Submitted by Rafael de Matteis null (rafamatteis@gmail.com) on 2017-11-08T12:06:38Z No. of bitstreams: 1 Dissertação_final_07_11.pdf: 1681500 bytes, checksum: 500c4cfcd27a41f039ae32bf6442d92c (MD5) / Approved for entry into archive by Luiz Galeffi (luizgaleffi@gmail.com) on 2017-11-21T13:44:53Z (GMT) No. of bitstreams: 1 matteis_r_me_jabo.pdf: 1681500 bytes, checksum: 500c4cfcd27a41f039ae32bf6442d92c (MD5) / Made available in DSpace on 2017-11-21T13:44:53Z (GMT). No. of bitstreams: 1 matteis_r_me_jabo.pdf: 1681500 bytes, checksum: 500c4cfcd27a41f039ae32bf6442d92c (MD5) Previous issue date: 2017-10-11 / Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) / Ao longo de várias décadas a raça Quarto de Milha foi selecionada para diferentes objetivos, formando grupos com aptidões ou habilidades distintas, como a linhagem de corrida, que apresenta melhor desempenho que qualquer outra linhagem ou raça em corridas de curta distância e a linhagem de trabalho, utilizada no manejo de bovinos a campo e em provas de caráter funcional. Considerando as diferenças nas medidas corporais e na musculatura que ocorrem entre as linhagens de corrida e de trabalho da raça Quarto de Milha, o objetivo deste trabalho foi analisar a ocorrência de relações entre alelos de polimorfismos da região cromossômica do gene da miostatina MSTN (ECA18), um regulador negativo do desenvolvimento muscular, e as duas linhagens da raça. Outro objetivo foi realizar análises de associação de polimorfismos dessa região cromossômica com valor genético estimado (EBV) do desempenho em corridas, dado pelo índice de velocidade máximo (IV max), e EBVs da altura à cernelha (AC), perímetro torácico (PT) e comprimento corporal (CC) na linhagem de corrida, e com EBVs da AC, PT e CC na linhagem de trabalho. Foram utilizadas informações genômicas, fenotípicas e de pedigree de 420 equinos, de ambos os sexos, registrados na associação Brasileira de criadores (ABQM), sendo 352 da linhagem de corrida e 68 da de trabalho. Na região genômica estudada (gene MSTN ± 2Mb), foram identificados 46 SNPs e 1 SINE – ERE1 comuns às linhagens de trabalho e de corrida, dos quais 32 SNPs e 1 SINE apresentaram alelos com frequências significativamente diferentes entre às mesmas. Também foi constatado que a porção dessa região mais próxima ao gene MSTN (± 1Mb) é menos polimórfica na linhagem de corrida em relação à de trabalho, o que pode ser consequência de maior pressão de seleção sobre essa região na linhagem de corrida e/ou em função do uso de animais da raça Puro Sangue Inglês na mesma. Em relação aos polimorfismos associados à fenótipos (p não ajustado < 0,05), destacaram-se os relacionados à altura de cernelha na linhagem de corrida devido ao seu grande número (p não ajustado < 0,05) e alto desequilíbrio de ligação. Ademais estes marcadores apresentaram frequências do alelo favorável significativamente maiores em relação à linhagem de trabalho. Tendo se em vista a possibilidade de associação genética entre características morfológicas e desempenho em equinos, esse resultado é de grande importância, fornecendo informações para futuros estudos de melhoramento genético animal. / For several decades the Quarter Horse breed was selected for different purposes, forming groups with different abilities, such as the racing line, which performs better than any other lineage or breed in short distance races and the lineage of work, used in the management of field cattle and in functional tests. Considering the differences in body measurements and musculature that occur between racing and working strains of the Quarter-Mile breed, the objective of this study was to analyse the occurrence of relations between polymorphic alleles of the chromosomal region of the myostatin (MSTN) gene (ECA18), a negative regulator of muscle development, and the two lineages of the breed. Other objective was to perform association analyses of these polymorphisms with estimated genetic value (EBV) of the performance in