The Mingan Archipelago along the north shore of the Gulf of St. Lawrence is well known for the diversity and rarity of its vascular plants. This diversity is often explained by a combination of the islands’ temperate maritime climate and its unusual regional geology where the islands are formed of calcareous sedimentary rock. Among the 80 species of rare plants on the islands, one in particular stands out, Cirsium scariosum (Meadow thistle), a species native to western North America, but with a disjunct populations on the Mingan islands over 3500 km away. Initially recognized as a separate species, Cirsium minganense, when it was first discovered in 1924 by Marie-Victorin, recent authors believe these Mingan populations are either the result of eastern migration during the Pleistocene or a contemporary anthropogenic introduction. Nevertheless, the question of how these populations arrived on the islands or whether they should be treated as a separate species has not been resolved. The eastern populations of Cirsium scariosum are now endangered and conservation efforts have been made to save this emblematic plant. To determine whether the Mingan populations might represent a separate species and to better understand the plants’ breeding system and genetic diversity for conservation, a phylogeny of closely related species and a population genetic analysis using genotyping by sequencing (GBS) was conducted. Results suggest the Mingan island populations are not closely related to the western Cirsium scariosum and that outcrossing and dispersal between islands could be occurring.

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

Michaux's sumac (Rhus michauxii) is a federally endangered rhizomatous shrub endemic to the southeastern United States, with two of the largest populations located at Maneuver Training Center--Fort Pickett, VA (Fort Pickett), and a nearby property, Deepwater. Michaux's sumac requires soil disturbance and fire to maintain healthy populations. Before being added to the endangered species list, 47% of populations were extirpated due to habitat loss, fire suppression, and hybridization with smooth sumac (Rhus glabra). Concerns with hybridization include hybrid swamping if hybrids are fertile, or outbreeding depression if hybrids display reduced fitness. I used genotyping-by-sequencing to estimate the extent of hybridization at Fort Pickett and Deepwater, and to assess how such hybridization may impact survival of Michaux's sumac as a distinct species at each of these locations. Additionally, population structure was examined using DAPC (discriminant analysis of principal components) and Admixture analyses to determine whether the colonies at Fort Pickett and Deepwater make up separate populations, meta-populations, or one large population. Analysis of 107,344 SNPs (single nucleotide polymorphisms) using Introgress and Admixture software suggested widespread hybridization at both Fort Pickett and Deepwater, with hybrids present in most of the sampled colonies. Population structure analyses revealed differentiation between the Fort Pickett and Deepwater populations, but little evidence of separate populations among the colonies sampled at Fort Pickett. These results are important for conservation planning to ensure the long-term survival of Michaux's sumac at Fort Pickett and Deepwater and can be used to help inform future management decisions. / Master of Science / Michaux's sumac (Rhus michauxii) is a small, federally endangered shrub endemic to the southeastern United States, with populations remaining in North Carolina, Virginia, and Georgia. To date, the largest known colonies of Michaux's sumac are in Virginia at Maneuver Training Center--Fort Pickett, VA (Fort Pickett), and at a nearby privately owned property called Deepwater. Michaux's sumac requires soil disturbance and fire to reduce competition and maintain healthy populations. It currently faces threats from habitat loss due to agricultural land use and fire suppression, and hybridization with a closely related species, smooth sumac (Rhus glabra). Hybridization is a threat to Michaux's sumac at Fort Pickett and Deepwater because it co-occurs with smooth sumac throughout the area. This study determined how much smooth sumac and Michaux's sumac are hybridizing in these locations and assessed whether hybridization is a threat to the long-term survival of the populations at each site. A secondary goal of the study was to gain a better understanding of how genetically similar the colonies within and between locations are to one another. Understanding the level of hybridization and the population structure of Michaux's sumac is important for making management decisions to protect the species. I found widespread hybridization between Michaux's and smooth sumac, with hybrid individuals at nearly all the colonies sampled. Additionally, there is evidence that Fort Pickett and Deepwater comprise two distinct populations, but the colonies inside each area are likely not separate populations. These results will inform future conservation management decisions for the species.

