<p>Many Single Nucleotide Polymorphisms (SNPs) found in coding or regulatory regions within the human genome lead to phenotypic differences that make prediction of physical appearance, based on genetic analysis, potentially useful in forensic investigations. Complex traits such as pigmentation can be predicted from the genome sequence, provided that genes with strong effects on the trait exist and are known. Phenotypic traits may also be associated with variations in gene expression due to the presence of SNPs in promoter regions. In this project, the identification of genes associated with these physical traits of potential forensic relevance have been collated from the literature using a text mining platform and hand curation. The SNPs associated with these genes have been acquired from public SNP repositories such as the International HapMap project, dbSNP and Ensembl. Characterization of different population groups based on the SNPs has been performed and the results and data stored in a MySQL database. This database contains SNP genotyping data with respect to physical phenotypic differences of forensic interest. The potential forensicrelevance of the SNP information contained in this database has been verified through in silico SNP analysis aimed at establishing possible relationships between SNP occurrence and phenotype. The software used for this analysis is MATCH&trade / .</p>

Recent Genome Wide Association Studies (GWAS) have identified a series of single nucleotide polymorphism (SNP)s that are associated with Alzheimer’s disease (AD). One of the SNPs, rs3851179 (G/A), is near the gene phosphatidylinositol-binding clathrin assembly protein (PICALM). To evaluate whether this SNP is associated with PICALM expression, we quantified PICALM mRNA in 56 brain cDNA samples. Using linear regression analysis, we analyzed PICALM expression relative to rs3851179, AD status, and cell type specific markers. An association was detected between rs3851179 and PICALM, microvessel mRNA, glial fibrillary acidic protein (GFAP) mRNA, and synaptophysin (SYN) mRNA. To gain clarity into other possible SNP mechanisms, we searched brain cDNA for PICALM splice variants. We identified several PICALM splice variants involving exons 13-19. To identify and gain an estimation of relative abundance of splice variants, we PCR-amplified across exons 13-20 in cDNA from six individuals, three rs3851179 GG individuals and three rs3851179 AA individuals. Sequencing the cloned isoforms we found that PICALM lacking exon 13 (delta 13) is the most abundant isoform. Other isoforms detected included deletion of exon 18-19. We targeted the latter part of the gene, exon 17-20, to investigate unequal allelic expression using next generation sequencing. Individuals heterozygous for rs76719109 (n= 35), located in exon 17, were used to study the abundance of G/T allele in cDNA and genomic DNA. When we analyzed the T:G allelic ratio, the variant lacking exons 18 and 19 showed unequal allelic expression (p-value < 0.001) in a subset of individuals. One individual was an outlier, showing overall unequal allelic expression, which maybe be harboring a rare mutation capable of modifying PICALM expression. The PICALM intronic SNP rs588076 was associated with delta 18-19 isoform splicing (p-value < 0.001). In conclusion, this study gained a greater insight into the role of AD genetics in PICALM expression and splicing.

Cell membrane receptors help to mediate communication between the cell and its environment. The largest group of these membrane receptors belong to the family of G protein-coupled receptors (GPCRs). GPCRs contain seven transmembrane (TM) helices and signal predominantly through heterotrimeric G proteins in response to diverse extracellular stimuli. Previously, three levels of amino acid conservation were proposed to understand the structure and function of a GPCR. This includes “signature” amino acids, “group –conserved” amino acids and amino acids conserved only within a specific subfamily. The group-conserved residues in class A GPCR family involve amino acid conservation of up to 99% when considered as a group of small and weakly polar residues (Ala, Gly, Ser, Cys and Thr). These group-conserved residues have been proposed as key determinants in helix-helix interactions. Therefore, I selected these residues for structure-function analysis in the amine and the prostanoid receptor sub-families of class A GPCRs. Molecular and biochemical assays clearly demonstrate the importance of group-conserved residues in β2-adrenergic receptor and thromboxane A2 receptor (TP) structure and function. These studies led to the identification of a non-synonymous single nucleotide polymorphic variant (nsSNP) A160T in TP to be a constitutively active mutant (CAM). Further, the TP-CAM was used as a pharmacological tool that enabled classification of well-known TP-blockers, into neutral antagonists and inverse agonists. The role of TP-A160T in prostanoid receptors, TP- Prostacyclin receptor (IP) heterodimerization and signaling was investigated. Activation of a GPCR ultimately leads to structural changes in its intracellular loops (ICLs), which in turn activates G-protein. TP activates its cognate G protein (Gαq), while IP mediates signaling, through Gαs. Using TP-IP chimeric receptors, molecular modelling, and site directed mutagenesis studies I determined the specific ICL regions required for G protein coupling in TP and IP. Significant challenges exist in expressing and purifying GPCR-CAMs in amounts required to pursue biophysical studies. Using tetracycline inducible HEK293S system, A160T was expressed at high-levels and CD spectropolarimetry studies were successfully pursued on the purified A160T. The CD spectra showed that the loss of thermal stability of the A160T mutant is due to the subtle changes in the secondary structure of the A160T protein. These studies involving molecular, biochemical and pharmacological approaches provide novel insights into the structure and function of prostanoid receptors TP and IP.

