No description available.

Although the Neophocaena is currently thought to be monotypic (¡§Neophocaena phocaenoides¡¨) with three ¡§subspecies¡¨, the taxonomy of this genus still remains uncertainty. The finless porpoise (¡§Neophocaena phocaenoides¡¨) is one of the small cetacean species under threats from human activities. At present, finless porpoise is listed in Appendix I of Convention on International Trade in Endangered Species of Wild Flora and Fauna (CITES). For conservation issue, it is important to define appropriate and unambiguous ¡§units¡¨. In this study, I intended to settle the taxonomic status of the specimens of finless porpoise from the southern part of the East China Sea (including the Taiwan Strait) in which the status has been under debate. Results from this study, indicated that they should belong to ¡§N. p. sunameri¡¨. Comparing the genotypes of the microsatellite of additional individuals of the ¡§N. p. asiaeorientalis¡¨ belonging to the VN-type group given in Xia and coworkers report with our data, three distinguished genetic groups were revealed: (1) the group occurring in the Taiwan Strait (i.e., the W-type group, currently recognized as ¡§N. p. phocaenoides¡¨); (2) the group occurred in the Yangtze Rive (i.e., the VN-type group, currently recognized as ¡§N. p. asiaeorientalis¡¨); (3) the group occurred in the Yellow Sea and the Taiwan strait (i.e., the IN-type + UN-type group, currently recognized as ¡§N. p. sunameri¡¨). Population differentiation was absent not only within the W-type group but also within the IN-type +UN-type group. I tried to detect the taxonomy of the two parapatric groups in where the W-type and IN-type +UN-type groups are co-exit sympatrically. No specimens with intermediate character state of the width of the dorsal denticles (i. e., hybrids) were presented in Matsu Islands on the Chinese coast where the W-type and UN-type groups were sympatric. Hybrid individual exhibiting the hybrid states of the 11 microsatellite loci between these two groups was also not found. According to E.O. Wiley¡¦s criteria for recognizing species, these two groups are eligible to be considered separate species. Based on Crandall and his coworkers¡¦ criteria of evolutionarily significant unit (ESU), the three groups, the W-type, IN-type +UN-type and VN-type groups, should be treated as three distinct ESUs.

Ancient DNA (aDNA) was isolated from the bones of 290 individuals and four species of extinct New Zealand moa. All sampled bones had been recovered from a small geographic area (~10 km radius) near Waikari in North Canterbury. A total of 217 specimens were 14C-AMS dated, providing a temporal framework for the genetic analyses and an unprecedented opportunity to study extinct megafauna at the population level. Taxon and sex were determined for each individual, using aDNA technology. This revealed a large excess of females (overall ♂:♀ = 1:5.1), and significant compositional differences for the moa assemblages between fossil sites. Balanced sex ratios were observed among juvenile moa, suggesting that a gender-bias developed as the birds matured, probably as a result of higher male mortality. Female territoriality and ecological niche-separation are discussed in this context. Mitochondrial DNA (mtDNA), amplified using a quantitative PCR procedure, provided a measure of DNA preservation in each radiocarbon-dated fossil. This assessment showed that DNA degrades over thousands of years according to an exponential decay model, and the average molecular half-life for the here targeted DNA fragment was estimated to be 521 years. By using high-throughput sequencing, six polymorphic moa microsatellite markers were identified and characterised. These are the first microsatellite primers developed exclusively for extinct taxa. A high-resolution genetic study of the four sympatric moa populations was carried out, combining information from mtDNA, microsatellites, sex-identification, and radiocarbon age. Genetic diversity, past demography, kinship, and other aspects of moa biology were analysed. The populations showed a remarkable extent of genetic stability throughout the 3000-4000 years preceding their extinction, suggesting that they were large and viable before suddenly disappearing. The results represent significant advances in aDNA research and thanks to the high resolution in microsatellite markers, moa have here been studied, almost as if they were still alive.

