Dissertations / Theses on the topic 'Genomic trait'

Genome-wide association studies have been used extensively to study hundreds of phenotypes and have determined thousands of associated SNPs whose underlying biology and causation is as yet largely unknown. Many previous studies attempted to clarify the causal biology by investigating overlaps of trait-associated variants with functional annotations, but lacked statistical rigor and examined incomplete subsets of available functional annotations. Additionally, it has been difficult to disentangle the relative contributions of different annotations that may show strong correlations with one another. In this thesis, we address these shortcomings and strengthen and extend the obtained results. Two methods, permutations and logistic regression, are applied in statistically rigorous analyses of genomic annotations and their observed enrichment or depletion of trait-associated SNPs. The genomic annotations range from genic regions and regulatory features to measures of conservation and aspects of chromatin structure. Logistic regressions in a number of trait-specific subsets identify genomic annotations influencing SNPs associated with both normal variation (e.g., eye or hair colour) and diseases, suggesting some generalities in the biological underpinnings of phenotypes. SNPs associated with phenotypes of the immune system are investigated and the results highlight the distinct aetiology for this subset. Despite the heterogeneity of the studied cancers, SNPs associated to different cancers are particularly enriched for conserved regions, unlike all other trait-subsets. Nonetheless, chromatin states are, perhaps surprisingly, among the most influential genomic annotations in all trait-subsets. Evolutionary conserved regions are rarely within the top genomic annotations despite their widespread use in prioritisation methods for follow-up studies. We identify a common set of enriched or depleted genomic annotations that significantly influence all traits, but also highlight trait-­‐specific differences. These annotations may be used for the computational prioritisation of variants implicated in phenotypes of interest. The approaches developed for this thesis are further applied to studies of a specific human complex trait (height) and gene expression in atherosclerosis.

Thesis (Ph.D. in Pharmacology) -- University of Colorado Denver, 2008.
Typescript. Includes bibliographical references (leaves 121-149). Free to UCD Anschutz Medical Campus. Online version available via ProQuest Digital Dissertations;

In multiple species, genome-wide association (GWA) studies have become an increasingly prevalent method of identifying the quantitative trait loci (QTLs) that underlie complex traits. Despite this, relatively few GWA analyses using high-density genomic markers have been carried out on highly quantitative traits in wheat. We utilized single-nucleotide polymorphism (SNP) data generated via a genotyping-by-sequencing (GBS) protocol to perform GWA on multiple yield-related traits using a panel of 329 soft red winter wheat genotypes grown in four environments. In addition, the SNP data was used to examine linkage disequilibrium and population structure within the testing panel. The results indicated that an alien translocation from the species Triticum timopheevii was responsible for the majority of observed population structure. In addition, a total of 50 significant marker-trait associations were identified. However, a subsequent study cast some doubt upon the reproducibility and reliability of plant QTLs identified via GWA analyses. We used two highly-related panels of different genotypes grown in different sets of environments to attempt to identify highly stable QTLs. No QTLs were shared across panels for any trait, suggesting that QTL-by-environment and QTL-by-genetic background interaction effects are significant, even when testing across many environments. In light of the challenges involved in QTL mapping, prediction of phenotypes using whole-genome marker data is an attractive alternative. However, many evaluations of genomic prediction in crop species have utilized univariate models adapted from animal breeding. These models cannot directly account for genotype-by-environment interaction, and hence are often not suitable for use with lower-heritability traits assessed in multiple environments. We sought to test genomic prediction models capable of more ad-hoc analyses, utilizing highly unbalanced experimental designs consisting of individuals with varying degrees of relatedness. The results suggest that these designs can successfully be used to generate reasonably accurate phenotypic predictions. In addition, multivariate models can dramatically increase predictive accuracy for some traits, though this depends upon the quantity and characteristics of genotype-by-environment interaction.
Ph. D.

Background Chronic Kidney Disease (CKD), has a high and increasing burden in sub-Saharan Africa. Environmental factors that have been associated to CKD are associated with multiple co-morbidities such as hypertension, diabetes, and HIV. Some genetics factors such APOL1 have been associated with the highest burden of CKD among population of African ancestries. Other emerging genetic factors such as Sickle Cell trait (SCT) have been investigated mostly among African Americans. Sickle Cell trait (SCT) has the highest burden in sub-Saharan Africans, because of a natural selection, attributed to its protective advantages against the severest form of Malaria, caused by Plasmodium falciparum. Many studies showed that SCT has an impact on the normal functioning of the kidneys among African Americans with some studies indicating significant association between SCT and CKD. However, no study has been reported from Sub-Saharan Africa, where most SCT carrier reside. Moreover, there are multiple other loci and variants in the genome that have been associated with CKD in many populations, and that are used for Polygenic Risk Score (PRS) models but have not been explored in populations living in Africa. Aims This project aimed to study in a sub-Saharan African cohort, the association between 1) Sickle cell trait (SCT) with Chronic Kidney disease (CKD), and 2) the association of CKD with 29 targeted single nucleotide polymorphisms (SNPs) identified in multiple Genome-Wide Association studies (GWAS). Methods Patients and controls: 300 Cameroonian adult participants were included: 150 CKD cases and 150 non-CKD age, sex, and comorbidities matched controls. Molecular methods: SCT heterozygosity was determined by RFLP-PCR using the restriction enzyme DdeI. A total of 29 targeted SNPs was genotyped using MassArray and TaqMan techniques, followed by Sanger sequencing in a subset of samples. 11 Statistical Analysis: Descriptive statistics and logistic regression, and Fisher exact test were used. Functional pathway analysis: following the identification SNPs with significant association with CKD, we performed functional pathway test using the Linux programme Cytoscape. Results The mean age of cases was 53 years (range 46-55 years), with 43% that were female; there were no age and sex significant differences with controls. We identified, an expected, association between CKD and various co-morbidities, demographic and anthropometric variables: hypertension (p value = 5.16X10-9 ), HIV (p value = 2.68x10- 9 ), diabetes (p value = 7.12X10-7 ), BMI (p value = 4.58X10-8 ) and age (p value = 4.5X10-8 ). HbAS carrier status was significantly associated CKD (p value= 4.3X10-9 ; Odds Ratio:7.05). Only three targeted SNPs (3/29) previously associated with CKD in GWAS among African Americans, European and Asian population, were significantly associated with CKD among this group of Cameroonians (KBTBD2 rs3750082, PTPRO rs7956634 and LPR2 rs4667594 with p values of 0.02335, 0.0408 and 0.0398). Genes protein-protein interactions analysis identified the two key functional pathways and one network cluster that could play a crucial role in kidney dysfunctions. Lastly, we distinguished that HbS carrier state doesn’t influence the relationship between APOL1 G1/G2 risk alleles and CKD (p value = 0.5725) in this group from subSaharan Africans. Conclusion and perspectives Our study illustrates a strong association between SCT and CKD, an important discovery that will have a major implication in preventative medicine policies and practices in both sub-Saharan African where there is a very high prevalence of SCT. The data also has global resonance, with the projected increase in the prevalence of 12 individual with SCT, due to migration and the improve life expectancy and genetic fitness of people living with both SCT and SCD. We identified a relatively low proportion of (3/29) of target SNPs positively associated with CKD among this group of Cameroonians. The study illustrates that the vast majority of targeted SNPs associated with CKD in GWAS studies in multiple populations including African American, Europeans, and Asians, are not relevant for sub-Saharan Africans, indicating the urgent need to include diverse populations, specifically those living in Africa. Therefore, the data support the possible bias in currently available Polygenic Risk Score generated from GWAS data, where population from sub-Saharan Africa are largely underrepresented. The data further indicate that there is potential to discover new loci associated with CKD when investigating populations of African ancestry living in Africa.

Yellowfin tuna (Thunnus albacares; YFT) represents one of the most important seafood commodities in the world. The rationale of this Ph.D. project was identified by prioritizing key issues as objectives for contributing to the conservation of YFT and helping to develop a more realistic stock assessment and sustainable management of this species. Specifically, in this work the current mismatch between the biology and/or ecology and the realized management strategies was highlighted, putting particular emphasis on YFT population structure, which is currently characterized by a high degree of uncertainty at both local and global scale. This general pattern was confirmed by the results obtained using a panel of microsatellite loci, which cannot reject the null hypothesis of the existence of only one panmictic population at the global scale. On the contrary, the access to more powerful and cost effective genetic tools would represent the first step for resolving YFT population structure at both global and local scale. After having evaluated the efficiency and usefulness of 2b-RAD genotyping technique for investigating population genetic structure in highly migratory fish species, a panel of 972 SNPs (Single Nucleotide Polymorphisms) was generated. Using this panel, three distinct populations were identified in the Atlantic, Indian and Pacific Oceans. Additionally, it was possible to define a subset of 33 outlier loci putatively under selection to delineate and separate sub-populations within both the Atlantic and the Pacific Oceans (following an east-west division). Finally, it was emphasized for the first time that in the Atlantic Ocean larger YFT females allocate a greater fraction of surplus energy to egg production than smaller ones, improving noticeably the spawning quality. This result sheds light on the important contribution that larger and most experienced spawners have for the YFT productivity.

Yellowfin tuna (Thunnus albacares; YFT) represents one of the most important seafood commodities in the world. The rationale of this Ph.D. project was identified by prioritizing key issues as objectives for contributing to the conservation of YFT and helping to develop a more realistic stock assessment and sustainable management of this species. Specifically, in this work the current mismatch between the biology and/or ecology and the realized management strategies was highlighted, putting particular emphasis on YFT population structure, which is currently characterized by a high degree of uncertainty at both local and global scale. This general pattern was confirmed by the results obtained using a panel of microsatellite loci, which cannot reject the null hypothesis of the existence of only one panmictic population at the global scale. On the contrary, the access to more powerful and cost effective genetic tools would represent the first step for resolving YFT population structure at both global and local scale. After having evaluated the efficiency and usefulness of 2b-RAD genotyping technique for investigating population genetic structure in highly migratory fish species, a panel of 972 SNPs (Single Nucleotide Polymorphisms) was generated. Using this panel, three distinct populations were identified in the Atlantic, Indian and Pacific Oceans. Additionally, it was possible to define a subset of 33 outlier loci putatively under selection to delineate and separate sub-populations within both the Atlantic and the Pacific Oceans (following an east-west division). Finally, it was emphasized for the first time that in the Atlantic Ocean larger YFT females allocate a greater fraction of surplus energy to egg production than smaller ones, improving noticeably the spawning quality. This result sheds light on the important contribution that larger and most experienced spawners have for the YFT productivity.