This dissertation brings to the fore the “Characterization of the SULT1A1 polymorphism in a South Africa Tswana population group.” The primary experimental group studied came from South African homogeneous Tswana individuals who participated voluntarily in an ongoing large-scale epidemiological Prospective Urban and Rural Epidemiological (PURE) study the North-West University (Potchefstroom Campus) participates in, as one of the 16 low- middleand high-income countries across the world. The primary aspect investigated was the comprehensive profile of the single nucleotide polymorphism (SNP) and copy number variation (CNP) of the SULT1A1 gene. Using the PCRbased RFLP method, SULT1A1 genotypes, and allele frequency distributions in an experimental group of 1 867 individuals were determined. According to the literature this is by far the largest and most homogeneous group from which such information has been acquired to date. The SULT1A1*1, SULT1A1*1/*2 and SULT1A1*2 genotypes were found to be present at a percentage of 43.76, 47.12 and 9.11 respectively. In comparison to similar studies in other population groups, results from this study indicate that there are ethnic differences in the SULT1A1 genotypes incidence. Asian group differs from Caucasian and Tswana groups because of its exceptionally high prevalence of individuals with the SULT1A1*1 genotype and a very low incidence of the SULT1A1*2 genotype. The SULT1A1*1 genotype profiles of Caucasian and Tswana groups were comparable, but notable differences were observed for the SULT1A1*2 genotype. Using a quantitative multiplex PCR method for the CNV study, the numbers of copies of the SULT1A1 gene in the Tswana population were determined, and the results showed 1 to ~5 copies: only 0.65% of the subjects had a single copy, whereas 59.69% of the subjects had 3 or more copies. This result shows a significant discrepancy between the Caucasian-American samples, which showed that only 26% from that group had more than three copies. However, there is a significant relationship with the African-American population, which presented 63% with 3 or more copies. This finding confirms results from a much smaller African-American study, and suggests a possible genetic link between the African Tswana and the heritage of the African-Americans. These findings were submitted for publication to the South African Journal of Science, as that journal specializes in publication of new knowledge that has a regional focus on Africa. Simultaneous phenotypic consequences of the SNP and CNP of the SULT1A1 gene, as well as the thermo-stable and thermo-labile forms of the sulfotransferases were determined. For this, the formation of [35S]-4-nitrophenyl sulphate from 4-nitrophenol and [35S]-3’-phosphoadenosine- 5’-phosphosulfate ([35S]-PAPS) in platelet homogenates were measured, with the data normalized to a common platelet count. This investigation required fresh blood for enzyme activity. These samples came from 98 Caucasian subjects who voluntarily participated in this part of the study. The experimental data presented a unique challenge to develop a statistical model to accommodate the complexity of the distribution of the data in the phenotype and genotype components, which could be achieved by the development of a mixed model. The model indicated that product formation increased through increasing copy number, but did not differ for SULT1A1*1 and SULT1A1*1/*2. However, the rate of increase in product for the thermo-stable forms of the SULTs was greater than that of thermo-labile forms. In contrast, copy number effect for SULT1A1*2 differed considerably from that of the other two genotypes. Since genotype is also a significant factor, it was concluded from Tukey post-hoc tests that the population group means for product formation differ significantly (for all levels). These results are presently being prepared for publication in an accredited international journal. Finally, perturbations in 23 biochemical parameters measured in the PURE study were analyzed as a function of the SULT1A1 SNP and CNP were evaluated. No group separation in this regard could be found. It could be shown however, that sulfonation of the iodothyronines, which are endogenous substrates for the SULTs, was influenced by the SULT1A1 genotype. The relative concentrations in plasma of the sulphonated iodothyronines may be expressed as T2S > T3S >> T4S, which coincides with the substrate preference of the SULT1A1 enzymes. This observation may, however, only be qualitatively interpreted as (1) the targeted metabolomics mass spectrometric method used for the quantitative analysis of these substances needs further development, and (2) the influence of deiodonation was not taken into account in these studies. In conclusion, three perspectives are given at the end of the thesis which might be considered for further investigations. / Thesis (Ph.D. (Biochemistry))--North-West University, Potchefstroom Campus, 2010.