lineages, given by the maximum velocity index (IV max), and EBVs of height at withers (HW), heart girth (HG) and body length (BL) in the racing line, and with EBVs of AC, PT and CC in the working line. We used genomic, phenotypic and pedigree information from 420 horses of both sexes, recorded in the Brazilian breeders' association (ABQM), 352 and 68 of the racing and working line, respectively. In the studied genomic region (MSTN gene ± 2Mb), 46 SNPs and 1 SINE - ERE1 were identified, common to the working and running strains, of which 32 SNPs and one SINE presented alleles with significantly different frequencies between them. It has also been found that the portion of this region closest to the MSTN gene (± 1Mb) is less polymorphic in the racing versus the working strain, which may be a consequence of higher selection pressure on that region in the racing line and / or due to the use of purebred English animals in it. In relation to the polymorphisms associated with the phenotypes (p not adjusted <0.05), those related to the height of the withers in the race line due to their large number (p not adjusted <0.05) and high linkage disequilibrium were the most prominent. In addition, these markers presented frequencies of the favorable allele significantly higher in relation to the working lineage. Considering the possibility of genetic association between morphological characteristics and performance in equines, this is a result of great importance, providing information for future animal breeding studies. / CNPq: 134521/2015-3

Submitted by Automa??o e Estat?stica (sst@bczm.ufrn.br) on 2016-01-04T22:02:35Z No. of bitstreams: 1 LeonardoCapistranoFerreira_TESE.pdf: 3396619 bytes, checksum: bffb880b6907328ac1ce5051faaf28fd (MD5) / Approved for entry into archive by Arlan Eloi Leite Silva (eloihistoriador@yahoo.com.br) on 2016-01-07T21:08:47Z (GMT) No. of bitstreams: 1 LeonardoCapistranoFerreira_TESE.pdf: 3396619 bytes, checksum: bffb880b6907328ac1ce5051faaf28fd (MD5) / Made available in DSpace on 2016-01-07T21:08:47Z (GMT). No. of bitstreams: 1 LeonardoCapistranoFerreira_TESE.pdf: 3396619 bytes, checksum: bffb880b6907328ac1ce5051faaf28fd (MD5) Previous issue date: 2014-10-06 / Coordena??o de Aperfei?oamento de Pessoal de N?vel Superior - CAPES / O desenvolvimento de doen?as complexas, como a pr?-ecl?mpsia, ? determinado por fatores ambientais e gen?ticos, al?m da poss?vel intera??o entre esses fatores. As doen?as hipertensivas da gravidez (DHGs) apresentam um amplo espectro cl?nico, que pode variar desde pr?-ecl?mpsia leve (hipertens?o e proteinuria) at? formas mais graves, como a ecl?mpsia (convuls?es) e s?ndrome HELLP (hem?lise, eleva??o das enzimas hep?ticas e plaquetopenia). O espectro cl?nico parece estar ligado a diferentes mecanismos patol?gicos. Este trabalho tem como objetivo identificar fatores (gen?ticos e ambientais) envolvidos no desenvolvimento das DHGs. Usando uma abordagem caso-controle, selecionamos um total de 1498 mulheres para os estudos epidemiol?gico e gen?tico, abrangendo 755 gr?vidas normotensas (controle); 518 pr?-ecl?mpsia; 84 eclampsia e 141 HELLP. As mulheres foram genotipados para 18 marcadores distribu?dos em cinco genes candidatos (FLT1, ACVR2A, ERAP1, ERAP2 e LNPEP). Como resultado das an?lises dos fatores ambientais, encontramos idade materna, paridade e o ?ndice de massa corporal pr?-gestacional como importantes fatores de risco associados ?s DHGs. As an?lises gen?ticas mostraram que os genes est?o associados de maneira fen?tipo-espec?fica: ACVR2A com pr?