Doctor of Philosophy
Department of Agronomy
Guihua Bai
Allan K. Fritz
Wheat pre-harvest sprouting (PHS), germination of physiologically matured grains in a wheat spike before harvesting, can cause significant reduction in grain yield and end-use quality. Many quantitative trait loci (QTL) for PHS resistance have been reported in different sources. To determine the genetic architecture of PHS resistance and its relationship with grain color (GC) in US hard winter wheat, a genome-wide association study (GWAS) on both PHS resistance and GC was conducted using in a panel of 185 U.S. elite breeding lines and cultivars and 90K wheat SNP arrrays. PHS resistance was assessed by evaluating sprouting rates in wheat spikes harvested from both greenhouse and field experiments. Thirteen QTLs for PHS resistance were identified on 11 chromosomes in at least two experiments, and the effects of these QTLs varied among different environments. The common QTLs for PHS resistance and GC were identified on the long arms of the chromosome 3A and 3D, indicating pleiotropic effect of the two QTLs. Significant QTLs were also detected on chromosome arms 3AS and 4AL, which were not related to GC, suggesting that it is possible to improve PHS resistance in white wheat. To identify markers closely linked to the 4AL QTL, genotyping-by-sequencing (GBS) technology was used to analyze a population of recombinant inbred lines (RILs) developed from a cross between two parents, “Tutoumai A” and “Siyang 936”, contrasting in 4AL QTL. Several closely linked GBS SNP markers to the 4AL QTL were identified and some of them were coverted to KASP for marker-assisted breeding. To investigate effects of the two non-GC related QTLs on 3AS and 4AL, both QTLs were transferered from “Tutoumai A” and “AUS1408” into a susceptible US hard winter wheat breeding line, NW97S186, through marker-assisted backcrossing using the gene marker TaPHS1 for 3AS QTL and a tightly linked KASP marker we developed for 4AL QTL. The 3AS QTL (TaPHS1) significantly interacted with environments and genetic backgrounds, whereas 4AL QTL (TaMKK3-A) interacted with environments only. The two QTLs showed additive effects on PHS resistance, indicating pyramiding these two QTLs can increase PHS resistance. To improve breeding selection efficiency, genomic prediction using genome-wide markers and marker-based prediction (MBP) using selected trait-linked markers were conducted in the association panel. Among the four genomic prediction methods evaluated, the ridge regression best linear unbiased prediction (rrBLUP) provides the best prediction among the tested methods (rrBLUP, BayesB, BayesC and BayesC0). However, MBP using 11 significant SNPs identified in the association study provides a better prediction than genomic prediction. Therefore, for traits that are controlled by a few major QTLs, MBP may be more effective than genomic selection.

Les nombreuses différences qui existent entre les organismes illustrent que le processus de variation est un phénomène universel en biologie. Ces variations sont particulièrement observables chez les espèces sexuées, entre mâles et femelles. Comprendre les différents facteurs biologiques, environnementaux et génétiques, à l'origine de ce dimorphisme sexuel est le cœur de mon sujet de thèse. Pour cela, j’ai établi un nouveau modèle d'étude, l’insecte semi-aquatique Microvelia longipes. Ces insectes ont évolué un dimorphisme sexuel spectaculaire où les mâles présentent une croissance extrême et hypervariable spécifiquement au niveau de la troisième paire de pattes. Pour étudier ce phénomène, nous avons, en premier lieu, émis l’hypothèse que cette croissance exagérée était associée à des pressions de sélection sexuelle. Nous avons mis en évidence la présence de compétition intense entre males, qui utilisent leurs pattes arrière comme arme, pour s’accoupler avec les femelles. Les males à pattes plus longues gagnent souvent dans ces combats, expliquant l’importance adaptative de ces pattes exagérées chez les mâles. De plus, nous montrons que l’intensité que mettent les mâles à se battre est associée aux variations de taille de pattes chez les mâles, de la même espèce ou d’espèces différentes. Nous avons également développé un génome et une approche transcriptomique comparant les sexes et les pattes afin d’identifier les gènes responsables de cette croissance exagérée. Ceci a permis de dresser une liste de gènes dont l’expression corrèle avec l’exagération de la croissance des pattes chez les mâles et d’identifier des régions génomiques associées à la sélection sexuelle
From the DNA molecule to the more complex phenotypes, variation is a universal process in life and living organisms. The innumerable differences that exist between species are probably one of the most manifest examples. Yet, all this diversity would never have occurred in nature without some pre-existing divergence within species. One of the most striking examples of intraspecies variation appears in sexual organisms, between males and females. Understanding the environmental and genetic factors influencing sexual divergence is a longstanding question in evolutionary biology. To this end, I focus here on a new insect model system, Microvelia longipes, which has the particularity to have evolved an extreme case of sexual dimorphism in the rear legs. Males display exaggerated long rear legs compared to females but also an extreme variability in these leg lengths from one male to another. We identified that M. longipes males use their exaggerated legs as weapons during male-male competition. Males with longer legs have more chance to access females on egg-laying sites and therefore increase their reproductive success. Moreover, fitness assays and comparative studies between Microvelia species revealed that the intensity of male competition was associated with the exaggeration and hypervariability of the rear legs in M. longipes males. In a second approach, we studied the developmental and genomic basis of this sexual dimorphism through a comparative transcriptomic analysis and identified genes and genomic regions associated with male exaggerated legs and ultimately with sexual selection. Overall, the integrative approach used in this work allows to establish Microvelia longipes as a promising new model system to study the influence of sexual selection in adaptive evolution

Ph.D. Dissertation Thesis
Recently, gene set analysis has become the first choice for gaining insights into the underlying complex biology of diseases through high-throughput genomic studies, such as Microarrays, bulk RNA-Sequencing, single cell RNA-Sequencing, etc. It also reduces the complexity of statistical analysis and enhances the explanatory power of the obtained results. Further, the statistical structure and steps common to these approaches have not yet been comprehensively discussed, which limits their utility. Hence, a comprehensive overview of the available gene set analysis approaches used for different high-throughput genomic studies is provided. The analysis of gene sets is usually carried out based on gene ontology terms, known biological pathways, etc., which may not establish any formal relation between genotype and trait specific phenotype. Further, in plant biology and breeding, gene set analysis with trait specific Quantitative Trait Loci data are considered to be a great source for biological knowledge discovery. Therefore, innovative statistical approaches are developed for analyzing, and vii interpreting gene expression data from Microarrays, RNA-sequencing studies in the context of gene sets with trait specific Quantitative Trait Loci. The utility of the developed approaches is studied on multiple real gene expression datasets obtained from various Microarrays and RNA-sequencing studies. The selection of gene sets through differential expression analysis is the primary step of gene set analysis, and which can be achieved through using gene selection methods. The existing methods for such analysis in high-throughput studies, such as Microarrays, RNA-sequencing studies, suffer from serious limitations. For instance, in Microarrays, most of the available methods are either based on relevancy or redundancy measures. Through these methods, the ranking of genes is done on single Microarray expression data, which leads to the selection of spuriously associated, and redundant gene sets. Therefore, newer, and innovative differential expression analytical methods have been developed for Microarrays, and single-cell RNA-sequencing studies for identification of gene sets to successfully carry out the gene set and other downstream analyses. Furthermore, several methods specifically designed for single-cell data have been developed in the literature for the differential expression analysis. To provide guidance on choosing an appropriate tool or developing a new one, it is necessary to review the performance of the existing methods. Hence, a comprehensive overview, classification, and comparative study of the available single-cell methods is hereby undertaken to study their unique features, underlying statistical models and their shortcomings on real applications. Moreover, to address one of the shortcomings (i.e., higher dropout events due to lower cell capture rates), an viii improved statistical method for downstream analysis of single-cell data has been developed. From the users’ point of view, the different developed statistical methods are implemented in various software tools and made publicly available. These methods and tools will help the experimental biologists and genome researchers to analyze their experimental data more objectively and efficiently. Moreover, the limitations and shortcomings of the available methods are reported in this study, and these need to be addressed by statisticians and biologists collectively to develop efficient approaches. These new approaches will be able to analyze high-throughput genomic data more efficiently to better understand the biological systems and increase the specificity, sensitivity, utility, and relevance of high-throughput genomic studies.
Netaji Subhas ICAR-International Fellowship (OM No. 18(02)/2016-EQR/Edn.)
ICAR-IASRI
University of Louisville, USA

This thesis develops and evaluates statistical methods for different types of genetic analyses, including quantitative trait loci (QTL) analysis, genome-wide association study (GWAS), and genomic evaluation. The main contribution of the thesis is to provide novel insights in modeling genetic variance, especially via random effects models. In variance component QTL analysis, a full likelihood model accounting for uncertainty in the identity-by-descent (IBD) matrix was developed. It was found to be able to correctly adjust the bias in genetic variance component estimation and gain power in QTL mapping in terms of precision.  Double hierarchical generalized linear models, and a non-iterative simplified version, were implemented and applied to fit data of an entire genome. These whole genome models were shown to have good performance in both QTL mapping and genomic prediction. A re-analysis of a publicly available GWAS data set identified significant loci in Arabidopsis that control phenotypic variance instead of mean, which validated the idea of variance-controlling genes.  The works in the thesis are accompanied by R packages available online, including a general statistical tool for fitting random effects models (hglm), an efficient generalized ridge regression for high-dimensional data (bigRR), a double-layer mixed model for genomic data analysis (iQTL), a stochastic IBD matrix calculator (MCIBD), a computational interface for QTL mapping (qtl.outbred), and a GWAS analysis tool for mapping variance-controlling loci (vGWAS).

Advances in molecular marker technologies have led to the development of high throughput genotyping techniques such as Genotyping by Sequencing (GBS), driving the application of genomics in crop research and breeding. They have also supported the use of novel mapping approaches, including Multi-parent Advanced Generation Inter-Cross (MAGIC) populations which have increased precision in identifying markers to inform plant breeding practices. In the first part of this thesis, a high density physical map derived from GBS was used to identify QTLs controlling key agronomic traits of wheat in a genome-wide association study (GWAS) and to demonstrate the practicability of genomic selection for predicting the trait values. The results from GBS were compared to a previous study conducted on the same association mapping panel using a less dense physical map derived from diversity arrays technology (DArT) markers. GBS detected more QTLs than DArT markers although some of the QTLs were detected by DArT markers alone. Prediction accuracies from the two marker platforms were mostly similar and largely dependent on trait genetic architecture. The second part of this thesis focused on MAGIC populations, which incorporate diversity and novel allelic combinations from several generations of recombination. Pedigrees representing a wild rice MAGIC population were used to model MAGIC populations by simulation to assess the level of recombination and creation of novel haplotypes. The wild rice species are an important reservoir of beneficial genes that have been variously introgressed into rice varieties using bi-parental population approaches. The level of recombination was found to be highly dependent on the number of crosses made and on the resulting population size. Creation of MAGIC populations require adequate planning in order to make sufficient number of crosses that capture optimal haplotype diversity. The third part of the thesis considers models that have been proposed for genomic prediction. The ridge regression best linear unbiased prediction (RR-BLUP) is based on the assumption that all genotyped molecular markers make equal contributions to the variations of a phenotype. Information from underlying candidate molecular markers are however of greater significance and can be used to improve the accuracy of prediction. Here, an existing Differentially Penalized Regression (DiPR) model which uses modifications to a standard RR-BLUP package and allows two or more marker sets from different platforms to be independently weighted was used. The DiPR model performed better than single or combined marker sets for predicting most of the traits both in a MAGIC population and an association mapping panel. Overall the work presented in this thesis shows that while these techniques have great promise, they should be carefully evaluated before introduction into breeding programmes.