This dissertation brings to the fore the “Characterization of the SULT1A1 polymorphism in a South Africa Tswana population group.” The primary experimental group studied came from South African homogeneous Tswana individuals who participated voluntarily in an ongoing large-scale epidemiological Prospective Urban and Rural Epidemiological (PURE) study the North-West University (Potchefstroom Campus) participates in, as one of the 16 low- middleand high-income countries across the world. The primary aspect investigated was the comprehensive profile of the single nucleotide polymorphism (SNP) and copy number variation (CNP) of the SULT1A1 gene. Using the PCRbased RFLP method, SULT1A1 genotypes, and allele frequency distributions in an experimental group of 1 867 individuals were determined. According to the literature this is by far the largest and most homogeneous group from which such information has been acquired to date. The SULT1A1*1, SULT1A1*1/*2 and SULT1A1*2 genotypes were found to be present at a percentage of 43.76, 47.12 and 9.11 respectively. In comparison to similar studies in other population groups, results from this study indicate that there are ethnic differences in the SULT1A1 genotypes incidence. Asian group differs from Caucasian and Tswana groups because of its exceptionally high prevalence of individuals with the SULT1A1*1 genotype and a very low incidence of the SULT1A1*2 genotype. The SULT1A1*1 genotype profiles of Caucasian and Tswana groups were comparable, but notable differences were observed for the SULT1A1*2 genotype. Using a quantitative multiplex PCR method for the CNV study, the numbers of copies of the SULT1A1 gene in the Tswana population were determined, and the results showed 1 to ~5 copies: only 0.65% of the subjects had a single copy, whereas 59.69% of the subjects had 3 or more copies. This result shows a significant discrepancy between the Caucasian-American samples, which showed that only 26% from that group had more than three copies. However, there is a significant relationship with the African-American population, which presented 63% with 3 or more copies. This finding confirms results from a much smaller African-American study, and suggests a possible genetic link between the African Tswana and the heritage of the African-Americans. These findings were submitted for publication to the South African Journal of Science, as that journal specializes in publication of new knowledge that has a regional focus on Africa. Simultaneous phenotypic consequences of the SNP and CNP of the SULT1A1 gene, as well as the thermo-stable and thermo-labile forms of the sulfotransferases were determined. For this, the formation of [35S]-4-nitrophenyl sulphate from 4-nitrophenol and [35S]-3’-phosphoadenosine- 5’-phosphosulfate ([35S]-PAPS) in platelet homogenates were measured, with the data normalized to a common platelet count. This investigation required fresh blood for enzyme activity. These samples came from 98 Caucasian subjects who voluntarily participated in this part of the study. The experimental data presented a unique challenge to develop a statistical model to accommodate the complexity of the distribution of the data in the phenotype and genotype components, which could be achieved by the development of a mixed model. The model indicated that product formation increased through increasing copy number, but did not differ for SULT1A1*1 and SULT1A1*1/*2. However, the rate of increase in product for the thermo-stable forms of the SULTs was greater than that of thermo-labile forms. In contrast, copy number effect for SULT1A1*2 differed considerably from that of the other two genotypes. Since genotype is also a significant factor, it was concluded from Tukey post-hoc tests that the population group means for product formation differ significantly (for all levels). These results are presently being prepared for publication in an accredited international journal. Finally, perturbations in 23 biochemical parameters measured in the PURE study were analyzed as a function of the SULT1A1 SNP and CNP were evaluated. No group separation in this regard could be found. It could be shown however, that sulfonation of the iodothyronines, which are endogenous substrates for the SULTs, was influenced by the SULT1A1 genotype. The relative concentrations in plasma of the sulphonated iodothyronines may be expressed as T2S > T3S >> T4S, which coincides with the substrate preference of the SULT1A1 enzymes. This observation may, however, only be qualitatively interpreted as (1) the targeted metabolomics mass spectrometric method used for the quantitative analysis of these substances needs further development, and (2) the influence of deiodonation was not taken into account in these studies. In conclusion, three perspectives are given at the end of the thesis which might be considered for further investigations. / Thesis (Ph.D. (Biochemistry))--North-West University, Potchefstroom Campus, 2010.

