The work focuses on the significance of pneumolysin in contribution to virulence of Streptococcus pneumoniae serotype 1 isolates. Methods include bioinformatics as well as in vitro assays. A SNP within nucleotide sequence of the second virulence factor, hyaluronidase, is a subject for screen of meningitis isolates.

Doctor of Philosophy / Department of Agronomy / Guihua Bai / Allan K. Fritz / Wheat leaf rust, caused by Puccinia triticina, is an important fungal disease worldwide. Growing resistant cultivars is an effective practice to reduce the losses caused by the disease, and using slow-rusting resistance genes can improve the durability of rust resistance in the cultivars. CI13227 is a winter wheat line that shows a high level of slow-rusting resistance to leaf rust and has been studied extensively. In this research, two recombinant inbreed line (RIL) populations derived from CI13227 x Suwon (104 RILs) and CI13227 x Everest (184 RILs) and one doubled haploid (DH) population derived from CI13227 x Lakin with 181 lines were used to identify quantitative trait loci (QTLs) for slow leaf rusting resistance. Each population and its parents were evaluated for slow-rusting traits in two greenhouse experiments. A selected set of 384 simple sequence repeat markers (SSRs), single nucleotide polymorphism markers (SNPs) derived from genotyping-by-sequencing (GBS-SNPs) or 90K-SNP chip (90K-SNPs) were analyzed in the three populations. Six QTLs for slow-rusting resistance, QLr.hwwgru-2DS, QLr.hwwgru-7BL, QLr.hwwgru-7AL, QLr.hwwgru-3B_1, QLr.hwwgru-3B_2, and QLr.hwwgru-1D were detected in the three populations with three stable QTLs, QLr.hwwgru-2DS, QLr.hwwgru-7BL and QLr.hwwgru-7AL. These were detected and validated by Kompetitive Allele-Specific PCR (KASP) markers converted from GBS-SNPs and 90K-SNPs in at least two populations. Another three QTLs were detected only in a single population, and either showed a minor effect or came from the susceptible parents. The KASP markers tightly linked to QLr.hwwgru-2DS (IWB34642, IWB8545 and GBS_snpj2228), QLr.hwwgru-7BL (GBS_snp1637 and IWB24039) and QLr.hwwgru-7AL (IWB73053 and IWB42182) are ready to be used in marker-assisted selection (MAS) to transfer these QTLs into wheat varieties to improve slow-rusting resistance in wheat.

Orientador: Celso Luis Marino / Resumo: Os resultados obtidos durante o desenvolvimento deste trabalho estão apresentados na forma de capítulos. O primeiro capítulo apresenta uma análise dos parâmetros genéticos de uma população F1 obtida a partir do cruzamento de duas variedades comerciais de cana-de-açúcar oriundas do programa de melhoramento do Centro de Tecnologia Canavieira, Piracicaba/SP. Também avaliamos marcadores moleculares microssatélites buscando uma relação entre os mesmos com as características agronômicas aqui estudadas (Peso do bolo úmido, Peso do bolo seco, Fibra, Lignina e Celulose). No segundo capítulo, o qual está em formato de artigo científico que será submetido para a revista Genome, com o título “A SNP genetic map constructed using restriction site-associated DNA sequencing approach for sugarcane”, apresenta o primeiro mapa genético com marcadores SNPs (Single nucleotide polymorphisms) obtidos via RADSeq utilizando a população F1 de mapeamento obtida a partir do cruzamento de uma variedade comercial dos Estados Unidos com S. spontaneum, oriundos do programa de melhoramento da Texas A&M AgriLife Research, Weslaco, TX, USA. Durante o doutorado realizei estágio na Texas A&M AgriLife Research, Weslaco, TX, USA, sob orientação do Dr. Jorge A. G. da Silva, onde foram realizadas as análises dos componentes lignocelulósicos e o screening de marcadores SSR. Também houve o estágio na Texas A&M AgriLife Genomics and Bioinformatics Service (Texas A&M University, College Station, TX, EUA), sob orientação... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: The results obtained during this work are presented in chapters. The first chapter shows an analysis of genetic parameters of an F1 population obtained from the crossing of two commercial varieties of sugarcane derived from the Sugar Cane Technology Center breeding program, Piracicaba / SP. We also screened microsatellites in this population seeking a relationship between them with agronomic traits like the weight of wet cane, dry cane weight, fiber, lignin and cellulose content. In the second chapter, which is in scientific paper format to be submitted to Genome journal, entitled "The SNP genetic map constructed using restriction site-associated DNA sequencing approach for sugarcane," presents the first genetic map with SNP markers (single nucleotide polymorphisms) obtained by RADSeq using the F1 population of mapping obtained from the crossing of a commercial variety of the United States with S. spontaneum, coming from the breeding program at Texas A & M AgriLife Research, Weslaco, TX, USA. During the doctoral stage at Texas A & M AgriLife Research, Weslaco, TX, USA, under the supervision of Dr. Jorge A. G. Silva, were carried out the analysis of lignocellulosic components and the screening of SSR markers. There was also a stage at Texas A & M AgriLife Genomics and Bioinformatics Service (Texas A & M University, College Station, TX, USA), under the supervision of Dr. Charles Johnson, where the genotyping for SNPs discovery was made by RadSeq protocol. The bioinformatics a... (Complete abstract click electronic access below) / Doutor

