oxford Nanopore technology for genotyping applications for sequencing (Genotyping By Sequencing - GBS), with the differential to obtain a high sequencing coverage (> 1,000x), how to develop a GBS platform to to identify sugarcane clones, safely and conveniently, this work used the MinION platform to perform genotyping based on the sequencing of 48 individuals. For this, using the genome of Sorghum bicolor as reference and a set of libraries of sugarcane transcripts, 20 pairs of primers were designed, which were used to obtain amplicons, in which SNPs molecular markers were identified (Single Nucleotide Polymorphisms). Six sequencing libraries were built, the first two being used in pilot trials. The alignment of the sequences obtained in the reference genome was performed using the BWA program. The identification and genotyping of the SNPs was performed using the SAMtools software. The identification of the sugarcane clones was done by calculating the genetic distance between individuals. The cluster analysis was performed using a script written in software R. The sequencing resulted in approximately 841 thousand sequences. The average size of the amplicons was 1.6 kb. High sequencing coverage (average 10,498X / amplicon) was obtained. Nine amplicons were selected, in which 356 SNPs sites were identified. The percentage of mismatches between the obtained and the reference sequences varied from 8% to 20% and the percentage of indels remained homogeneous (~ 6%). The duplicates of the same individual used as biological control formed a knot with a consistency of 94% in the obtained dendrogram, however they did not present perfect genetic identity between them. It is suggested that this fact is mainly associated with the high rate of sequencing error of the Oxford Nanopore sequencing technology, evidencing the difficulty of its use in applications that require a genetic identification with a high degree of security, as occurs in problems involving clonal identification in sugar cane.Item Depressão endogâmica e variabilidade genética de populações para produção de milho verde(Universidade Federal de Goiás, 2020-03-30) Cascão, Luma Mariano; Resende, Marcela Pedroso Mendes; http://lattes.cnpq.br/2080097211870591; Melo, Patrícia Guimarães Santos; http://lattes.cnpq.br/1508679345970114; Melo, Patrícia Guimarães Santos; Resende, Marcela Pedroso Mendes; Vidotti, Mirian Suzane; Reis, Edésio Fialho dosThe production of vegetable corn is an activity of great importance for several regions of Brazil. Despite this, breeding programs have devoted little effort to developing and recommending cultivars specifically for this purpose. Then, it is essential that programs for the improvement of public institutions seek to serve this niche market, which has a relevant social role, as it is conducted mainly in small areas. This work aimed to estimate inbreeding depression and the genetic components of three populations for the production of vegetable corn. The populations evaluated have a different genetic basis: a variety of open pollination, called UFG-Samambaia (P1), a population obtained by crossing two older hybrids (P2) and a third population obtained by crossing of the modern hybrids (P3). Progenies of these three populations were obtained by sampling self-fertilized S0 plants. S1 progenies, three S0 populations and two checks were evaluated in a triple lattice 14 x 14 with plots of a four meter line. They were evaluated the agronomic traits: ears weight, plant height, ears height, relative position of the ear, breaking and lodging plants, days to anthesis, days to silking; and quality traits of ears: mass weight, ears weight without straw, length of ears without straw, ears diameter, ear alignment, ear stuffing, grain color. Statistical analyzes were performed using a mixed model approach. Inbreeding depression was estimated for all characters and the components of means (m + a ’and d) and variance. Genetic variability was observed for most traits among P1 progenies. The progenies of the P2 and P3 populations did not show genetic variability for most characters. The three populations suffered an impact when subjected to self-fertilization due to the effects of inbreeding. Inbreeding depression in P1 has higher rates for most characters: plant height, ear height, relative ear position, mass weight, length of ears without straw, alignment of ears and stuffing; In P2, the male flowering characters, weight of ears without straw and diameter of ears show a higher index and in P3, the characters of ear weight, female flowering, breakage and lodging and grain color. In general, the quality characters of the ear, important for the production of green corn, the greater depression due to inbreeding than the agronomic characters. This shows that, inbreeding depression must be considered in the selection process, with the frequency of favorable alleles increasing throughout the improvement process.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.Item Caracterização de microssatélites e desenvolvimento de marcadores SSR em khaya grandifoliola C. DC(Universidade Federal de Goiás, 2019-11-26) Sousa, Rodrigo Carlos Batista de; Soares, Thannya Nascimento; http://lattes.cnpq.br/5590256762396056; Novaes, Evandro; http://lattes.cnpq.br/0568272239145336; Novaes, Evandro; Coelho, Alexandre Siqueira Guedes; Soares, Thannya Nascimento; Guimaraes, Rejane AraujoAfrican mahogany (Khaya spp.) cultivation attracts increasing interest from producers, since their wood has similar characteristics to those of Brazilian mahogany with high commercial value in the European market. Despite its timber value throughout the world and its ecological importance in Africa, where it is classified as vulnerable to extinction, little is known about the species' levels of genetic diversity. Thus, this work aims to identify and characterize microsatellite regions in the transcriptome of Khaya grandifoliola, as well as to develop markers for studies of the genetic variability of the species. From the transcripts developed by Soares et al., (2019), microsatellite regions were identified and PCR primers were designed. Microsatellite sequences were classified according to the type and number of repetitions, as well as their location within transcripts. Using the microsatellite loci genetic parameters were estimated, such as the number of alleles per loci (K), expected and observed heterozygosity (He and Ho), intrapopulational fixation index (f), probability of exclusion of paternity and of identity (PE and PI). Within the African Mahogany transcripts, 37,925 microsatellite regions were detected, with 54% being mononucleotides, 29% dinucleotides and 15% trinucleotides. From 40 microsatellite loci, 12 were selected for labelling with fluorophores (6-FAM and HEX), forming two multiplex panels. The genotyping performed with the individuals identified an average of 3 alleles per locus. The expected (He = 0.53) and observed heterozygosity (Ho = 0.50) values used to estimate the genetic diversity in K. grandifoliola individuals were reasonable, given the low number of alleles per locus. The values found for PE (0.96) and PI (4.70x10-6) were similar to those found in studies of the same genus. Thus, these estimates indicate that the set of microsatellite markers is efficient in discriminating individuals. The SSR markers were also successfully transferred to other Khaya species. Therefore, these markers can be efficiently used in population studies with K. grandifoliola and other Khaya species.