Nel corso dell’ultimo secolo, i programmi di miglioramento genetico hanno portato a notevoli progressi nelle razze bovine nonostante le conoscenze scarse o assenti relative ai geni coinvolti e alle loro funzioni. In questa tesi il genoma bovino è stato studiato con tecnologie massive, impiegando metodiche d’analisi sia tradizionali sia innovative per identificare i geni che controllano i fenotipi complessi e dare supporto al sistema allevatoriale. Nella prima parte del lavoro pannelli SNP a media densità sono stati utilizzati per l’individuazione di ”selection signature” condivise tra razze bovine da latte o da carne, identificando geni candidati specifici per l’attitudine produttiva, e di regioni associate ai fenotipi produttivi in razze da latte. L’associazione è stata effettuata sia con una regressione classica sia con un approccio “gene-centrico” innovativo. Regioni e geni associati significativamente ai fenotipi legati alla produzione lattea sono risultati essere razza specifici. Nella seconda parte, i dati dal sequenziamento dell’esoma e da pannelli SNP ad alta densità sono stati combinati per identificare mutazioni deleterie nella razza Frisona. Diversi approcci sono stati combinati per filtrare e ordinare le varianti genetiche. Alcuni geni che controllano meccanismi biologici di base, quali la fertilità e lo sviluppo, sono stati identificati come candidati ad essere deleteri. Per queste indagini sono stati utilizzati alcuni strumenti bioinformatici già disponibili e, quando necessario, sono stati sviluppati nuovi approcci e procedure. / In the last century, advanced breeding methods have increased the rate of genetic gain in cattle but, with a few exceptions, genes and molecular functions underlying phenotypic variation are still largely unknown. In this thesis, the bovine genome was studied with high-throughput technologies using established and innovative procedures to search for genes controlling complex traits and support bovine breeding. In the first part a medium density marker panel was used to detect selection signatures shared by dairy or by beef breeds, identify candidate genes for specific production aptitudes, and genomic regions associated to production traits in dairy cattle. Genome wide association was run using a classic regression and an innovative gene-centric method. Regions and genes significantly associated to milk traits were specific for each breed. In a second part, data from exome sequences and high-density marker panels were combined to identify deleterious mutations in Italian Holstein. Different approaches were combined to filter and prioritize genetic variants. A set of candidate deleterious genes were found, that control basic biological mechanisms such as development and fertility. State of the art bioinformatics tools were used in these investigations and, whenever necessary, new pipelines and approaches were developed.

The release of the Illumina BovineSNP50 BeadChip in late 2007 has drawn attention from cattle breeders around the world to develop breeding programs that leverage association of these single nucleotide polymorphism (SNP) with economically important quantitative trait loci (QTL). In that context this project has come to study applications of the SNP panel in beef cattle. Analysis of linkage disequilibrium (LD) existing in Angus, Charolais, and crossbred animals revealed the pattern of LD within each breed group, as well as the persistence of LD phase between pairs of the breed groups. This is important for genomic selection where SNP are trained in one population and used to predict breeding value for animals in another population. Detection of chromosome regions potentially carrying QTL or causative mutations affecting the phenotypic variation in economically important traits was presented at individual SNP and haplotype levels. There were 269 SNP associated (P<0.001) with birth weight (BWT), weaning weight (WWT), average daily gain (ADG), dry matter intake (DMI), mid-test metabolic weight (MMWT), residual feed intake (RFI). They explained 1.64% - 8.06% of the phenotypic variation in these traits. There were 520 SNP associated (P<0.001) with carcass quality traits, namely hot carcass weight, back fat thickness, ribeye area, marbling scores, lean yield grade by Beef Improvement Federation, steak tenderness, and six rib dissection traits. These SNP explained 1.90 - 5.89% of the phenotypic variance of the traits. Many of the significant SNP were located on chromosome 6. Six haplotypes were found associated (P<0.05) with ADG, DMI, and RFI. In order for genomic selection to happen in beef cattle, higher density SNP panels should be made available at low genotyping cost. However, the cost of genotyping animals for high density SNP chip is still high, thus genotype imputation has come to practice. The last chapter of this thesis compared two approaches presently used in genotype imputation, investigated factors affecting imputation accuracy, as well as the impact of imputation accuracy on genomic estimated breeding value (GEBV). It proved that the highest possible accuracy of GEBV is attainable with sufficiently large groups of reference animals. / Ontario Ministry of Agriculture, Food and Rural Affairs. Ontario Cattlemen’s Association. Ontario Farm Innovation Program. Agriculture and Agri-Food Canada’s Growing Forward Program. Agriculture Adaptation Council. Ontario Research and Development Program. MITACS Accelerate. Beef Improvement Opportunities.

