Dezoito galinhas de uma população experimental utilizada em um cruzamento recíproco entre as linhagens de frangos de corte (TT) e de postura (CC) foram sequenciadas pela tecnologia de nova geração na plataforma Illumina com uma cobertura média de 10X. A descoberta de variantes genéticas foi realizada em uma região de locos de característica quantitativa (Quantitative Trait Locus, QTL), associado anteriormente com peso e percentagem de gordura abdominal no cromossomo 3 da galinha (GGA3), entre os marcadores microssatélites LEI0161 e ADL0371 (33,595,706-42,632,651 pb). O programa SAMtools foi utilizado na identificação de 136.054 SNPs únicos e 15.496 INDELs únicas nos 18 animais sequenciados e após a filtragem das mutações, 92.518 SNPs únicos e 9.298 INDELs únicas foram mantidas. Uma lista de 77 genes foi analisada buscando genes relacionados ao metabolismo de lipídios. Variantes localizadas na região codificante (386 SNPs e 15 INDELs) foram identificadas e associadas com vias metabólicas importantes. Variantes nos genes LOC771163, EGLN1, GNPAT, FAM120B, THBS2 e GGPS1 foram identificadas e podem ser responsáveis pela associação do QTL com a deposição de gordura na carcaça em galinhas. / Eighteen chickens from a parental generation used in a reciprocal cross with broiler and layer lines were sequenced by new generation technology with an average of 10-fold coverage. The DNA sequencing was performed by Illumina next generation platform. The genetic variants discovery was performed in a quantitative trait loci (QTL) region which was previously associated with abdominal fat weight and percentage in chicken chromosome 3 (GGA3) between the microsatellite markers LEI0161 and ADL0371 (33,595,706-42,632,651 bp). SAMtools software was used to detect 136,054 unique SNPs and 15,496 unique INDELs for the 18 chickens, and after quality filtration 92,518 unique SNPs and 9,298 unique INDELs were retained. One list of 77 genes was analised and genes related to lipid metabolism were searched. Variants located in coding region (386 SNPs and 15 INDELs) were identified and associated with important metabolic pathways. Loss of functional variants in the genes LOC771163, EGLN1, GNPAT, FAM120B, THBS2 and GGPS1 may be responsible for the QTL associated with fat deposition in chicken.

京都大学 / 0048 / 新制・課程博士 / 博士(医学) / 甲第22002号 / 医博第4516号 / 新制||医||1038(附属図書館) / 京都大学大学院医学研究科医学専攻 / (主査)教授 滝田 順子, 教授 松田 文彦, 教授 山田 亮 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

京都大学 / 0048 / 新制・論文博士 / 博士(医学) / 乙第13326号 / 論医博第2194号 / 新制||医||1043(附属図書館) / (主査)教授 小川 誠司, 教授 滝田 順子, 教授 河本 宏 / 学位規則第4条第2項該当 / Doctor of Medical Science / Kyoto University / DFAM

京都大学 / 0048 / 新制・課程博士 / 博士(社会健康医学) / 甲第22889号 / 社医博第113号 / 新制||社医||11(附属図書館) / 京都大学大学院医学研究科社会健康医学系専攻 / (主査)教授 川上 浩司, 教授 松田 文彦, 教授 中島 貴子 / 学位規則第4条第1項該当 / Doctor of Public Health / Kyoto University / DFAM

Sorghum crop has become attractive to breeders due to its drought tolerance, and many uses including a human food source, animal feed, industrial fibre and bioenergy crop. Sorghum, like any other plant, is a host to a variety of microbes that can have neutral, negative or positive effects on the plant. While the majority of microorganisms are beneficial, pathogens colonize plant tissues and overwhelm its defence mechanisms. This colonization is a direct threat to the sorghum productivity. The development of microbiome-based approaches for sustainable crop productivity and yield is hindered by a lack of understanding of the main biotic factors affecting the crop microbiome. Metabarcoding has proven to be a valuable tool which has been widely used for characterizing the microbial diversity and composition of different environments and has been utilized in many research endeavours. This study analyses the relationship between the microbiota and their response to natural pathogen infection in sorghum disease groups (R, MR, S and HS) and identifies the most dominant pathogen in the highly susceptible disease group. The study also, assesses the spore viability through the use of the automated cell counter and confirms Fusarium graminearum (dominant pathogen linked to the HS disease group) through sequencing of the marker genes, to subsequently characterize pathways likely to be involved in pathogen infection resistance. To achieve the objectives, a combination of 16S rRNA (V3/V4 regions) and ITS (ITS1/ITS4) of the internal transcribed spacer regions were amplified and sequenced using NGS technologies to study the microbiota in response to natural infection. Additionally, comparative transcriptional analysis of sorghum RILs in response to Fusarium graminearum infection was conducted through RNA-Seq. Upon natural infection, the foliar symptoms assessment of the RILs was conducted and four disease groups; resistant (R), moderately resistant (MR), susceptible (S) and highly susceptible (HS) were designated. The results of the present metabarcoding study indicate that resistant sorghum leaves (R group) supported a large diversity of fungal and bacterial microbes. The