As a large number of single nucleotide polymorphisms (SNPs) and microsatellite markers are available, high resolution mapping employing multiple markers or multiple allele markers is an important step to identify quantitative trait locus (QTL) of complex human disease. For many complex diseases, quantitative phenotype values contain more information than dichotomous traits do. Much research has been done on conducting high resolution mapping using information of linkage and linkage disequilibrium. The most commonly employed approaches for mapping QTL are pedigree-based linkage analysis and population-based association analysis. As one of the methods dealing with multiple alleles markers, mixed models are developed to work out family-based association study with the information of transmitted allele and nontransmitted allele from one parent to offspring. For multiple markers, variance component models are proposed to perform association study and linkage analysis simultaneously. Linkage analysis provides suggestive linkage based on a broad chromosome region and is robust to population admixtures. One the other hand, allelic association due to linkage disequilibrium (LD) usually operates over very short genetic distance, but is affected by population stratification. Combining both approaches plays a synergistic role in overcoming their limitations and in increasing the efficiency and effectiveness of gene mapping.

Kawasaki disease (KD) is the most common cause of paediatric acquired heart disease which may be attributed to the combined effects of infection, immunological response, and genetic susceptibility. Acute coronary artery lesions (CALs) develop in 20-48 % KD children. In addition, chronic CALs develop in approximately 20-30% of untreated KD children. Although KD children treated with IVIG, 2-6% still develop chronic CALs. According to recent epidemiological studies, Asian populations have a much higher incidence of KD. Taiwan has the third highest annual incidence in the world (69 per 100,000 children < 5 years of age between 2003 and 2006). Several studies have shown that KD patients spontaneously produce high levels of IL- 10. Plasma or serum IL-10 levels of KD children in acute phase were nearly 8-33 fold and 4-5 fold higher than those of healthy controls and those of the acute febrile children, respectively. The elevated IL-10 levels during the acute phase of KD not only decreased during subacute and convalescent phase, but also decreased immediately after IVIG administration, coincidently rapid improvement of inflammatory symptoms. The above studies show a correlation of high IL-10 levels with inflammatory features of KD, but do not answer the question of whether high levels of IL-10 may be simply a byproduct of acute KD, or whether it may play a role in the pathogenesis of KD. Therefore, a family-based linkage study of 134 case-parents trios, a case-control study of 247 KD children and 129 normal controls, and a matched case-control study of 76 KD cases with acute coronary artery lesions (CALs) and 76 KD controls without acute CALs were carried out to evaluate the association of genetic single nucleotide polymorphisms (SNP) in IL-10 promoter (-1082, -819, and -592) with the risk of KD and acute CALs. Based on the Transmission Disequilibrium test (TDT) results, significant undertransmission of haplotype ATA and overtransmission of haplotype (ACC+GCC) were found for KD (p = 0.023 and 0.011, respectively), even after 1,000 times permutation (p = 0.026 and 0.010, respectively). In addition, the TC and CC genotype of IL-10-819T>C were significantly associated with the decreased risk of acute CALs (AOR, 0.93; 95% CI, 0.47-1.81 and AOR, 0.07; 95% CI, 0.01-0.62, respectively), as compared to TT genotype. The carries of AC and CC genotype in IL-10-592A>C were with significantly decreased risk of acute CALs (AOR, 0.90; 95%CI, 0.46-1.75 and AOR, 0.17; 95%CI, 0.03-0.87, respectively), as compared to those with AA genotype. Furthermore, as compared with ATA/ATA diplotype, GCC+ACC/GCC+ACC diplotype of IL10 was associated with the decreased risk of acute CALs (AOR, 0.18; 95% CI, 0.04-0.72). In conclusion, the haplotype and diplotype of IL10-1082/-819/-592 were significant differences in the transmission in KD families and that the IL10-819 and -592 SNPs played important role for the sequelae of acute CALs.