The possibility of identifying single nucleotide polymorphisms (SNPs) that would be useful for rapid bacterial typing was investigated. Neisseria meningitidis was the organism chosen for modelling the approach since informative SNPs could be found amongst the sequence data available for multi-locus sequence typing (MLST) at http://www.mlst.net. The hypothesis tested was that a small number of SNPs located within the seven gene fragments sequenced for MLST provide information equivalent to MLST. Preliminary investigations revealed that a small number of SNPs could be utilised to highly discriminate sequence types (STs) of clinical interest. Laboratory procedures demonstrated that SNP fingerprinting of N. meningitidis isolates is achievable. Further tests showed that laboratory identification of a defining SNP in the genome of isolates was to be a practical method of obtaining relevant typing information. Identification of the most discriminating SNPs amongst the ever-increasing amount of MLST sequence data summoned the need for computer-based assistance. Two methods of SNP selection devised by the author of this thesis were translated into computer-based algorithms by contributing team members. Software for two computer programs was produced. The algorithms facilitate the optimal selection of SNPs useful for (1) distinguishing specific STs and (2) differentiating non-specific STs. Current input information can be obtained from the MLST database and consequently the programs can be applied to any bacterial species for which MLST data have been entered. The two algorithms for the selection of SNPs were designed to serve contrasting purposes. The first of these was to determine the ST identity of isolates from an outbreak of disease. In this case, isolates would be tested for their membership to any of the STs known to be associated with disease. It was shown that one SNP per ST could distinguish each of four hyperinvasive STs of N. meningitidis from between 92.5% and 97.5% of all other STs. With two SNPs per ST, between 96.7% and 99.0% discrimination is achieved. The SNPs were selected from MLST loci with the assistance of the first algorithm which scores SNPs according to the number of base mismatches in a sequence alignment between an allele of an ST of interest and alleles belonging to all other STs at a specified locus. The second purpose was to determine whether or not isolates from different sources belong to the same ST, regardless of their actual ST identity. It was shown that with seven SNPs, four sample STs of N. meningitidis could, on average, be discriminated from 97.1% of all other STs. The SNPs were selected with the aid of the second algorithm which scores SNPs at MLST loci for the relative frequency of each nucleotide base in a sequence alignment as a measure of the extent of their polymorphism. A third algorithm for selecting SNPs has been discussed. By altering the method of scoring SNPs, it is possible to overcome the limitations inherent in the two algorithms that were utilised for finding SNPs. In addition, the third approach caters for finding SNPs that distinguish members of a complex from non-members.