-ecl?mpsia precoce (rs1424954, p=0,002); FLT1 com s?ndrome HELLP (rs9513095, p=0,003), e ERAP1 com ecl?mpsia (rs30187, p=0,03). Nossos resultados sugerem que diferentes mecanismos gen?ticos, juntamente com fatores ambientais espec?ficos, contribuem na determina??o do espectro cl?nico das DHGs. Al?m disso, o refinamento fenot?pico parece ser um passo essencial na busca por genes de doen?as complexas / The development of complex diseases such as preeclampsia are determined by both environmental and genetic factors, but there is also interaction among these factors. Preeclampsia is a pregnancy-specific disorder characterized by de-novo hypertension and proteinuria after 20th week of gestation. There is a broad spectrum of clinical presentations related to hypertensive disorders of pregnancy (HDP) that can range from mild preeclampsia to eclampsia (seizures) or HELLP syndrome (Hemolysis, Elevation of Liver enzymes, Low Platelets). Those clinical outcomes might be linked to different pathological mechanisms. Our work aims to identify factors (i.e. genes and environmental) associated with the HDP?s clinical spectrum. Using a case-control approach, we selected a total of 1498 pregnant women for epidemiological and genetic studies, encompassing 755 normotensive (control); 518 preeclampsia; 84 eclampsia; and 141 HELLP. Women were genotyped for 18 SNPs across 5 candidate genes (FLT1, ACVR2A, ERAP1, ERAP2 and LNPEP). For the environmental factors, we found maternal age, parity status and pre-gestational body mass index as important risk factors associated with disease. Genes were associated in a phenotype-specific manner: ACVR2A with early preeclampsia (rs1424954, p=0.002); FLT1 with HELLP syndrome (rs9513095, p=0.003); and ERAP1 with eclampsia (rs30187, p=0.03). Our results suggest that different genetic mechanisms along with specific environmental factors might determine the clinical spectrum of HDP. In addition, phenotype refinement seems to be an essential step in the search for complex disease genes

Nowadays intensive research is conducted for application of genetic polymorphisms for degraded samples analysis, identification and kinship determination. Another area of research in forensic genetics is biogeographical and phenotypic traits (eye, hair and skin color) determination. First part of presented work dealt with population study on the Czech popu- lation using Investigator DIPplex (QIAGEN, Germany) marker set containing 30 autosomal insertion-deletion polymorphisms. Power of Discrimination (PD), which is the probability of random selection of two persons with different genotypes, was 99.9999999999% for the whole marker set. This part of study concluded that ana- lyzed marker set is suitable as an additional marker panel for identification and kinship determination in the Czech Republic. Second part of the presented study was devoted to population research of Cen- tral Croatia using Mentype Argus X-8 kit (QIAGEN, Germany) containing 8 short tandem repeat polymorhisms located on X choromosomes (X-STR) divided into 4 linkage groups. PD for the whole kit reached 99.9999% and 99.99999999% for males and females, respectively. This kit could be used in Central Croatian population for kinship analysis and for identification as an additional marker panel. The next part of the presented study was the...

Trichome formation in Arabidopsis lyrata is a naturally occurring trait with phenotypic polymorphisms within wild populations. In Swedish accessions of A. lyrata, three genetic polymorphisms situated in the coding region of GL1, an important transcription factor in trichome production, have been identified, and these are candidates for being the cause of a glabrous phenotype. In this study a complementation test has been performed to clarify which mutation/mutations that are detrimental for trichome formation. A set of constructs has been transformed into A. thaliana, a close relative to A. lyrata, and subsequent generations of plants were examined for phenotype, genotype and gene expression. A SNP (Single Nucleotide Polymorphism) in the R3 MYB domain of GL1, resulting in a change of an alanine to aspartic acid, was identified as the critical polymorphism. The other two mutations, two indels, were harmless to protein function. The inserted constructs were under control of the native GL1 promoter. Plants that, because of the SNP, lacked trichome production, became totally glabrous.