genera Methylorubrum, Enterobacter and Sphingomonas with reported plant growth promoting traits were more abundant and highly enriched in the R and MR group, with members of the latter genus significantly enriched in the R group. The resistant fungal group had a majority of OTUs showing similarity to well-known plant growth-promoting fungal genus including Papiliotrema (Tremellaceae family), which are known biocontrol agents. The yeast Hannaella was also highly linked with the resistant plants. Some Hannaella species are known to produce indole acetic acid (IAA) for promoting plant growth. Metabarcoding was also used to assess the major potential disease-causing taxa associated with the highly diseased group. It identified fungal pathogenic species, that have not previously been identified as pathogens of sorghum such as Ascochyta paspali and Ustilago kamerunensis (which are known pathogenic fungi of grass species) and were associated with the susceptible disease groups (S and HS). These analyses revealed the potential sorghum fungal pathogen Epicoccum sorghinum, and was highly linked with the S disease group. It further expanded the identification of a reportedly economically importance species causing sorghum related diseases Fusarium graminearum (anamorph Gibberella zeae). This species has also been identified in this study to be highly associated with the RILs showing major disease symptoms. Fusarium graminearum a significant pathogen in winter cereals and maize has been associated with stalk rot of sorghum and sorghum grain mould. The presence of Fusarium graminearum in sorghum can be a toxicological risk, since this species has the potential to produce mycotoxins. It was further shown that natural pathogen infection results in distinct foliar microbial communities in sorghum RILs. The co-occurrence taxa represented by Tremellomycetes and Dothiomycetes fungal classes and Bacillaceae and Sphingomonadaceae bacterial family had more central roles in the network. The modules which are located centrally on the network have been expected to play important ‘topological roles’ in interconnecting pairs of other fungal and bacterial taxa in the symbiont–symbiont co-occurrence network. These taxa having a central role, are considered to be keystone microbes, and have been suggested to be drivers of microbiome structure and functioning. The results of bacterial and fungal community composition, community co-occurrences further suggested the importance of keystone taxa which may disproportionately shape the structure of foliar microbiomes. The foliar disease symptom assessments revealed that sorghum RIL 131 was highly diseased and RIL 103 did not show any visible disease symptoms and were subsequently used for transcriptomic analysis. Gene expression patterns were studied between the identified RIL that did not show visible symptoms (resistant RIL no 103) and the RIL that showed major disease symptoms (susceptible RIL no 131). Fusarium graminearum the dominant potential pathogen found in this study to be associated with the highly susceptible plants was used to inoculate RILs at seedling stage in a greenhouse and samples were collected in triplicates at 24 hours post infection (hpi), 48 hpi, 7 days post infection (dpi) and 14 dpi. Prior to that, ITS and UBC genes confirmed the identity of Fusarium graminearum, and the automated haemocytometer confirmed the cell/spore viability. Using RNA-Seq analysis it was shown that the resistant RIL had defence related pathways from early response (24- 48 hpi) to late response (7-14 dpi). And the more the infection progressed, the more the defence related genes were up-regulated in terms of fragments per kilobase of exon model per million reads mapped (FPKM) and False Discovery Rate (FDR ≤ 0.05) values. Transcriptome time series expression profiling was used to characterize the plant response to Fusarium graminearum with the Dirichlet Process Gaussian Process mixture model software (DPGP) in susceptible and resistant RILs. The susceptible RIL (number 131) transcriptional response upon Fusarium graminearum infection presented differences of the closely related clustered expression profiles across all timepoints in both RILs. Group 2 exclusively clustered the genes encoding the sesquiterpene metabolism pathway, which is one of the major physiological change occurring in response to fungal infection and has been previously reported to produce the mycotoxins associated with Fusarium head blight (FHB) of cereals. This pathway presented an increase from the initial infection phase to the late infection phase in group 4, the genes encoding starch sucrose, metabolism and cyanoamino acid pathways presented a pattern that had a sharp decline from 48 hpi -14 dpi (at a later stage of infection). This could suggest that, as the time progresses in the susceptible RIL the pathways which are important in plant defence declines at a late infection stage. Group 3 presented a pattern increase of the 5-lipoxygenase (LOX 5) gene expressed from 48 hpi-14 dpi