Genetic basis of variation for root traits and response to heat stress in durum wheat

Durum wheat is the second most important wheat species worldwide and the most important crop in several Mediterranean countries including Italy. Durum wheat is primarily grown under rainfed conditions where episodes of drought and heat stress are major factors limiting grain yield. The research presented in this thesis aimed at the identification of traits and genes that underlie root system architecture (RSA) and tolerance to heat stress in durum wheat, in order to eventually contribute to the genetic improvement of this species. In the first two experiments we aimed at the identification of QTLs for root trait architecture at the seedling level by studying a bi-parental population of 176 recombinant inbred lines (from the cross Meridiano x Claudio) and a collection of 183 durum elite accessions. Forty-eight novel QTLs for RSA traits were identified in each of the two experiments, by means of linkage- and association mapping-based QTL analysis, respectively. Important QTLs controlling the angle of root growth in the seedling were identified. In a third experiment, we investigated the phenotypic variation of root anatomical traits by means of microscope-based analysis of root cross sections in 10 elite durum cultivars. The results showed the presence of sizeable genetic variation in aerenchyma-related traits, prompting for additional studies aimed at mapping the QTLs governing such variation and to test the role of aerenchyma in the adaptive response to abiotic stresses. In the fourth experiment, an association mapping experiment for cell membrane stability at the seedling stage (as a proxy trait for heat tolerance) was carried out by means of association mapping. A total of 34 QTLs (including five major ones), were detected. Our study provides information on QTLs for root architecture and heat tolerance which could potentially be considered in durum wheat breeding programs.

Candidate genes affecting fat deposition, carcass composition and meat quality traits in pigs

Pig meat quality is determined by several parameters, such as lipid content, tenderness, water-holding capacity, pH, color and flavor, that affect consumers’ acceptance and technological properties of meat. Carcass quality parameters are important for the production of fresh and dry-cure high-quality products, in particular the fat deposition and the lean cut yield. The identification of genes and markers associated with meat and carcass quality traits is of prime interest, for the possibility of improving the traits by marker-assisted selection (MAS) schemes. Therefore, the aim of this thesis was to investigate seven candidate genes for meat and carcass quality traits in pigs. In particular, we focused on genes belonging to the family of the lipid droplet coat proteins perilipins (PLIN1 and PLIN2) and to the calpain/calpastatin system (CAST, CAPN1, CAPN3, CAPNS1) and on the gene encoding for PPARg-coactivator 1A (PPARGC1A). In general, the candidate genes investigation included the protein localization, the detection of polymorphisms, the association analysis with meat and carcass traits and the analysis of the expression level, in order to assess the involvement of the gene in pork quality. Some of the analyzed genes showed effects on various pork traits that are subject to selection in genetic improvement programs, suggesting a possible involvement of the genes in controlling the traits variability. In particular, significant association results have been obtained for PLIN2, CAST and PPARGC1A genes, that are worthwhile of further validation. The obtained results contribute to a better understanding of biological mechanisms important for pig production as well as for a possible use of pig as animal model for studies regarding obesity in humans.

New perspectives of genetic disorders in cattle

In the last decades a negative trend in inbreeding has accompanied the evident improvement in productivity and performance of bovine domestic population, predisposing to the occurrence of recessively inherited disorders. The objectives of this thesis were: a) the study of genetic diseases applying a “forward genetic approach” (FGA); b) the estimation of the prevalence of deleterious alleles responsible for eight recessive disorders in different breeds; c) the collection of well-characterized materials in a Biobank for Bovine Genetic Disorders. The FGA allowed the identification of seven new recessive deleterious variants (Paunch calf syndrome - KDM2B; Congenital cholesterol deficiency - APOB; Ichthyosis congenita - FA2H; Hypotrichosis - KRT71; Hypotrichosis - HEPHL1; Achromatopsia - CNGB3; Hemifacial microsomia – LAMB1) and of seven new de novo dominant deleterious variants (Achondrogenesis type II - two variants in COL2A1; Osteogenesis imperfecta - COL1A1; Skeletal-cardio-enteric dysplasia - MAP2K2; Congenital neuromuscular channelopathy - KGNG1; Epidermolysis bullosa simplex - KRT5; Classical Ehlers-Danlos syndrome - COL5A2) in different breeds, associated with a large spectrum of phenotypes affecting different systems. The FGA was based on the sequence of a clinical, genealogical, gross- and/or histopathological and genomic study. In particular, a WGS trio-approach (patient, dam and sire) was applied. The prevalence of deleterious alleles was calculated for the Pseudomyotonia congenita, Paunch calf syndrome, Hemifacial microsomia, Congenital bilateral cataract, Ichthyosis congenita, Ichthyosis fetalis, Achromatopsia and Hypotrichosis. A particular concern resulted the allelic frequency of 12% for the Paunch calf syndrome in Romagnola cattle. In respect to the Biobank for Bovine Genetic Diseases, biological materials of clinical cases and their available relatives as well as controls used for the allelic frequency estimations were stored at -20 °C. Altogether, around 16.000 samples were added to the biobank.