The natural environments of organisms present a multitude of biotic and abiotic challenges that require both short-term ecological and long-term evolutionary responses. Though most environmental response studies have focused on effects at the ecosystem, community and organismal levels, the ultimate controls of these responses are located in the genome of the organism. Soil nematodes are highly responsive to, and display a wide variety of responses to changing environmental conditions, making them ideal models for the study of organismal interactions with their environment. In an attempt to examine responses to environmental stress (desiccation and freezing), genomic level analyses of gene expression during anhydrobiosis of the Antarctic nematode Plectus murrayi was undertaken. An EST library representative of the desiccation induced transcripts was established and the transcripts differentially expressed during desiccation stress were identified. The expressed genome of P. murrayi showed that desiccation survival in nematodes involves differential expression of a suite of genes from diverse functional areas, and constitutive expression of a number of stress related genes. My study also revealed that exposure to slow desiccation and freezing plays an important role in the transcription of stress related genes, improves desiccation and freezing survival of nematodes. Deterioration of traits essential for biological control has been recognized in diverse biological control agents including insect pathogenic nematodes. I studied the genetic mechanisms behind such deterioration using expression profiling. My results showed that trait deterioration of insect pathogenic nematode induces substantial overall changes in the nematode transcriptome and exhibits a general pattern of metabolic shift causing massive changes in metabolic and other processes. Finally, through field observations and molecular laboratory experiments the validity of the growth rate hypothesis in natural populations of Antarctic nematodes was tested. My results indicated that elemental stoichiometry influences evolutionary adaptations in gene expression and genome evolution. My study, in addition to providing immediate insight into the mechanisms by which multicellular animals respond to their environment, is transformative in its potential to inform other fundamental ecological and evolutionary questions, such as the evolution of life-history patterns and the relationship between community structure and ecological function in ecosystems.

Background Atlantic salmon (Salmo Salar) is a key aquaculture species in several countries. Since its critical role in economic sector and scientific research, this species has been relatively extensively investigated, in comparison with other farmed and wild aquatic species. However, the genetic components associated with growth and fillet-related traits are lack consistency, and the issue of sea louse disease in both wild and famed salmon is still unsolved. Objectives Overall aim of this project was to understand the genetic basis of growth-related traits and host resistance to sea lice using three large commercial farmed salmon populations. Specifically, the method of quantitative trait loci (QTL) mapping, genome-wide association study (GWAS), and genomic prediction (GS) were utilized to dissect the genetic architectures associated with traits of interest in our experimental populations. Prior to this, linkage mapping was performed to construct a high-density linkage map for Atlantic salmon. Results Linkage map A linkage map was firstly constructed underlying a SNP array containing 132 K validated SNPs. 96,396 SNPs were successfully assigned to 29 chromosomes that correspond to the linkage group number of European Atlantic salmon. 6.5 % of unassigned contigs, which was equal to 1 % of recent whole genome reference assembly (GCA_000233375.4) anchored to exist chromosomes by referring to linkage mapping result. Genetic components associated with growth traits Heritabilities of growth-related traits were about 0.5 to 0.6 in adult and juvenile farmed salmon. The QTL mapping and GWAS suggested the growth-related traits are likely a polygenic genetic architecture with no major QTL segregating. The prediction accuracy estimated by genomic prediction showed that approximately 5,000 SNP markers could achieve the highest accuracy in body weight and length in juvenile salmon within population. Genetic components associated with lice resistance The heritability of lice resistance was 0.22 to 0.33 using pedigree and genetic relationship matrices respectively. GWAS indicated that the host resistance to sea lice was likely polygenic with no individual SNP surpassed the genome-wide significance threshold. Genomic prediction showed that about 5 to 10 K SNPs was able to achieve the asymptote of accuracy in closely related animals, while the greatest advantage of genomic prediction was observed in non-sibling test within population. Conclusions As the growth-related traits and lice resistance are both likely polygenic and population-specific, the genomic prediction is an efficient approach to capture the genetic variances of the traits in selection candidates in experimental population, especially for traits with low heritability such as flesh colour and lice resistance. Family-based selection method is the better choice than mass selection to accumulate the genetic effects in corresponding SNP platform. Given the high cost of genotyping and field data collection, the genotyping-by-sequencing and genotype imputation are likely the way to make significant improvements in relevant research.

 

The domesticated apple (Malus x domestica Borkh.), belonging to the Malus genus of the Rosaceae family, is one of the edible pomaceous fruits. Since it is one of the important commercial fruit crops worldwide, the quality of the fruit is crucial to breeders and farmers as it ultimately determines acceptance of a cultivar for consumption. Fruit quality is also a critical determinant factor that is used to estimate the potential of apples to have a long shelf life. The introduction of marker-assisted selection (MAS) has allowed hastening of traditional breeding and selection of high-quality apple cultivars. The availability of genetic linkage maps, constructed by positioning molecular markers throughout the apple genome, enables the detection and analysis of major genes and quantitative trait loci (QTLs) contributing to the quality traits of a given genotype. 
herefore, the primary aim of this study was to construct a genetic linkage map of the &lsquo
Golden Delicious&rsquo
x &lsquo
Dietrich&rsquo
population for the identification of QTLs associated with fruit quality traits and then to examine the apple fruit pulp proteome with a specific focus on fruit firmness. In this regard, genomic DNA was extracted from leaves of the &lsquo
Golden Delicious&rsquo
x Dietrich&rsquo
population and used in megaplex PCR reactions. The PCR products were analysed prior to scoring of alleles. Polymorphic markers were then used to construct genetic linkage maps. The genetic linkage maps constructed in this study comprise of 167 simple sequence repeats (SSR) markers, 33 of these were newly developed markers. The 17 linkage groups of apple were constructed and aligned to existing apple genetic maps. The maps span 1,437.8 cM and 1,491.5 cM for &lsquo
Golden Delicious&rsquo
and &lsquo
Dietrich&rsquo
, respectively.

The main objective of this thesis was to perform a comprehensive investigation of the possibilities for the improvement of meat quality traits focusing on the development of innovative tools. The study was carried out sampling 1,327 Piemontese young bulls. Animals were fattened in 115 farms and slaughtered at the same commercial abattoir. Information about farms fattening system was collected through on field surveys. After slaughter, the following carcass traits were recorded: carcass weight, carcass conformation, age at slaughter and carcass daily gain. Individual samples of the Longissimus thoracis muscle were collected and transferred to the laboratory for meat quality analyses: muscle pH, colour parameters of lightness (L*), redness (a*), yellowness (b*), hue angle (h*), chroma (C*), purge losses, cooking losses, and Warner Bratzler shear force, all measured at 7 d after slaughter. On each meat sample, 5 spectra were collected in a reflectance mode at the abattoir with a portable top-ranking visible near-infrared spectrometer and an hand-held spectrometer. Calibration equations were developed after conventional meat quality assessment using Bayesian methods. The ability of spectroscopy in predicting meat quality traits was evaluated comparing the performances of the two spectrometers. Genetic correlations between carcass and measured meat quality traits were investigated, as well as genetic relations of meat quality traits with predictions obtained by spectral data. All the sampled young bulls were genotyped with the “GeneSeek Genomic Profiler Bovine LD” (GGP Bovine LD) array containing 30,111 SNPs. A combination of Genome-Wide Association and Pathway Analysis was performed to identify the genomic regions and biological pathways contributing to the variability of carcass and meat quality traits. Genomic variance components and SNP effects were estimated with bayesian methodology and a SNP-BLUP model. Genomic heritability and direct genomic breeding values were computed, assessing the possibility of implement genomic selection for meat quality traits. Six main typologies of fattening system were identified within the Piemontese breed. Carcass traits were deeply affected by production system, while little effects on meat quality, limited to colour traits, were observed. The small effect of beef production system showed that the variability of meat quality traits mainly depends on individual animal factors, shifting the possibilities for their improvement to genetic aspects. All the meat quality traits showed not negligible heritabilities, allowing their improvement through selection. They also displayed genetic relationships with carcass traits, indicating a possible modification as a correlated response to selection for growth rate and muscularity, traits currently included in the breeding goal of the Piemontese breed. However, the establishment of a direct selection procedure relies on the availability of phenotypes collected within a routine recording scheme. Predictions of colour traits and purge losses were satisfactory, whereas pH, cooking losses and shear force predictabilities were rather poor. However, all the predicted traits except shear force showed moderate heritabilities and were highly correlated with measured traits, allowing their use for selection purposes. From genetic architecture point of view of carcass and meat quality traits, our investigation highlighted that, besides myostatin, other genes contribute to explain the variability in carcass and growth characteristics. Moreover, association of pathways related to transporter activity (oxygen, calcium, ion and cation) was found with meat color parameters. Genomic heritabilities were higher than pedigree-based heritabilies for purge losses and all colour traits, while they were similar for the other meta quality traits. The accuracy of prediction of genomic breeding values was satisfactory and allows to consider genomic selection as a valid tool to improve meat quality traits in Piemontese breed.
La ricerca alla base di questa tesi di dottorato è stata condotta nell'ambito del progetto "QualiPiem" - Strumenti innovativi per la selezione della qualità della carne nella razza bovina Piemontese. Obiettivo principale è stato valutare la possibilità di migliorare la qualità della carne nei bovini di razza Piemontese, ponendo particolare attenzione agli aspetti applicativi oltre che a quelli conoscitivi. Lo studio ha previsto la comprensione delle basi genetiche dei caratteri di qualità della carne, la messa a punto di strumenti innovativi per il rilievo dei fenotipi, potenzialmente applicabili su larga scala a livello operativo, e l'impiego di informazioni genomiche per la selezione. Operativamente, il progetto ha previsto il campionamento di 1,327 vitelloni registrati nel Libro Genealogico italiano della razza Piemontese. Gli animali sono stati ingrassati in 115 allevamenti e macellati nella stessa struttura commerciale tra aprile 2015 e febbraio 2017. Le informazioni sui sistemi di ingrasso adottati negli allevamenti sono state raccolte attraverso indagini in campo basate sul colloquio con gli allevatori e analizzate per studiare l'effetto del sistema di allevamento sull'efficienza produttiva e sulla qualità della carne. Dopo la macellazione, sono stati raccolti i seguenti fenotipi: peso della carcassa a caldo, conformazione della carcassa, età al macello ed accrescimento giornaliero in carcassa. Ventiquattro ore dopo la macellazione, sono stati raccolti campioni individuali del muscolo Longissimus thoracis tra la quinta e la sesta vertebra toracica. I campioni sono stati quindi scansionati per effettuare la misura dell'area del muscolo. Inoltre, su ciascun campione di carne, direttamente al macello, sono stati raccolti 5 spettri in riflettanza con due spettrometri portatili: un ASD LabSpec 2500 (range dello spettro tra 350 e 1,830 nm, con acquisizione ogni nm) ed un JDSU (range dello spettro tra 905 e 1,649 nm, con acquisizione ogni 6 nm). Le equazioni di calibrazione sono state sviluppate con metodologie bayesiane e la capacità predittiva della spettroscopia è stata valutata confrontando le prestazioni dei due spettrometri. La valutazione della qualità della carne è stata eseguita con le tradizionali metodologie di analisi in laboratorio 7 giorni dopo la macellazione ed ha incluso il pH, il colore (L *, a *, b *, h *, C *), le perdite di sgocciolamento, le perdite di liquidi in cottura e la tenerezza. Sono state studiate le relazioni fenotipiche e genetiche tra i caratteri di efficienza produttiva e quelli di qualità della carne. Inoltre, si è provveduto ad indagare le relazioni genetiche tra i tratti di qualità della carne misurati in laboratorio e le loro predizioni ottenute con la spettrometria nel vicino-infrarosso. Tutti gli animali campionati sono stati genotipizzati utilizzando il supporto “GeneSeek Genomic Profiler Bovine LD” (GGP Bovine LD) contenente 30.111 SNP. E' stato eseguito uno studio combinando Genome-wide Association e Pathway Analysis per identificare le regioni genomiche e i processi biologici che contribuiscono a spiegare la variabilità dei caratteri di qualità della carne. Le componenti di varianza e gli effetti degli SNP sono stati stimati congiuntamente con la metodologia SNP-BLUP. Sono state stimate le ereditabilità genomiche e predetti gli indici genomici, valutando quindi la possibilità di implementare la selezione genomica per migliorare la qualità della carne nella razza Piemontese. I risultati ottenuti hanno evidenziato la presenza di sei principali tipologie di ingrasso nel contesto della razza piemontese, ognuna caratterizzata da specifiche tecniche gestionali. I caratteri produttivi sono risultati profondamente influenzati dal sistema di produzione, mentre è emerso un effetto minimo sulla qualità della carne, limitato al colore. L'effetto limitato del sistema di produzione ha dimostrato che la variabilità dei caratteri di qualità della carne dipende principalmente da fattori animale-specifici e che i miglioramenti possono essere apportati agendo a livello dei singoli animali, guardando con particolare attenzione all'aspetto genetico. E' importante, quindi, che i caratteri di qualità abbiano riportato valori di ereditabilità non trascurabili, lasciandone presupporre un possibile miglioramento attraverso la selezione. Tuttavia, l'inserimento di tali caratteri tra gli obiettivi di selezione dipende dalla disponibilità di fenotipi raccolti all'interno di un processo di registrazione routinario. Da un punto di vista fenotipico, i caratteri del colore e le perdite di sgocciolamento sono stati predetti in modo soddisfacente con con entrambi gli spettrometri utilizzati in questo studio. La capacità predittiva della spettrometria del vicino infrarosso per il pH, le perdite di cottura e la tenerezza è risultata meno favorevole. Tuttavia, i fenotipi predetti a partire dai dati spettrali sono risultati ereditabili e le elevate correlazioni genetiche tra questi ed i fenotipi osservati potrebbero consentire di utilizzare la spettroscopia a fini selettivi. Per quanto riguarda l'architettura genetica dei caratteri indagati, il presente studio ha evidenziato che oltre alla miostatina sono presenti diversi geni che contribuiscono a spiegare quote della variabilità esistente, soprattutto per quanto riguarda l'accrescimento in carcassa. Inoltre, è stata messa in evidenza un'associazione tra pathway metabolici inerenti all'attività di trasporto cellulare (ossigeno, calcio, ioni e catione) ed i caratteri di qualità della carne relativi al colore. L'utilizzo delle informazioni genomiche, congiunto alle parentele pedigree, ha prodotto stime di ereditabilità maggiori rispetto a quelle tradizionali per le perdite di sgocciolamento ed il colore della carne, mentre per gli altri caratteri non sono state evidenziate differenze di rilievo. Gli indici genomici che ne sono conseguiti hanno mostrato una capacità predittiva soddisfacente, permettendo di considerare la selezione genomica come un possibile strumento per migliorare i caratteri di qualità della carne nella razza Piemontese.