Aquaculture plays an important role in economic development and food security in many countries in the world. World aquaculture production in 2006 was 51.7 million tonnes with an estimated value of US$ 78.8 billion (FAO, 2009). World production will need to increase however by 30-40 million tonnes from its current production level by 2030 to meet growing global demand for fish. In this context, aquaculture in Vietnam has developed rapidly over the past decade and the fisheries sector ranked fourth in terms of export value in 2008 (Vietnamnet, 2008). Total fisheries production in Vietnam in 2007 was 4.149 million tonnes, of which fisheries production from catch and aquaculture were 2.064 and 2.085 million tonnes, respectively. A variety of aquatic species are cultured in Vietnam, but shrimps (mainly Black Tiger shrimp Penaeus monodon, and Pacific white shrimp Litopenaeus vannamei) and ‘tra’ or ‘basa’ catfish are the most common species used in aquaculture. The giant freshwater prawn (GFP), Macrobrachium rosenbergii, is one of the most important crustacean species in inland aquaculture in many countries across the world where this species is either native or exotic. GFP is suitable for culture in a variety of farming systems, including monoculture or polyculture in ponds, pens, and integrated or rotational rice-prawn culture models. The GFP industry worldwide relies totally on wild or unimproved stocks, a practice that threatens the long-term sustainability of GFP farming due to low productivity and vulnerability of farmed stocks to disease. The current status of GFP aquaculture highlights the need for initiation of a systematic stock improvement program for the species to improve economically important traits. Large-scale selective breeding programs have been instigated for some finfish, salmonids and GIFT tilapia for example, and some selective breeding trials have been conducted on crustacean species, namely marine penaeid shrimp and freshwater crayfish. Examples of selective breeding programs on aquatic species have demonstrated that significant genetic gains can be achieved for growth rates with gains of around 10-20% per generation. While a selective breeding program is an option for GFP stock improvement, an alternative approach to improving GFP productivity, potentially with more immediate effect and one that is less expensive, is crossbreeding which may produce heterosis or hybrid vigour in crossbred offspring. Therefore, a crossbreeding strategy was trialed in the current study as a starting point for a stock improvement program for the GFP industry in Vietnam. The current study assessed the growth performance of three GFP strains (two wild Vietnamese strains from the Dong Nai and Mekong rivers, and a single domesticated Hawaiian strain) and their reciprocal crosses in a complete 3x3 diallel cross, i.e. three purebred and six crossbred strains. The diallel cross was carried out over two consecutive generations (G1 and G2). Juveniles for the experiments were produced using single-pair matings. Juveniles from each strain combination were stocked into three replicate hapas for 15 weeks. Growth data (body weight, carapace length, standard length) from the G1 and G2 were pooled for all subsequent analyses as there was no effect of generation on growth traits. Results showed that the Hawaiian strain performed best among purebred strains, and crosses with the Dong Nai or Mekong strains as dams and the Hawaiian strain as sires grew significantly faster than did the purebred Dong Nai or Mekong strains. These results suggest potential for heterosis among some crosses. Growth data were analyzed in depth by partitioning the strain combination (cross) effect into three components: strain additive genetic effects, heterotic effects, and strain reciprocal effects. Strain additive genetic and reciprocal effects were significant sources of variation for all growth traits measured. Strain additive genetic effects were highest for the Hawaiian strain and lowest for the Mekong strain for all growth traits. Reciprocal effects influenced negatively on growth rate of crosses with the Hawaiian (H) strain as dams and the Dong Nai (D) or Mekong (M) as sires compared with their reciprocal crosses (DH and MH). Heterotic effects for all growth traits were small and not significantly different from zero (P > 0.05). These results indicate that a crossbreeding approach based on the strains evaluated here provides only limited potential for improving growth rates based simply on heterotic outcomes and that a likely more productive option would be to trial artificial selection on a diverse synthetic stock. The current study also employed genetic markers (microsatellites) to characterize levels and patterns of genetic diversity in three purebred strains of GFP that originated from the diallel cross above. All three purebred strains showed relative high levels of genetic diversity in terms of allele number and individual heterozygosity across the six marker loci screened. Levels of genetic diversity present in the three purebred strains combined into a single stock were compared with that from a combination of three wild river stocks to assess the impact of domestication on genetic diversity of a ‘synthetic’ population. Results demonstrated that there was no significant loss of genetic diversity in the three purebred strains combined compared with a reference set containing the three wild populations. Therefore, a synthetic population formed from these purebred strains successfully captured the majority of genetic variation present in the wild broodstock. This synthetic population provides a potential stock for a future selective breeding program for GFP in Vietnam. The current study was also the first attempt to identify single nucleotide polymorphisms (SNPs) in key growth genes in GFP. Two key candidate genes were targeted, actin and crustacean hyperglycemic hormone (CHH), that are potentially linked to growth performance in GFP. The study screened SNPs in GFP females only, because growth performance of GFP males is influenced strongly by social rank. The study identified four SNPs in intron 3 of the CHH gene that were significantly correlated with individual body weight at harvest, while no SNPs detected in the actin gene were associated with growth traits in GFP. This finding however, needs to be confirmed using larger sample sizes and other GFP lines. The current study has produced important basic knowledge relevant to implementation of an effective stock improvement program for GFP in Vietnam. Results indicate that a selective breeding strategy rather than a crossbreeding approach is likely to be the best strategy for improving GFP culture stocks in Vietnam. In addition, the study demonstrates that application of modern molecular genetic technologies can be efficient in developing a genetically diverse, synthetic population for stock improvement and for identifying potential markers correlated with important commercial traits in GFP. Integration of DNA techniques with traditional breeding practices can facilitate GFP stock improvement in Vietnam and accelerate the industry development when improved lines are available. Some limitations of the current study and recommendations for further work are discussed.

