Submitted by Erika Demachki (erikademachki@gmail.com) on 2014-10-22T18:36:07Z No. of bitstreams: 2 Dissertação - Cristyene Gonçalves Benicio - 2012.pdf: 2894781 bytes, checksum: 3c9043dba7034429c44217077fc3cac5 (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) / Approved for entry into archive by Jaqueline Silva (jtas29@gmail.com) on 2014-10-22T20:22:44Z (GMT) No. of bitstreams: 2 Dissertação - Cristyene Gonçalves Benicio - 2012.pdf: 2894781 bytes, checksum: 3c9043dba7034429c44217077fc3cac5 (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) / Made available in DSpace on 2014-10-22T20:22:44Z (GMT). No. of bitstreams: 2 Dissertação - Cristyene Gonçalves Benicio - 2012.pdf: 2894781 bytes, checksum: 3c9043dba7034429c44217077fc3cac5 (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) Previous issue date: 2012-08-30 / Rice (Oryza sativa L.) has great social and economic importance worldwide. Produce food for a growing world population, promoting increased productivity in environmentally appropriate conditions, it one of the great challenges of breeding programs. Rice production based on seasonal rainfall, typical of upland rice (rainfed), today represents about 40% of Brazilian production. The agricultural irrigation consumes much of the planet's fresh water, and restricting the use of water resources is a reality. With the rising cost of water for agriculture and potential shortages in some regions of the planet, the development of plants more efficient in the water use is a priority demand of breeding programs. This study aimed to evaluate and compare the polymorphism of a set of microsatellite markers (SSRs) and SNPs (Single Nucleotide Polymorphisms) and use them for mapping QTL for yield components under two irrigation conditions. The parentals Douradão (drought tolerant) and Primavera (susceptible to drought) resulted in a segregating population consisting of 221 F2:5, which were genotyped with fluorescent SSR markers in analyzer ABI3100 (Applied Biosystems) and SNP markers developed for the GoldenGate platform based on Veracode technology (Illumina). Among the 86 SSRs, 11 (12.8%) did not amplify and 41 (54.7%) were polymorphic. Among the 1920 SNPs, 316 (16.45%) did not amplify for both parentals and 46 (2.87%) were polymorphic. The parentals and their progeny were evaluated in two trials (with and without water deficit) in 12x19 rectangular lattice design with two replications. The composite interval mapping analysis identified 53 QTL, 10 of which related to ISS (index of susceptibility to drought) and five to productivity in water stress condition. Among the identified QTL it were found putative genes related to plant abiotic stress defense mechanisms. Families CNAx15128-70-B, CNAx15128-118-B, CNAx15128-74-B and CNAx15128-120-B showed higher yield under drought and lower ISS. These families may be evaluated by rice breeding programs aiming the development of superior cultivars. / A cultura do arroz (Oryza sativa L.) possui grande importância social e econômica no mundo inteiro. Produzir alimento para uma população mundial crescente, promovendo um aumento da produtividade e em condições de produção ambientalmente adequadas, é um dos grandes desafios dos programas de melhoramento. A produção de arroz em regime de irrigação natural, baseada em chuvas sazonais, típica de arroz de terras altas (sequeiro), representa hoje cerca de 40% da produção nacional. A irrigação agrícola consome grande parte da água potável do planeta, e a restrição do uso dos recursos hídricos é uma realidade. Com o aumento do custo da água para agricultura e potencial escassez em algumas regiões do planeta, o desenvolvimento de plantas mais eficientes no seu uso é uma demanda prioritária dos programas de melhoramento genético. Este trabalho teve como objetivo avaliar e comparar o polimorfismo de um conjunto de marcadores microssatélites (SSRs) e SNPs (Single Nucleotide Polymorphisms) e utilizá-los para o mapeamento de QTL para componentes de produção sob duas condições de irrigação. Os parentais Douradão (tolerante à seca) e Primavera (suscetível à seca) deram origem a uma população segregante composta por 221 famílias F2:5, que foram genotipadas com marcadores SSRs fluorescentes em