Genetic variation is the raw material of evolution. The sources of this variation within a population, and its maintenance within a species, have been mysterious since the birth of the field of evolutionary genetics. In this work, I study divergently adapted freshwater and marine populations of the threespine stickleback (Gasterosteus aculeatus) as an evolutionary model to track the origin of adaptive genetic variation and to describe the evolutionary processes maintaining variation across the genome. The stickleback is a small fish with a large geographic range encompassing the northern half of the Northern Hemisphere and composed of coastal marine habitats, freshwater lakes, and river systems. Populations of stickleback adapt rapidly to changes in habitat, and fossil evidence suggests that similar adaptive transitions have been ongoing in this lineage for at least ten million years. In this work, I develop a significant extension of restriction site-associated DNA sequencing (RAD-seq) to generate phased haplotype information to estimate gene tree topologies and divergence times at thousands of loci simultaneously. I find anciently derived clades of variation associated with marine and freshwater habitats in genomic regions involved in recent adaptive divergence; some divergence times extend to over ten million years ago. This history of adaptive divergence has had profound effects on genetic variation elsewhere in the genome: chromosomes harboring freshwater-adaptive variants retain anciently derived variation in linked genomic regions, while marine chromosomes have much more recent ancestry. I present a conceptual model of asymmetric selective and demographic processes to explain this result, which will form a nucleus for future research in this species. Lastly, by incorporating genome-wide recombination rates estimated from multiple genetic maps, I describe a recombination landscape that is favorable to the maintenance of marine-freshwater genomic divergence. Low recombination rates in key chromosomal regions condense widespread divergence of the physical genome, encompassing many megabases, into a small number of Mendelian loci. Combined, my results demonstrate the interconnectedness of evolutionary processes taking place on ecological and geological timescales. The genetic variation available for adaptive evolution today is a product of the long-term evolutionary history of a species.

Viral sequence data are increasingly being used to estimate evolutionary and epidemiological parameters to understand the dynamics of viral diseases. This thesis focuses on developing novel and improved computational methods for high-throughput analysis of large viral sequence datasets. I have developed a novel computational pipeline, Pipelign, to detect potentially unrelated sequences from groups of viral sequences during sequence alignment. Pipelign detected a large number of unrelated and mis-annotated sequences from several viral sequence datasets collected from GenBank. I subsequently developed ANVIL, a machine learning-based recombination detection and subtyping framework for pathogen sequences. ANVIL's performance was benchmarked using two large HIV datasets collected from the Los Alamos HIV Sequence Database and the UK HIV Drug Resistance Database, as well as on simulated data. Finally, I present a computational pipeline named Phlow, for rapid phylodynamic inference of heterochronous pathogen sequence data. Phlow is implemented with specialised and published analysis tools to infer important phylodynamic parameters from large datasets. Phlow was run with three empirical viral datasets and their outputs were compared with published results. These results show that Phlow is suitable for high-throughput exploratory phylodynamic analysis of large viral datasets. When combined, these three novel computational tools offer a comprehensive system for large scale viral sequence analysis addressing three important aspects: 1) establishing accurate evolutionary history, 2) recombination detection and subtyping, and 3) inferring phylodynamic history from heterochronous sequence datasets.