White mold (Sclerotinia sclerotiorum Lib. de Bary) is one of the most important diseases of common bean in the U.S. with seed yield losses up to 100%. White mold resistance is hard to incorporate into breeding materials because of low heritability, cumbersome screening methods, and few sources of resistance. A Multi-parent Advanced Generation Inter-Crosses population was created to develop resistant germplasm and map the genetics factors controlling the resistance. A seedling straw test method was used to identify resistant lines. Twenty genotypes were found to be resistant based on its response when inoculated with isolate 1980 of white mold. GWAS using quantitative, polynomial and binomial phenotypic distribution data, identified 30 genomic regions associated with resistance on Pv01, Pv02, Pv04, Pv05, Pv07, Pv08, Pv10 and Pv11. Cumulative R2 values were 57% for binomial distribution using 13 genomic intervals, 41% for polynomial using 8 intervals, and 40% for quantitative using 11 intervals.

Acca sellowiana, known as feijoa or pineapple guava, is a Myrtaceae fruit tree species native to Uruguay and Brazil. The species stand out for its highly aromatic fruits, with nutraceutical and therapeutic value. Despite its agronomically promising valuable, genetics studies on this species are limited. Linkage genetic maps are valuable tools for genetic and genomic studies, and can be employed in breeding programs to support the development of molecular breeding strategies. The lack of a high number of polymorphic markers is one of the main limitation to development saturated genetic maps. Recently, novel genotyping methods based on next generation sequencing technology allow to detect and genotype thousands of markers in mapping populations. This represents a rapid and cost-effective strategy, remarkably useful for minor species with limited genomic resources. In this study, we constructed a high-density integrated genetic linkage map of A. sellowiana using two populations, H5 (\'TCO × BR\' , n = 160) and H6 (\'TCO × DP\', n = 184), which have the same female parent. Genotyping by sequencing (GBS) approach was used to simultaneously discover and genotype single nucleotide polymorphism (SNP) markers in both populations. Two strategies were carried out to identify SNP markers: a reference pipeline using the reference genome of the closely-related species Eucalyptus grandis, and a de-novo pipeline that do not require a reference genome. After quantitative genotype calling, 5,350 and 4,227 high quality SNP markers were selected for mapping in H5 and H6 populations, respectively. The two resulting maps of populations H5 and H6 comprised 1,236 and 1,302 markers distributed over the expected 11 linkage groups. The H5 and H6 maps spanned a map length of 1,593 cM and 1,572 cM, with an average inter-marker distance of 1:29 cM and 1:21 cM, respectively. A high degree of collinearity was observed between the two maps. In addition, a large proportion of markers were common to both maps and were used to construct the composite genetic linkage map. A novel approach to estimate recombination of two connected populations is described, where the meiosis information of all individuals is captured in a single estimator using a multipoint maximum likelihood estimation. The composite map consisted of 641 SNPs markers with a total map length of 1011 cM. This composite map represent the best consensus ordering of markers, a valuable reference framework for future studies in A. sellowiana. The large number of SNPs identified allowed us to construct high-density genetic maps, molecular tools which represent a relevant contribution for future genetic research and breeding efforts in A. sellowiana. / Acca sellowiana, conhecida como feijoa, pineapple guava ou goiabeira-serrana, é uma árvore frutífera nativa do Uruguai e do Brasil, pertencente a família Myrtaceae. A espécie destaca-se por suas frutas altamente aromáticas, com reconhecido valor nutracêutico e terapêutico. Apesar do promissor valor agronômico, os estudos genéticos nesta espécie são limitados. Os mapas genéticos são valiosas ferramentas em tais estudos, sendo empregados no desenvolvimento de estratégias de melhoramento molecular nos programas de melhoramento. No entanto, a falta de um elevado número de marcadores polimórficos nas populações de mapeamento é uma das principais limitações no desenvolvimento de mapas genéticos saturados. Recentemente, novos métodos de genotipagem baseados em tecnologia de sequenciamento de nova geração permitem identificar e genotipar milhares de marcadores em populações de mapeamento. Esta rápida e eficiente estratégia é muito útil para culturas pouco estudadas, com recursos genômicos limitados. Neste estudo, foram construídos mapas genéticos saturados em A. sellowiana. Foram usadas duas populações de mapeamento, H5 (\'TCO × BR\', n = 160) e H6 (\'TCO × DP\', n = 184), conectadas geneticamente pelo mesmo genitor feminino. A estratégia de genotipagem por sequenciamento (genotyping by sequencing; GBS) foi usada para simultaneamente identificar e genotipar marcadores de polimorfismos de nucleotídeo único (single nucleotide polymorphism; SNP) em ambas populações. No processo de detecção de SNPs, duas estratégias foram implementadas: na primeira foi empregado o genoma de referência de especie relacionada Eucalyptus grandis; na segunda, foi empregado uma abordagem de novo, que não requer genoma de referência. Após o processo de genotipagem quantitativo, 5350 e 4227 SNPs de alta qualidade foram selecionados para mapeamento em H5 e H6, respectivamente. Os mapas integrados H5 e H6 compreendem 1236 e 1302 marcadores distribuídos no 11 grupos de ligação esperados. Os mapas genético abrangeram um comprimento total de 1593 cM e 1572 cM, com uma distância média entre marcadores de 1:29 cM e 1:21 cM, nas populações H5 e H6, respectivamente. Um alto nível de colinearidade foi observado entre os dois mapas. Além disso, uma grande proporção de marcadores foram mapeados em ambos mapas e posteriormente usados na construção de um mapa genético integrado, considerando a informação de ambas populações simultaneamente. Foi apresentada uma nova abordagem para estimar as frações de recombinação em duas populações conectadas, onde a informação das meioses de todos os indivíduos é capturado num único estimador, usando uma estimativa de máxima verossimilhança multiponto. O mapa integrado composto contém 641 marcadores SNP com um comprimento total de 1011 cM. Este mapa representa o melhor ordenamento consenso de marcadores, sendo una valiosa referencia para futuros estudos nesta espécie. O grande número de SNPs identificados permitiu-nos a construção de mapas genéticos de alta densidade, ferramentas moleculares que representam uma contribuição relevante para futuras pesquisas genéticas e avanços no melhoramento genético em A. sellowiana.

