Recent advances in next generation sequencing have provided unprecedented opportunities for high-throughput genomic research, inexpensively producing millions of genomic sequences in a single run. Analysis of massive volumes of data results in a more accurate picture of the genome complexity and requires adequate bioinformatics support. We explore computational challenges of applying next generation sequencing to particular applications, focusing on the problem of reconstructing viral quasispecies spectrum from pyrosequencing shotgun reads and problem of inferring informative single nucleotide polymorphisms (SNPs), statistically covering genetic variation of a genome region in genome-wide association studies. The genomic diversity of viral quasispecies is a subject of a great interest, particularly for chronic infections, since it can lead to resistance to existing therapies. High-throughput sequencing is a promising approach to characterizing viral diversity, but unfortunately standard assembly software cannot be used to simultaneously assemble and estimate the abundance of multiple closely related (but non-identical) quasispecies sequences. Here, we introduce a new Viral Spectrum Assembler (ViSpA) for inferring quasispecies spectrum and compare it with the state-of-the-art ShoRAH tool on both synthetic and real 454 pyrosequencing shotgun reads from HCV and HIV quasispecies. While ShoRAH has an advanced error correction algorithm, ViSpA is better at quasispecies assembling, producing more accurate reconstruction of a viral population. We also foresee ViSpA application to the analysis of high-throughput sequencing data from bacterial metagenomic samples and ecological samples of eukaryote populations. Due to the large data volume in genome-wide association studies, it is desirable to find a small subset of SNPs (tags) that covers the genetic variation of the entire set. We explore the trade-off between the number of tags used per non-tagged SNP and possible overfitting and propose an efficient 2LR-Tagging heuristic.

<p>Genetic variation is a natural occurrence in the genome that contributes to the phenotypic differences observed between individuals as well as the phenotypic outcomes of various diseases, including infectious disease and cancer. Single nucleotide polymorphisms (SNPs) have been identified as genetic factors influencing host susceptibility to infectious disease while the study of copy number variation (CNV) in various cancers has led to the identification of causal genetic factors influencing tumor formation and severity. In this work, we evaluated the association between genomic variation and disease phenotypes to identify SNPs contributing to host susceptibility in Staphylococcus aureus (<italic>S. aureus</italic>) infection and to characterize a nervous system brain tumor, known as oligodendroglioma (OD), using the CNV observed in tumors with varying degree of malignancy.</p><p>Using SNP data, we utilized a computational approach, known as in silico haplotype mapping (ISHM), to identify genomic regions significantly associated with susceptibility to <italic>S. aureus</italic> infection in inbred mouse strains. We conducted ISHM on four phenotypes collected from <italic>S. aureus</italic> infected mice and identified genes contained in the significant regions, which were considered to be potential candidate genes. Gene expression studies were then conducted on inbred mice considered to be resistant or susceptible to <italic>S. aureus</italic> infection to identify genes differentially expressed between the two groups, which provided biological validation of the genes identified in significant ISHM regions. Genes identified by both analyses were considered our top priority genes and known biological information about the genes was used to determine their function roles in susceptibility to <italic>S. aureus</italic> infection.</p><p> We then evaluated CNV in subtypes of ODs to characterize the tumors by their genomic aberrations. We conducted array-based comparative genomic hybridization (CGH) on 74 ODs to generate genomic profiles that were classified by tumor grade, providing insight about the genomic changes that typically occur in patients with OD ranging from the less to more severe tumor types. Additionally, smaller genomic intervals with substantial copy number differences between normal and OD DNA samples, known as minimal critical regions (MCRs), were identified among the tumors. The genomic regions with copy number changes were interrogated for genes and assessed for their biological roles in the tumors' phenotype and formation. This information was used to assess the validity of using genomic variation in these tumors to further classify these tumors in addition to standard classification techniques. </p><p> The studies described in this project demonstrate the utility of using genetic variation to study disease phenotypes and applying computational and experimental techniques to identify the underlying genetic factors contributing to disease pathogenesis. Moreover, the continued development of similar approaches could aid in the development of new diagnostic procedures as well as novel therapeutics for the generation of more personalized treatments. The genomic regions with copy number changes were interrogated for genes and assessed for their biological roles in the tumors' phenotype and formation. This information was used to assess the validity of using genomic variation in these tumors to further classify these tumors in addition to standard classification techniques.