Recent theoretical developments have led to a renewed interest in the potential role of chromosomal rearrangements in speciation. Australian morabine grasshoppers (genus Vandiemenella, viatica species group) provide an excellent study system to test this potential role, because they show extensive chromosomal variation: 12 chromosomal races/species with parapatric distributions. The research in this thesis involves the application of molecular genetic analyses to examine patterns of gene introgression among chromosomal races of Vandiemenella at three different spatial scales: local-scale hybrid zone analysis, island-scale phylogeography, and continental-scale phylogeography. The aims of these multi-scale analyses are to investigate whether chromosomal races represent genetically distinct taxa with limited gene flow, and to infer the historical biogeography of Vandiemenella and evolutionary origins of their parapatric distributions. Karyotype and 11 nuclear markers revealed a remarkably narrow hybrid zone with substantial linkage disequilibrium and strong deficits of heterozygotes between the chromosome races P24(XY) and viatica17 on Kangaroo Island, suggesting that the zone is maintained by a balance between dispersal and selection against hybrids (tension zone). Selection that maintains the stable hybrid zone is unlikely to be operating only on loci linked to rearranged chromosomes. Island-scale and continental-scale phylogeography using multiple nuclear markers indicated that Vandiemenella chromosome races/species generally represent genetically distinct taxa with reduced gene flow between them. In contrast, analyses of a mitochondrial gene showed the presence of distinctive and geographically localised phylogroups that do not correspond with the distribution of the Vandiemenella taxa. These discordant population genetic patterns are likely to result from introgressive hybridization between the taxa and range expansions and contractions. Overall, our molecular analyses favour the allopatric mode of diversification for the evolution of Vandiemenella and do not support the stasipatric speciation model of White (1978). Patterns of genetic differentiation between the chromosomal races analysed at three different spatial scales show dynamic responses of the grasshoppers to past climatic fluctuations, leading to opportunities for long-term isolation and allopatric fixation of new chromosome variants and molecular mutations at many loci. Further analyses are necessary to assess potential roles of chromosomal rearrangements in facilitating diversification in Vandiemenella by reducing recombination within the rearranged chromosome segments.

L’autisme et la déficience mentale sont deux syndromes neuro-développementaux impliquant des facteurs génétiques. Notre travail a consisté à rechercher de nouveaux gènes candidats ou facteurs de susceptibilité chez 106 patients atteints d’autisme et 68 de déficience mentale non syndromique sporadique.Nous avons observé une association entre l’allèle 4 d’un marqueur microsatellite GXAlu localisé en 17q11.2 dans l’intron 27b du gène NF1 et des patients atteints de déficience mentale non-syndromique.Nous avons contribué à la mise en évidence d’une augmentation d’expression du transcrit NLGN4X, chez un patient autiste avec un retard mental non-syndromique présentant une mutation dans le promoteur du gène NLGN4X.L’étude de la région 22q13 par MLPA, nous a permis de mettre en évidence une délétion de novo d’au moins 1Mb chez un patient autiste.Les variations de nombre de copies (CNV) ont été étudiées chez des autistes par QPCR. Nous avons identifié 27 variations réparties sur 17 gènes parmi les 36 explorés. Les CNV observés dans les gènes ITGA6, TAGLN3, HOXA1, DLG4 et UBE2C sont intéressants en raison de l’implication de ces gènes dans le développement cérébral ou la fonction neuronale.L’ensemble de ces résultats nécessite des expériences complémentaires de validation. / Autism and mental retardation are two neurodevelopmental syndromes involving genetic factors. Our work consists in finding new candidate genes or susceptibility factors. 106 autistic patients and 68 sporadic non-syndromic mentally retardated patients were studied.We have shown an association between allele 4 of a microsatellite marker GXAlu locasized in 17q11.2, in intron 27b of the NF1 gene and patients with non-syndromic mental retardation.We contributed to the study on the NLGN4X gene. We demonstrated an increase of expression of NLGN4X transcript, in an autistic patient with non-syndromic mental retardation linked to a mutation in the NLGN4X gene promoter.We study the 22q13 region with MLPA method, we have demonstrated a deletion de novo of at least 1Mb in an autistic patient.The copy number variations (CNV) have been investigated in an autistic population by QPCR. We identified 27 variations on 17 genes among the 36 investigated. The CNV observed in ITGA6, TAGLN3, HOXA1, DLG4 and UBE2C genes are interesting because of the involvement of these genes in brain development or neuronal function.These results require further experiments for validation.