Denna uppsats fokuserar på att undersöka EU:s taxonomins påverkan på gröna obligationer emitterade av svenska fastighetsföretag. Vår studie fann att EU:s taxonomi kommer att påverka de flesta emittenters gröna ramverk, eftersom aktörerna kommer att vilja vara mer taxonomi-förenad för att uppfylla marknadens efterfrågan. Det finns även en trend som visar att fastighetsföretagen övergår till nya former av hållbar finansiering. Detta på grund av att de vill expandera sina portföljer för att möta behovet på marknaden. Fastighetsföretagen kommer att fortsätta arbeta med miljöcertifieringar trots att taxonomin inte ställer krav på detta. Branschexperterna har en förhoppning att taxonomin kan uppdateras och därmed ska fånga upp klimatpåverkan som orsakas av exempelvis byggmaterialen och produktionsfasen. Utöver det hoppas också braschaktörerna att taxonomin antar en gemensam standard för alla EU-länder angående vilka byggnader som kan klassificeras som gröna. För den svenska fastighetsbranschen är det av väsentlig betydelse att arbeta hållbart vid produktion-och förvaltningsfasen. EU:s taxonomiregleringar kan eventuellt utgöra ett hinder för fastighetsföretagens klimatarbete, på grund av att regleringarna sätter fokus på byggnadens energiprestanda snarare än andra hållbarhetsparametrar. / This thesis focuses on the EU taxonomy’s impact on green bonds issued by Swedish real estate companies. Our research found that most of the issuers’ green bond frameworks will be affected by the EU Taxonomy, since market participants would aim to become more taxonomy-compliant in order to meet the market’s demand. There is also a new trend showing real estate companies having a transition towards new categories of sustainable financing, which would allow them to expand their portfolios to comply with market development. Real estate companies will continue working with building certifications despite the lack of such requirements in the EU Taxonomy. There is an expectation that the Taxonomy’s criteria will be expanded with regards to the construction materials and the production process. Moreover, there are also expectations of the taxonomy adopting a common standard for EU countries when it comes to classification of green buildings. It is of particular importance for the Swedish real estate industry to take into consideration the sustainability aspects of both the production process and the facility management. The EU taxonomy could possibly become an obstacle to the climate work of Swedish real estate companies, on the ground that the taxonomy focuses on the energy performance of buildings rather than the environmental impacts.

No description available.