INTRODUÇÃO: Embora todos os indivíduos com anemia falciforme (AF) apresentem o mesmo defeito molecular nos genes da beta-globina, existe uma considerável variabilidade fenotípica entre eles. A síntese continuada da hemoglobina fetal (HbF) é o mais potente modificador da morbimortalidade da AF. A HbF diminui a polimerização da desoxi-HbS, reduzindo a intensidade da anemia hemolítica crônica e dos fenômenos vaso-oclusivos, consequentemente, as complicações sistêmicas da AF. Há uma grande variação na taxa de síntese de HbF (1% a 30%) em indivíduos com AF. Vários estudos demonstraram que o tratamento com hidroxiureia (HU) diminui a morbimortalidade desta hemoglobinopatia, principalmente, por estimular a síntese de HbF. Na dose máxima tolerada (DMT), a HU geralmente aumenta os níveis de HbF entre 10% e 40%. Contudo, há uma grande variabilidade de resposta, a DMT é muito variável, cerca de 25% dos portadores de AF não respondem e não há preditores de resposta definidos à HU. Estudos polimorfismos de nucleotídeo único (SNPs) demonstraram a influência de modificadores epigenéticos na regulação da expressão da HbF. Estes elementos são, principalmente, o oncogene BCL11A, a região intergênica HMIP e o polimorfismo Xmn1-HBG2. Estes 3 quantitative trait loci (QTLs) detêm 20% a 50% do controle da expressão dos genes HBG (genes envolvidos na síntese da HbF). OBJETIVOS: Avaliar o comportamento epidemiológico e a associação dos SNPs Xmn1- HBG2; BCL11A rs7482144, rs4671393 e rs11886868; HMIP-2 rs9399137 e rs9402686 com a expressão da HbF e com o comportamento dos parâmetros hematimétricos em portadores de AF tratados com HU. PACIENTES E MÉTODOS: Neste estudo pioneiro de coorte prospectivo foram incluídos sequencialmente indivíduos com AF, em uso regular de HU por pelo menos 6 meses, que não receberam transfusão sanguínea 3 meses antes de ingressar no estudo e que não faziam uso de drogas que estimulassem a síntese de HbF. Foram coletados 4 ml de sangue venoso periférico para extração do DNA genômico. A genotipagem dos polimorfismos foi realizada por meio da reação da cadeia de polimerase em tempo real. RESULTADOS: Foram avaliados 121 pacientes, entre 1 ano e 9 meses-54 anos (19 ± 14) anos idade, que estavam recebendo doses regulares de HU entre 8,6-42,8 (23 ± 7,6) mg/kg/dia, durante 6- 254 (102± 67) meses. Não encontramos correlação entre a contagem de leucócitos, de neutrófilos e de reticulócitos; hemoglobina total; volume corpuscular médio e a concentração de hemoglobina corpuscular média, com os valores basais da HbF. A HbF basal (r=0,40; P < 0,001), a hemoglobina total basal (r=0,26; P = 0,005) e o tempo de exposição (r = -0,30; P = 0,001) foram associadas significativamente com maiores taxas de HbF ao final do estudo. Não houve correlação dos polimorfismos com os parâmetros hematimétricos, com o tempo de exposição e com a DMT de HU. Os SNPs HMIP-2 rs9399137 e rs9402686 foram responsáveis por 5,7% e 8,4% do total de variação da HbF basal (P= 0,01 e P=0,002). Não houve correlação, porém, entre os demais polimorfismos com a variação dos níveis basais de HbF. Os SNPs BCL11A rs1427407, rs4671393 e rs11886868 foram responsáveis, respectivamente, por uma variação de 7,6%, 4,5% e 4,3% nos níveis de HbF final (P=0,017; P=0,025 e P=0,029). Ainda, houve uma associação do rs1427407 (B = 0,29; P = 0,035) e do rs4671393 (B = 0,28; P = 0,036) em relação aos valores do delta HbF (variação da HbF final menos a HbF inicial). CONCLUSÃO: Estes dados sugerem que os indivíduos com AF com SNP BCL11A rs1427407 respondem mais favoravelmente ao tratamento com HU, no incremento dos níveis de HbF. São necessários