In order to get full understanding of how evolution proceeds in natural settings it is necessary to reveal the genetic basis of the phenotypic traits that play a role for individual fitness in different environments. There are a few possible approaches, most of which stem from traditional mapping efforts in domestic animals and other model species. Here we set the stage for gene mapping in natural populations of birds by producing a large number of anchor markers of broad utility for avian genetical research and use these markers to generate a genetic map of the collared flycatcher (Ficedula albicollis). The map reveals a very high degree of synteny and gene order conservation between bird species separated by as much as 100 million years. This is encouraging for later stages of mapping procedures in natural populations since this means that there is a possibility to use the information from already characterized avian genomes to track candidate genes for detailed analysis in non-model species. One interesting aspect of the low degree of rearrangements occurring in the avian genomes is that this could play a role in the low rate of hybridization barriers formed in birds compared to for instance mammals. An analysis of Z-linked gene markers reveals relatively long-range linkage disequilibrium (LD) in collared flycatchers compared to other outbred species but still, LD seems to decay within &lt; 50 kb indicating that &gt; 20.000 markers would be needed to cover the genome in an association scan. A detailed scan of 74 Z-linked genes evenly distributed along the chromosome in both the collared flycatcher and the pied flycatcher (Ficedula hypoleuca) indicates that there are regions that evolve under directional selection, regions that might harbor loci of importance for adaptive divergence and/or hybrid inviability.

Australia has the highest incidence of melanoma in the world. Melanocytic nevi and mutations in the CDKN2A gene are the main risk factors for the development of cutaneous melanocytic melanoma, and particularly in those of European descent. My study uses genetic epidemiological methods to investigate causes of variation in the number of melanocytic nevi and pigmentary traits such as freckles, eye colour, hair colour and skin colour collected on a sample of adolescent twins and siblings from the Brisbane Twin Nevus Study (1992-2006). Information was available for 2524 individuals from 973 families (from the first visit when the twins were aged 12 years), and from a repeat visit (two years later) for 1598 individuals from 791 families. Using the twin study design extended to siblings and parents, variance components analyses showed that the proportion of phenotypic variance explained by genetic factors ranged from 43 to 99 percent for the traits studied. The atypical nevus count and freckles showed sex differences in the magnitude of genetic and environmental effects. Genetic correlations among counts of three types of nevus (flat, raised and clinically atypical) ranged from 0.46 to 0.63. Nevus count was genetically correlated with skin colour (r=0.23). I analysed genome-wide linkage data using a total of 1190 microsatellite (STR) markers from three scans for 644 families with 1646 twins and siblings, plus genotypes for 1033 parents. These were combined with an additional 169 families with genome-wide association 100K SNP (single nucleotide polymorphism) data, where I selected a linkage analysis panel of 13,000 SNPs making a total of 3365 individuals from 811 families (each individual had more than 200 markers typed). Suggestive linkages for flat nevus count (FNC) were identified on chromosomes 2p25 and 9p21 with lod scores of 3.19 and 2.62 respectively. For raised nevus count (RNC), a suggestive QTL with a lod score of 2.20 was found on chromosome 2q37.2, and for atypical nevus count (ANC) a lod score of 2.71 was found on chromosome 7p14.1. There was suggestive evidence of linkage for freckling on chromosomes 2 and 9. Eye colour was strongly linked (lod=17.86) to chromosome 15, at the OCA2 locus. I have also carried out genetic association analyses using the 100K SNP data in 169 families, and additional fine mapping using SNPs (as well as STR markers) in the complete data set. A sample size of 169 families (461 twins) for genome-wide association data means that statistical power is low. From the 100K SNP data, the best association