</p><p> The studies described in this project demonstrate the utility of using genetic variation to study disease phenotypes and applying computational and experimental techniques to identify the underlying genetic factors contributing to disease pathogenesis. Moreover, the continued development of similar approaches could aid in the development of new diagnostic procedures as well as novel therapeutics for the generation of more personalized treatments.</p> / Dissertation

Graves¡¦ disease (GD), an organ specific autoimmune disease, requires two signals to activate the T cells. In addition to the specific binding of T cell receptor to the antigenic peptide-MHC complex, an antigen-independent costimulatory pathway reportedly require generate subsequent cytokines and cell surface molecules. This regulation of T-cell response is a highly-organized multiple step program. T cell costimulatory signals is found to regulate the magnitude and duration of various type of autoimmune diseases. This study is to test whether genetic polymorphism of these costimulatory genes is related with the disease susceptibility or progression. We anticipated that the candidate genetic makers are beneficial for importing GD management. We recruited 262 GD patients from the Outpatient Department of Endocrine and 200 healthy controls from the Health Screening Center of Chang Gung Memorial Hospital in Kaohsiung.The GD patients were divided into three groups: recurred within 9 months (n=91), between 10-36 months (n=65), and more than 36 months (n=106). Clinical and laboratory attributes included: the genotypes of CTLA-4, CD28, ICOS, PD-1 and CD40; serum levels of T4, T3 and TSH; goiter size and TSH-receptor antibodies at the beginning and end of treatment. Genomic DNA was extracted from peripheral blood leucocytes by kit. The single nuclotide polymorphisms of the candidate genes were genotyped by polymerase chain reaction- restriction fragment length polymorphism and TaqMan® SNP Genotyping Assays with specific primers. Linkage disequilibuium between pairs of polymorphism was estimated by Haploview software. Haplotype analyses were performed using the Hap-Clustering program. Variance and correlation of data was statistically analyzed by Chi-square, general liner model, multiple logistic regression analysis and Kaplan-Meier plot. A p value <0.01 was considered significant. The results showed:(1) Genetic polymorphism within the costimulatory molecules affected the susceptibility and progression of GD; (2) GD patients carried more risk alleles than the controls; (3) Within the GD group, patients harboring more risk alleles wound relapse earlier after drug withdrawal; (4) Number of risk alleles, goiter size and TBII levels at end of treatment were independent predictors of disease relapse; (5) A risk score calculation based on odds ratio of risk alleles correlated with patients¡¦ relapse time after drug withdrawal. We concluded that patients¡¦ genetic makers of costimulatory molecules may be helpful in choosing appropriate treatment for GD.

The genus Chrysopsis (Asteraceae) contains eleven species native to Florida, including the newly described species, Chrysopsis delaneyi. Populations of this endemic plant species inhabit the Lake Wales Ridge (LWR) and the Atlantic Ridge (AR) of the Florida peninsula. Differences in morphology have been demonstrated within C. delaneyi, based on their locations. My objective was to determine the relationships between the LWR and the AR populations by analysis of chloroplast sequence and nuclear sequence variation. Approximately 160 samples of C. delaneyi and its sister species C. scabrella have been collected from fifteen sites throughout Florida. Six single base differences were detected, one insertion, and one variable short duplication. A total of four haplotypes (i.e.: groups that have different combinations of polymorphisms) have been found. For the most part, one haplotype is found in LWR populations and is indistinguishable from that found in C. scabrella. Another haplotype is found primarily in AR populations and is more similar to haplotypes found in the more distantly related C. highlandsensis and C. floridana. One haplotype is found within populations of C. scabrella. The last haplotype in one AR population contains two polymorphic loci, one site is representative of the AR populations, and the other site is that of the LWR populations. Only one mixed population has been found, at the northern end of the AR range. These results are not consistent with taxonomic relationships inferred from morphological characteristics; hence the results suggest that chloroplast DNA (cpDNA) relationships may be the consequence of one or more instances of chloroplast capture.