analisador ABI3100 (Applied Biosystems) e marcadores SNPs desenvolvidos para a plataforma GoldenGate com tecnologia VeraCode (Illumina). Dentre os 86 SSRs, 11 (12,8%) não amplificaram e 41 (54,7%) foram polimórficos. Dentre os 1.920 SNPs, 316 (16,45%) não amplificaram para ambos parentais e 46 (2,87%) foram polimórficos. Os genitores e sua progênie foram avaliados em dois ensaios (com e sem déficit hídrico) no delineamento em látice retangular 12x19 com duas repetições. Através da análise de mapeamento por intervalo composto foram detectados 53 QTL, dos quais 10 relacionados ao ISS (índice de susceptibilidade à seca) e cinco à produtividade em condição de déficit hídrico. Dentre os QTLs identificados foram encontrados genes putativos relacionados a mecanismos de defesa da planta em resposta a estresses abióticos. As famílias CNAx15128-70-B, CNAx15128-118-B, CNAx15128-74-B e CNAx15128-120-B apresentaram maior produtividade sob déficit hídrico e menores ISS. Estas famílias poderão ser avaliadas pelo programa de melhoramento genético do arroz visando o desenvolvimento de cultivares superiores.

Introduction: In Africa, it is estimated that cardiovascular disease (CVD) will affect approximately 1.3 million people per annum over the following 20 years. C-reactive protein (CRP) is a predictor of CVD risk and certain CRP gene polymorphisms can result in altered CRP concentrations. The distribution of CRP gene polymorphisms is ethnic-specific and extrapolating information from other populations to the black South African population, reported to harbour considerable genetic variation, should be avoided. This highlights the fact that genetic research among black South Africans is necessary. Objectives: The main aim of this dissertation was to determine the association between various polymorphisms (reported and novel [single nucleotide polymorphisms (SNPs)] within the CRP gene with CRP concentrations [measured as high sensitivity (hs)-CRP concentrations] in a black South African population undergoing an epidemiological transition. Interactions between specific CRP polymorphisms and certain environmental factors on hs-CRP concentrations were also investigated. Methods: This cross-sectional study (n=1,588) was nested within the Prospective Urban and Rural Epidemiological (PURE) study. Genotyping was performed using Illumina VeraCode technology on the BeadXpress® platform. Hs-CRP concentrations were measured by the use of a sequential multiple analyser computer (SMAC) through a particle-enhanced immunoturbidometric assay. Results: All the SNPs adhered to the assumptions of Hardy-Weinberg equilibrium, although the distribution of several SNPs differed from that reported in other population groups. Three SNPs (rs3093058, rs3093062 and rs3093068) were associated with a significant (p ≤ 0.05) increase in CRP concentrations. Five SNPs (rs1205, rs1341665, rs2794520, rs7553007 and rs2027471) were associated with a significant (p ≤ 0.05) decrease in CRP concentrations. This difference in effect was most probably due to changes in gene function brought about by the localisation of these SNPs in the CRP gene. Men and urban individuals were more likely to present with significant associations between the SNPs investigated and CRP concentrations. The difference in the prevalence of the alleles associated with higher CRP concentrations in this population compared to non-African populations could possibly explain the increased CRP concentrations that are observed in the black South African population. Gene-gender (rs1205, rs1341665 and rs2027474) as well as gene-environmental (rs3093068) interactions were also observed. Conclusions: CRP concentrations are in themselves a complex trait and there are many factors at play that influence their expression. Numerous factors (both genetic and environmental) are involved and no single factor acting alone is likely to have enough of an influence to be used as a clinical diagnostic test of CRP concentrations. These results provide valuable information on the regulation of CRP in a black South African population as well as contribute to the literature of CRP on a global level. / Thesis (MSc (Nutrition))--North-West University, Potchefstroom Campus, 2013.