Les microbes sont affectés par les perturbations environnementales qui affectent la stabilité fonctionnelle des communautés microbiennes. Cependant, leurs réponses sont complexes, difficiles à élucider et les mécanismes de la stabilité fonctionnelle sont encore mal compris. Dans cette thèse, j'ai étudié les réponses microbiennes aux perturbations environnementales, des populations uniques aux communautés complexes. Dans le cas d'une population unique, nous avons étudié la réponse transcriptionnelle de populations bactériennes uniques dont la niche varie le long d'un gradient environnemental. Pour aborder les conséquences des perturbations au niveau de la communauté, nous avons établi et testé un protocole de cryoconservation de communautés microbiennes complexes afin d'améliorer la reproductibilité des études expérimentales avec des assemblages de communautés microbiennes aquatiques naturelles comme sources d'inoculum. En outre, nous avons exposé expérimentalement des communautés microbiennes aquatiques complexes à des perturbations pulsées afin d'étudier les conséquences de ces perturbations sur les changements structurels de la communauté et les paramètres fonctionnels généraux, tels que l'efficacité de la croissance bactérienne. Enfin, nous avons inspecté plus en détail les conséquences des perturbations pulsées sur les processus impliqués dans le cycle de l'azote. Au cours de cette thèse, je me suis particulièrement intéressé aux isolats et aux communautés provenant d'habitats aquatiques côtiers qui fournissent d'importants services écosystémiques
Microbes are impacted by environmental disturbances affecting the functional stability of microbial communities. However, their responses are complex, difficult to elucidate and the mechanics of functional stability are still poorly understood. In this thesis, I investigated microbial responses to environmental disturbances from single populations to complex communities. For the single population approach, we addressed the transcriptional response of single bacterial populations with varying niche breadths along an environmental gradient. To address the consequences of disturbances at the community level, we have established and tested a protocol for cryopreserving complex microbial communities to improve the replicability of experimental studies with natural microbial aquatic community assemblies as inoculum sources. Furthermore, we have experimentally exposed complex aquatic microbial communities to pulsed disturbances to study the consequences of such disturbances on community structural changes and broad functional parameters, such as bacterial growth efficiency. Finally, we have inspected in more detail the consequences of pulsed disturbances on processes involved in nitrogen cycling. During this thesis, I particularly focused on isolates and communities that originated from coastal aquatic habitats that provide important ecosystem services

The aim of this work was to identify markers associated with production traits in the pig genome using different approaches. We focused the attention on Italian Large White pig breed using Genome Wide Association Studies (GWAS) and applying a selective genotyping approach to increase the power of the analyses. Furthermore, we searched the pig genome using Next Generation Sequencing (NSG) Ion Torrent Technology to combine selective genotyping approach and deep sequencing for SNP discovery. Other two studies were carried on with a different approach. Allele frequency changes for SNPs affecting candidate genes and at Genome Wide level were analysed to identify selection signatures driven by selection program during the last 20 years. This approach confirmed that a great number of markers may affect production traits and that they are captured by the classical selection programs. GWAS revealed 123 significant or suggestively significant SNP associated with Back Fat Thickenss and 229 associated with Average Daily Gain. 16 Copy Number Variant Regions resulted more frequent in lean or fat pigs and showed that different copies of those region could have a limited impact on fat. These often appear to be involved in food intake and behavior, beside affecting genes involved in metabolic pathways and their expression. By combining NGS sequencing with selective genotyping approach, new variants where discovered and at least 54 are worth to be analysed in association studies. The study of groups of pigs undergone to stringent selection showed that allele frequency of some loci can drastically change if they are close to traits that are interesting for selection schemes. These approaches could be, in future, integrated in genomic selection plans.

The aim of this work was to identify markers associated with production traits in the pig genome using different approaches. We focused the attention on Italian Large White pig breed using Genome Wide Association Studies (GWAS) and applying a selective genotyping approach to increase the power of the analyses. Furthermore, we searched the pig genome using Next Generation Sequencing (NSG) Ion Torrent Technology to combine selective genotyping approach and deep sequencing for SNP discovery. Other two studies were carried on with a different approach. Allele frequency changes for SNPs affecting candidate genes and at Genome Wide level were analysed to identify selection signatures driven by selection program during the last 20 years. This approach confirmed that a great number of markers may affect production traits and that they are captured by the classical selection programs. GWAS revealed 123 significant or suggestively significant SNP associated with Back Fat Thickenss and 229 associated with Average Daily Gain. 16 Copy Number Variant Regions resulted more frequent in lean or fat pigs and showed that different copies of those region could have a limited impact on fat. These often appear to be involved in food intake and behavior, beside affecting genes involved in metabolic pathways and their expression. By combining NGS sequencing with selective genotyping approach, new variants where discovered and at least 54 are worth to be analysed in association studies. The study of groups of pigs undergone to stringent selection showed that allele frequency of some loci can drastically change if they are close to traits that are interesting for selection schemes. These approaches could be, in future, integrated in genomic selection plans.

Watercress (Nasturtium officinale R. Br.; Brassicaceae) has a long history of human use for medicine and consumption. In recent years, it has received a large deal of attention as one of the most nutrient-dense foods. Despite this, watercress remains largely underdeveloped with limited breeding resources through which to meet current and future intensifying market demands, such as for a more compact morphology, enhanced nutritional benefits and resource-use efficiency. The aim of this PhD has been to characterize the genetic structure of nutritional and morphological traits in watercress and develop molecular breeding tools that will inform and facilitate future work on this crop. To this end, Chapter 1 provides an overview of pre-existing knowledge on watercress and reviews the opportunities offered by Next Generation Sequencing tools for undeveloped crops. Chapter 2 describes the application of RNASeq towards de novo assembly and functional annotation the watercress transcriptome for the first time. Differential expression analysis resulted in a catalogue of significant genes for antioxidant capacity and glucosinolate content in watercress and identified orthologs to known phenylpropanoid and glucosinolate biosynthetic pathway genes. In Chapter 3, the first genetic linkage map and QTL analysis were completed for this crop, utilizing Genotyping-By-Sequencing for marker discovery. In a novel undertaking to identify QTL for chemopreventive qualities in a plant genome, the toxicity of watercress to human cancer cells was mapped successfully explaining 20 % of variation in this trait. As the development of new cultivars remains central to this work, Chapter 4 reports on the first commercial trials of the new ‘Boldrewood’ accession, aimed at informing its commercialization process. Excitingly, this study also highlighted previously unknown trends in phytonutrient character of the crops across a temporal gradient, which suggests the potential for increasing consumer health benefit by alternations to crop management practices. The sum of this work has resulted in significant advances in the understanding of watercress genetics and genomics and the production of valuable resources for its future preservation and advancement.

This thesis focuses on the genomic study of symbionts of two different groups of hymenopterans: bees and ants. Both groups of insects have major ecological impact, and investigating their microbiomes increases our understanding of their health, diversity and evolution. The study of the bee gut microbiome, including members of Lactobacillus and Bifidobacterium, revealed genomic processes related to the adaptation to the gut environment, such as the expansion of genes for carbohydrate metabolism and the acquisition of genes for interaction with the host. A broader genomic study of these genera demonstrated that some lineages evolve under strong and opposite substitution biases, leading to extreme GC content values. A comparison of codon usage patterns in these groups revealed ongoing shifts of optimal codons. In a separate study we analysed the genomes of several strains of Lactobacillus kunkeei, which inhabits the honey stomach of bees but is not found in their gut. We observed signatures of genome reduction and suggested candidate genes for host-interaction processes. We discovered a novel type of genome architecture where genes for metabolic functions are located in one half of the genome, whereas genes for information processes are located in the other half. This genome organization was also found in other Lactobacillus species, indicating that it was an ancestral feature that has since been retained. We suggest mechanisms and selective forces that may cause the observed organization, and describe processes leading to its loss in several lineages independently. We also studied the genome of a species of Rhizobiales bacteria found in ants. We discuss its metabolic capabilities and suggest scenarios for how it may affect the ants’ lifestyle. This genome contained a region with homology to the Bartonella gene transfer agent (GTA), which is a domesticated bacteriophage used to transfer bacterial DNA between cells. We propose that its unique behaviour as a specialist GTA, preferentially transferring host-interaction factors, originated from a generalist GTA that transferred random segments of chromosomal DNA. These bioinformatic analyses of previously uncharacterized bacterial lineages have increased our understanding of their physiology and evolution and provided answers to old and new questions in fundamental microbiology.