Deficiência intelectual é uma condição heterogênea e complexa, diagnosticada em 1-3% da população mundial. Desequilíbrios cromossômicos e variações no número de cópias (CNVs) são as causas mais frequentes de DI e, até recentemente, a maior parte desse desequilíbrio era averiguado por análises citogenéticas convencionais. Antes da utilização de microarrays cromossômicos (CMA), a causa etiológica da DI ainda permanecia desconhecida em ~60% dos pacientes. A aplicação de CMA tem revolucionado o diagnóstico da DI e de muitas outras doenças congênitas, permitindo explicar a etiologia molecular de parte da DI através da identificação de CNVs patogênicas. Nos países desenvolvidos, CMA é considerado como primeiro teste para avaliar pacientes com múltiplas anomalias congênitas, DI e/ou autismo. Contudo, nos países em desenvolvimento, a detecção de alterações ainda é feita principalmente por métodos citogenéticos convencionais. O objetivo desse estudo foi identificar, através do uso de SNP arrays, o espectro de anomalias cromossômicas presente em uma amostra de 40 pacientes com DI idiopática moderada e grave, apresentando ou não aspectos dismórficos e anomalias congênitas. Em especial, essa coorte de pacientes, em sua maioria (~2/3), não havia sido previamente cariotipada. Embora mundialmente desde 2010 a recomendação seja de realizar arrays antes de cariótipo, a maioria dos pacientes relatados em estudos já havia sido cariotipada antes de array ser oferecido a eles como teste. Foram identificadas alterações raras em 18 pacientes (45%). Em 12 (30%) desses Pacientes, as CNVs eram sabidamente patogênicas; esta taxa diagnóstica está muito acima da taxa de detecção reportada na literatura (~20%) e possíveis causas desta discrepância são discutidas. Outros 6 Pacientes (15%) apresentaram variantes raras de significado incerto (variants of unknown significance - VUS). Um aspecto adicional investigado foram os mecanismos envolvidos na formação de alguns dos rearranjos estruturais; enquanto nosso foco inicial era o uso de arrays para detecção de CNVs, se tornou evidente no decorrer do projeto que o padrão dos SNPs obtido nos arrays revelava, a partir do DNA, informação valiosa sobre a estrutura dos cromossomos e a composição heterogênea de células em uma amostra (mosaicismo). Esses resultados são discutidos em detalhes em duas situações: (1) A descrição de uma deleção terminal 1p36, associada a dissomia uniparental (UPD) em mosaico de segmentos de 1pter de diferentes tamanhos. Sugerimos que essa composição reflita eventos recorrentes de captura de telômero, embora processo similar nunca tenha sido descrito, e propomos um possível mecanismo responsável por originar esse desequilíbrio complexo. (2) Três dos nossos pacientes apresentam 4 cópias ou uma combinação de 3-4 cópias de segmentos proximais, na maior parte superpostos, de 15q11q13. Possíveis mecanismos de origem desses rearranjos são discutidos / Intellectual disability (ID) is a complex and heterogeneous condition affecting about 1-3% of the general population. Chromosomal imbalances and copy-number variations (CNVs) have been recognized as the most frequent causes of ID and, until recently, most of these imbalances were diagnosed by cytogenetic analysis. Before the application of microarray analysis (CMA), the underlying cause of ID remains unknown in ~60% of patients. The use of CMA has revolutionized the diagnosis of ID and several other congenital disorders, and have made it possible to identify pathogenic CNVs that could explain the molecular etiology of ID. In developed countries, CMA is considered the first-tier technique for the analysis of patients with multiple congenital anomalies, ID, and/or autism spectrum disorders. However, in developing nations, detection of alterations is still performed mainly by conventional cytogenetic techniques. The aim of this study was identifying, using a high-density resolution SNP microarray, chromosomal imbalances in a total of 40 patients presented with moderate-to-severe ID, associated or not with dysmorphic features and congenital anomalies. Particularly, most of the patients in the cohort (~2/3) was not karyotyped previously. Although CMA has been recommended as the first-tier test since 2010 all over the world, the majority of the patients in the reported studies were karyotyped before CMA was offered as a diagnostic test. Rare CNVs were detected in 18 patients (45%). Among those patients, 12 (30%) carried pathogenic CNVs. This yield is much higher than reported in the literature (~20%), and possible causes for this discrepancy are discussed. Six patients (15%) carried variant of unknown significance (VUS). Furthermore, mechanisms involved in structural rearrangements found in some patients were investigated. Even though the main focus of this dissertation was the detection of CNVs using high resolution SNP arrays, throughout the course of this project it was clear that the SNP patterns found could reveal crucial information about the structure of chromosomes and the heterogeneous composition of cells (mosaicism). Those results are discussed in detail in two situations: (1) One description of a terminal 1p36 deletion, associated with mosaic uniparental disomy (UPD) of different sized 1pter segments. We hypothesized that this composition reflects recurrent telomere capture events, although a similar process has never been described so far, and proposed a possible mechanism responsible for originating this complex imbalance. (2) Three of our patients carried four copies or a four-three copies-combination of a proximal, partially overlapping, 15q11q13 segment. Possible mechanisms responsible for this complex rearrangement are discussed