Made available in DSpace on 2016-03-07T19:20:17Z (GMT). No. of bitstreams: 0 Previous issue date: 2015-07-31. Added 1 bitstream(s) on 2016-03-07T19:23:57Z : No. of bitstreams: 1 000858103.pdf: 6986071 bytes, checksum: 61cc82fb4f22cd71ec70c868dc8f37e5 (MD5) / Objetivou-se com este estudo realizar associação genômica ampla, visando detectar regiões cromossômicas associadas a características indicadoras de precocidade sexual de bovinos da raça Nelore, bem como avaliar metodologias para a predição de valores genômicos visando à seleção destas características. Foram utilizados dados de animais da raça Nelore, pertencentes a fazendas que integram os programas de melhoramento genético da DeltaGen® e Paint® (CRV Lagoa). As características associadas à precocidade sexual utilizadas neste estudo foram a idade ao primeiro parto (IPP), a ocorrência de prenhez precoce de novilhas (P16) e o perímetro escrotal (PE). Após o controle de qualidade e consistência dos dados fenotípicos, permaneceram para as análises informações de 68.170, 72.675 e 83.911 animais com fenótipo e de 1.738, 1.770 e 1.680 animais genotipados para IPP, P16 e PE, respectivamente, e 412.993 SNPs. No Capítulo 2, as estimativas dos efeitos dos SNPs foram obtidas utilizando-se a metodologia single-step (WssGBLUP). Todos os animais foram utilizados aplicando-se modelo animal unicaracterística para predizer os valores genéticos e, posteriormente, as soluções dos efeitos dos SNPs foram obtidas a partir destes valores genéticos. Foram identificadas as 10 janelas de 150 SNPs que capturaram a maior proporção da variância explicada pelos marcadores. As 10 janelas de maior efeito obtidas para a P16 estão localizadas nos cromossomos 5, 6, 7, 14, 18, 21 e 27 e somadas explicaram 7,91% da variância genética total. Para o PE, estas janelas estão nos cromossomos 4, 8, 11, 13, 14, 19, 22 e 23, explicando 6,78% da variância total. Com as análises de GWAS foi possível identificar regiões cromossômicas associadas com P16 e PE. A identificação dessas regiões possibilita o melhor entendimento e avaliação destas características, além de indicar genes candidatos para estudos futuros de investigação de... / The objective of this study was to perform genome-wide association to detect chromosomal regions associated with indicator traits of sexual precocity of Nellore cattle, and evaluating methodologies for prediction of genomic values to use for selection of these traits. Data from Nellore animals belonging to farms integrating animal breeding programs of DeltaGen® and Paint® (CRV Lagoa), were used. Age at first calving (AFC), the occurrence of early pregnancy of heifers (EP) and scrotal circumference (SC) were used as traits associated with sexual precocity. After quality control and consistency of phenotypic data, information of 68,170; 72,675 and 83,911 animals with phenotype, and of 1,738; 1,770 and 1,680 genotypes for AFC, EP and SC, respectively, and 412,993 SNPs, remained for analysis. In chapter 2, the estimates of the SNP effects were obtained using the single-step method (WssGBLUP). All animals were used applying single trait animal model to predict the genetic values and, subsequently, the solutions of the SNP effects were obtained from these genetic values. The 10 windows of 150 SNPs that captured the greatest proportion of variance explained by markers were identified. The 10 windows with greater effect obtained for EP are located on chromosomes 5, 6, 7, 14, 18, 21 and 27 and together explained 7.91% of the total genetic variance. For SC, these windows are on chromosomes 4, 8, 11, 13, 14, 19, 22 and 23, explaining 6.78% of the total variance. With GWAS analysis it was possible to identify chromosomal regions associated with EP and SC. Identifying these regions enables better understanding and evaluation of these traits, besides indicating candidate genes for future research studies of causal mutations. In Chapter 3, two multi-step methods were used to estimate the marker effects - GBLUP and IBLASSO; besides the single-step method (ssGBLUP). Observed phenotype was used as the dependent variable to estimate the genomic value ...