for total nevus count (TNC) was with SNP rs2420070, p=6.0×10-6 on chromosome 10, and included another two nearby SNPs; rs7086663, p=2.0×10-4 and rs7090904, p=1.5×10-4. These 3 SNPs also showed possible association with FNC; rs2420070, p=3.9×10-6, rs2420070, p=1.3×10-4 and rs2420070, p=8.9×10-5. For raised nevus count the top three associated SNPs were rs1885238, p=1.8×10-5 on chromosome 9; rs10503048, p=3.7×10-5 on chromosome 18 and rs4769189, p=4.0×10-5 on chromosome 13. SNP rs1412341 which is located near CDKN2A on chromosome 9, was also associated with p=2.8×10-4. There were a total 18 SNPs which showed evidence of association with atypical nevus count, the strongest signal being with rs951099 (p=3.7×10-5) on chromosome 9. In a fine-mapping dataset, I studied the association of CDKN2A SNP rs2218220 with TNC, FNC, RNC and ANC. The best SNP, rs2218220, gave p values of 2.8×10-10, 7.7×10-8, 2.7×10-12 and 9.1×10-8, respectively. A SNP, rs1800407 (R419Q) located in the OCA2 gene (chromosome 15q11.2-15q12) showed evidence of association with eye colour and particularly with blue and green eye colours, (p=1.7×10-12 and p=6.0×10-7). SNP rs12913832 from the Hect Domain and RCC1-like Domain 2 gene (HERC2) on chromosome 15q13.1, was also strongly associated with eye colour p=3.6×10-155. This SNP was associated with blue (p= 7.9×10-150) and brown (p=5.3×10-158), but not green eye colour. In addition I confirmed the association of the MC1R SNP rs1805007 and freckling (p=4.8×10-12). This SNP was also associated with FNC (p=3.5×10-8), a finding not previously described in the literature. I also carried out multi-allelic association analysis using STR markers with these traits and uncovered suggestive findings for several regions. Finally, I conducted a multivariate association analysis searching for SNPs with pleiotropic effects. The most interesting results for all types of nevi were with rs801840, p=3.5×10-5, and rs10487075, p=4.9×10-5, both on chromosome 7q21.13. Another four SNPs on chromosome 8p23.1 also showed associations, rs7009724, p=1.4×10-4, rs10503389, p=1.9×10-4, rs7832398, p=6.2×10-4 and rs7005133, p=6.9×10-4 (close to a candidate gene, MFHAS1, implicated in sarcoma risk). In conclusion I have characterised a number of definite and possible genetic factors influencing important risk factors for melanoma.

Thesis (MSc)--Stellenbosch University, 2015. / ENGLISH ABSTRACT: Linkage disequilibrium (LD) is defined as the non-random association of alleles at two or more loci within a population. It is sensitive to a variety of locus-specific- and demographic factors, and can thus provide much insight into the micro-evolutionary factors that have shaped species of interest. It can also be exploited to identify the genomic regions determining complex traits of interest, which can then be applied as performance evaluation markers in marker-assisted selection (MAS). The South African abalone, Haliotis midae, supports a rapidly developing aquaculture production industry, in which genetic improvement potential is high. This species also represents an opportunistic model for studying the effects of early domestication in a shellfish species. The aim of this study was therefore to quantify and characterise levels of genome-wide LD within the South African abalone, and to demonstrate its utility within population genetic investigations and the characterisation of complex traits. Estimates of LD between 112 mapped microsatellite markers within wild and cultured H. midae revealed that levels of LD in abalone are high relative to other aquaculture species. This was attributed primarily to small effective population sizes produced by a combination of natural- and anthropogenic factors. The decay of LD with genetic distance was evident in both cultured cohorts, but almost absent in wild cohorts, likely reflecting the differences in size, age and sampling of wild populations relative to cultured. Putative evidence for the effects of recombination, selection, and epistasis were also evident in distinctive locus-specific patterns of LD on some of the linkage groups, many of which could represent the effects of domestication. The effects of selection associated with the domestication event were further investigated using a candidate locus LD mapping approach to determine the proportion of candidate loci under selection associated with artificial selection for