timepoints. The loss and silencing of LOX5 function have in the past described to be linked with enhanced disease resistance. In this study the LOX5 was expressed and this could suggest that LOX5 might have a function as a susceptibility factor in disease caused by Fusarium graminearum in sorghum RILs. CBL-interacting protein kinase 6 (CIPK6) gene was also associated with this group. This gene has been associated with negative regulation of immune response to Pseudomonas syringae in Arabidopsis as plants overexpressing CIPK6 were more susceptible to Pseudomonas syringae. Transcriptional response of a resistant RIL (number 103) to infection with Fusarium graminearum presented an increase in genes encoding metabolic and biosynthesis of metabolites pathways in group 1 and group 4 at early infection phase and a sharp decline in the late infection phase. An increase in the genes encoding pathways in earlier infection state could suggest the establishment of a beneficial energy balance for defence. Additionally, genes encoding phenylpropanoid (PAL), galactose and glycolysis pathway were amongst the genes increased at early stages of infection in group 1. Sugar can play a significant role in resistance to fungal pathogens through phenylpropanoid metabolism stimulation, and previous studies showed that the phenylpropanoid pathway could play a role in resistance of wheat to Fusarium graminearum and deoxynivalenol. Overall, this study represents a first step in understanding the molecular mechanisms involved in resistance to Fusarium graminearum. This analysis has also identified the reported beneficial microbes and defence related genes and pathways. Together, the current findings suggest that different ‘resident’ consortia found in naturally infected and uninfected sorghum plants may be viable biocontrol and plant-growth promoting targets. Cultivation studies may shed light on the nature of the putative symbiotic relationships between bacteria and fungi. These results have consequences for crop breeding, and the analysis of microbial diversity and community composition can be useful biomarkers for assessing disease status in plants. The transcriptome and metabarcoding data generated will help guide further research to develop novel strategies for management of disease in sorghum RILs through the integrative approach considering both beneficial microbes and defence related genes. This provides the baseline information and will positively impact in the development of Fusarium graminearum resistant genotypes in future through the integration/incorporation of beneficial microorganisms (bacteria and fungi) and resistant genes in breeding strategies. / Life and Consumer Sciences / D. Phil. (Life Sciences)

Y-chromosome testing has become more prevalent in recent years as a means of identifying forensic samples using STRs or identifying biomarkers for disease or determining geographic origins of populations. Additionally, Y-chromosome analysis is especially useful in paternity testing as the Y chromosome is inherited paternally and the male-specific region of the Y chromosome does not undergo any recombination events, allowing the genotypic data of both the father and son to be identical. Though in most cases a father-son pair will have the same Y-allelic data, random mutations like allele insertions and deletions can occur, which can interfere and result in incorrect conclusions in regards to paternity testing, forensic analysis, or genealogy. Though the exact mechanism of Y loci mutability is unknown, postulations of factors that can cause mutations have been studied, as well as attempts to determine mutation rate specific to each locus. A multi-generational pedigree consisting of 9 males was analyzed using two different methodologies: capillary electrophoresis and next-generation sequencing. The samples were amplified using either a ForenSeq™ Signature DNA Prep Kit (Verogen, San Diego, CA) or a YFiler™ Plus PCR Amplification Kit (Thermo Fisher Scientific, Waltham, MA). Between the two methods, five Y-STR loci were identified as being discordant between a father-son pair. Next-generation sequencing identified an allele insertion at DYS385a/b, resulting in a potential tri-allelic locus, but was disproved after comparison with the capillary electrophoresis data of the sample. The capillary electrophoresis data identified four discordances between father-son pairs, one of which was an allele mutation with a gain of a repeat at DYS458. At DYS 389II, an allele insertion was identified, but was contradicted after comparison with the next-generation sequencing data. There was a potential null allele at DYS518 and either an OL variant allele or a 2 base pair deletion at DYS481. Following peak height ratio, stutter, and comparative analysis between the genotypic data of the two analysis methods, two of these discordances were proven to be errors, one was a definitive mutational event, and the other two could neither be confirmed nor denied due to differences in loci tested in each kit.