Made available in DSpace on 2016-03-07T19:20:44Z (GMT). No. of bitstreams: 0 Previous issue date: 2015-07-29. Added 1 bitstream(s) on 2016-03-07T19:24:25Z : No. of bitstreams: 1 000858097.pdf: 325868 bytes, checksum: b5d70c189e8328bfce207cd5135d7627 (MD5) / Para o capítulo 2 o objetivo do trabalho foram avaliar a qualidade das predições de mérito genético entre os métodos BLUP e GBLUP na presença de imprecisão nos dados. Para o capítulo 3 o objetivo do trabalho foi comparar os métodos BLUP, GBLUP e BAYESR considerando ou não a interação genótipoambiente em ovinos multirraciais. Os dados utilizados para a realização do capítulo 2 foram simulados com três níveis de imprecisão nos dados fenotípicos, 0%, 25% e 50% em três características com magnitude de herdabilidade de 0,02, 0,15 e 0,30, respectivamente, as metodologias BLUP e GBLUP foram aplicadas nesse dados e seus desempenhos foram comparados. Para a comparação das metodologias os parâmetros de erro quadrático médio, variância do erro de predição, viés, acurácia e eficiência de seleção foram utilizados. Melhores resultados foram obtidos pelo método BLUP em relação ao método GBLUP. O método GBLUP não apresentou vantagem em relação ao método BLUP, exceto quando a magnitude da herdabilidade foi de 0,02 e não houve imprecisão nos dados fenotípicos. Para o capítulo 3 foram utilizados 4.288 fenótipos e genótipos de dois rebanhos núcleos de informação (Information Nucleus Flock) oriundos do Australian Sheep Cooperative Research Center program (CRC). Para acessar a acurácia das estimativas, foi utilizada a validação cruzada. Os métodos BLUP, GBLUP e BAYESR, foram utilizados para estimar os valores genéticos sob dois modelos, univariado, o qual não considera a interação genótipo-ambiente e o modelo bivariado com o efeito da interação é considerado. As acurácias dos modelos univariados variaram de 0,17 à 0,27 para o ambiente 1 e de 0,19 à 0,20 para o ambiente 2. As acurácias dos modelos bivariados variam de 0,14 à 0,23 para o ambiente 1 e para o ambiente 2 as acurácias foram de 0,19. Não houve benefício da aplicação da seleção genômica sobre o método BLUP no ambiente 2 para... / In Chapter 2 the objective of the work was to evaluate the quality of the genetic merit of predictions between BLUP and GBLUP methods in the presence of uncertainty in the data. In chapter 3 the objective was to compare the BLUP methods, GBLUP and BAYESR considering whether or not to genotypeenvironment interaction in multi-racial sheep. The data used for the realization of Chapter 2 were simulated with three levels of inaccuracy in phenotypic data, 0%, 25% and 50% in three features with magnitude of heritability of 0.02, 0.15 and 0.30, respectively, the BLUP and GBLUP methodologies were applied this data and their performances were compared. To compare the methodologies the mean square error parameters, prediction error variance, bias, accuracy and selection efficiency were used. Better results were obtained by BLUP method over the GBLUP method. The GBLUP method showed no advantage over the BLUP method, except when the magnitude of heritability was 0.02 and there was no inaccuracy in phenotypic data. For chapter 3 we were used 4,288 phenotypes and genotypes dual-core herds of information (Information Nucleus Flock) coming from the Australian Sheep Cooperative Research Center program (CRC). To access the accuracy of the estimates, cross-validation was used. Methods BLUP, GBLUP and BAYESR, were used to estimate breeding values under two models, univariate, which does not consider the genotype-environment interaction and the bivariate model with the interaction effect is considered. The accuracies of the univariate models ranged from 0.17 to 0.27 for the environment 1 and 0.19 to 0.20 for the environment 2. The accuracies of bivariate models ranging from 0.14 to 0.23 for the environment 1 to the environment and the accuracies were 0.19. There was no benefit from the application of genomic selection on BLUP method in environment 2 for gastrointestinal resistance feature. On the other hand, for the application of 1 atmosphere genomic ...