faster growth rate in cultured abalone. Two loci (15%) were found to be significantly associated with differences in size of individual animals, both of which could be linked with genes potentially involved in growth and development. These markers could therefore find application in MAS programmes for abalone. Several promising candidates for natural selection were also identified based on similarity with known genes. As the latter represented the majority, natural selection, rather than artificial selection, appears to be predominant during the early stages of domestication in abalone. While some conclusions within the current study were speculative, both the direct and indirect applications of LD were clearly demonstrated. Linkage disequilibrium data can provide a unique perspective on many of the commonly used population genetic estimates, and is therefore of great value in population genetic investigations. Furthermore, these results also highlighted the effectiveness of the candidate locus approach in species with both limited molecular resources and extensive LD. / AFRIKAANSE OPSOMMING: Koppelingsonewewig (KO) word gedefinieer as die nie-lukrake assosiasie van allele by twee of meer lokusse binne 'n populasie. Koppelingsonewewig is sensitief vir 'n verskeidenheid van lokus-spesifieke- en demografiese faktore, en kan dus insiggewend wees m.b.t. mikro-evolusionêre faktore wat spesies van belang beïnvloed het. Dit kan ook benut word om die genoom-gebiede onderligend tot komplekse eienskappe te bespeur; wat dan aangewend kan word vir prestasie-evaluering m.b.v. merkerbemiddelde seleksie (MBS). Die Suid-Afrikaanse perlemoen, Haliotis midae, ondersteun 'n vinnig ontwikkelende akwakultuur produksie bedryf, waarin genetiese verbeteringspotensiaal hoog is. Hierdie spesie verteenwoordig ook 'n opportunistiese model vir die bestudering van die gevolge van vroeë domestiseering in 'n skulpvis spesie. Die doel van hierdie studie was dus om vlakke van genoom-wye KO binne die Suid-Afrikaanse perlemoen te kwantifiseer en te karakteriseer, en om die toepassing hiervan binne populasiegenetiese ondersoeke en die karakterisering van komplekse eienskappe te demonstreer. Ramings van KO tussen 112 gekarteerde mikrosatelliet-merkers binne wilde en gekultiveerde H. midae het aan die lig gebring dat die vlakke van KO in perlemoen hoog was, in vergelyking met ander akwakultuur spesies. Dit word hoofsaaklik toegeskryf aan klein effektiewe populasiegroottes wat deur 'n kombinasie van natuurlike- en antropogeniese faktore teweeg gebring word. Die verval van KO met genetiese afstand was duidelik waarneembaar in gekultiveerde kohorte, maar amper afwesig in die wilde kohorte, waarskynlik a.g.v. verskille in populasiegrootte, ouderdom, en streekproef-neemings metodieke van die verskeie populasies. Vermeende bewyse vir die gevolge van rekombinasie, seleksie en epistase kon ook gesien word a.g.v. lokus-spesifieke patrone van KO op sommige van die koppelingsgroepe, moontlik ‘n gevolg van domestisering. Die gevolge van seleksie wat verband hou met die domestiseringsgebeurtenis is verder ondersoek m.b.v 'n kandidaat-lokus KO karteringsbenadering om die verhouding van kandidaat lokusse wat geassosieer is met kunsmatige seleksie (vir vinniger groeikoers in perlemoen) te bepaal. Twee lokusse (15%) was beduidend geassosieer met verskille in grootte tussen individuele diere. Beide van die lokusse was gekoppel met gene wat potensieel betrokke is by groei en ontwikkeling. Hierdie merkers kan dus moontlik aangewend word in MBS programme vir perlemoen. Verskeie belowende kandidaat lokusse vir natuurlike seleksie is ook geïdentifiseer gebaseer op ooreenkoms met bekende gene. Gegewe dat die laasgenoemde die meerderheid van die merkers verteenwoordig, kan daar afgelei word dat natuurlike seleksie, eerder as kunsmatige seleksie, oorheersend is in die vroeë stadia van domestisering in perlemoen. Terwyl sommige gevolgtrekkings binne die huidige studie spekulatief was, is beide die direkte en indirekte toepassings van KO duidelik gedemonstreer. Koppelingsonewewig-data kan 'n unieke perspektief gee op baie van die algemeen gebruikte populasie genetiese skattings, en is dus van groot waarde in populasie genetiese ondersoeke. Verder demonstreer hierdie resultate ook die doeltreffendheid van die kandidaat lokus benadering in spesies met beide beperkte molekulêre hulpbronne en uitgebreide KO.