Understanding the composition, evolution, and function of the cotton (Gossypium) genome is complicated by the joint presence of two genomes in its nucleus (AT and DT genomes). Specifically, read-mapping (a fundamental part of next-generation sequence analysis) cannot adequately differentiate reads as belonging to one genome or the other. These two genomes were derived from progenitor A-genome and D-genome diploids involved in ancestral allopolyploidization. To better understand the allopolyploid genome, we developed PolyCat to categorize reads according to their genome of origin based on homoeo-SNPs that differentiate the two genomes. We re-sequenced the genomes of extant diploid relatives of tetraploid cotton that contain the A1 (Gossypium herbaceum), A2 (Gossypium arboreum), or D5 (Gossypium raimondii) genomes. We identified 24 million SNPs between the A-diploid and D-diploid genomes. These analyses facilitated the construction of a robust index of conserved SNPs between the A-genomes and D-genomes at all detected polymorphic loci. This index can be used by PolyCat to assign reads from an allotetraploid to its genome-of-origin. Continued characterization of the Gossypium genomes will further enhance our ability to manipulate fiber and agronomic production of cotton. We re-sequenced 34 allotetraploid cotton lines, representing all 7 tetraploid cotton species. The analysis of these genomes-using PolyCat and PolyDog-provides us with the beginnings of a HapMap-like resource for cotton species, including indices of both homoeo-SNPs and allele-SNPs. With this information, we explore the phylogenetic relationships among cotton species, including the newly characterized species G. ekmanianum and G. stephensii. We examine gene conversion both recent and ancient, discovering that recent gene conversion is extremely rare, and ancient gene conversion is far less extensive than previously believed, with many previously identified conversion events being more probably due to autapamorphic SNPs in the descent of diploid relatives. In order to carry out these experiments, many tools for next-generation sequence analysis were developed. These tools, along with PolyCat and PolyDog, comprise the tool suite BamBam.