Made available in DSpace on 2016-03-07T19:21:18Z (GMT). No. of bitstreams: 0 Previous issue date: 2015-08-21. Added 1 bitstream(s) on 2016-03-07T19:25:30Z : No. of bitstreams: 1 000858092.pdf: 1898150 bytes, checksum: e3ce9484168acf98f02ece6694eaec3c (MD5) / Painéis comerciais contendo milhares de SNPs a custo acessível revolucionaram os estudos genéticos na pecuária, principalmente por meio das análises de associação ampla e seleção genômica. A seleção genômica tem um aspecto prático, por ser diretamente aplicado aos programas de melhoramento, possibilitando aumento de acurácia das avaliações para as características quantitativas, como a produção de leite e seus constituintes. Como base nisso objetivou-se com esta tese verificar a distribuição das frequências dos polimorfismos e calcular o desequilíbrio de ligação (DL) dos segmentos cromossômicos no genoma de bovinos da raça Guzerá; estudar a associação dos marcadores com a produção de leite e seus constituintes; e comparar diferentes modelos para avaliação genômica com diferentes distribuições a priori para o efeito dos marcadores. Dessa forma, foi avaliado o DL entre marcadores de um painel de 50 k da Illumina® e estimado o tamanho efetivo populacional. Para isto foram utilizados 50 touros e 853 vacas Guzerá que também participaram dos estudos de associação e seleção genômica. A média de r2 foi de 0,16 para a distância 100 kb no genôma destes animais. A densidade do painel de 50 k foi considerada suficiente para proporcionar DL entre os segmentos cromossômicos para a predição de valores genéticos genômicos. Já as estimativas do tamanho efetivo populacional foram reduzidas com o decorrer das gerações, indicando aumento da intensidade de seleção para a raça ao longo das gerações. O baixo tamanho efetivo observado para as gerações recentes (137) indicaram a importância de se considerar a endogamia nas decisões de acasalamentos para manter a diversidade genética da raça. As avaliações genômicas foram realizadas pelos métodos GBLUP, BayesC, BayesCπ, Lasso e por meio de dois modelos multicaracterística para a produção de leite (PL), gordura (PG) e proteína (PP). As acurácias... / Commercial panels containing thousands of SNPs revolutionized genetic studies in livestock, especially with the genome-wide association study and genomic selection. The genomic selection is also directly applied to breeding programs enabling increasing on accuracy of the genetic evaluation for quantitative traits such as milk yield and its constituents. Thus, the aim of this thesis was to study the distribution of frequencies of polymorphisms and the linkage disequilibrium (LD) in the Guzerá cattle; was also to study the association of the markers with the dairy traits and to compare different models for genomic evaluation with different prior distributions for the effect of markers. The LD and the effective size were estimated using a 50 k Illumina® panel for 50 sires and 853 cows. For 100 kb the average of r2 was 0.16. The density of this 50 k panel was considered sufficient to provide LD between chromosomal segments for estimation of genomic breeding values. The effective size was reduced over the course of generations, indicating increase intensity of selection. The low estimate for effective size for recent generations indicated the importance of considering inbreeding for mating to maintain the genetic diversity of this breed. Genomic evaluations were performed by GBLUP, BayesC, BayesCπ, Lasso and two multi-trait models for milk yield (MY), fat (MF) and protein (MP). The accuracies for predictions ranged from 0.65 to 0.80. Bayesian prediction, GBLUP and multi-traits models were equivalent for predict the genomic breeding values. However, the best option was GBLUP considering overall fit, lower computational requirement and facility of convergence. The results indicated that genomic predictions were adequate to assist animal selection. In other study, the percentages of explained variance for each SNP were calculated. Windows, composed of seven adjacent SNPs deviated substantially from the other genomic regions were ...