estudos com populações maiores para validarmos estes achados. / INTRODUCTION: Although all individuals with sickle cell anemia (SCA) have the same molecular defect in the beta-globin genes, considerable phenotypic variability exists between them. Continued synthesis of fetal hemoglobin (HbF) is the most powerful SCA morbimortality modifier. HbF decreases the polymerization of deoxy-Hb, reducing the intensity of chronic hemolytic anemia and vaso-occlusive phenomena, and consequently systemic complications of SCA. There is a large variation in the HbF synthesis rate (1 to 30%) in patients with SCA. Several studies show that treatment with hydroxyurea (HU) decreases the morbimortality of this hemoglobinopathy, mainly by stimulating HbF synthesis. At the maximum tolerated dose (MTD), HU generally increases HbF levels from 10 to 40%. However, there is great variability in response as the MTD is highly variable, about 25% of SCA patients do not respond and there are no response predictors set for HU. Single nucleotide polymorphism studies (SNPs) demonstrate the influence of epigenetic modifiers in the regulation of HbF expression. These elements are, mainly, the BCL11A oncogene, the HMIP intergenic region and the Xmn1-HBG2 polymorphism. These 3 quantitative trait loci (QTLs) hold 20 to 50% of HBG gene expression control (genes involved in HbF synthesis). OBJECTIVE: To study the epidemiological behaviors and the association of SNPs Xmn1- HBG2; BCL11A rs7482144, rs4671393 and rs11886868; HMIP-2 rs9399137 and rs9402686 with HbF expression and with the behavior of hematimetric parameters in SCA patients treated with HU. PATIENTS AND METHODS: In this pioneering prospective cohort study, we included SCA patients, in regular treatment with HU at least for 6 months, who had not received blood transfusions in the 3 months prior to entering in the study and who didn‘t use drugs that stimulate HbF synthesis. We collected 4 ml of venous blood to proceed with the genomic DNA extraction. The polymorphism genotyping was done by real-time polymerase chain reaction. RESULTS: We evaluated 121 individuals with SCA aged between 1 year 9 months and 54 years (19 ± 14) who were receiving HU doses between 8.6 and 42.8 (23 ± 7.6) mg/kg/day for 6 to 254 (102 ± 67) months. No correlation was found between total leukocyte, neutrophils and reticulocytes counts; total hemoglobin; mean corpuscular volume and the concentration of mean corpuscular hemoglobin with baseline values of HbF. Basal HbF (r = 0.40; P <0.001), total baseline hemoglobin (r = 0.26; P = 0.005) and exposure time to HU (r = -0.30; P = 0.001) were significantly associated with higher HbF rates at the end of the study. There was no correlation of polymorphisms with the hematological parameters, exposure time and the MTD of HU. The SNPs HMIP-2, rs9399137 and rs9402686 accounted for 5.7% and 8.4% of the total variation of baseline HbF (P = 0.01 and P = 0.002). There was no correlation, however, between the other polymorphisms and variation in baseline HbF levels. The SNPs BCL11, rs1427407, rs4671393 and rs11886868 were responsible, respectively, for a variation of 7.6%, 4.5% and 4.3% in the final HbF levels (P = 0.017, P = 0.025 and P = 0.029). Still, there was an association of rs1427407 (B = 0.29; P = 0.035) and rs4671393 (B = 0.28; P = 0.036) in relation to delta HbF values (final minus initial HbF variation). CONCLUSIONS: These data suggest that individuals with SCA who have SNP rs1427407 BCL11A respond more favorably to HU treatment, with increased HbF levels. Studies with larger populations are necessary to validate these findings.