The objective - To identify Zemaitukai mtDNA D-loop region and genetic relationships between Zemaitukai and some other breeds based on mtDNA sequence variation. Methods - To perform a phylogenetic analysis of 10 Zemaitukai, mtDNA D-loop 49 horses in the 20 different horse breeds sequence were included from GenBank (http://www.ncbi.nlm.nih.gov/GenBank). DNA was extracted from hair roots using the DNEasy® Tissue Kit (Qiagen). 1,280 bp fragment of mtDNA D-loop were amplify out in PTC-100™ termocycler. Amplified products were sequenced on a LI-COR® 4200S-2 automated sequencer. Sequencher v 4.1.4. software package was used to generate the actual DNA sequence for each of the animals. Multiple alignments of sequences were performed with CLUSTAL X 1.8 (Thompson et al., 1997). The Neighbor-joining tree (Saitou and Nei, 1987) of mtDNA sequences was constructed from Jukes-Cantor distances, performed on the pairwise deletion using the MEGA software (Kumar et al., 1993). Results –Within Zemaitukai breed 19 polymorphic sites were detected and 6 haplotypes. At the individual level 4 zemaitukai haplotypes were private to one individuals, 1 haplotype-between 2 individuals and 1 haplotype was shared between 4 individuals. On the Neighbor-joining tree showed one Zemaitukai haplotype closer genetic relationships to the Icelandic and to the Norwegian Fiord horse haplotypes. Zemaitukai breed formed a separate branch with the ancient DNA haplotype. The phylogenetic analysis reflects the presence... [to full text]

Submitted by YURI TANI UTSUNOMIYA null (yuri.tani@yahoo.com.br) on 2018-01-08T12:45:05Z No. of bitstreams: 1 UTSUNOMIYA.pdf: 11784469 bytes, checksum: 9fc7d258b6e5e683b47b78ad25853acc (MD5) / Approved for entry into archive by Alexandra Maria Donadon Lusser Segali null (alexmar@fcav.unesp.br) on 2018-01-09T09:34:15Z (GMT) No. of bitstreams: 1 utsunomiya_yt_dr_jabo.pdf: 11784469 bytes, checksum: 9fc7d258b6e5e683b47b78ad25853acc (MD5) / Made available in DSpace on 2018-01-09T09:34:15Z (GMT). No. of bitstreams: 1 utsunomiya_yt_dr_jabo.pdf: 11784469 bytes, checksum: 9fc7d258b6e5e683b47b78ad25853acc (MD5) Previous issue date: 2017-12-06 / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / O gene 1 do adenoma pleomórfico (PLAG1) apresenta evidência de seleção positiva recente e associação com tamanho corporal e fertilidade em um grande número de raças bovinas ao redor do mundo. Tendo em vista sua recentemente descoberta função como fator de transcrição para o gene do fator de crescimento semelhante à insulina 2 (IGF2), o PLAG1 possui papel emergente como um dos principais reguladores do crescimento e da reprodução em bovinos. Apesar de sua importância, a variante de sequência de DNA responsável pelos efeitos pleiotrópicos atribuídos ao PLAG1 em bovinos permanece desconhecida. Também não está claro se a mesma mutação explica as associações fenótipo-genótipo encontradas em diferentes populações bovinas. Além disso, ainda é incerto onde e quando ocorreu a pressão de seleção responsável pelo aumento da frequência da mutação do PLAG1. No presente trabalho, reportamos o desenvolvimento de um pacote para o software estatístico R, o qual é direcionado à análise de haplótipos como preditores para variantes genéticas não observadas. Através da aplicação desta ferramenta a dados genômicos de bovinos oriundos de diversas regiões do mundo, encontramos evidência indicando que um único alelo derivado do PLAG1 aumentou em frequência rapidamente em bovinos Bos taurus do noroeste europeu entre os séculos XVI e XVIII. Este período é reconhecido como a última onda de aumento de estatura em bovinos por meio de registros arqueológicos. Os dados também sugerem que o alelo foi introgredido em B. taurus não europeu e raças Bos indicus entre os séculos XIX e XX, adquirindo uma distribuição quase global no último século. Análises de DNA antigo revelaram que esta mutação segrega em gado do noroeste europeu há pelo menos 1.000 anos. Em conjunto, estes resultados implicam um papel central da mutação do PLAG1 em recentes mudanças de tamanho corporal em bovinos. / The pleomorphic adenoma gene 1 (PLAG1) presents both evidence of recent positive selection and association with body size and fertility in a wide range of worldwide cattle breeds. Considering its recently uncovered function as a transcription factor for the insulin-like growth factor 2 gene (IGF2), PLAG1 is emerging as a major