Made available in DSpace on 2018-08-01T22:57:28Z (GMT). No. of bitstreams: 1 tese_10266_Dissertação Final Iana Pedro da Silva Quadros.pdf: 2554686 bytes, checksum: 3716e4642d5c167349ceddb1c5ee793f (MD5) Previous issue date: 2016-08-31 / A mandioca é típica dos trópicos e fonte de segurança alimentar para mais de 600 milhões de pessoas, utilizada na alimentação humana e animal e na indústria, pela extração de amido e produção de biocombustível. O Brasil é o segundo país em produção, entretanto o incremento em produção é baixo para atender o crescente mercado. A compreenção da arquitetura genética de caracteres agronomicamente importantes é útil para delinear cruzamentos e possibilita a identificação de loci controladores de características quantitativas (QTL), no intuito de seleção assistida e clonagem de genes candidatos. Neste trabalho objetivou-se identificar, mapear e caracterizar QTL para as características de altura das plantas (AP), produtividade de parte aérea (PPA), produtividade total de raízes fresca (PTR), teor de matéria seca da raiz (MS) e produtividade de amido (PROD-AMD) de mandioca. Para isto foi utilizada uma população F1 de 141 indivíduos, oriunda do cruzamento entre as cultivares Fécula Branca e BRS Formosa, mantida em delineamento em blocos, com duas repetições e 16 plantas por parcela para as análises fenotípicas. A genotipagem dos indivíduos foi realizada usando SNPs, microssatélites e minissatélites. O mapa foi construído com abordagem multiponto e a detecção dos QTL realizada por análise de contraste entre médias e intervalo, considerando os diferentes tipos de segregação do QTL. Variabilidade foi observada para todas as características e altas correlações fenotípicas, exceto para MS, com destaque para PTR e PROD-AMD (0,98), bem como alta herdabilidade para AP (74,29%). Também, segregação transgressiva foi detectada para todas as características, indicando complementariedade de alelos dos pais na progênie segregante. O mapa genético representou regiões dos 18 cromossomos da mandioca e foi composto por 283 marcadores em 32 grupos de ligação. Uma região do cromossomo 10 apresentou evidência de pleitropia. Para AP, PPA e PROD-AMD um QTL comum foi identificado, bem como para PTR e PROD-AMD, três QTL comuns foram verificados. O MS apresentou QTL exclusivos. Estes resultados indicam o controle quantitativo das características estudadas, com QTL de grande e pequeno efeito detectados. Estes são úteis no melhoramento da cultura visando maior produtividade.