Made available in DSpace on 2014-06-11T19:26:06Z (GMT). No. of bitstreams: 0 Previous issue date: 2012-03-13Bitstream added on 2014-06-13T20:33:37Z : No. of bitstreams: 1 bizari_dc_me_jabo.pdf: 336489 bytes, checksum: 0801c01531c7ce877e08321205d11d07 (MD5) / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / No presente estudo, cinco novos genes codificantes de proteínas foram selecionados para o mapeamento do cromossomo 6 bubalino (BBU6). Os novos genes (muc1, ppp1r7, psmd4, tshb e gtf2b) foram testados com a tecnologia de PCR resultando em produtos de PCR adequados ao mapeamento utilizando-se um painel de células somáticas híbridas irradiadas, denominado BBURH5000. Os resultados obtidos mostraram uma freqüência de retenção (FR) do produto de PCR de cada gene nas diferentes linhagens do painel com variação de 13,3% (gtf2b) a 26,6% (psmd4). A análise comparativa entre os mapas RH do BBU6 e a sequência do cromossomo 3 bovino permitiu indicar a localização dos novos genes no cromossomo 6 bubalino / In this study, five new protein coding genes were select for mapping buffalo chromosome 6. The new genes (muc1, ppp1r7, psmd4, tshb and gtf2b) were tested using PCR technology resulting in PCR products suitable for mapping using a radiation hybrid panel (BBURH5000). The retention frequency of the PCR products in each hybrid cell line of the panel showed the percentage from 13,3% (gtf2b) to 26,6% (psmd4). Comparative analysis between the buffalo chromosome 6 RH map and the sequence from bovine chromosome 3 allowed to assign the location of the new genes on buffalo chromosome 6

Made available in DSpace on 2014-06-11T19:35:11Z (GMT). No. of bitstreams: 0 Previous issue date: 2013-02-01Bitstream added on 2014-06-13T18:46:30Z : No. of bitstreams: 1 matos_mc_dr_jabo.pdf: 4821384 bytes, checksum: 0c887753a87a7ee387b394c1e0625fe2 (MD5) / Análises de associação genômica ampla (GWAS) para idade ao primeiro parto (IPP) e duração do período gestacional (PG) em bovinos da raça Nelore foram conduzidas utilizando painel de ~ 777.000 polimorfismos de nucleotídeo de sítio único (SNP). As análises de associação foram conduzidas em três grupos amostrais distintos com seus respectivos dados fenotípicos: 1) IPP em meses para 96 fêmeas, 2) valores genéticos preditos (EBVs) para IPP e PG para 831 touros, e 3) EBVs para IPP e PG para 1.278 fêmeas. Para cada conjunto de dados e para cada marcador, efeitos de substituição alélica foram estimados por meio do método dos quadrados mínimos ponderados e corrigidos para estratificação populacional. Os marcadores apresentando maiores efeitos estimados foram considerados como indicativos de evidência da associação da região cromossômica com o fenótipo investigado. Realizou-se a prospecção de genes candidatos nas regiões detectadas por diferentes metodologias (busca de SNP intragênicos, mapeamento de genes potencialmente em LD com SNP e construção de redes de termos funcionais, além de revisão manual para evidência em processo reprodutivo baseado em literatura científica). Grande número de regiões genômicas foram indicadas pelos efeitos de substituição alélica estimados, os quais apresentaram distribuição esperada para uma característica poligênica. Os resultados obtidos revelaram funções biológicas relacionadas a processos reprodutivos e sugeriram os genes PRKCD (protein kinase C delta type), PRKCE (protein kinase C epsilon type), ITHI-1 (inter-alpha-trypsin inhibitor heavy chain H1 precursor), ITHI-3 (inter-alphatrypsin inhibitor heavy chain H3), ITHI-4 (inter-alpha-trypsin inhibitor heavy chain H4 precursor), BT.62377 (sarcoplasmic/endoplasmic reticulum calcium... / Genome-wide scans for age at first calving (AFC) and gestation length (GL) in Nellore cattle were performed using a panel of over 777,000 single nucleotide polymorphisms (SNP). Association analyses were carried out in three distinct sample groups and their respective phenotypic data: 1) AFC, in months, for 96 cows, 2) AFC and GL estimated breeding values (EBVs) for 831 sires, and 3) AFC and GL EBVs for 1,278 cows. For each dataset and each marker, allele substitution effects were estimated via ordinary least squares and corrected for population stratification. Markers exhibiting high estimated effects were considered as indicative of evidence of association between the chromosomal region and phenotype investigated. Different methodologies were applied for the prospection of candidate genes within the detected