regulator of bovine growth and reproduction. In spite of its importance, the causal DNA sequence variant underlying the pleiotropic effects of PLAG1 in cattle remains unknown. It is also unclear whether the same mutation accounts for the phenotype-genotype associations detected across different cattle populations. Furthermore, when and where the selective pressure responsible for increasing the frequency of the PLAG1 mutation occurred is still uncertain. Here, we report the development of a package for the R statistical software to analyze haplotypes as surrogates for unobserved genetic variants. By applying this tool to genomic data of worldwide cattle breeds, we found evidence that a single bovine PLAG1 derived allele increased rapidly in frequency in Northwestern European Bos taurus populations between the 16th and 18th centuries. This period is recognized as the last wave of increase in bovine stature from archaeological data. The data also suggested that the allele was introgressed into non-European B. taurus and Bos indicus breeds towards the 19th and 20th centuries, achieving an almost global distribution in the last century. Ancient DNA analyses further revealed that this mutation has been segregating in Northwestern European cattle for at least 1,000 years. Altogether, these results implicate a major role of the PLAG1 mutation in recent changes in body size in cattle. / 2014/01095-8 / 2016/07531-0

Doctor of Philosophy / Department of Plant Pathology / Bikram S. Gill / H13, a dominant resistance gene transferred from Aegilops tauschii into wheat (Triticum aestivum), confers a high level of antibiosis against a wide range of Hessian fly (HF, Mayetiola destructor) biotypes. Previously, H13 was mapped to the distal arm of chromosome 6DS, where it is flanked by markers Xcfd132 and Xgdm36. A mapping population of 1,368 F2 individuals derived from the cross: PI372129 (h13h13) / PI562619 (Molly, H13H13) was genotyped and H13 was flanked by Xcfd132 at 0.4cM and by Xgdm36 at 1.8cM. Screening of BAC-based physical maps of chromosome 6D of Chinese Spring wheat and Ae. tauschii coupled with high resolution genetic and Radiation Hybrid mapping identified nine candidate genes co-segregating with H13. Candidate gene validation was done on an EMS-mutagenized TILLING population of 2,296 M₃ lines in Molly. Twenty seeds per line were screened for susceptibility to the H13-virulent HF GP biotype. Sequencing of candidate genes from twenty-eight independent susceptible mutants identified three nonsense, and 24 missense mutants for CNL-1 whereas only silent and intronic mutations were found in other candidate genes. 5’ and 3’ RACE was performed to identify gene structure and CDS of CNL-1 from Molly (H13H13) and Newton (h13h13). Increased transcript levels were observed for H13 gene during incompatible interactions at larval feeding stages of GP biotype. The predicted coding sequence of H13 gene is 3,192 bp consisting of two exons with 618 bp 5’UTR and 2,260 bp 3’UTR. It translates into a protein of 1063 amino acids with an N-terminal Coiled-Coil (CC), a central Nucleotide-Binding adapter shared by APAF-1, plant R and CED-4 (NB-ARC) and a C-terminal Leucine-Rich Repeat (LRR) domain. Conserved domain analysis revealed shared domains in Molly and Newton, except for differences in sequence, organization and number of LRR repeat in Newton. Also, the presence of a transposable element towards the C terminal of h13 was indicative of interallelic recombination, recent tandem duplications and gene conversions in the CNL rich region near H13 locus. Comparative analysis of candidate genes in the H13 region indicated that gene duplications in CNL encoding genes during divergence of wheat and barley led to clustering and diversity. This diversity among CNL genes may have a role in defining differences in the recognition specificities of NB-LRR encoding genes. Allele mining for the H13 gene in the core collection of Ae. tauschii and hexaploid wheat cultivars identified different functional haplotypes. Screening of these haplotypes using different HF biotypes would help in the identification of the new sources of resistance to control evolving biotypes of HF. Cloning of H13 will provide perfect markers to breeders for HF resistance breeding programs. It will also provide an opportunity to study R-Avr interactions in the hitherto unexplored field of insect-host interaction.