Oral and oropharyngeal squamous cell carcinoma (OOSCC) is a malignant neoplasm of epithelial origin that accounts for 90 to 95% of tumors in oral cavity. Alcohol and tobacco consumption are main risk factors, but the formation of reactive oxygen species (ROS) and presence of chronic inflammatory processes have been shown to favor the carcinogenesis process. Human serum paraoxonase 1 (PON1) is a protein with an important antioxidant action and prevents oxidative stress induced by ROS, in turn, high levels of tumor necrosis factor-alpha (TNF-α) and transforming growth factor-beta (TGF-β) are commonly found in inflammatory processes, and changes in these proteins have been related to development of different neoplasms. Present study aims to investigate the prognostic value of functional polymorphisms in PON1, TNF-α and TGF-β genes in OOSCC. This is a prospective cohort study with patients attended at the Advanced Oncology Center of the North-Riograndense League against Cancer. Data collection of clinical variables was done through the form: gender, age, tumor site, TNM (primary tumor, regional nodule and distant metastasis) classification, clinical stage; and through interview: smoking habits and alcohol intake by the patient. A total of 163 samples from patients with OOSCC and 146 control samples were genotyped by real-time PCR. It was observed that 76.1% of the population was males, 84% older than 52 years, with a more frequent intra-oral clinical presentation (53.4%), in the tongue region (21.5%), tumors greater than 4cm (56.45%), presence of nodal involvement (58.9%) and stages III and IV (79.15%). There was a positive association between drinking and smoking habits in patients with OOSCC and between clinical stage and tumor site (p <0.05). The polymorphisms were in Hardy-Weinberg equilibrium, with exception of rs662 of PON1. TNF-α wild-type GG homozygous genotype (rs1800629) was associated with intra-oral lesions, clinical stage of the most advanced disease (III and IV), and decreased overall disease survival, whereas the polymorphic AA genotype was associated with lip lesion, clinical stage I and II and a longer overall disease survival (p <0.05). It was observed association of TGF-β polymorphic AG and AA genotypes (rs1800469) with larger diameter tumors (T3 and T4) (p <0.05). Finally, the polymorphic TT genotype of PON1 (rs662) in recessive model was associated with a shorter disease survival time within threshold of significance (p = 0.05). In view of the findings, it is suggested that wild-type GG homozygous genotype of TNF-α rs1800629 and TGF-β rs1800469 polymorphic AG and AA genotypes may exert an influence on more aggressive biological behavior of OOSCC and that AG genotype of TNF-α rs1800629 and TT genotype of PON1 rs662 could be prognostic markers in OOSCC. In the clinical practice of oncology, these genotypes can be used to perform early diagnosis, knowledge of the biological behavior of the tumor and choice of appropriate individualized therapy / O carcinoma de células escamosas oral e orofaríngeo (CCEO) é uma neoplasia maligna de origem epitelial que representa 90 a 95% dos tumores da cavidade oral. O consumo de álcool e de tabaco são os principais fatores de risco, mas a formação de espécies reativas de oxigênio (EROs) e a presença de processos inflamatórios crônicos têm-se mostrado favorável ao processo de carcinogênese. A paraoxonase de soro humano 1 (PON1) é uma proteína com importante ação antioxidante e previne o estresse oxidativo induzido pelas EROs, por sua vez, elevados níveis do fator de necrose tumoral-alfa (TNF-α) e do fator de crescimento transformante-beta (TGF-β) são comumente encontrados em processos inflamatórios, e alterações nessas proteínas têm sido relacionadas com o desenvolvimento de diferentes neoplasias. O presente estudo tem por objetivo investigar o valor prognóstico dos polimorfismos funcionais nos genes da PON1, TNF-α e TGF-β no CCEO. Trata-se de um estudo coorte prospectivo com pacientes atendidos no Centro Avançado de Oncologia da Liga Norte-Riograndense contra o Câncer. Realizou-se a coleta de dados das variáveis clínicas por meio de formulário: gênero, idade, localização do tumor, classificação TNM (Tumor primário, nódulo regional e metástase à