Submitted by DONICER EDUARDO MONTES VERGARA null (donicer.montes@unisucre.edu.co) on 2016-04-11T17:24:33Z No. of bitstreams: 1 H.Tese-Donicer- Defensa Definitivo -08-04-2016.pdf: 1794206 bytes, checksum: a97a3f4dcd0f3e1489260272006d51af (MD5) / Approved for entry into archive by Juliano Benedito Ferreira (julianoferreira@reitoria.unesp.br) on 2016-04-12T14:43:11Z (GMT) No. of bitstreams: 1 montesvergara_de_dr_jabo.pdf: 1794206 bytes, checksum: a97a3f4dcd0f3e1489260272006d51af (MD5) / Made available in DSpace on 2016-04-12T14:43:11Z (GMT). No. of bitstreams: 1 montesvergara_de_dr_jabo.pdf: 1794206 bytes, checksum: a97a3f4dcd0f3e1489260272006d51af (MD5) Previous issue date: 2016-03-24 / Características reprodutivas, como a ocorrência de prenhez precoce, são mais importantes economicamente ao comparar-se com as características de crescimento. Desta forma, o aumento da taxa de fertilidade e emprego de animais geneticamente superiores é determinante no progresso da produtividade nas fazendas comerciais de produção de carne bovina. A seleção modifica as frequências alélicas de uma população ao transmitir as variantes gênicas mais interessantes. Considerando o desequilíbrio de ligação, alguns locos adjacentes às mutações favoráveis são transmitidos ao longo das gerações. Estes são conhecidos como assinaturas de seleção e podem ser identificados com o uso de “chips” de SNP e metodologias estatísticas adequadas. Com o objetivo de identificar assinaturas de seleção recentes em QTL previamente mapeados para características reprodutivas de fêmeas bovinas ligadas à precocidade sexual, foram genotipadas 2.035 fêmeas da raça Nelore (Bos taurus indicus) com o chip “Illumina BovineHD BeadChip”. Posteriormente foi inferida a fase de ligação dos SNPs e a reconstrução dos haplótipos. A detecção de assinaturas de seleção foi realizada por meio da aplicação da metodologia “Relative Extended Haplotype Homozygosity” (REHH). A identificação de genes que contribuem para a importância da característica nestas regiões foi feita com a ferramenta Map Viewer do “National Center for Biotechnology Information”- NCBI e GBrowse carregada com o genoma bovino versão UMD 3.1. Foram detectadas 2.756 regiões núcleo, com tamanho médio 27,6 ± 29,1 Kb, abrangendo 70,1 Mb dos 25 cromossomos estudados. Dos SNPs utilizados, 17.312 participaram da formação das regiões núcleo, com o mínimo de 10 no BTA27 e o máximo de 20 SNPs nos cromossomos 1, 3-7, 9-15,18-21, e 23-24. Foram identificadas 40 assinaturas de seleção recentes com diferentes níveis de significância e 56 genes A maioria dos genes localizados nas regiões de assinaturas de seleção tem relação com os processos biológicos de metabolismo mitocondrial, desenvolvimento pós-embrionário, regulação da taxa de ovulação e fertilidade, resposta imune, metabolismo de triglicerídeo, proliferação celular e neurônios receptores olfativos. A investigação de mecanismos regulatórios da expressão dos genes associados aos processos biológicos descritos pode oferecer conhecimentos sobre os mecanismos moleculares que afetam a característica ocorrências de prenhez precoce, na raça Nelore. / Some reproductive traits such as early pregnancy are more profitable than those related to growth. Increasing fertility rate and using genetically superior animals are crucial in productivity of meat commercial farms. Artificial selection modifies allele frequencies of a cattle population by transmitting the most significant gene variants. Considering linkage disequilibrium, some loci adjacent to favorable mutations are transmitted across generations. Known