Ecological genetics and conservation genomics of wolf (Canis lupus)

In the present work, we apply both traditional and Next Generation Sequencing (NGS) tools to investigate some of the most important adaptive traits of wolves (Canis lupus). In the first part, we analyze the variability of three Major Histocompatibility Complex (MHC) class II genes in the Italian wolf population, also studying their possible role in mating choice and their influence on fitness traits. In the second section, as part of a larger canid genome project, we will exploit NGS data to investigate the transcript-level differences between the wolf and the dog genome that can be correlated to domestication.

"Ancestry, gender and language - The role of culture in economic development"

This thesis is a combination of research questions in development economics and economics of culture, with an emphasis on the role of ancestry, gender and language policies in shaping inequality of opportunities and socio-economic outcomes across different segments of a society. The first chapter shows both theoretically and empirically that heterogeneity in risk attitudes can be traced to the ethnic origins and ancestral way of living. In particular, I construct a measure of historical nomadism at the ethnicity level and link it to contemporary individual-level data on various proxies of risk attitudes. I exploit exogenous variation in biodiversity to build a novel instrument for nomadism: distance to domestication points. I find that descendants of ethnic groups that historically practiced nomadism (i) are more willing to take risks, (ii) value security less, and (iii) have riskier health behavior. The second chapter evaluates the nature of a trade-off between the advantages of female labor participation and the positive effects of female education. This work exploits a triple difference identification strategy relying on exogenous spike in cotton price and spatial variation in suitability for cotton, and split sample analyses based on the exogenous allocation of land contracts. Results show that gender differences in parental investments in patriarchal societies can be reinforced by the type of agricultural activity, while positive economic shocks may further exacerbate this bias, additionally crowding out higher possibilities to invest in female education. The third chapter brings novel evidence of the role of the language policy in building national sentiments, affecting educational and occupational choices. Here I focus on the case of Uzbekistan and estimate the effects of exposure to the Latin alphabet on informational literacy, education and career choices. I show that alphabet change affects people's informational literacy and the formation of certain educational and labour market trends.

Multidisciplinary approach to horse welfare in different management systems

From its domestication until nowadays, the horse has assumed multiple roles in human society. Over time, this condition and the lack of specific regulation have led to the development of different kinds of management systems for this species. This Ph.D. research project aims to investigate horses' welfare in different management practices and housing systems, considering a multidisciplinary approach, taking into account biological function, naturalness, and affective dimension. The results are presented in five articles that evidence risk factors that can mine horse welfare, and examine tools and parameters that can be employed for its assessment. Our research shows the importance of considering the evolutionary history and the species-specific and behavioural needs of horses in their management and housing. Sociality, free movement, diet composition and foraging routine, and the workload that these animals undergo are important factors that should be taken into account. Furthermore, this research has evidenced the importance of employing different parameters (e.g., behaviour, endocrinological parameters, and immune activity) in welfare assessment and proposes the use of horsehair DHEA (dehydroepiandrosterone) as a possible useful additional non-invasive measure for the investigation of long-term stress conditions. Finally, our results underline the importance of considering the affective dimension in welfare research. Recently, Judgement Bias Tests (JBT), which are based on the influence of affective states on the decision-making process, have been widely employed in animal welfare research. However, our studies show that the use of spatial JBT in horses can have some limitations. Still today several management systems do not fulfill species-specific needs of horses, thus the implementation of specific regulations could ameliorate horse welfare. A multidisciplinary approach to welfare assessment is fundamental, but it should be always remembered the individual and its own characteristics, which can influence not only physiological, immunological, and behavioural responses but also emotional and cognitive dimensions.

Exploring mediterranean durum wheat wild relatives and elite diversity panel for future breeding

Durum wheat (Triticum durum) is an important crop that has been used for millennia for human consumption, and modern breeding can take advantage of the wide variability useful for the adaptation to new challenges. Novel beneficial alleles can be found in wild relatives and landraces thus enhancing crop adaptation to many biotic and abiotic stresses. This dissertation considers the source of variability from both before and after wheat domestication, that caused a loss of potentially useful alleles. Chapter 1. is the thesis introduction, which outlines the importance of wheat in the world, providing an historical overview of the domestication, the evolution mechanisms that led to the current forms of durum wheat and the use of wild relatives as a source of germplasm for future breeding programs is crucial. Moreover, the emergence of Z. tritici has been considered as the main pathogen of wheat since it contains extremely high levels of genetic variability and is thus difficult to control. Chapter 2. Considers the contribution of the phenotypic diversity of 242 accessions of Aegilops tauschii from the Open Wild Wheat Consortium, involved in wheat domestication, provided with whole-genome resequencing. The accessions were phenotyped both in the field and in controlled conditions and A k-mer-based GWAS was performed to identify genomic regions involved in useful traits. Chapter 3. Describes the genetic basis of resistance to Z. tritici in a durum wheat elite diversity panel representative of the germplasm bred in Mediterranean. Quantitative trait loci (QTL) analysis results revealed several loci involved in the STB response that were found in several chromosome regions with a high infection rate. The genomic regions associated with STB resistance identified in this study could be of interest for marker assisted selection (MAS) in durum wheat breeding programs.

Applied genomics in livestock: genome-wide association studies and population genomics analysis in pig and rabbit breeds

The domestication and selection processes in pigs and rabbits have resulted in the constitution of multiple breeds with broad phenotypic diversity. Population genomics analysis and Genome-wide association study analysis can be utilized to gain insights into the ancestral origins, genetic diversity, and the presence of lethal mutations across these diverse breeds. In this thesis, we analysed the dataset obtained from three Italian Pig breeds to detect deleterious alleles. We screened the dataset for genetic markers showing homozygous deficiency using two approaches single marker and haplotype-based approach. Moreover, Genome-wide association study analyses were performed to detect genetic markers associated with pigs' reproductive traits. In rabbits, we investigated the application of SNP bead chip for detection signatures of selection in rabbits using different methods. This analysis was implemented for the first time in different fancy and meet rabbit breeds. Multiple approaches were utilized for the detection of the selection of signatures including Fst analysis, ROH analysis, PCAdapt analysis, and haplotype-based analysis. The analysis in pigs was able to identify five putative deleterious SNPs and nine putative deleterious haplotypes in the analysed Italian Pig breeds. The genomic regions of the detected putative deleterious genomic markers harboring loss of function variants such as the Frameshift variant, start lost, and splice donor variant. Those variants are close to important candidate genes such as IGF2BP1, ADGRL4, and HGF. In rabbits, multiple genomic regions were detected to be under selection of signature. These genomic regions harbor candidate genes associated with coat color phenotype (MC1R, TYR, and ASIP), hair structure (LIPH), and body size (HMGA2 and COL2A1). The described results in rabbits and pigs could be used to improve breeding programs by excluding the deleterious genetic markers carriers and incorporating candidate genes for coat color, body size, and meat production in rabbit breeding programs to enhance desired traits