distância), estadiamento clínico (EC); e por meio de entrevista: hábitos de fumo e ingestão alcoólica pelo paciente. Foram genotipadas 163 amostras de pacientes com CCEO e 146 amostras controle por meio de PCR em tempo real. Observou-se que 76,1% da população era do gênero masculino, sendo 84% com mais de 52 anos, com apresentação clínica mais frequente intra-oral (53,4%), na região da língua (21,5%), tumores maiores que 4cm (56,45%), presença de envolvimento nodal (58,9%) e em estágios III e IV (79,15%). Evidenciou-se associação positiva entre os hábitos de beber e fumar com pacientes portadores de CCEO e entre o EC e a localização do tumor (p<0,05). Os polimorfismos encontravam-se em equilíbrio de Hardy-Weinberg, com exceção do rs662 da PON1. O genótipo homozigoto selvagem GG do TNF-α (rs1800629) associou-se com lesões intra-orais, EC da doença mais avançado (III e IV) e menor sobrevida global da doença, enquanto o genótipo AA polimórfico associou-se a lesão de lábio, EC I e II e maior sobrevida global da doença (p<0,05). Observou-se associação dos genótipos AG e AA polimórfico do TGF-β (rs1800469) com tumores de maior diâmetro (T3 e T4) (p < 0,05). Por fim, o genótipo TT polimórfico da PON1 (rs662) no modelo recessivo apresentou associação com menor tempo de sobrevida da doença dentro do limiar de significância (p=0,05). Diante dos achados, sugere-se que o genótipo GG selvagem do rs1800629 do TNF-α e os genótipos AG e AA polimórfico do rs1800469 do TGF-β podem exercer influência no comportamento biológico mais agressivo do CCEO e que o genótipo AG do rs1800629 do TNF-α e o genótipo TT polimórfico do rs662 da PON1 poderiam ser marcadores com valor prognóstico no CCEO. Na prática clínica da oncologia, esses genótipos podem ser utilizados para realização de diagnóstico precoce, conhecimento do comportamento biológico do tumor e escolha da terapêutica individualizada adequada. / Lagarto, SE

Submitted by Marlene Santos (marlene.bc.ufg@gmail.com) on 2016-06-08T20:29:50Z No. of bitstreams: 2 Tese - Alex Silva da Cruz - 2015.pdf: 4189617 bytes, checksum: f21e8815a51e44f144dd811005f32bdd (MD5) license_rdf: 19874 bytes, checksum: 38cb62ef53e6f513db2fb7e337df6485 (MD5) / Approved for entry into archive by Luciana Ferreira (lucgeral@gmail.com) on 2016-06-09T11:41:47Z (GMT) No. of bitstreams: 2 Tese - Alex Silva da Cruz - 2015.pdf: 4189617 bytes, checksum: f21e8815a51e44f144dd811005f32bdd (MD5) license_rdf: 19874 bytes, checksum: 38cb62ef53e6f513db2fb7e337df6485 (MD5) / Made available in DSpace on 2016-06-09T11:41:47Z (GMT). No. of bitstreams: 2 Tese - Alex Silva da Cruz - 2015.pdf: 4189617 bytes, checksum: f21e8815a51e44f144dd811005f32bdd (MD5) license_rdf: 19874 bytes, checksum: 38cb62ef53e6f513db2fb7e337df6485 (MD5) Previous issue date: 2015-10-19 / Fundação de Amparo à Pesquisa do Estado de Goiás - FAPEG / Genomic selection in a dairy cattle breeding is a new strategy in national livestock. Genome wide association study (GWAS) is known as a strategy that involve the use of molecular markers panels distributed throughout the genome which are selected for the identification of chromosomal regions that are important for the interest traits. The aim of this study was apply the GWAS strategy for 305-day milk yield in Girolando cows. We did the genotype from 404 Girolando and after quality control analysis remained 337 individuals and 45.622 markers. The GWAS analysis resulted in 52 SNPs associated to 305-day milk yield. Of these, 23 SNPs were linked to Known genes and only 3 SNPs were linked to NUB1, SLC24A2 and DGAT1 genes that already were associated with cattle lactation. The other SNPs have no relationships described in the cattle lactation literature. In addition, the milk production QTL analysis resulted in 52 SNPs and 14 genes linked or close to 1Mb of the SNP marker. The ARS-BFGL-NGS-414 SNP on BTA19 at 47.9Mbp is located near to GH1 gene. This gene is commonly accepted as causal gene for Quantitative Character Locus of milk production mainly affecting the yield in liters and solid milk components. Thus, our data suggest that NUB1 and SLC24A2 genes could be considered as candidate genes to understand the milk production in Girolando breed. Like this DGAT1 and GH1 genes are valuable predictive markers to be added to genomic selection of dairy cattle in breeding program. / A seleção genômica, aplicada em bovino em associação à produção de leite é uma inovação estratégica na pecuária nacional, e que poderá se tornar uma ferramenta prática importante para a atividade. Estudos de Associação Ampla do Genoma (GWAs) caracteriza-se como uma estratégia que envolve o uso de painéis de marcadores moleculares distribuídos por todo o genoma, selecionados para a identificação de regiões dos cromossomos associadas com um fenótipo de interesse. O objetivo deste estudo foi aplicar a estratégia de GWAS para a característica de lactação total ajustada em 305 dias de vacas Girolando. Inicialmente, foram genotipados 404 vacas Girolando que