La sélection variétale consiste à créer de nouvelles variétés répondant aux exigences du marché pour plusieurs caractères d’intérêt agronomique. L’objectif de la thèse était d’étudier l’apport des prédictions génomiques pour optimiser les programmes de sélection chez le blé tendre. Dans un premier chapitre, nous avons testé des méthodes visant à améliorer la précision les prédictions génomiques d’un caractère cher à mesurer en utilisant un caractère corrélé moins cher à mesurer, sans augmenter le budget alloué au phénotypage. Nous avons utilisé un modèle de prédiction génomique multi-caractère. Nous avons développé un indice appelé CDmulti permettant d’optimiser le choix d’un sous-ensemble de lignées à phénotyper pour deux caractères corrélés. Nous avons montré que les prédictions génomiques multi-caractères étaient particulièrement intéressantes lorsque les lignées de la population de validation, ou au moins une partie d’entre elles, pouvaient être phénotypées pour la force boulangère, caractère corrélé à la note de panification et dont le phénotypage est moins coûteux. En effet, cette approche permettait de réduire le budget alloué au phénotypage sans diminuer la précision des prédictions de la qualité boulangère. Dans un deuxième chapitre, nous avons développé un pipeline de simulations stochastiques pour comparer des schémas de sélection produits in silico à partir du génotypage et du phénotypage d’une population de référence. Un cycle dure cinq ans, comprenant un an pour les croisements, un an pour la production d’haploïdes doublés, un an de multiplication, une étape de sélection qui peut être basée soit sur les valeurs phénotypiques (stratégie PS) soit sur les prédictions génomiques (stratégie GPS), et une dernière année de sélection phénotypique. Pour la stratégie GPS, nous avons la possibilité de faire les croisements au hasard parmi les meilleurs descendants du cycle précédent, ou d’optimiser les croisements grâce aux prédictions génomiques. Nous montrons que la stratégie GPS avec optimisation des croisements est systématiquement significativement supérieure aux autres pour tous les paramètres testés (héritabilité du caractère, budget, intensité de sélection relative à deux étapes clé). L’efficacité de la stratégie GPS sans optimisation de croisement est similaire à PS. En revanche, la perte de diversité génétique était plus rapide pour GPS avec ou sans prédiction de croisement. Des modules complémentaires seront ajoutés à cet outil d’aide à la décision pour lui permettre de simuler des schémas de sélection plus réalistes
Breeding consists in creating new varieties which combine qualities for several traits of agronomic interest to answer to the market demand. The objective of the phD was to propose strategies using genomic predictions to optimize bread wheat breeding programs in terms of genetic gain under economic constraint. In a first chapter, we tested methods aiming at improving genomic prediction accuracy of a trait that is expensive to measure using a correlated cheap trait, without increasing the budget allocated to phenotyping. We used a multi-trait genomic prediction models. We also developed an index called CDmulti to optimize the choice of a subset of lines to phenotype for two different correlated traits. We showed that multi-trait genomic predictions could be particularly interesting when lines of the validation set, or at least part of them, could be phenotyped for dough strength, which is correlated to bread-making quality and which is cheaper to phenotype. Indeed, this approach allowed to reduce the budget allocated to phenotyping without decreasing the genomic prediction accuracy of bread-making quality. In a second chapter, we developed a stochastic simulation pipeline to compare breeding scheme produce in silico, using genotyping and phenotyping of a reference population. One cycle lasts five years, including one year for crossing, one year for double haploids production, one year for seed multiplication, one year of selection based on either phenotypic value (PS strategy) or genomic predictions (GPS strategy), and one last year of phenotypic selection. For GPS strategy, we can mate the best lines of previous cycle at random or optimise mating using genomic predictions. We showed that GPS strategy with mating optimization is systematically significantly superior to other strategies for all tested parameters (trait heritability, budget, relative intensity of selection at two key steps). The efficiency of GPS strategy without mating optimization was similar to PS. However, the loss of genetic diversity was more intense for GPS strategies, with or without mating optimization. Some complementary modules will be added to this decision tool to simulate more realistic breeding schemes

The entire dissertation/thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file (which also appears in the research.pdf); a non-technical general description, or public abstract, appears in the public.pdf file. Title from PDF of title page (University of Missouri--Columbia, viewed on January 6, 2010). Vita. Thesis advisor: Jeremy Taylor. "July 2009" Includes bibliographical references.

Here I used microarrays to identify genes that are activated or repressed by nicotine and caffeine in Drosophila melanogaster. I compared genotypes with differential resistance to each drug in order to select genes that may be involved in resistance to the drugs. Comparison of the genes differentially expressed by both drugs leads me to propose that there are common mechanisms of metabolic resistance to caffeine and nicotine, in particular cytochrome P-450-mediated mechanisms. Caffeine seems to have a more dramatic influence on gene expression than nicotine, in particular on expression of genes involved in energy metabolism. Next, I extended the studies on nicotine resistance to ask whether there are differences in response between two populations of Drosophila. The gene expression patterns of both populations were evaluated separately and in a combined analysis. Most of the differentially expressed genes were up-regulated by nicotine in both populations and in the combined analysis. The induced transcripts were mainly related to protein, nucleic acid, amino acid and energy metabolism, and response to stimulus and stress. Those findings suggest that amino acid and energy metabolism may be important biological processes affected by nicotine and be interesting targets for further investigation related to the nicotine response in Drosophila. The two populations displayed considerable differences in gene expression profiling that may be the result of the observed phenotypic variation for nicotine response between the two populations. Most of the differential expression induced by nicotine seems to be specific to the more resistant population. Finally, I focused on genes whose expression showed significant correlation with survival time on nicotine food. Using a regression approach, it was possible to map quantitative trait transcripts associated to nicotine response. Control expression of alkaline phosphatase and ornithine aminotransferase displayed significant correlation to survival time in drug food. They seem to be linked to regulation of GABA/glutamate neurotransmission and detoxification mechanisms, which ultimately counteracts the stimulatory effects of nicotine.

Doctor of Philosophy
Department of Agronomy
Geoffrey Morris
Climate change has been anticipated to affect agriculture, with most the profound effect in regions where low input agriculture is being practiced. Understanding of how plants evolved in adaptation to diverse climatic conditions in the presence of local stressors (biotic and abiotic) can be beneficial for improved crop adaptation and yield to ensure food security. Great genetic diversity exists for agroclimatic adaptation in sorghum (Sorghum bicolor L. Moench) but much of it has not been characterized. Thus, limiting its utilization in crop improvement. The application of next-generation sequencing has opened the plant genome for analysis to identify patterns of genome-wide nucleotide variations underlying agroclimatic adaptation. To understand the genetic basis of adaptive traits in sorghum, the genetic architecture of sorghum inflorescence traits was characterized in the first study. Phenotypic data were obtained from multi-environment experiments and used to perform joint linkage and genome-wide association mapping. Mapping results identified previously mapped and novel genetic loci underlying inflorescence morphology in sorghum. Inflorescence traits were found to be under the control of a few large and many moderate and minor effect loci. To demonstrate how our understanding of the genetic basis of adaptive traits can facilitate genomic enabled breeding, genomic prediction analysis was performed with results showing high prediction accuracies for inflorescence traits. In the second study, the sorghum-nested association mapping (NAM) population was used to characterize the genetic architecture of leaf erectness, leaf width, and stem diameter. About 2200 recombinant inbred lines were phenotyped in multiple environments. The obtained phenotypic data was used to perform joint linkage mapping using ~93,000 markers. The proportion of phenotypic variation explained by QTL and their allele frequencies were estimated. Common and moderate effects QTL were found to underlie marker-trait associations. Furthermore, identified QTL co-localized with genes involved in both vegetative and inflorescence development. Our results provide insights into the genetic basis of leaf erectness and stem diameter in sorghum. The identified QTL will also facilitate the development of genomic-enable breeding tools for crop improvement and molecular characterization of the underlying genes Finally, in a third study, 607 Nigerian accessions were genotyped and the resulting genomic data [about 190,000 single nucleotide polymorphisms (SNPs)] was used for downstream analysis. Genome-wide scans of selection and genome-wide association studies (GWAS) were performed and alongside estimates of levels of genetic differentiation and genetic diversity. Results showed that phenotypic variation in the diverse germplasm had been shaped by local adaptation across climatic gradient and can provide plant genetic resources for crop improvement.

With the intense use of high throughput genomic technologies, our knowledge about the cattle and pig genomes has rapidly evolved. Over the last years, many investigations have been already carried out to identify major genes and mutations underlying different morphological, productive, and reproductive traits in cattle and pigs. This thesis is the result of research activities focused on the investigation of genomic features to find novel candidate gene markers associated with pigmentation in two Italian local cattle breeds (Reggiana and Modenese) and in an Italian heavy pig breed, the Italian Large White breed. In the first study that we proposed, we detected signatures of selection in the genome of these two autochthonous cattle breeds using genome-wide SNP information in comparative FST analyses. Results show top FST values detected for the melanocortin 1 receptor (MC1R) gene region on BTA18, and for the agouti signalling protein (ASIP) gene region on BTA13. The second aim of this thesis was to investigate the pigmentation process of the iris in the Italian Large White pig breed. This is a white-coloured breed not affected by albinism. For this aim, we carried out several genome-wide association studies using high density SNP datasets and designed to contrast groups of pigs with different colour of iris. The results indicated that the eye pigmented patterns, the total absence of pigmentation in the both eyes, and heterochromia iridis defect were associated with SNPs close to the SLC45A2 (on chromosome 16, SSC16), EDNRB (SSC11) and KITLG (SSC5) genes, respectively. In addition, other associated genomic regions with eye depigmented patterns were also identified. This thesis demonstrates how population genomic approaches designed to take advantage from the diversity between livestock genetic resources could provide interesting hints to explain pigmentation related traits not yet completely investigated in these species.