Masters of Science / Genetic analysis for resistance to Woolly Apple Aphid in apple rootstock breeding populations MC Selala MSc Thesis, Department of Biotechnology, Faculty of Science, University of the WesternCape. The Woolly Apple Aphid (WAA) Eriosoma lanigerum (Hausm.) (Homoptera: Aphididae) is economically one of the most important pests in apple commercial production in the Western Cape province, South Africa. The apple cultivar Northern Spy possesses a single major gene (Er1) responsible for E. lanigerum resistance. This cultivar has been used as a commercial rootstock in apple breeding programmes. There are other genes also implicated in resistance to E. lanigerum from other cultivars. Manipulation and pyramiding of the E. lanigerum resistance genes (Er1, Er2 and Er3) might provide a necessary control for commercial apple production. The aim of this study was to construct a genetic linkage map for apple using microsatellite markers. The use of marker-assisted selection would greatly benefit local apple breeding programmes. Ninety six seedlings from a Northern Spy × Cox Orange Pippin mapping population were used for genetic linkage construction. Phenotypic data collection and analysis were performed to determine the E. lanigerum infestation patterns and the levels of resistance conferred by the Er1 gene from Northern Spy using 52 in vitro propagated seedlings in the greenhouse. Classification and quantification analysis showed association patterns between first assessments (30 days) to second assessment (60 days) in all replicate blocks. Roots and shoots data showed that it could be useful in quantitative trait loci (QTL) analysis, but may be used in different QTLs beingidentified due to the variations between roots and shoots data. A preliminary linkage map was constructed using a mapping population from Northern Spy × Cox Orange Pippin (96 seedlings).Fluorescently labelled published and predicted microsatellite markers were used in map construction. Primers were optimised using single apple cultivar and the detection of polymorphisms using nine apple cultivars. Optimised markers were multiplexed for high throughput data generation using the Polymerase Chain Reaction (PCR) technique. Multiplexed PCR products were pooled and analysed on an ABI 310 PRISM™ Genetic Analyser to determine allele fragment sizes, and the inherited segregation types in the seedlings. Computer software GenoTyper® 2.5.2 and JoinMap® 3.0 was used in data analysis from ABI 310 PRISM™Genetic Analyser and linkage map construction. Seventy two markers were used in linkage map construction, which produced nine linkage groups with some segments from the same linkage group. Twenty-one markers were aligned on the map 20 published and one predicted. Only one linkage group consisted of five markers while other linkage groups had two markers each. This study has proved that th preliminary linkage map could be used as the basis of a complete linkage map of Northern Spy × Cox Orange Pippin.

The power of microsatellite markers lies in their ability to identify. Whether it is the identification of genes and associating them with known phenotypes or identifying and discerning individuals from one another, the role they play in the genetic field has been immense. Parentage testing of horses today is done via molecular means as opposed to serology. Microsatellite marker panels are decided upon by bodies such as the International Society for Animal Genetics (ISAG) in order to uphold international genotyping standards. The current horse microsatellite marker panel is not fully characterized and many markers are amplified by primers originally designed for linkage studies and were never intended for multiplex PCR analysis. The aim of this study was to refine and validate the current marker panel used for horses through sequencing of the repeat elements and flanking regions as well as the design of new primers for the setup of a marker panel incorporating more microsatellites and better primers. Sequencing of microsatellite flanking regions revealed that much variation lies within the regions flanking a microsatellite repeat element. Sequencing of the repeat element showed that not all markers are simple repeats, as was previously thought. The primers used to amplify microsatellite markers for horses were re-designed in the course of this study, utilizing knowledge gained from flanking region variation and repeat element length. New primers and known allele sizes allowed for the implementation of a nomenclature system in horses based on repeat element length as opposed to alphabet letters. By incorporating more markers into the panel it was hoped that a greater discriminatory power would be achieved. Measures of genetic diversity such as Observed Heterozygosity and Polymorphism Information Content showed negligible differences between the two panels however genotyping data from the old ISAG panel of nine markers showed that the probability of excluding an individual in a parentage test was better when using more markers. / Dissertation (MSc)--University of Pretoria, 2010. / Production Animal Studies / unrestricted

Cañahua (Chenopodium pallidicaule Aellen) is a poorly studied, annual subsistence crop of the high Andes of South America. Its nutritionally value (high in protein and mineral content) and ability to thrive in harsh climates (drought, extreme elevations, etc.) make it an important regional food crop throughout the Andean region. The objectives of this study were to develop genetic markers and to quantify genetic diversity within cañahua. A set of 43 wild and cultivated cañahua genotypes and two related species (C. quinoa and C. petiolare) were evaluated for polymorphism using 192 microsatellite markers derived from random genomic sequences produced by 454 pyro-sequencing of cañahua genomic DNA. In addition, another and 424 C. quinoa based microsatellite markers were evaluate as potential cross-species marker loci. A total of 48 polymorphic microsatellite marker loci were identified which detected a total of 168 alleles with an average of 3.5 alleles per marker locus and an average heterozygosity value of 0.47. A cluster analysis, based on Nei genetic distance, grouped the cultivated cañahua into a single dominant branch clearly separated from wild cañahua genotypes and the outgroup species. Within the cultivated genotypes, two dominant subclades were present that were further partitioned by AMOVA analysis into five model-based clusters. Significant correlations were found between genetic distance and morphological traits. The isolation by distance test displayed no significant correlation between geographic collection origin and genotypic data, suggesting that cañahua populations have moved extensively, presumably via ancient food exchange strategies among native peoples of the Andean region. The molecular markers reported here are a significant resource for ongoing efforts to characterize the extensive Bolivian and Peruvian cañahua germplasm banks, including the development of core germplasm collections needed to support emerging breeding programs.

No description available.