após procedimento de controle de qualidade resultou em um total de 337 indivíduos e 45.622 marcador. O GWAS resultou em 52 SNPs associados a lactação ajustada em 305 dias. Destes, 23 SNPs apresentaram-se ligados a genes conhecidos e somente 3 SNPs estão ligados aos genes NUB1, SLC24A2 e DGAT1, descritos relacionados a lactação em bovinos. Os demais SNPs não apresentam relações descrita na literatura a lactação em bovinos. Para o QTL de produção de leite (MY), dos 52 SNPs, foram identificados 14 genes ligados ou próximos a 1Mb de distância do SNP marcador. Em particular, o SNP ARS-BFGL-NGS-414 associado ao QTL de lactação bovina, constituído de aproximadamente 47,9 Mbp localizado no BTA19 está localizado muito próximo do gene GH1 (Hormônio do Crescimento 1), comumente aceito como gene causal para o Lócus de Caráter Quantitativo (QTL) de produção de leite, afetando principalmente o rendimento em litros e componentes sólidos do leite. Dessa forma, nossos dados sugerem que os genes NUB1, e SLC24A2 poderiam ser considerados como genes candidatos para ajudar a explicar a produção de leite em animais da raça Girolando, assim como os genes DGAT1 e GH1, são considerados como valiosos marcadores preditivos a serem adicionados à seleção genômica do gado leiteiro em programas de melhoramento.

There is a continuous development of different crop varieties in the crop trade. The cultivated crops tend to be more and more alike which require an effective method for crop identification. Crop type and crop type purity has become a quality measure in crop trade both nationally and internationally. A number of well known quality attributes of interest in the crop trade can be correlated to the specific crop type and therefore it is of great importance to reliably be able to identify different crop varieties. It is well known from the literature that there exist genomic variations at the nucleotide level between different crop varieties and these variations might potentially be useful for automated variety identification. This project deals with the crop variety identification area where the possibilities of distinguishing between different wheat varieties are investigated. Experience from performing wheat variety identification at protein level has shown unsatisfactory results and therefore DNA-based techniques are proposed instead. DNA-based techniques are dependent upon the availability of sequence data from the wheat genome and some work has concerned examining the availability of sequence data from wheat. But the focus of the work has been on defining a method for computational detection of single nucleotide variations in ESTs from wheat and to experimentally test that method. Results from these experiments show that the method defined in this project detects polymorphic variations that can be correlated to variety variations

Palmer amaranth (Amaranthus palmeri) is a major weed in United States cotton and soybean production systems. Originally native to the Southwest, the species has spread throughout the country. In 2004 a population of A. palmeri was identified with resistance to glyphosate, a herbicide heavily relied on in modern no-tillage and transgenic glyphosate-resistant (GR) crop systems. This project aims to determine the degree of genetic relatedness among eight different populations of GR and glyphosate-susceptible (GS) A. palmeri from various geographic regions in the United States by analyzing patterns of phylogeography and diversity to ascertain whether resistance evolved independently or spread from outside to an Arizona locality (AZ-R). Shikimic acid accumulation and EPSPS genomic copy assays confirmed resistance or susceptibility. With a set of 1,351 single nucleotide polymorphisms (SNPs), discovered by genotyping-by-sequencing (GBS), UPGMA phylogenetic analysis, principal component analysis, Bayesian model-based clustering, and pairwise comparisons of genetic distances were conducted. A GR population from Tennessee and two GS populations from Georgia and Arizona were identified as genetically distinct while the remaining GS populations from Kansas, Arizona, and Nebraska clustered together with two GR populations from Arizona and Georgia. Within the latter group, AZ-R was most closely related to the GS populations from Kansas and Arizona followed by the GR population from Georgia. GR populations from Georgia and Tennessee were genetically distinct from each other. No isolation by distance was detected and A. palmeri was revealed to be a species with high genetic diversity. The data suggest the following two possible scenarios: either glyphosate resistance was introduced to the Arizona locality from the east, or resistance evolved independently in Arizona. Glyphosate resistance in the Georgia and Tennessee localities most likely evolved separately. Thus, modern farmers need to continue to diversify weed management practices and prevent seed dispersal to mitigate herbicide resistance evolution in A. palmeri.