The ability to identify germplasm and select traits accurately is fundamental to successful plant breeding. Pedigrees and molecular markers facilitate these processes; however misleading experimental results can occur when incorrect relationships and/or cultivar names are recorded. Molecular markers can identify these inconsistencies, and with advances in genotyping technology these diagnostics can be done faster and more objectively. This study aimed to develop molecular marker assays and graphical genotyping methodologies for cultivar identification, seed purity assessment and trait selection in oat (Avena sativa L.). KBioscience’s Allele-Specific PCR (KASP™) and genotyping-by-sequencing (GBS) technologies were applied to a set of current Canadian oat cultivars to evaluate their utility for identifying cultivars and detecting intra-cultivar variation. Both KASP™ and GBS detected different extents of heterogeneity among a set of 160 seeds that originated from four seed sources of four cultivars. In both cases, the detected variation did not appear to be limited to a specific cultivar or seed source, reinforcing that all cultivars are heterogeneous. Graphical genotyping localized heterogeneity to specific chromosome regions, thereby distinguishing physical contamination from true genetic heterogeneity and heterozygosity. Pre-existing genotype data for 700 oat cultivars and breeding lines were also used to construct graphical genotypes for pedigree validation and discovery of potential sources for favourable quantitative trait loci (QTL) alleles. This methodology used historical QTLs and anchoring markers to identify 25 putative “high oil” allele carriers. The results from this study will provide diagnostic tools for cultivar identification and pedigree validation, in addition to meaningful information about existing heterogeneity and possible QTL locations in current cultivars.

As a result of its unique evolutionary history, the modern dog (Canis lupus familiaris) has a simplified genetic landscape that makes it a strong model for investigating the genetic basis of breed specific traits and diseases. This thesis applies genomic methodologies to a complex disease, myxomatous mitral valve disease (MMVD), with the primary aim of improving our understanding of its genetic basis. MMVD is an acquired disease of the dog that causes valvular dysfunction and may result in the development of congestive heart failure (CHF). In dogs, MMVD is the most frequent cause of cardiovascular morbidity and mortality, and despite a thorough understanding of the clinical aspects, the genetic mechanisms that drive disease onset and progression are uncertain. Current MMVD research supports a polygenic mode of inheritance and exemplifies the difficulty in identifying disease risk variants in complex traits. In this thesis, genomic workflows are used to investigate MMVD in an Australian population of Cavalier King Charles Spaniels (CKCS), a breed disproportionately affected by the trait. I first assessed the strength of MMVD phenotypes for use in comparative genomic studies. Then, through bioinformatic approaches, I investigated the genetic landscape of the disease in this breed. Using genomic tools developed for the dog and a combined approach of objective phenotyping, I was able to thoroughly explore the genetics and genomics of MMVD in the CKCS using different types of genomic analyses. In doing so, I was able to demonstrate the utility of pedigreed breeds in the investigation of complex traits and the versatility of genomic datasets. Throughout this thesis MMVD associated loci, candidate genes and putative functional variants are reported.

Traditional chicken breeds exhibit a range of phenotypic diversity, which in some cases is far removed from that of their jungle fowl ancestors. This diversity includes plumage pattern and colouration, feather stlUcture, comb morphology, egg colour, and numerous other behavioural and morphological characteristics. Extensive research over the last century has identified that a number of these phenotypic traits are inherited in a Mendelian fashion, enabling them to be studied at the genetic level with relative ease. Typically, the genetic mapping of these traits has required establishing resource mapping populations through inter-crossing or back-crossing to select for the trait(s) of interest. However, recent advances in technology have demonstrated that it is possible to fine-map phenotypic traits by comparing the DNA of different breeds. Through the contrasting of single-nucleotide polymorphisms (SNPs) in a range of breeds exhibiting the trait of interest, to breeds in which the trait is absent, it is possible to take advantage of countless recombination events that have taken place since the different breeds were established, enabling the trait to be mapped at higher resolution than might be achieved through a resource mapping population.

The selection on genetic values predicted from markers could substantially increase the rate of genetic gain in animals by increasing accuracy of prediction and reducing generation interval, especially for difficult to measure traits, such as feed efficiency. Feed efficiency is the most important trait in animal production due to its impacts on cost of production and environmental factors. Many metrics measure the feed efficiency, such as ratio of gain to feed (FER), the ratio of feed to gain (FCR) and residual feed intake (RFI). Nevertheless, in ovine, no study with the aim of understand the genetic variants or the accuracy of genomic estimated breeding value (GEBV) for feed efficiency traits was published yet. Moreover, before to apply the genomic information, it is necessary to understand and characterized the population structure, for instance, by linkage disequilibrium (LD). Both genome-wide association studies (GWAS) and genomic selection (GS) leverage LD between marker and causal mutation. Based on the above considerations, the aim of this study was to map LD in ovine, characterized by Brazilian Santa Inês sheep; to search genetic variants for feed efficiency traits (FER, FCR and RFI) through GWAS; and to verify the accuracy of GEBV for RFI. In total, 396 samples (animals) of Longissimus dorsi muscle were collect. A high-density panel of SNP (Illumina High-Density Ovine SNP BeadChip®) comprising 54,241 SNPs was used to obtain the genotyping data. The phenotype data was comprised of 387 animals. The average LD between adjacent markers for two LD metrics, r² and |D\'|, were 0.166 and 0.617, respectively. The degree of LD estimated was lower than reported in other species and it was characterized by short haplotype blocks. Consequently, for genomic analyses, high-density panels of marker are recommended. Many markers were associated to feed efficiency traits in GWAS, mainly to RFI trait. Few candidate genes were reported in this study, highlighting NRF-1 (nuclear respiratory factor 1), which controls mitochondrial biosynthesis, the most important process responsible by a great fraction of the produced energy. Finally, we verified the accuracy of GEBV for RFI using few Bayesian regression models, and we found low accuracy, ranging from 0.033 (BayesB with π=0.9912) to 0.036 (BayesA), which might be explained by the low relationship among animals and small training population.
A seleção com base nos valores genéticos genômicos preditos pode aumentar substancialmente a taxa de ganho genético em animais por meio do aumento da acurácia de predição e redução do intervalo de gerações, especialmente para características de difícil e/ou onerosa mensuração, como eficiência alimentar. A eficiência alimentar é uma das características mais importantes na produção animal devido principalmente aos seus impactos econômicos e ambientais. Muitas métricas representam a eficiência alimentar, por exemplo: a relação do ganho de peso e consumo alimentar (EA), a proporção do consumo alimentar e ganho de peso (CA) e o consumo alimentar residual (CAR). Em ovinos, nenhum estudo com o objetivo de buscar variantes genéticas ou verificar a acurácia do valor genético genômico estimado para eficiência alimentar foi publicado. Adicionalmente, antes de aplicar a informação genômica, é necessário compreender e caracterizar a estrutura da população, como por meio do desequilíbrio de ligação (LD). O estudo de associação genômica (GWAS) e seleção genômica (GS) consideram o LD entre marcador e a mutação causal. Com base nas considerações acima, o objetivo deste estudo foi mapear o LD em ovinos, caracterizado pela raça ovina Santa Inês; localizar variantes genéticas para as características de eficiência alimentar (EA, CA e CAR) utilizando a abordagem GWAS; e verificar a acurácia da estimação dos valores genéticos genômico para o CAR. No total, foram coletadas 396 amostras (animais) do músculo Longissimus dorsi, para posterior genotipagem utilizando o painel de alta densidade (Illumina High-Density Ovine SNP BeadChip®), compreendendo 54.241 SNPs. O banco fenotípico é composto por 387 animais. O LD médio entre marcadores adjacentes para duas métricas de LD, r² e |D\'|, foram 0,166 e 0,617, respectivamente. O grau de LD estimado foi menor que o relatado em outras espécies e foi caracterizado por blocos de haplótipos curtos. Consequentemente, para as análises genômicas são recomendados painéis de marcadores de alta densidade. No GWAS, foram encontrados muitos marcadores associados aos fenótipos, em especial, à característica CAR. Alguns genes candidatos foram relatados neste estudo, destacando-se o NRF-1 (fator respiratório nuclear 1), que controla a biossíntese mitocondrial, o processo mais importante responsável por grande parte da produção de energia. Finalmente, verificamos a acurácia do valor genético genômico estimado para o CAR usando modelos de regressão Bayesiana, e encontramos baixos valores para acurácia (0,033 a 0,036) o que pode ser explicado pelo baixo grau de relacionamento entre os indivíduos e tamanho reduzido da população de treinamento.

This thesis presents novel investigations of three common ageing phenotypes in human population studies, using microarray technology to assess ‘transcriptome-wide’ expression in whole blood to identify mechanisms and biomarkers. Muscle strength is related to frailty and is predictive of disability in older persons. I assessed the association between transcript abundance in the InCHIANTI peripheral blood samples (N=695) and muscle strength. One gene (CEBPB) passed the multiple testing criteria, and is involved in macrophage-mediated repair of damaged muscle. I extended this work with a meta-analysis of over 7,781 individuals in four collaborating cohorts; expression of over 222 genes were significantly associated with strength, less than half of which have previously been linked to muscle in the literature. CEBPB did not replicate in these younger cohorts. I then performed the first human analysis of gene expression and cognitive function (and separately with decline in cognitive ability over nine years) in the InCHIANTI cohort (N=681), and one gene was identified; CCR2, a chemokine receptor. Evidence in mice has implicated this gene in the accumulation of β-amyloid and cognitive impairment. Finally, in a collaborative project with the Framingham Heart Study I studied age-related inflammation – another hallmark of ageing - using a novel approach to ‘transcriptome-wide’ analysis; each transcript was assessed for the proportion of the association between age and interleukin-6 (IL6) that it statistically mediated. Very few of the genes associated with IL6 alone also mediated the relationship with age. Findings include; SLC4A10, the strongest mediator, not previously linked to inflammation, and interleukin-1 beta and perforin, a cytokine and cytotoxic protein, respectively. These novel analyses highlight key molecular pathways associated with age-related phenotypes in whole blood and provide links between mouse models and humans. They provide biological insight and directions for future research.

Quantitative Trait Loci (QTL) mapping has been widely used to identify genetic loci attributable to the variation observed in complex traits. In recent years, gene expression phenotypes have emerged as a new type of quantitative trait for which QTL can be mapped. Locating sequence variation that has an effect on gene expression (eQTL) is thought to be a promising way to elucidate the genetic architecture of quantitative traits. This thesis explores a number of methodological aspects of eQTL mapping (also known as “genetical genomics”) and considers some practical strategies for applying this approach to livestock populations. One of the exciting prospects of genetical genomics is that the combination of expression studies with fine mapping of functional trait loci can guide the reconstruction of gene networks. The thesis begins with an analysis in which correlations between gene expression and meat quality traits in pigs are investigated in relation to a pork meat quality QTL previously identified. The influence on power due to factors including sample size and records of matched subjects is discussed. An efficient experimental design for two-colour microarrays is then put forward, and it is shown to be an effective use of microarrays for mapping additive eQTL in outbred crosses under simulation. However, designs optimised for detecting both additive and dominance eQTL are found to be less effective. Data collected from livestock populations usually have a pedigreed structure. Many family-based association mapping methods are rather computationally intensive, hence are time-consuming when analysing very large numbers of traits. The application of a novel family-based association method is demonstrated; it is shown to be fast, accurate and flexible for genetical genomics. Furthermore, the results show that multiple testing correction alone is not sufficient to control type I errors in genetical genomics and that careful data filtering is essential. While it is important to limit false positives, it is desirable not to miss many true signals. A multi-trait analysis based on grouping of functionally related genes is devised to detect some of the signals overlooked by a univariate analysis. Using an inbred rat dataset, 13 loci are identified with significant linkage to gene sets of various functions defined by Gene Ontology. Applying this method to livestock species is possible, but the current level of annotations is a limiting factor. Finally, the thesis concludes with some current opinions on the development of genetical genomics and its impact on livestock genetics research.