Introduction: In Africa, it is estimated that cardiovascular disease (CVD) will affect approximately 1.3 million people per annum over the following 20 years. C-reactive protein (CRP) is a predictor of CVD risk and certain CRP gene polymorphisms can result in altered CRP concentrations. The distribution of CRP gene polymorphisms is ethnic-specific and extrapolating information from other populations to the black South African population, reported to harbour considerable genetic variation, should be avoided. This highlights the fact that genetic research among black South Africans is necessary. Objectives: The main aim of this dissertation was to determine the association between various polymorphisms (reported and novel [single nucleotide polymorphisms (SNPs)] within the CRP gene with CRP concentrations [measured as high sensitivity (hs)-CRP concentrations] in a black South African population undergoing an epidemiological transition. Interactions between specific CRP polymorphisms and certain environmental factors on hs-CRP concentrations were also investigated. Methods: This cross-sectional study (n=1,588) was nested within the Prospective Urban and Rural Epidemiological (PURE) study. Genotyping was performed using Illumina VeraCode technology on the BeadXpress® platform. Hs-CRP concentrations were measured by the use of a sequential multiple analyser computer (SMAC) through a particle-enhanced immunoturbidometric assay. Results: All the SNPs adhered to the assumptions of Hardy-Weinberg equilibrium, although the distribution of several SNPs differed from that reported in other population groups. Three SNPs (rs3093058, rs3093062 and rs3093068) were associated with a significant (p ≤ 0.05) increase in CRP concentrations. Five SNPs (rs1205, rs1341665, rs2794520, rs7553007 and rs2027471) were associated with a significant (p ≤ 0.05) decrease in CRP concentrations. This difference in effect was most probably due to changes in gene function brought about by the localisation of these SNPs in the CRP gene. Men and urban individuals were more likely to present with significant associations between the SNPs investigated and CRP concentrations. The difference in the prevalence of the alleles associated with higher CRP concentrations in this population compared to non-African populations could possibly explain the increased CRP concentrations that are observed in the black South African population. Gene-gender (rs1205, rs1341665 and rs2027474) as well as gene-environmental (rs3093068) interactions were also observed. Conclusions: CRP concentrations are in themselves a complex trait and there are many factors at play that influence their expression. Numerous factors (both genetic and environmental) are involved and no single factor acting alone is likely to have enough of an influence to be used as a clinical diagnostic test of CRP concentrations. These results provide valuable information on the regulation of CRP in a black South African population as well as contribute to the literature of CRP on a global level. / Thesis (MSc (Nutrition))--North-West University, Potchefstroom Campus, 2013.

Introduction: Cardiovascular disease (CVD) is the leading cause of global mortality and its prevalence is increasing among black South Africans in spite of their favourable lipid profile. Apolipoprotein E (ApoE) is a well-described risk factor for CVD and certain polymorphisms within this gene alter the lipid profile. The author hypothesised that there are population-specific effects within the ApoE gene that are responsible for the favourable lipid profile observed in black South Africans whose effects are being altered by environmental factors. Objectives: The main aim of this study was to investigate the associations between specific ApoE single nucleotide polymorphisms (SNPs) and the lipid profile of a black South African population, taking into account certain environmental and phenotypic factors in order to explore the interaction effects between these variables. Methods: Genotyping within this cross-sectional study (n=1 588), nested within the Prospective Urban and Rural Epidemiology (PURE) study, was achieved using Illumina‘s® GoldenGate Genotyping Assay with VeraCode® technology on the BeadXpress® platform (proprietary multiplex fluorescent hybridisation assays on a bead array substrate) or the Bio-Rad CFX Manager© (version 2.0). The Konelab20i™ auto analyser was used for quantitative determination of serum total cholesterol; high-density lipoprotein cholesterol (HDL-C) and triglyceride (TG) concentrations. Low-density lipoprotein cholesterol concentrations were estimated by the Friedewald equation. Results: All SNPs adhered to the assumptions of the Hardy-Weinberg