regions (intragenic SNP mining, mapping of genes potentially in linkage disequilibrium with SNP, networking of functional terms, and manual review of genes previously found to be involved in reproductive processes). Large amounts of genomic regions were indicated by the estimated allele substitution effects, which presented a distribution consistent with a polygenic trait. The results obtained revealed biological functions related to reproductive processes and suggested PRKCD (protein kinase C delta type), PRKCE (protein kinase C epsilon type), ITHI-1 (inter-alpha-trypsin inhibitor heavy chain H1 precursor), ITHI-3 (interalpha- trypsin inhibitor heavy chain H3), ITHI-4 (inter-alpha-trypsin inhibitor heavy chain H4 precursor), BT.62377 (sarcoplasmic/endoplasmic reticulum calcium ATPase 3), EFCAB6 (uncharacterized gene), TPT1 (translationally-controlled tumor protein) and AMH (muellerian-inhibiting factor precursor), and ZBTB16 (zinc finger and BTB domain-containing protein 16) and PIK3R1 (Phosphatidylinositol 3-kinase... (Complete abstract click electronic access below)

Made available in DSpace on 2015-06-17T19:34:21Z (GMT). No. of bitstreams: 0 Previous issue date: 2015-02-27. Added 1 bitstream(s) on 2015-06-18T12:48:59Z : No. of bitstreams: 1 000834512.pdf: 473043 bytes, checksum: 44d24e6dcb2fb5220f4b7b5945c123fe (MD5) / CNVs (copy number variation - variação no número de cópias) são segmentos de DNA de tamanho igual ou maior a 1 Kb e estão presentes em número variável de cópias em comparação com um genoma referência e podem estar associadas com a expressão gênica e variâncias fenotípicas. Assim, esse trabalho teve como objetivo identificar regiões com variações no número de cópias nos segmentos de DNA em um total de 366 indivíduos de 5 raças bovinas autóctones de corte espanholas, distribuídos em 25 famílias formadas por pai-mãe-progênie, denominados trios. Os animais pertencentes às raças Asturiana de los Valles (75 indivíduos, 25 trios), Avileña-Negra Ibérica (74 indivíduos, 24 trios completos, um trio com pai repetido), Morucha (Mo, 75 indivíduos, 25 trios), Pirenaica (74 indivíduos, 24 trios completos, um trio com pai repetido) e Retinta (68 indivíduos, 18 trios completos, 7 trios com pais repetidos) foram genotipados com o painel Illumina BovineHD Beadchip de 777K A identificação das CNVs foi realizada por meio do modelo das cadeias ocultas de Markov implementado no software PennCNV. As regiões de CNV (copy number variation region - CNVR) foram determinadas pela sobreposição de agrupamentos das CNVs identificados em diferentes animais. Genes candidatos localizados nas CNVR encontradas foram investigados por meio de análises nas plataformas NCBI e Ensembl. Foram detectadas 8061 CNVs, sendo 2852 cópias e 5592 deleções e 1293 regiões, sendo 876 deleções e 314 cópias, cobrindo 3,6% do genoma autossômico bovino. Foram encontrados dentro dessas regiões 1.263 genes, com alguns deles fazendo parte de processos biológicos como crescimento e sistema imune. Encontrou-se um grande número de CNVs sendo compartilhadas entre as raças Asturiana de los Valles e Morucha, o que sugere proximidade entre essas raças durante seu... / Copy number variation (CNV) are DNA segments that are present at variable copy number compared to a reference genome. Classes of CNVs include insertions, deletions, duplications and inversions. CNVs can be associated with gene expression and phenotypic variation, providing genetic variability among individuals and, thus, are an important tool to production and healthy traits selection. The goal of this study was to identify regions with copy number variation in a total of 366 individuals from 5 autochthonous Spanish breeds of beef cattle, distributed into 25 families for breed, composed of sire-dam-offspring, called trios. The animals belonged to Asturiana de los Valles (75 individuals, 25 trios), Avileña-Negra Ibérica (74 individuals, 24 complete trios, one sire-repeated trio), Morucha (Mo, 75 individuals, 25 trios), Pirenaica (74 individuals, 24 24 complete trios, one sire-repeated trio) e Retinta (68 individuals, 18 complete trios, 7 sire-repeated trios) and were genotyped with the Illumina BovineHD Beadchip. The PennCNV software performed the CNVs identification. The CNV regions (CNVR) were determined by the overlapping of the CNVs. Candidates genes placed within the found CNVRs were investigated by analysis into the NCBI and Ensembl data platform. It has been detected a total of 8,061 CNV, which 2852 are gain and 5592 are loss of a DNA segment. A great amount of sharing CNVs between Asturiana de los Valles and Morucha breeds had been observed, which suggests a proximity during their formation process. We found also 1,293 regions of CNVs, spanning 3.6% of the autosomal bovine genome and 1,263 genes were present within these regions, and were involved in biological processes such as growth and immune system