Amb l'objectiu d'obtenir nous coneixements sobre la base molecular de la lactació en cabres de la raça Murciano-Granadina (MUG), hem dut a terme una anàlisi RNA-Seq de mostres de la glàndula mamària (N=7) obtingudes en tres punts temporals diferents: 78 dies (T1, lactació primerenca), 216 dies (T2, lactació tardana) i 285 dies (T3, període sec) després del part. Aquest experiment ens va permetre identificar 1654 gens expressats diferencialment (DE), les funcions dels quals estaven relacionades principalment amb el metabolisme de les proteïnes, lípids i carbohidrats, homeòstasi del calci, mort cel·lular programada, remodelació tissular i immunitat. A més, vam realitzar un estudi d'associació del genoma complet (GWAS) que va incloure 822 cabres amb registres per set fenotipus lleters mesurats durant la primera lactació amb la finalitat de contribuir a dilucidar l'arquitectura genòmica de la producció i la composició de la llet. Aquest estudi ens va permetre detectar 24 quantitative trait loci (QTL). No obstant això, només tres QTL van mostrar significació estadística a nivell genòmic, és a dir, QTL1 (cromosoma 2, 130,72-131,01 Mb) per al percentatge de lactosa de la llet, QTL6 (cromosoma 6, 78,90-93, 48) Mb) per al percentatge de proteïna i QTL17 (cromosoma 17, 11.20 Mb) per als percentatges de proteïna i matèria seca. Mitjançant l'anàlisi del patró de segregació de polimorfismes d'un sol nucleòtid (SNP) dels genes de les caseïnes en bezoars (ancestre de la cabra domèstica) i cabres domèstiques d'Europa, Àfrica, Pròxim Orient i Extrem Orient, es va determinar que del 36,1% (CSN2) al 55,1% (CSN1S2) dels SNPs són compartits entre bezoar i cabra domèstica. Així mateix, més del 50% dels SNP dels gens de les caseïnes van ser compartits per 2 o més poblacions de cabra doméstica situades en diferents continents, i del 18 al 44% dels SNP van ser compartits per les quatre poblacions domèstiques esmentades anteriorment. Aquests resultats ens permeten concloure que una part important de la diversitat existent en els gens de les caseïnes caprines va emergir abans de la domesticació de les cabres. Un altre objectiu de la Tesi va ser caracteritzar la variació del nombre de còpies (CNV) en una població de 1036 cabres MUG. Mitjançant l'ús del programari PennCNV i QuantiSNP, vam identificar 4617 i 7750 CNV autosòmics, respectivament, que posteriorment van ser acoblats en 486 regions CNV o CNVR. Els gens que mapegen dins de CNV mostren un enriquiment de funcions relacionades amb la transducció olfactiva, els transportadors ABC i el desenvolupament embrionari. Un dels CNVR identificats en el nostre estudi coincideix amb la posició del gen de la proteïna de senyalització agouti (ASIP), que afavoreix la síntesi de feomelanina groga/vermella. En diversos estudis, l'augment del nombre de còpies del gen ASIP va ser associat amb un patró de pigmentació blanc en cabres. No obstant això, al realitzar un experiment de qPCR amb l'objectiu de quantificar el nombre de còpies del gen ASIP en poblacions de cabres amb diferents patrons de pigmentació, vam esbrinar que el CNV de ASIP no solsament segrega en cabres Saanen (blanques), sinó també en cabres MUG (negres/marrons) i cabres Malaguenyes (vermelles/rosses). Aquest resultat indica l'absència d'una relació simple i lineal entre el nombre de còpies del gen ASIP i la diŀlució del patró de pigmentació en cabres. Finalment, hem investigat l'arquitectura genòmica de la coloració de la capa en cabres MUG mitjançant la combinació de diferents tècniques experimentals. Aquesta anàlisi ha revelat l'existència d'una estreta associació entre una mutació aminoacídica (c.801C> G, p.Cys267Trp) al gen de receptor de la melanocortina 1 (MC1R) i el color negre/marró de les cabres MUG, la qual cosa implica que l'herència de la pigmentació en aquesta raça és monogènica.
Con el objetivo de obtener nuevos conocimientos sobre la base molecular de la lactación en cabras de la raza Murciano-Granadina (MUG), se llevó a cabo un análisis RNA-Seq de muestras de la glándula mamaria (N=7) obtenidas en tres puntos temporales distintos, es decir, 78 días (T1, lactación temprana), 216 días (T2, lactación tardía) y 285 días (T3, período seco) después del parto. Este experimento permitió identificar 1654 genes expresados diferencialmente (DE), cuyas funciones estaban relacionadas principalmente con el metabolismo de las proteínas, lípidos y carbohidratos, homeostasis del calcio, muerte celular programada, remodelación tisular e inmunidad. Con la finalidad de contribuir a dilucidar la arquitectura genómica de la producción y la composición de la leche, realizamos un estudio de asociación del genoma completo (GWAS) que incluyó 822 cabras con registros para siete fenotipos lecheros medidos durante la 1ª lactación. Este estudio permitió detectar 24 quantitative trait loci (QTL). No obstante, sólo tres QTL mostraron significación estadística a nivel genómico, es decir, QTL1 (cromosoma 2, 130,72-131,01 Mb) para el porcentaje de lactosa de la leche, QTL6 (cromosoma 6, 78,90-93,48) Mb) para el porcentaje de proteína y QTL17 (cromosoma 17, 11.20 Mb) para los porcentajes de proteína y materia seca. Mediante el análisis del patrón de segregación de polimorfismos nucleotídicos sencillos (SNP) de los genes de las caseínas en bezoares (ancestro de la cabra doméstica) y cabras domésticas de Europa, África, Cercano Oriente y Lejano Oriente, se determinó que del 36,1% (CSN2) al 55,1% (CSN1S2) de los SNPs son compartidos por el bezoar y la cabra doméstica. Asimismo, más del 50% de los SNP de los genes de las caseínas fueron compartidos por 2 o más poblaciones de cabra doméstica ubicadas en diferentes continentes, y del 18 al 44% de los SNP fueron compartidos por las cuatro poblaciones domésticas mencionadas anteriormente. Estos resultados nos permiten concluir que una parte importante de la diversidad existente en los genes de las caseínas caprinas emergió antes de la domesticación de las cabras. Otro objetivo de la Tesis consistió en caracterizar la variación del número de copias (CNV) en una población de 1036 cabras MUG. Mediante el uso del software PennCNV y QuantiSNP, identificamos 4617 y 7750 CNV autosómicos, respectivamente, que posteriormente fueron ensamblados en 486 regiones CNV o CNVR. Los genes que mapean dentro de CNVR muestran un enriquecimiento de funciones relacionadas con la transducción olfativa, los transportadores ABC y el desarrollo embrionario. Uno de los CNVR identificados en nuestro estudio coincide con la posición del gen de la proteína de señalización agouti (ASIP), que favorece la síntesis de feomelanina amarilla/roja. En diversos estudios, el aumento del número de copias del gen ASIP fue asociado con un patrón de pigmentación blanco en cabras. Sin embargo, al realizar un experimento de qPCR con el objetivo de cuantificar el número de copias del gen ASIP en poblaciones de cabras con diferentes patrones de pigmentación, averiguamos que el CNV del gen ASIP no sólo segrega en cabras Saanen (blancas), sino también en cabras MUG (negras/marrones) y cabras Malagueñas (rojas/rubias). Este resultado indica la ausencia de una relación simple y lineal entre el número de copias del gen ASIP caprino y la dilución del patrón de pigmentación. Finalmente, hemos investigado la arquitectura genómica de la coloración de la capa en cabras MUG mediante la combinación de distintas técnicas experimentales. Este análisis reveló la existencia de una estrecha asociación entre una mutación aminoacídica (c.801C> G, p.Cys267Trp) en el gen del receptor de la melanocortina 1 (MC1R) y el color negro/marrón de las cabras MUG, lo que implica que la herencia de la pigmentación en dicha raza es monogénico.
In order to obtain new insights into the molecular basis of lactation in Murciano-Granadina (MUG) goats, we carried out a RNA-Seq analysis of mammary gland samples (N = 7) obtained in three different time points, that is, 78 days (T1, early lactation), 216 days (T2, late lactation) and 285 days (T3, dry period) after parturition. This experiment allowed the identification of 1654 differentially expressed (DE) genes, the functions of which were mainly related to protein, lipid and carbohydrate metabolism, calcium homeostasis, programmed cell death, tissue remodeling and immunity. In order to help elucidate the genomic architecture of milk production and composition, we also carried out a genome-wide association study (GWAS) including 822 goats with records for seven dairy phenotypes measured during the first lactation. This study allowed the detection of 24 quantitative trait loci (QTL). However, only three QTL showed statistical significance at the genome-wide level, that is, QTL1 (chromosome 2, 130.72-131.01 Mb) for the percentage of lactose in milk, QTL6 (chromosome 6, 78.90-93, 48) Mb) for the percentage of protein and QTL17 (chromosome 17, 11.20 Mb) for the percentages of protein and dry matter. By analyzing the segregation patterns of single nucleotide polymorphisms (SNPs) mapping to the casein genes in bezoars (ancestor of the domestic goat) and domestic goats of Europe, Africa, the Near East and the Far East, it was determined that about 36.1% (CSN2) to 55.1% (CSN1S2) of casein SNPs are shared between bezoars and domestic goats. Besides, more than 50% of the SNPs of the casein genes were shared by 2 or more domestic goat populations located on different continents, and 18 to 44% of the SNPs were shared by the four previously mentioned domestic populations. These results allow us to conclude that an important part of the diversity existing in the caprine casein genes emerged before the domestication of goats. Another objective of the Thesis consisted of characterizing copy number variation (CNV) in a population of 1036 MUG goats. Using the PennCNV and QuantiSNP software, we identified 4617 and 7750 autosomal CNVs, respectively, which were subsequently assembled into 486 CNV regions (CNVR). Genes located within CNV show an enrichment of functions related to olfactory transduction, ABC transporters and embryonic development. Interestingly, one of the CNVR identified in our study coincides with the position of the agouti signaling protein (ASIP) gene, which favors the synthesis of yellow/red pheomelanin. In several studies, increased copy number of the ASIP gene was associated with a white pigmentation in goats. However, when conducting a qPCR experiment with the objective of quantifying the number of copies of the ASIP gene in goat populations with different coat colors, we found that the ASIP CNV not only segregates in Saanen (white) goats, but also in MUG (black/brown) and Malagueñas goats (brown/blond). This result indicates the absence of a simple and linear relationship between the number of copies of the goat ASIP gene and the dilution of pigmentation. Finally, we have investigated the genomic architecture of coat color in MUG goats by combining different experimental techniques. This analysis revealed the existence of a close association between a missense mutation (c.801C>G, p.Cys267Trp) in the melanocortin receptor 1 (MC1R) gene and the black/brown color of MUG goats, which implies that the inheritance of pigmentation in this breed is monogenic.
Universitat Autònoma de Barcelona. Programa de Doctorat en Producció Animal