Stress can induce prolonged deleterious effects on many characteristics in chickens (Gallus gallus). Particular interest has been paid to early life stress. Social isolation as an early life stressor results in increased plasma corticosterone levels. Moreover, it induces behavioural and physiological changes as well as gene expression modifications in the hypothalamus. In the first part of my study, I aim to inquire into social isolation impacts on the short and long-term. Short and long-term effects were assessed by immune system, behaviour and weight. 82 male chickens were assigned to three groups (stress, control and enrichment). The stress group was exposed to social isolation, the enrichment group was provided with enrichment substrates while the control group was left untreated. According to my knowledge, this is the first study that investigates the effects of social isolation on the interuleikn-6 levels as an indicator of immune system response. My findings suggest that social isolation induces short and long-term effects on immune response as well as on body weight. In the second part of my study, I aim to develop a method investigating effects of early stress on DNA methylation in blood and sperm. For this purpose, two methods GBS (Genotyping by sequencing) and MeDIP (Methylated DNA immuneprecipitation) were f using pooled DNA from all individuals for the first time. Moreover, I developed a protocol for extracting sperm DNA from frozen testis. Combining both methods has many advantages, such as cost effectiveness and the ability to evaluate epigenetic signatures in large number of individuals

The neonate is still at risk of acquiring Group B Streptococcus (GBS) infection upon delivery even with the implementation of early onset GBS neonatal disease preventative protocols. GBS was reported as the most prevalent organism causing neonatal morbidity and mortality in the USA and Australia in the 1990s. GBS is also known to cause disease in children, women, the immunocompromised adult and the elderly, but it is the preterm neonates who are at greatest risk of GBS neonatal disease. The aim of this study was to determine the prevalence of lower genital tract (LGT) colonisation with GBS in Brisbane women of child bearing age. We also aimed: (i) to compare the GBS LGT prevalence rate of Indigenous and non Indigenous women; (ii) to determine whether previously reported risk factors for LGT colonisation with GBS were also risk factors associated with GBS colonisation of women in this study; (iii) to further develop and optimise a rapid PCR assay that could detect maternal LGT GBS colonisation; and (iv) to serotype the GBS strains that were isolated from pregnant and non pregnant women who participated in this study. This study recruited 374 women of childbearing age attending public medical providers and found an overall GBS prevalence of 98/374 (26.2%) for these Brisbane women, a rate higher than previously reported in Australia. When the GBS prevalence for pregnant women (25.6%) was compared to non pregnant women (27.2%) they were similar. We also compared the GBS LGT colonisation rate of women attending different medical providers. The GBS LGT prevalence rate for pregnant women attending the Mater was 36/118 (30.5%), whilst those women attending the Redlands Hospital antenatal clinic had a LGT GBS prevalence rate of only 7/53 (13.2%). By comparison, the LGT GBS prevalence rate for non pregnant women attending Biala Sexual Health clinic was 21/69 (30.4%) and 34/127 (26.8%) of women attending the Brisbane Family Planning Queensland were also GBS positive. The seven women recruited from Inala community centre tested negative for GBS LGT colonisation. The LGT GBS prevalence of Australian Aboriginal women was 5/22 (22.7%), a rate which was not significantly different from non-Aboriginal women 78/288 (27.1%). Established early onset GBS neonatal disease preventative policies have been recently revised. The CDC now recommends that all pregnant women are screened for LGT GBS colonisation during late gestation, and that any GBS isolates be tested for resistance to antibiotics if the GBS positive women have an allergy to penicillin. Queensland's Department of Health recommend that Queensland medical agencies implement a non screening based preventative protocol, where clinicians monitor: women prior to labour for reported risk factors associated with maternal GBS colonisation: women in labour for 'obstetric risk factors'. A number of risk factors have previously been reported in association with GBS LGT colonisation. However, in this current study we found that only one risk factor was significantly associated with current GBS: previous reported LGT GBS colonisation was significantly associated with maternal LGT GBS colonisation reported in this study. Women who previously tested positive for GBS were significantly more likely to be GBS positive in subsequent tests (OR 4.7; 95%CI, 1.8-12.5) compared to women with no previous history of GBS colonisation. An assessment of adverse pregnancy outcomes, preterm deliveries, and GBS colonisation data was made. It was established that 30 women had previously given birth to one or more preterm neonates and of these 30 women, nine (30%) of them tested positive for GBS in this current study. Of the 71 women who had given birth to neonates and who had suffered an adverse pregnancy outcome 25.3% also tested positive for GBS in this current study. GBS was identified in up to 30% of all mothers who had delivered