Autism is a severe childhood neuropsychiatric condition characterized by impairments in socialization and communication, and by restricted and repetitive behaviours. Autism spectrum disorder (ASD) is a complex and largely unknown disease with a strong genetic basis, multiple genes involved and environmental factors determining its phenotype. Interestingly, the DLX1/DLX2 and DLX5/DLX6 bigene clusters are located in autism susceptibility loci and Dlx genes are involved in GABAergic interneurons differentiation and migration to the cortex during forebrain development. Dlx gene expression is controlled by different cis-regulatory elements. Of these, 4 are active in the forebrain, URE2, I12b, I56ii and I56i. In order to determine the role of the DLX genes in ASD, variants were found in gene exons and in cis-regulatory elements in autistic individuals. A single nucleotide polymorphism (SNP), a change of an adenine for a guanine, was identified in I56i enhancer. Finding a SNP in I56i was very surprising considering that it is located in a Dlx binding motif highly conserved among >40 species. We showed, using in vitro approaches, that the presence of this SNP affects the affinity of Dlx for their binding site and reduces the transcriptional activation of the enhancer. The SNP also affects activity of the I56i enhancer in transgenic mice. In order to determine the real impact of the SNP in vivo, mutant mice harboring the SNP in their I56i enhancer were produced. That involved the insertion of the I56i enhancer with the SNP, using homologous recombination in mouse embryonic stem cells to replace the wild type version of the enhancer. With these mutant mice, we demonstrated that, in vivo, this SNP reduces Dlx5 and Dlx6 expression in the forebrain. Furthermore, this decrease in Dlx5/Dlx6 expression could affect the differentiation and/or migration of specific populations of inhibitory interneurons in the forebrain. No distinct iv behavioural phenotypes were observed between wild type mice and those carrying the SNP, during social interaction and anxiety tests. Therefore, these results suggest that even a subtle change in a regulatory element can have an impact in the development of the forebrain and may even contribute to disorders such as autism.

Single nucleotide polymorphism (SNP) methodology is being used as a means to determine genetic merit in beef cattle by interrogating animal genomes and associating the findings with performance traits. The ability to predict future trait performance is highly attractive to beef cattle producers as they can make important management and financial decisions earlier and with more certainty. To fully realize the potential of SNP testing technology the methodology must be vetted to assure producer confidence. The purpose of this project is to assess three sources of information for beef cattle trait assessment. These information sources are: SNP testing, Expected Progeny Differences (EPDs) and direct animal measures. To conduct this study, young beef bulls (n=181) consigned to the SIU Beef Evaluation Station were utilized in an 84-day period to obtain direct measures. The SIU Beef Evaluation Station uses the Calan-Broadbent confinement feeding system which allows researchers to monitor individual animal feed intake and weight gain. Feed efficiency traits are important to the cattle industry since feed is generally among the largest input cost to producers. The evaluation of bulls also assesses reproductive and carcass traits which are also important to the producer’s financial success.Individual animal performance information was sent to the bull’s respective breed association for determination of EPD’s. Blood samples were submitted to a commercial company for SNP testing (Igentiy Gold and Igenity Beef Profile, Neogen, Lincoln, NE). Data was analyzed using pairwise comparisons by source of information. Pearson correlations were used to determine the direction and the strength for sources of information to vary together. Data was determined to be correlated when the correlation coefficient was 0.3 < r < - 0.3. No correlation was observed between RFISIU :RFINEO (r = 0.042), RFINEO:F/GSIU (r = - 0.09), RFISIU:ADGNEO (r = 0.091), RFISIU:ADGSIU (r = - 0.039), RFINEO:ADGNEO (r = 0.236), BWNEO:BWSIU (r = 0.115), FRAMESIU:BWSIU (r = 0.111), FRAMESIU:BWEPD (r = 0.159), FRAMESIU:ADGSIU (r = 0.148), FRAMESIU:ADGNEO (r = -0.005), BWSIU:BWEPD (r = 0.256), and BWNEO:BWEPD (r = 0.226). Correlations were observed between RFISIU:F/GSIU (r = 0.455), ADGSIU :ADGNEO (r = 0.353), and FRAMESIU:BWNEO (r = 0.326).This study determined that beef bulls should continue to be performance tested due to discrepancies between sources of information for key animal performance traits. Assessment of SNPs used in the commercial test should continue.

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With the development of sequencing technologies, more and more sequence variants are available for investigation. Different types of variants in the human genome have been identified, including single nucleotide polymorphisms (SNPs), short insertions and deletions (indels), and large structural variations such as large duplications and deletions. Of great research interest is the functional effects of these variants. Although many programs have been developed to predict the effect of SNPs, few can be used to predict the effect of indels or multiple variants, such as multiple SNPs, multiple indels, or a combination of both. Moreover, fine grained prediction of the functional outcome of variants is not available. To address these limitations, we developed a prediction framework, HMMvar, to predict the functional effects of coding variants (SNPs or indels), using profile hidden Markov models (HMMs). Based on HMMvar, we proposed HMMvar-multi to explore the joint effects of multiple variants in the same gene. For fine grained functional outcome prediction, we developed HMMvar-func to computationally define and predict four types of functional outcome of a variant: gain, loss, switch, and conservation of function. / Ph. D.