Over the last years we have come to realize that the history of our species is not as simple as we once thought. We are now faced with complex demographic scenarios, events of admixture with human species and the realization that our differences with Neanderthals might be of gradient, not quality. Knowing all of this, we have to face the question of what did in fact change since the emergence of our species, to what extent, when did it happened in our evolution, and what consequences those changes bring for complex traits. This thesis tries to contribute answers to these questions, either through in silico analysis of open, publicly available genomic databases, or, when possible, in vitro, in collaboration with other research groups. Chapter 1 outlines the questions that are treated in this thesis and summarizes the results and arguments of each chapter. First, I present an overview of the current understanding of human evolution since the split between the Neanderthal/Denisovan lineage and the Homo sapiens branch. Then, I show what kind of core questions arise from the state of the field, namely what can be done to explore the relationship between genotype and phenotype over evolutionary time in humans. I follow with a succinct summary of the main methods and results of each chapter, showing how they try to answer each of these questions, as well as a final note on challenges and future steps. Chapter 2 explores the effects of Homo sapiens variants in gene expression in specific brain tissues, using the GTEx consortium eQTL database. We highlight the effect of regulation in human evolution, present contrasts with previous literature regarding directional gene regulation, and presents genes that correlate with brain volume GWAS signals. Chapter 3 presents the result of our collaboration with the team of Dr. Giuseppe Testa, showing how neurodevelopmental disease modeling can inform our understanding of human evolution. We show how BAZ1B, a gene implicated in Williams-Beuren syndrome, regulates neural crest stem cell induction and migration. Our work suggests that the BAZ1B regulatory network has undergone changes in human evolution, shaping the facial morphology of our species and validating previously-standing hypothesis about the biology of craniofacial morphology in humans. Chapter 4 applies an open large-scale database of allele age estimations (GEVA) to Homo sapiens specific variants in order to map species-specific genetic variation over time. We also apply gene expression predictions via machine learning and other time-sensitive genomic analysis,and present genes that have undergone changes in specific windows of human evolution.
En los últimos años nos hemos dado cuenta de que la historia de nuestra especie no es tan simple como una vez pensamos. Nos enfrentamos ahora a escenarios demographicos complejos, eventos de admixtura en el pasado con otras especies humanas y la realización de que nuestras diferencias con los Neandertales son de grado, no de cualidad. Sabiendo esto, tenemos que preguntarnos qué cambios tuvieron lugar desde la aparición de nuestra especie, hasta qué punto el fenotipo cambió, cuándo ocurrió en nuestra historia evolutiva y cuales son las consequences de esos cambios para rasgos complejos. Esta tesis intenta contribuir respuestas a estas preguntas a través de análisis in silico de bases de datos genomicas públicas, o, cuando es posible, in vitro. El Capítulo 1 delinea las preguntas que trato en esta tesis y resume los argumentos y resultados de cada capítulo. Primero determino las claves de nuestro conocimiento actual en evolución humana desde la separación entre el lineaje Neanderthal/Denisovano y la rama Homo sapiens. Después, muestro qué tipo de preguntas centrales surgen del estado del campo; específicamente, qué puede hacerse para explorar la relación entre genotipo y fenotipo en tiempo evolutivo en humanos. A continuación presento un resumen de los métodos y resultados de cada capítulo, mostrando cómo intentan resolver cada una de estas preguntas, así como una última nota sobre pasos futuros y retos. El Capítulo 2 explora el efecto de variantes Homo sapiens en expressión genética en tejidos cerebrales específicos, usando la base de datos de eQTL del consorcio GTEx. Los resultados resaltan el efecto de la regulación genómica en evolución humana, presenta contrastes con literatura anterior respecto a la direccionalidad de regulación genómica, y presentan genes que se correlacionan con señales de volumen cerebral en GWAS. El capítulo 3 presenta los resultados de nuestra colaboración con el grupo del Dr. Giuseppe Testa, mostrando cómo el modelaje de desórdener neurodevelomentales puede informar nuestra comprensión de la evolución humana. En este capítulo demostramos cómo BAZ1B, un gen implicado en el síndrome de Williams-Beuren, regula la inducción y migración de células madre de la cresta neuronal. Nuestro trabajo sugiere que la red reguladora de BAZ1B ha cambiado a lo largo de la evolución humana, cincelando la morfología facial de nuestra especie tal y como había sido predicho en la literatura anterior. El capítulo 4 aplica una base de datos de estimaciones de edad de variantes (GEVA) a variantes specíficas de Homo sapiens para localizar en el tiempo variación específica de nuestra especie en el tiempo. También aplicamos predicciones de expresión genética a través de Machine Learning y otros análisis, y presentamos genes que han cambiado en ventanas específicas de nuestra historia evolutiva.

This study focuses on integrating and applying computational techniques for modelling quantitative traits and complex diseases, such as hypertension and diabetes, using the rat model system and translating the findings to humans. Complex disease traits are heritable, highly polygenic, and influenced by environmental factors. Human studies, like Genome Wide Association Studies (GWAS), have identified many genetic determinants underlying these traits but have provided little information about the functional effects of these variants and mechanisms regulating the disease. This study takes a systems-level approach for looking at the genetic regulation of complex traits in the rat by analysing multiple phenotypes, genomewide genetic variation and gene expression data in multiple tissues. I integrated these multi-modality datasets in the BXH/HXB rat Recombinant Inbred (RI) lines, an established model of the human metabolic syndrome, to identify candidate genes, pathways and networks associated with complex disease phenotypes. I evaluated methods for Expression Quantitative Trait Locus (eQTL) analysis and used sparse Bayesian regression approaches to map eQTLs in the RI lines, delineating a new, large eQTL data resource for the rat genetic community. I have also developed and applied signal processing and time series analysis methods to physiological traits to extract more detailed indices of blood pressure, and integrated these with genetic, expression and eQTL data to inform on the regulation of these traits. Then, using publicly available data, I used comparative genomics approaches to elucidate a set of genes and pathways that can play a role in human diseases. This study has provided a valuable resource for future work in the rat, by means of new eQTLs in multiple tissues, and physiological time series phenotypes and approaches. This has enabled an integrative analysis of these data to give new insights into the regulation of complex traits in rats and humans.

Kyoto University (京都大学)
0048
新制・課程博士
博士(農学)
甲第20427号
農博第2212号
新制||農||1048(附属図書館)
学位論文||H29||N5048(農学部図書室)
京都大学大学院農学研究科応用生物科学専攻
(主査)准教授 谷口 幸雄, 教授 今井 裕, 教授 廣岡 博之
学位規則第4条第1項該当

BACKGROUND: Genome-wide association studies (GWAS) have identified single nucleotide polymorphisms (SNPs) associated with diseases of the colon including inflammatory bowel diseases (IBD) and colorectal cancer (CRC). However, the functional role of many of these SNPs is largely unknown and tissue-specific resources are lacking. Expression quantitative trait loci (eQTL) mapping identifies target genes of disease-associated SNPs. This study provides a comprehensive eQTL map of distal colonic samples obtained from 40 healthy African Americans and demonstrates their relevance for GWAS of colonic diseases. RESULTS: 8.4 million imputed SNPs were tested for their associations with 16,252 expression probes representing 12,363 unique genes. 1,941 significant cis-eQTL, corresponding to 122 independent signals, were identified at a false discovery rate (FDR) of 0.01. Overall, among colon cis-eQTL, there was significant enrichment for GWAS variants for IBD (Crohn's disease [CD] and ulcerative colitis [UC]) and CRC as well as type 2 diabetes and body mass index. ERAP2, ADCY3, INPP5E, UBA7, SFMBT1, NXPE1 and REXO2 were identified as target genes for IBD-associated variants. The CRC-associated eQTL rs3802842 was associated with the expression of C11orf93 (COLCA2). Enrichment of colon eQTL near transcription start sites and for active histone marks was demonstrated, and eQTL with high population differentiation were identified. CONCLUSIONS: Through the comprehensive study of eQTL in the human colon, this study identified novel target genes for IBD- and CRC-associated genetic variants. Moreover, bioinformatic characterization of colon eQTL provides a tissue-specific tool to improve understanding of biological differences in diseases between different ethnic groups.

The linkage era left a rich legacy of pedigree samples that can be used for modern genome-wide association sequencing (GWAS) or next-generation sequencing (NGS) studies. Family designs are naturally equipped to detect rare variants, control for population stratification, and facilitate the study of parent-of-origin effects. Unfortunately, pedigree likelihoods are notoriously hard to compute, and current software for association mapping in pedigrees is prohibitively slow in processing dense marker maps. In a recent release of the comprehensive genetic analysis software MENDEL, we implemented an ultra-fast score test for association mapping with pedigree-based GWAS or NGS study data. Our implementation (a) works for random sample data, pedigree data, or a mix of both
(b) allows for covariate adjustment, including correction for population stratification
(c) accommodates both univariate and multivariate quantitative traits
and (d) allows missing values in multivariate traits. In this paper, we assess the capabilities of MENDEL on the Genetic Analysis Workshop 18 sequencing data. For instance, when jointly testing the 4 longitudinally measured diastolic blood pressure traits, it takes MENDEL less than 51 minutes on a standard laptop computer to read, quality check, and analyze a data set with 959 individuals and 8.3 million single-nucleotide polymorphisms (SNPs). Our analysis reveals association of one SNP in the q32.2 region of chromosome 1. MENDEL is freely available on http://www.genetics.ucla.edu/software webcite.

Domestication is the process by which animals become adapted to the environment provided by humans. The process of domestication has let to a number of correlated behavioural, morphological and physiological changes among many domesticated animal species. An example is the changes of plumage colour in the chicken. Plumage colour is one of the most readily observable traits that make distinction between breeds as well as between strains within a breed. Understanding the genetic architecture of pigmentation traits or indeed any trait is always a great challenge in evolutionary biology. The main aim of this study was to map quantitative trait loci (QTLs) affecting the red and metallic green coloration in the chicken plumage. In this study, a total of 572 F8 intercross chickens between Red Junglefowl and White Leghorn were used. Phenotypic measurements were done using a combination of digital photography and photography manipulating software. Moreover, all birds were genotyped with 657 molecular markers, covering 30 autosomes. The total map distance covered was 11228 cM and the average interval distance was 17 cM. In this analysis, a total of six QTLs (4 for red and 2 for metallic green colour) were detected on four different chromosomes: 2, 3 11 and 14. For red colour, the most significant QTL was detected on chromosome 2 at 165 cM. An additional QTL was also detected on the same chromosome at 540 cM. Two more QTLs were detected on chromosomes 11 and 14 at 24 and 203 cM respectively. Additionally, two epistatic pairs of QTLs were also detected. The identified four QTLs together can explain approximately 36% of the phenotypic variance in this trait. In addition, for metallic green colour, one significant and one suggestive QTLs were detected on chromosomes 2 and 3 at 399 and 247 cM respectively. Moreover, significant epistatic interactions between these two QTLs were detected. Furthermore, these two QTLs together can explain approximately 24% of the phenotypic variance in this trait. These findings suggest that the expression of pigmentation in the chicken plumage is highly influenced by both the epistatic actions and pleiotropic effects of different QTLs located on different chromosomes.