Made available in DSpace on 2014-11-10T11:09:51Z (GMT). No. of bitstreams: 0 Previous issue date: 2014-02-27Bitstream added on 2014-11-10T11:57:53Z : No. of bitstreams: 1 000791427.pdf: 858212 bytes, checksum: 73468dc580b32c2569a024a91ace55d2 (MD5) / O objetivo do presente trabalho foi avaliar a acurácia de predição dos valores genéticos genômicos para características de diferentes herdabilidades, em populações simuladas de aves com diferentes níveis de endogamia. Os dados fenotípicos e genotípicos foram simulados com base na estrutura populacional de uma população experimental de aves poedeiras. Foram simulados os fenótipos e os genótipos de aves para características de taxa de postura total de ovos (PTO) e peso dos ovos as 32 semanas de idade (PO), com herdabilidades de 0,15 e 0,37 respectivamente. Foi simulada uma população histórica a fim de gerar desequilíbrio de ligação na população e esta deu origem as populações recentes em que foram simulados três cenários populacionais, visando maximizar (REC1), minimizar (REC2) e aleatorizar (REC3) os acasalamentos endogâmicos. Ao longo de 10 gerações recentes, os animais foram selecionados com base nos maiores valores genéticos preditos (VGP), utilizando o BLUP (best linear unbiased prediction) tradicional. O genoma das aves foi simulado ao longo dos 958 Mb do genoma Gallus gallus 4.0 com 3.747 QTL (loci de caracteres quantitativos) aleatoriamente distribuídos e 49.978 marcadores SNP uniformemente distribuídos. A fim de alterar as frequências alélicas e gerar variabilidade genética ao longo das gerações, foram simulados eventos de deriva genética, taxa de recombinação e mutação recorrente. Para avaliar os efeitos da endogamia nas populações recentes, foram calculados os desequilíbrios de ligação (DL), o tamanho efetivo da população (Ne) e as tendências genéticas em todos os cenários de populações recentes em ambas as características simuladas. Para predizer os valores genéticos genômicos preditos (VGGP), as populações recentes foram subdivididas em populações de treinamento e validação. Nas subpopulações de treinamento, os 960 animais ... / The objective of this study was to evaluate the prediction accuracy of genomic breeding values for traits of different heritability in simulated populations with different inbreeding. Phenotypic and genotypic data were simulated based on the population structure of an experimental population of White Leghorn hens at Embrapa Suínos e Aves. The phenotypes and genotypes were simulated for the rate of total egg production (PTO) and egg weight to 32 weeks of age (PO) with heritability of 0.15 and 0.37, respectively. The historical population was simulated to generate linkage disequilibrium in the population. Three scenarios in recent populations were simulated for each trait: REC1, REC2 and REC3 to maximize inbreeding, minimize inbreeding and random mating, respectively. The animals were selected based on the largest breeding values along 10 generations. The genome of the birds was simulated with eight macro-chromosomes and 19 micro-chromosomes with 3.747 QTL randomly distributed and 49.978 SNPs markers evenly spaced along the 958 cM. Recombination, random drift and recurrent mutation were simulated in order to generate genetic variability. The linkage disequilibrium (LD), effective population (Ne) and genetic trends were calculated for all scenarios. Each recent population was divided in training and validation sets In order to predict the genomic breeding values. The training set included the genotypes and phenotypes of 960 animals, which had higher breeding values’ accuracy. The validation set had 1120 animals of the last generation of the recent population. The average inbreeding ranged from 0.06 ± 0.30 to 0.22 ± 0.12 for PTO and 0.05 ± 0.03 to 0.20 ± 0.12 for PO. The REC1 populations had higher inbreeding along generations compared, both for PTO and PO, compared to REC2 and REC 3, and consequently higher level of LD. The highest accuracy for PTO and PO were ...