Thesis (PhD (Genetics))--Stellenbosch University, 2010. / ENGLISH ABSTRACT: The South African abalone, Haliotis midae, is a commercially valuable mollusc and is mostly exported to the Far East. Genetics research on H. midae has increased substantially since a genetic improvement programme was introduced in 2006 by collaboration between Stellenbosch University, government and industry partners. The development of molecular markers, QTL-mapping, gene-expression and genome manipulations are the main focuses of the research currently being conducted. The end goal is to create high quality and fast growing animals for the industry. The present study focused on the development of microsatellite markers and the detection of quantitative trait loci (QTL) affecting growth traits (shell length, shell width, wet weight) in this species. A combination of three methods, namely selective genotyping and bulked segregant analysis (pooling analysis), single marker regression and interval mapping were used to identify putative QTL in two full-sib families from two different farmed locations. Additional methods and protocols were developed that can assist the industry in other molecular research aspects. A total of 125 microsatellite loci were characterised. A total of 82 of these loci were isolated using second generation sequencing, a first for any abalone species. A preliminary, low-density framework linkage map was constructed containing 50 loci that mapped to 18 linkage groups. The observed genome length was 148.72cm with coverage of ±47%. QTL analyses revealed two putative QTL for shell width and wet weight, with 17% and 15% variance explained, that mapped on one linkage group in the first family and three putative QTL, for shell length, shell width and wet weight, with 33%, 28.5% and 31.5% variance explained, that mapped on one linkage group in the second family. Additional methods and protocols developed include an automated high-throughput DNA isolation protocol, a real-time PCR assay for H. midae x H. spadicea hybrid verification, a triploid verification microsatellite assay and a pre- and post-PCR multiplex setup and optimisation protocol. Future studies focussing on QTL and marker assisted selection (MAS) should verify the QTL found in this study and also utilise additional family structures and determine QTL-marker phase within the commercial populations. / AFRIKAANSE OPSOMMING: Die Suid-Afrikaanse perlemoen, Haliotis midae, is ’n kommersieel waardevolle weekdier en word hoofsaaklik na die Verre-Ooste uitgevoer. Genetiese navorsing op H. midae het aansienlik toegeneem sedert ’n genetiese verbeteringsprogram in 2006 deur samewerking tussen die Universiteit van Stellenbosch, die regering en industrievennote ingebring is. Die ontwikkeling van molekulêre merkers, KEL-kartering, geen-uitdrukking en genoom manipulasies is die hooffokusse van die navorsing wat tans uitgevoer word. Die einddoel is om hoë kwaliteit en snelgroeiende diere vir die industrie te skep. Die huidige studie het op die ontwikkeling van mikrosatelliet merkers en die opsporing van groeiverwante (skulplengte, -breedte en nat gewig) kwantitatiewe eienskap lokusse (KEL) in hierdie spesie gefokus. ’n Kombinasie van drie metodes, naamlik selektiewe genotipering en versamelde segregaat analise (samevoegingsanalise), enkel merker regressie en intervalkartering is gebruik om waarskynlike KEL in twee vol-sibbe families van twee verskillende produksiegebiede te identifiseer. Aanvullende metodes en protokolle is ontwikkel wat die industrie in ander molekulêre navorsingsaspekte kan ondersteun. ’n Totaal van 125 mikrosatelliet lokusse is beskryf. ’n Totaal van 82 van hierdie lokusse is deur die gebruik van derde generasie volgordebepaling geïsoleer, ’n eerste vir enige perlemoen spesie. ’n Voorlopige, laedigtheid raamwerkkoppelingskaart is saamgestel met 50 lokusse wat op 18 koppelingsgroepe gekarteer is. Die waarneembare genoomlengte was 148.72cm met ’n dekking van ±47%. KEL-analises het twee waarskynlike KEL vir skulpbreedte en nat gewig blootgelê wat 17% en 15% variasie verduidelik en is op een koppelingsgroep in die eerste familie gekarteer asook drie waarskynlike KEL, vir skulplengte, -breedte en nat gewig wat 33%, 28.5% en 31.5% variasie verduidelik en is op een koppelingsgroep in die tweede familie gekarteer. Aanvullende metodes en protokolle wat ontwikkel is, sluit ’n geoutomatiseerde hoë-deurgang DNS-isolasieprotokol, ’n intydse PKR-proef vir H. midae x H. spadicea hibried verifikasie, ’n triploïed verifikasie mikrosatellietproef en veelsoortige pre- en post-PKR opstelling en optimaliseringsprotokol in. Toekomstige studies wat fokus op KEL en merker ondersteunde seleksie (MOS) behoort die KEL wat in hierdie studie gevind is te verifieer en ook bykomende familie strukture te benut om KEL-merker fases binne die kommersiële populasie te bepaal.