Statistical association tests of quantitative traits have been widely used in the past decade, to locate loci associated with a disease trait. For instance, Genome Wide Association Studies (GWAS) have led to tremendous success in finding susceptible genes or associated loci. However, most of the past studies were based on unrelated samples focusing on quantitative or qualitative traits. The analysis of polychotomous traits in family samples is very challenging. This dissertation describes three projects related to methods to conduct association tests beyond continuous traits, such as multinomial traits, bivariate traits, and tests involving haplotypes. The first project focuses on developing a statistical approach to test the association between common or low-frequency variants with a multinomial trait in family samples. It is an important issue because there is no computer efficient software available for this type of question. We employ Laplace approximation in conjunction with an efficient grid-search strategy to obtain an approximate maximum log-likelihood function and the Maximum Likelihood Estimate (MLE) of the variance component. We also successfully incorporate the kinship matrix to adjust for the familial correlation, based on a regression framework. Extensive simulation studies are performed to evaluate the type-I error rate and power in scenarios with causal variant with different Minor Allele Frequency (MAF). In the second project, we propose an approach to test the association between a genetic variant and a bivariate trait arising from a combination of a quantitative and a binary trait in family samples, based on Extended Generalized Estimating Equations (EGEE). Multiple phenotype-genotype association tests are often reduced to univariate tests, decreasing efficiency and power. Our approach is shown to be much more powerful and efficient than univariate association tests adjusted for multiple testing. The third project involves the development of a general framework for meta-analysis of haplotype association tests, applicable to both unrelated and family samples. Although meta-analysis has been widely used in single-variant and gene-based tests, there are few existing methods to meta-analyze haplotype association tests. A predominant advantage of our novel approach is that it accommodates cohort-specific haplotypes as well as haplotypes common to all cohorts. The cohort participants may be either related or unrelated. Our approach consists of two stages: in the first stage, each cohort performs a haplotype association test, reports the estimates of effect size, variance, haplotypes, and their frequency. In the second stage, a generalized least square method is applied to combine the results of all the cohorts into one vector of meta-analysis coefficients. Our approach is shown to have the correct type-I error rate in scenarios with different between and within cohort variation. We also present an application to exome-chip data from a large consortium. Through the three projects, we are able to tackle the problem of conducting association tests for non-continuous traits in family samples. All the approaches achieve the correct type-I error rate and are computationally efficient. We hope these approaches will not only facilitate analyses of categorical traits in family samples, but will also provide a basis for future methodological development of statistical approaches for non-continuous traits.