Parasitic copepods including Lepeophtheirus salmonis have been the focus of strong concern for the health of wild and farmed salmonids in the Pacific and Atlantic Oceans. Salmon are highly valuable species from both socioeconomic and ecological perspectives. The host-parasite dynamics of Lepeophtheirus salmonis and the Atlantic and Pacific salmonids have changed over evolutionary time to the point that both Atlantic and Pacific salmon and Atlantic and Pacific Lepeophtheirus salmonis are genetically distinct. Recent human interference with the natural population dynamics of this parasite and its hosts may have altered the population genetic structure of Lepeophtheirus salmonis, particularly because salmon farms may provide more stable conditions for parasite population growth. High abundance of Lepeophtheirus salmonis on salmon farms causes damage to the farmed salmon and leads to increased infection intensities in nearby wild hosts. Some Atlantic Lepeophtheirus salmonis have developed resistance to the anti-parasitic drugs they are repeatedly exposed to. No drug resistance has yet been detected within the Pacific Ocean, where only one drug is available, and heavily relied on, to treat Lepeophtheirus salmonis infections. Control of Lepeophtheirus salmonis abundance on Pacific salmon farms is important to maintain the health of farmed salmon and is also important to protect wild salmonids from increased infections originating from salmon farms. The goal of this thesis was to characterize and employ a large suite of molecular markers to assess the population structure of Lepeophtheirus salmonis in the Pacific Ocean. Until this point, the primary focus of Lepeophtheirus salmonis population genetics research has been limited to the Atlantic Ocean and has relied on a small number of available molecular markers. Available expressed sequence tag DNA libraries were screened to identify putative polymorphic loci, which were then experimentally evaluated. We characterized 22 novel microsatellite loci and 87 single nucleotide polymorphisms within 25 nuclear loci for Lepeophtheirus salmonis. We used these genetic markers, as well as 5 microsatellite loci previously developed for use in Atlantic Lepeophtheirus salmonis population studies, to genotype 562 Lepeophtheirus salmonis that were collected from12 Pacific Ocean sampling locations. We compared Lepeophtheirus salmonis genotypes among: (1) seven wild host populations and five farmed host populations within the Pacific Ocean; (2) geographically separated wild host populations, ranging from the Bering Sea to the southwest end of Vancouver Island, British Columbia; and (3) temporally separated cohorts of farmed Atlantic salmon from two geographically distant farm locations on the northwest coast of Vancouver Island and the Campbell River area east of central Vancouver Island. Our analyses failed to resolve significant population structure among sampled Pacific Lepeophtheirus salmonis and, therefore, supports a hypothesis of high gene flow throughout the Northeast Pacific Ocean. It is important to understand the biology and population dynamics of Lepeophtheirus salmonis because it is a consequential parasite of wild and farmed salmonids in the Pacific Ocean. Both the molecular tools developed for this study and the population genetics information generated from this study have contributed to our overall understanding of the evolutionary history and population dynamics of Lepeophtheirus salmonis. / Graduate