equilibrium, yet the frequency of the SNPs often differed from that reported in other ethnic groups. The well-reported rs429358 and rs7412 SNPs (as the constituent SNPs of the haplotype-genotypes) presented with the strongest associations with various components of the blood lipid profile in the black South African cohort under investigation. Two gene-environment (rs405509 and rs7412) interaction effects on TG remained significant after conducting post hoc tests. Two genotype-phenotype interaction effects between the rs7412 SNP and body mass index and gamma-glutamyl transferase on the HDL-C concentrations remained significant after conducting post hoc tests. Conclusions: The variety of associations between these particular SNPs and the blood lipid profile determined in the present cohort strongly indicates that it is integral to any public health investigation into CVD development that these SNPs be investigated. This study further produced greater insight into the biological mechanisms underlying serum lipid and cholesterol concentrations in a black South African population. Therefore, from these results it is evident that the lipid profile of black South Africans is most definitely influenced by not only genetic variations in the ApoE gene and certain environmental factors, but by the interaction between these factors as well. The present study is the largest study to date to investigate the effect of polymorphisms in the ApoE gene on the lipid profile of black South Africans. / MSc (Nutrition), North-West University, Potchefstroom Campus, 2014

Introduction: Cardiovascular disease (CVD) is the leading cause of global mortality and its prevalence is increasing among black South Africans in spite of their favourable lipid profile. Apolipoprotein E (ApoE) is a well-described risk factor for CVD and certain polymorphisms within this gene alter the lipid profile. The author hypothesised that there are population-specific effects within the ApoE gene that are responsible for the favourable lipid profile observed in black South Africans whose effects are being altered by environmental factors. Objectives: The main aim of this study was to investigate the associations between specific ApoE single nucleotide polymorphisms (SNPs) and the lipid profile of a black South African population, taking into account certain environmental and phenotypic factors in order to explore the interaction effects between these variables. Methods: Genotyping within this cross-sectional study (n=1 588), nested within the Prospective Urban and Rural Epidemiology (PURE) study, was achieved using Illumina‘s® GoldenGate Genotyping Assay with VeraCode® technology on the BeadXpress® platform (proprietary multiplex fluorescent hybridisation assays on a bead array substrate) or the Bio-Rad CFX Manager© (version 2.0). The Konelab20i™ auto analyser was used for quantitative determination of serum total cholesterol; high-density lipoprotein cholesterol (HDL-C) and triglyceride (TG) concentrations. Low-density lipoprotein cholesterol concentrations were estimated by the Friedewald equation. Results: All SNPs adhered to the assumptions of the Hardy-Weinberg equilibrium, yet the frequency of the SNPs often differed from that reported in other ethnic groups. The well-reported rs429358 and rs7412 SNPs (as the constituent SNPs of the haplotype-genotypes) presented with the strongest associations with various components of the blood lipid profile in the black South African cohort under investigation. Two gene-environment (rs405509 and rs7412) interaction effects on TG remained significant after conducting post hoc tests. Two genotype-phenotype interaction effects between the rs7412 SNP and body mass index and gamma-glutamyl transferase on the HDL-C concentrations remained significant after conducting post hoc tests. Conclusions: The variety of associations between these particular SNPs and the blood lipid profile determined in the present cohort strongly indicates that it is integral to any public health investigation into CVD development that these SNPs be investigated. This study further produced greater insight into the biological mechanisms underlying serum lipid and cholesterol concentrations in a black South African population. Therefore, from these results it is evident that the lipid profile of black South Africans is most definitely influenced by not only genetic variations in the ApoE gene and certain environmental factors, but by the interaction between these factors as well. The present study is the largest study to date to investigate the effect of polymorphisms in the ApoE gene on the lipid profile of black South Africans. / MSc (Nutrition), North-West University, Potchefstroom Campus, 2014