Oenococcus oeni est une espèce de bactérie lactique adaptée à l'environnement hostile de la fermentation du vin. Elle montre un degré de spécialisation remarquable face au stress provoqué par le faible pH et la forte teneur en éthanol, ce qui lui permet de proliférer là où la plupart des bactéries ne survivent pas. Cette bactérie est très importante dans la production de vin, car elle réalise la fermentation malolactique, qui se produit après la fermentation alcoolique, et au cours de laquelle l'acide malique est métabolisé en acide lactique et où le vin est désacidifié. L'espèce accumule des mutations plus vite que les autres espèces de bactéries lactiques, ce qui a probablement accéléré le processus de domestication. Son degré de spécialisation a été démontré par la présence de populations spécifiques adaptées aux vins rouges ou aux vins blancs dans la même région. Dans cette étude, nous avons utilisé des approches de séquençage haut débit et de génomique pour élucider la diversité des souches d’O. oeni, identifier leurs caractéristiques génomiques et mesurer leur dispersion dans différents environnements ainsi que leur dynamique au cours des fermentations. En raison de son importance pour la vinification, plusieurs centaines de souches ont été isolées et séquencées. Dans ce travail, nous avons augmenté la collection de génomes en séquençant des souches de cidre et de kombucha et en effectuant des analyses phylogénétiques afin de clarifier la structure de la population de l'espèce. En calculant un pangénome à l'échelle de l'espèce, nous avons effectué une analyse génomique comparative afin d'explorer des gènes spécifiques à une ou plusieurs sous-populations. Avec le séquençage de nouvelle génération, nous avons produit des génomes entièrement circularisés à partir des principales sous-populations et analysé leurs arrangements génomiques. Ces nouveaux génomes ont été annotés avec de nouveaux pipelines automatiques et une curation manuelle pour la première fois depuis la publication du génome de référence PSU-1. L’évolution des communautés bactériennes au cours de la fermentation, du moût de raisin au vin fini, a été examinée par le séquençage de fragments 16S dans quatre exploitations du bordelais. À l’aide d’amorces universelles et spécifiques, nous avons comparé la biodiversité des espèces dans des vins issus d’agriculture biologique ou conventionnelle. De plus, en se basant sur les groupes phylogénétiques de souches d’O. oeni nouvellement définis, nous avons développé une méthode de qPCR pour analyser la dispersion des groupes de souches d’O. oeni et leur dynamique au cours des fermentations. Cette nouvelle méthode a également été utilisée pour analyser la diversité des souches d’O. oeni dans les vins de base de Cognac et au cours de la production de cidre, deux produits qui se distinguent des productions de vins traditionnels par la non-utilisation de sulfites. Les deux autres espèces du genre Oenococcus, O. kitaharae et O. alcoholitolerans, se retrouvent également dans les environnements de boissons fermentées. O. kitaharae ne possède pas de gène malolactique fonctionnel, mais O. alcoholitolerans, découvert plus récemment, serait capable de réaliser la réaction malolactique. Nous l’avons caractérisée, ainsi que sa tolérance aux facteurs de stress de l'environnement vin. Constatant qu'elle était incapable de survivre dans le vin, nous avons produit un génome entièrement circularisé d'O. alcoholitolerans et effectué une analyse de génomique comparative afin d'identifier les gènes d'O. oeni lui permettant de tolérer le pH et l'éthanol, ce qui manque à O. alcoholitolerans et à O. kitaharae. En conclusion, nous avons utilisé les nouvelles technologies de séquençage de nouvelle génération pour produire des génomes de haute qualité et effectuer des analyses comparatives approfondies à l’échelle de l’espèce qui nous ont permis d’identifier des gènes susceptibles d’expliquer l’adaptation d’O. oeni à l’environnement. / Oenococcus oeni is a lactic acid bacteria species adapted to the inhospitable environment of fermenting wine, where it shows a remarkable degree of specialization to the stress of low pH and high ethanol that allows it to proliferate where most bacteria fail to survive. The bacteria is supremely important in wine production, because it carries out malolactic fermentation, a process that occurs after alcoholic fermentation, where malic acid is metabolised into lactic acid and the pH of the wine is raised. The species has only a small genome and accumulates mutations several orders of magnitude faster than other lactic acid bacteria due to a loss of DNA mismatch repair genes. This has likely sped up the process of domestication to wine. The degree of specialization has been demonstrated by finding specific populations adapted to red or white wines in the same region. In this study, we used high throughput sequencing and genomics approaches to elucidate the diversity of O. oeni strains, to identify their genomic characteristics and measure their dispersion in different environments as well as their dynamics during fermentation. Because of its importance to wine-making, several hundred strains have been isolated and sequenced. In this work, we have expanded upon the collection of genomes by sequencing strains from cider and kombucha and performing phylogenetic analyses to clarify the population structure of the species. By calculating a species-wide pangenome, we performed comparative genomics to explore gene clusters that were specific to one or more sub-populations. With next generation sequencing, we produced fully circularized genomes from the major sub-populations and analysed their genomic arrangements. These new genomes were annotated with new, automatic pipelines and manual curation for the first time since the publication of the reference genome PSU-1. The evolution of bacterial communities over the course of fermentation, from grape must to finished wine, was examined with 16S amplicon sequencing in four Bordeaux wineries. Using a universal and a specific primer-set, we compared the biodiversity in wines resulting from organic or conventional farming practices. In addition, with the newly defined phylogenetic groups, we developed a qPCR experiment to detail the composition of O. oeni in the fermentations and cemented the dispersal of even rarely isolated strain sub-populations in grape must. This new method was also used to analyse the diversity of O. oeni strains in the base wines of Cognac and during the production of cider, two products that are distinguished from traditional wine production by not using sulfite. The two other species in the Oenococcus genus, kitaharae and alcoholitolerans, are also found in the environments of fermenting beverages. O. kitaharae does not have a functional malolactic gene, but the more recently discovered O. alcoholitolerans was thought capable of performing the malolactic reaction. We characterized this, as well as the species tolerance for the stressors of the wine environment. Finding it unable to survive in wine, we produced a fully circularized genome of O. alcoholitolerans and performed a comparative genomics analysis to identify the O. oeni genes that enable it to tolerate the pH and ethanol, which O. alcoholitolerans and O. kitaharae lacks. In conclusion, we have used the new technologies of next generation sequencing to produce high-quality genomes and performed extensive, species-wide comparative analyses that allowed us to identify patterns in gene presence that provide likely explanations for environmental adaptation.