Introdução: Mucopolissacaridose IVA é uma doença lisossômica, autossômica recessiva, causada pela deficiência da enzima N-acetilgalactosamina-6-sulfatase. É uma doença rara e a incidência varia de 1:76.000 a 1:640.000 recém-nascidos vivos. Até o momento 319 diferentes mutações causadoras da doença já foram identificadas, o que demonstra a ampla variabilidade genética. Objetivo: Caracterizar o genótipo de pacientes com MPS IVA, analisar 6 polimorfismos intragênicos e identificar os haplótipos presentes em nossos pacientes, através do estudo molecular do gene GALNS. Métodos: O estudo foi realizado em 45 pacientes provenientes das regiões Nordeste, Sudeste, e Sul do Brasil, com diagnóstico bioquímico confirmado para MPS IVA. A análise molecular foi realizada através de PCR seguida de sequenciamento, pelo método de Sanger, a fim de identificar as mutações causadoras da doença. Para o estudo de haplótipos foram analisados 6 polimorfismos intragênicos através de PCR em Tempo Real, pelo método Taqman, em pacientes e controles. Resultados: A análise do gene GALNS, nos 45 pacientes, permitiu a identificação de 18 diferentes mutações, e a caracterização de 6 haplótipos distintos. Das 18 mutações encontradas, 5 apresentaram uma alta frequência (p.Ser341Arg, p.Arg386Cys, p.Gly301Cys, p.Arg94Leu e p.Gly116Ser), além disso, foram encontradas 4 novas mutações em outros três pacientes (p.Gly115Arg, p.Asn45Gly, p.Thr394Ala e c.759-2A>G). Dentre as mutações encontradas com maior frequência, a mutação p.Ser341Arg foi identificada em um maior número de pacientes, sendo a maioria proveniente da região Nordeste. Além disso, todos os pacientes com esta mutação apresentaram um único haplótipo. Conclusão: Os resultados obtidos permitiram a identificação de 18 mutações dentre elas 4 novas mutações. A alta frequência da mutação p.Ser341Arg no Nordeste do Brasil, principalmente no estado da Paraíba nos leva a inferir um possível efeito fundador da doença. Esta mutação foi observada somente na população brasileira e todos os pacientes com mutação em homozigose apresentaramum único haplótipo. Estas análises são importantes para identificar portadores nas famílias, para diagnóstico pré-natal, e também como forma de identificar uma origem comum em mutações frequentes em determinadas populações. / Background: Mucopolysaccharidosis IVA is an autosomal recessive lysosomal disease, caused by deficiency of N-acetilgalactosamina-6-sulfatase. It is a rare disease and the incidence ranges from 1: 76,000 to 1:640,000 live births. To date 319 mutations have been identified in this gene, demonstrating the wide variability of disease causing mutations. Objective: Analyze and characterize the genotype of patients with MPS IVA, through molecular analysis of GALNS. Methods: Molecular analysis of 45 patients with confirmed biochemical diagnosis for MPS IVA was performed. Mutation analysis was performed by PCR followed by Sanger sequencing. Haplotype analysis was performed using 6 intragenic polymorphisms by Real-Time PCR. Results: In this study we found 18 different mutations among 45 Brazilian patients and identified 5 common mutations (p.Ser341Arg, p.Arg386Cys, p.Gly301Cys, p.Arg94Leu e p.Gly116Ser). Four novel mutations were also identified through molecular analysis, including: p.Gly115Arg, p.Asn45Gly, p.Thr394Ala e c.759-2A>G. Patients are distributed in Northeast, Southeast and South regions of Brazil. Six different haplotypes were identified among patients. The p.Ser341Arg mutation showed the highest frequency, and most patients are located in the Northeast, additionally, all patients with this mutation show the same haplotype.Conclusion: These analyzes are important to identify carriers in families, for prenatal diagnosis, and in order to identify the mutation origin when certain recurrent mutation is associated with the same haplotype. In this study, we observed a high frequency of p.Ser341Arg mutation in Northeast, mainly in the state of Paraíba. This mutation was detected with higher frequency among patients, and showed only a haplotype. This mutation is unique for the Brazilian population and thus, we could suggest that a possible founder effect for this mutation could exist.