Made available in DSpace on 2014-11-10T11:09:51Z (GMT). No. of bitstreams: 0 Previous issue date: 2014-02-19Bitstream added on 2014-11-10T11:57:52Z : No. of bitstreams: 1 000791334.pdf: 1246832 bytes, checksum: a218fc15109d0f914149e0a8bee3fbf4 (MD5) / Painéis de marcadores genéticos de alta densidade (HD) possuem forte desequilíbrio de ligação, que permite melhores predições de valores genômicos. Entretanto, genotipar animais com estes painéis apresenta custo elevado, tornando-se uma limitação para a genotipagem de todos os candidatos à seleção. Uma alternativa para a redução desses custos é utilizar imputação de genótipos. A imputação é um método em que marcadores de uma população genotipada com painéis de baixa densidade (LD) são inferidos utilizando informações provenientes de uma população referência genotipada com painéis HD. O objetivo deste trabalho foi comparar em diferentes cenários metodologias de imputação de marcadores moleculares de polimorfismos de nucleotídeos únicos (SNP) em bovinos de corte da raça Canchim. Foram utilizadas informações de 285 animais da raça Canchim, 114 do grupo genético “MA” e 1 touro da raça Charolês genotipados com painel Illumina BovineHD BeadChip (786.799 SNP), nascidos entre 1999 e 2005 e provenientes da base de dados genômicos da Embrapa Pecuária Sudeste, São Carlos, SP. A edição dos dados foi realizada no software R e em linguagem C++. Para a frequência mínima de alelos (MAF) foram aplicados 3 diferentes critérios: sem remover MAF (QC1); SNP com MAF menor que 0,0025 (QC2) e menor que 0,10 (QC3) foram excluídos. O painel HD original foi reduzido para painéis de baixa densidade (LD) 3K, 6K, 9K, 50K, 20K, 80K e 90K, selecionando os marcadores em comum entre o painel HD original e os painéis comerciais Illumina Bovine3K (3K), BovineLD (6K), GeneSeek Genomic Profiler (GGP) Beef LD (9K), BovineSNP50 (50K), GGP Indicus LD (20K) ,GGP Beef HD (80K) e GGP Indicus HD (90K). Os animais foram divididos em diferentes cenários, denominados de população referência e imputação, sendo o cenário 1 (C1): População referência formada por animais nascidos ... / High-density panels (HD) have strong level linkage disequilibrium among genetic markers (i.e. single nucleotide polymorphism - SNP), which allows better predictions of genomic breeding values. However, HD genotyping still expensive and became a limitation for the quantity of candidate animals used in genomic studies. As an alternative to decrease costs, imputation methods are powerful tools to infer missing marker genotypes from low-density (LD) panels to HD. Imputation uses information from a reference population of animals genotyped with a HD panel to impute variants that are not directly genotyped in LD panels. The objective of this study was to compare different scenarios and methodologies of imputation for the Canchim cattle. Data set was provided by Embrapa Pecuária Sudeste and comprised 285 Canchim animals, 114 MA genetic group animals, and 1 ancestor Charolais bull. Animals born between 1999 and 2005 were genotyped with the Illumina BovineHD panel (786,799 SNP). Data editing was performed in the R software and in C ++ language. Multiple scenarios combining different minor allele frequencies (MAF) thresholds for SNPs were tested: no MAF filter (QC1), and exclusion of SNPs with MAF lower than 0.0025 (QC2) and MAF lower than 0.10 (QC3). LD panels were created by masking SNPs originally present in the HD panel, and then assigning markers into the Illumina Bovine3K (3K), Illumina BovineLD (6K), Beef LD GeneSeek Genomic Profiler (9K), Indicus LD GeneSeek Genomic Profiler (20K), Illumina BovineSNP50 (50K), GeneSeek Genomic Profiler Beef HD (80K) and GeneSeek Genomic Profiler Indicus HD (90K) panels. Reference and target populations were defined as scenario 1 (C1), reference animals were born up until 2004 and target animals were born in 2005; scenario 2A (C2A), reference animals from Canchim breed and target animals from MA genetic group; scenario 2B (C2B), reference animals from MA genetic ...