their neonate preterm, 27.4% of women who had previously suffered miscarriages and 16.7% of women who had previously had stillbirths. In this study we found that Australian Aboriginal women also had a greater risk of delivering neonates who suffered from an adverse pregnancy outcome in comparison to all other women. Twenty one of the 22 Aboriginal women had previously been pregnant at least once, and nine (42.9%) of these women had at least one prior adverse pregnancy outcome while seven (33.3%) of these women had previously delivered at least one neonate preterm. Of the 21 Aboriginal women who had a previous pregnancy more than half the total number of Aboriginal women (11/21) had either delivered one or more neonates preterm or had suffered from one or more adverse pregnancy outcomes. When the incidence of adverse pregnancy outcomes was compared for Aboriginal and all other women the results were surprising. Overall, this study found 216 women including Aboriginal women had previously been pregnant and of these women 71 (32.8%) of them suffered an adverse pregnancy outcome. By comparison, only 62 of 195 (31.8%) non Aboriginal women but nine out of 21 (41.9%) Australian Aboriginal women suffered from a previous adverse pregnancy outcome. The clinical LGT GBS isolates found in this study of Brisbane women were typed and all nine GBS serotypes plus non typeable GBS serotypes were detected. Seventy women tested GBS culture positive and vaginal and/or perianal samples obtained from these women were evaluated. GBS serotype III was the serotype most frequently isolated from this total population, from 47.4% of pregnant women and 51.7% of non pregnant women. From some women only a single GBS serotype was isolated: in these women we found that GBS serotype III (50%) was the predominant isolate, followed by GBS serotype Ia isolated from 16.7% women. In addition 4.2% of women were colonised with GBS serotypes; Ib, II and V, whilst GBS serotypes IV and VII were isolated from 2.1% women. Non typeable GBS strains confirmed by latex agglutination tests accounted for 11.9% of all strains isolated from these Brisbane women. This study identified multiple serovars in 15 clinical samples and found that 22 (31.4%) women were colonised with mixed GBS serotypes in samples collected from both vaginal and perianal regions. In five women the combination of serotypes III/Ia were identified and in other women combinations of serotypes III/II, III/IV, III/V, III/VIII, Ia/IV and Ib/NT were also detected. In two instances three serotype combinations were detected in samples from one woman and these included serotypes III/Ib/II and III/Ia/Ib. Isolates were also typed for women who were colonised in both vaginal and perianal regions and it was found that only 10 participants had identical isolates in both regions. GBS serotype III was the predominant serotype detected in women tested in this study and this is the serotype that has previously been associated with invasive infections in neonates. GBS neonatal disease is a world wide economic, health and social burden affecting different ethnic groups and is preventable. Currently no vaccine technology is available for the prevention of GBS neonatal disease and the most effective EOGND preventative protocol would be to test for maternal GBS colonisation during labour, or screen women for GBS at &gt36 weeks' gestation and administer intrapartum antibiotic prophylaxis (IAP) to all women who tested positive for GBS. In this current study we utilised a rapid bsp PCR assay to detect LGT GBS colonisation in women of child bearing age. The PCR assay identified 62.5% of all vaginal and perianal positive culture GBS samples. The specificity of the PCR assay was 89% while the positive and negative predictive values were 56.8% and 91.1% respectively. This PCR assay using the current parameters is not an effective GBS detection assay but could be further optimised in the near future. This PCR assay could be an effective test in the future with the development of an alternative DNA extraction method to InstaGene (BioRad). However, this PCR assay if used in conjunction with the current culture method is able to detect a further 8.9% of women colonised with asymptomatic GBS. Brisbane women aged between 26 to 35 years who are pregnant and who are attending public health care agencies are at greatest risk of being colonised with GBS. No disparity was identified when ethnicity or social standing were assessed. The overall results of this study demonstrate that the LGT GBS prevalence rate in Brisbane women is 26.2% but this rate was higher at 30.5% for women attending a Brisbane sexual health clinic and for pregnant women attending the Mater Mothers' antenatal clinic. GBS serovar III has been identified as the dominant serovar in our population group and this strain has been reported as the major cause of GBS disease in neonates and infants aged to three months. Disparity (11.1%) was reported when the incidence of adverse pregnancy outcomes amongst Aboriginal women was compared to non Aboriginal women. From the outcomes of this study it has been suggested that Queensland adopt a screening based GBS preventative protocol. It has also been suggested that an Australian wide GBS prevention strategy may further reduce the incidence of neonatal disease.

Thesis (M.Com. (Economics & Economic History)) - Rhodes University, 2009. / A thesis submitted in partial fulfilment of the requirements for the degree of Masters in Commerce (Financial Markets)