Made available in DSpace on 2016-06-02T20:21:35Z (GMT). No. of bitstreams: 1 6190.pdf: 937316 bytes, checksum: ab23c07a84b6ef5293322fb74683c2b5 (MD5) Previous issue date: 2014-01-24 / Financiadora de Estudos e Projetos / The Beef cattle production is a very important economic activity for Brazil, which is a global producer and exporter of bovine-derived products and currently contains the world s largest beef cattle herd. However, the majority Brazilian cattle are adapted to a tropical climate and have low meat and carcass quality. The crossbreeding between Charolais and Zebu animals resulted in development of Canchim breed. This breed shows better resistance to high temperatures and parasites, as well as better meat and carcass quality. New genotyping and computational technologies can enable the use of single nucleotide polymorphism (SNP) in breeding programs. The high demand for meat quality and the aggressive competition among other beef exporting countries justifies studies focused on improving carcass traits, such as ribeye area (REA), which can provide more efficiency production of meat cuts for consumption. The objective in this study was to validate SNPs selected in a previous genomewide association study (GWAS) for REA performed by Random Forest methodology in 400 animals genotyped with the BovineHD BeadChip ( Illumina®) which yielded a set of 197 SNPs. First, we analyzed the linkage disequilibrium (LD), and then we annotated the associated regions. After verifying this set of SNPs, we selected four SNPs located on BTA4, BTA10, BTA22 and BTA27 for validation purposes. These SNPs were genotyped by RFLPPCR in approximately 712 bovine. We analyzed the genetic effect of these SNPs the using GLM procedure in SAS (P &#8804; 0,05), which identified SNPs in BTA4 and BTA27 as contributing some genetic effect on REA. Furthermore, we found significant additive effect (P&#8804; 0,05) for the SNP on BTA 27, and a significant dominance effect for the SNP in BTA 4 using the ASReml software. The GWAS for REA identified one region between 34989224pb and 36989224pb using haplotype association analysis with the PLINK software that indicated two regions (P&#8804; 0,05) in the SFRP1 and ANK1 genes associated with REA. / A bovinocultura de corte brasileira se destaca na economia nacional, sendo o Brasil atualmente um dos principais produtores e exportadores de produtos cárneos de origem bovina, apresentando o maior rebanho comercial do mundo. No entanto, a maioria dos rebanhos bovinos são caracterizados por animais com maior adaptabilidade a ambientes tropicais e baixa qualidade de carcaça e carne. Cruzamentos entre raças taurinas e zebuínas originaram a raça Canchim, sendo esta vantajosa em relação à produtividade, conformação da carcaça e resistência ao calor e a parasitas. Com as novas tecnologias de genotipagem e computacionais se renovou o interesse em viabilizar o uso da informação de marcadores genéticos do tipo SNP em programas de seleção e melhoramento. O mercado interno mais exigente e maior competição entre países exportadores justificam estudos em características de carcaça, como área de olho de lombo (AOL), que pode proporcionar maior rendimento em cortes de alto valor agregado. Diante deste contexto, o objetivo desse trabalho foi validar SNPs selecionados por estudo prévio de associação genômica ampla (GWAS) para área de olho de lombo, realizada por Random Forest em uma população composta por 400 animais Canchim e genotipados em BovineHD BeadChip (Illumina®) e que resultou em um conjunto de 197 SNPs. Inicialmente estudou-se o desequilíbrio de ligação no genoma bovino da raça Canchim e realizou-se anotação das regiões associadas. A mineração desse conjunto resultou em 4 SNPs, os quais foram selecionados para as análises de validação e localizam-se nos cromossomos BTA4, BTA10, BTA22 e BTA27. Os marcadores selecionados foram genotipados pela técnica RFLP-PCR em uma população de 712 bovinos da raça Canchim. Analisou-se o efeito desses marcadores sobre o valor genético aditivo (VGA) de AOL por meio de análise de variância que indicou a influência dos SNPs localizados nos BTA4 e BTA27. Além disso, tais SNPs significativos nas análises de validação foram analisados quantos aos efeitos aditivos e de dominância pelo teste Wald F, tendo sido observado efeito 6 de dominância significativo no SNP do BTA4 e efeito aditivo significativo no SNP do BTA 27. A análise de associação haplotípica com área de olho de lombo realizada na região 34989224pb a 36989224pb no BTA27 por meio de análise de regressão logística indicaram duas regiões nos genes SFRP1 e ANK1 associadas com a característica.