as signatures of selection, such locations can be identified by the SNP chips, and appropriate statistical methods. To determine recent selection signature in quantitative trait loci (QTL) previously mapped for reproductive cow features linked to sexual precocity, 2,035 Nelore (Bos taurus indicus) females were genotyped by Illumina Bovine chip. After, inferring the connection phase of SNPs allowed haplotype reconstruction. Selection signatures were detected by Relative Extended Haplotype Homozygosity (REHH) method. Genes supposedly important were recognized by Map Viewer from the National Center for Biotechnology Information (NCBI), and also through a loaded GBrowse with bovine genome UMD, version 3.1. A total of 2,756 core regions were detected, with an average size of 27.6 ± 29.1 Kb, covering 70.1 Mb of 25 chromosomes. 17,312 SNPs are involved in the formation of core regions with at least 10 on BTA27, and a maximum of 20 SNPs on 1, 3-7, 9-15, 18-21, and 23-24 chromosomes. We identify 40 possible recent selection signatures, with different levels of significance, and 56 positional candidate genes. Most of genes located in selection signature regions are related to biological processes of mitochondrial metabolism, post-embryonic development, ovulation rate regulation and fertility, immune response, triglyceride metabolism, cell proliferation, and olfactory receptor neurons. The investigation of regulatory mechanisms of gene expression associated with biological processes described can provide knowledge on the molecular mechanisms affecting characteristic of early pregnancy occurrences in Nellore.

Pyrenophora semeniperda (anamorph Drechslera campulata) is a necrotrophic fungal seed pathogen of a variety of grass genra and species, including Bromus tectorum, an exotic grass that has invaded many natural ecosystems of the U.S. Intermountain West. As a natural seed pathogen of B. tectorum, P. semeniperda has potential as a biocontrol agent due to its effectiveness at killing dormant B. tectorum seeds; however, few genetic resources exist for this fungus. Here, the genome assembly of a P. semeniperda isolate using 454 GS-FLX genomic and paired-end pyrosequencing techniques is presented. The total assembly is 32.5 Mb and contains 11,453 gene models greater than 24 amino acids. The assembly contains a variety of predicted genes that are involved in pathogenic pathways typically found in necrotrophic fungi. In addition, 454 sequence reads were used to identify single nucleotide polymorphisms between two isolates of P. semeniperda. In total, 20 SNP markers were developed for the purposes of recombination assesment of 600 individual P. semeniperda isolates representing 36 populations from throughout the U.S. Intermountain West. Although 17 of the fungal populations were fixed at all SNP loci, linkage disequilibrium was determined in the remaining 18 populations. This research demonstrates the effectiveness of the 454 GS-FLX sequencing technology, for de novo assembly and marker development of filamentous fungal genomes. Many features of the assembly match those of other Pyrenophora genomes including P. tritici-repentis and P. teres f. teres, which lend validity to our assembly. These findings present a significant resource for examining and furthering our understanding of P. semeniperda biology.

No description available.

No description available.

京都大学 / 新制・課程博士 / 博士(経済学) / 甲第23668号 / 経博第651号 / 新制||経||300(附属図書館) / 京都大学大学院経済学研究科経済学専攻 / (主査)教授 佐々木 啓明, 教授 柴田 章久, 准教授 高橋 修平 / 学位規則第4条第1項該当 / Doctor of Economics / Kyoto University / DGAM