Coal gasification stripped gas liquor (CGSGL) wastewater contains large quantities of complex organic and inorganic pollutants which include phenols, ammonia, hydantoins, furans, indoles, pyridines, phthalates and other monocyclic and polycyclic nitrogen-containing aromatics, as well as oxygen- and sulphur-containing heterocyclic compounds. The performance of most conventional aerobic systems for CGSGL wastewater is inadequate in reducing pollutants contributing to chemical oxygen demand (COD), phenols and ammonia due to the presence of toxic and inhibitory organic compounds. There is an ever-increasing scarcity of freshwater in South Africa, thus reclamation of wastewater for recycling is growing rapidly and the demand for higher effluent quality before being discharged or reused is also increasing. The selection of hybrid fixed-film bioreactor (HFFBR) systems in the detoxification of a complex mixture of compounds such as those found in CGSGL has not been investigated. Thus, the objective of this study was to investigate the detoxification of the CGSGL in a H-FFBR bioaugmented with a mixed-culture inoculum containing Pseudomonas putida, Pseudomonas plecoglossicida, Rhodococcus erythropolis, Rhodococcus qingshengii, Enterobacter cloacae, Enterobacter asburiae strains of bacteria, as well as the seaweed (Silvetia siliquosa) and diatoms. The results indicated a 45% and 79% reduction in COD and phenols, respectively, without bioaugmentation. The reduction in COD increased by 8% with inoculum PA1, 13% with inoculum PA2 and 7% with inoculum PA3. Inoculum PA1 was a blend of Pseudomonas, Enterobacter and Rhodococcus strains, inoculum PA2 was a blend of Pseudomonas putida iistrains and inoculum PA3 was a blend of Pseudomonas putida and Pseudomonas plecoglossicida strains. The results also indicated that a 70% carrier fill formed a dense biofilm, a 50% carrier fill formed a rippling biofilm and a 30% carrier fill formed a porous biofilm. The autotrophic nitrifying bacteria were out-competed by the heterotrophic bacteria of the genera Thauera, Pseudaminobacter, Pseudomonas and Diaphorobacter. Metagenomic sequencing data also indicated significant dissimilarities between the biofilm, suspended biomass, effluent and feed microbial populations. A large population (20% to 30%) of unclassified bacteria were also present, indicating the presence of novel bacteria that may play an important role in the treatment of the CGSGL wastewater. The artificial neural network (ANN) model developed in this study is a novel virtual tool for the prediction of COD and phenol removal from CGSGL wastewater treated in a bioaugmented H-FFBR. Knowledge extraction from the trained ANN model showed that significant nonlinearities exist between the H-FFBR operational parameters and the removal of COD and phenol. The predictive model thus increases knowledge of the process inputs and outputs and thus facilitates process control and optimisation to meet more stringent effluent discharge requirements. / Thesis (PhD)--University of Pretoria, 2017. / Chemical Engineering / PhD / Unrestricted

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