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GENOME-WIDE DETECTION OF QTL AND CNVS IN DAIRY CATTLE POPULATION
Full text linkThe QTL involved in susceptibility/resistance of infectious diseases and in the productive traits variations, are characterized by genetic heterogeneity and multifactorial inheritance, involving gene polymorphisms from different alternative pathways. With the availavility of single nucleotide polymorphism (SNP) genotyping arrays, the genome-wide association studies (GWAS) have been frequently used to determine the genetic component of complex trait. The Copy Number Variations (CNVs) are another genomic marker that can be possibly used in GWAS and that can be identified from SNP chips themselves.
The aims and related discussions for each of the studies presented in this thesis were grouped into three different chapters.
• Chapter 1 described the QTL mapping analysis to identify the existence of genetic variability associated to the CLA, VA and D9D contents in milk of the Italian Brown Swiss dairy cattle breed. For this study a selective DNA pooling in a daughter design was adopted, using the Illumina Bovine SNP50 Bead Chip to genotype the pools. Milk samples from 60 animals with higher values (after correction for environmental factors) and 60 animals with lower values for each of these traits from each of five half-sib families were pooled separately. Allele frequencies were compared between pools of high and low value at the sire and marker level for each SNPs for which the sires were heterozygous. An R procedure was implemented to perform data analysis. A correction for multiple tests was applied using the proportion of false positives approach. BTA 19 showed the largest number of markers in association with CLA. Associations between SNPs and the VA and D9-desaturase traits were found on several chromosomes. A bioinformatics survey identified genes with an important role in pathways for milk fat and fatty acids metabolism within 1 Mb distance from SNP markers associated with fatty acids contents. This is the first available mapping for fatty acid content in the Brown Swiss population.
• Chapter 2 described a genome-wide association study for somatic cell score (SCS) in the Valdostana Red Pied cattle, with a selective DNA pooling analysis, using the Illumina BovineHD BeadChip. The phenotypes of 275 sires for SCS were expressed as Deregressed Proofs (DP-EBVs) for SCS. The sires were ranked according to DP-EBVs for SCS and the 20% high and 20% low sires included in the pools. The multiple marker test was performed in R software. On BTAs 1, 2, 3, 4, 9, 13, 15, 17, 21 and 22 the largest number of markers in association to the trait was found identifying novel genomic regions related to mastitis (1-Mb SNP windows) and confirming others already mapped. The largest number of significant SNPs exceeding the threshold for genome-wide significant signal was found on BTA 15, located at 50.43-51.63 Mb. The genomic regions identified in this study contribute to a better understanding of the genetic control of the mastitis immune response in cattle and may allow the inclusion of more detailed QTL information in selection programs.
• Chapter 3 described a genome wide CNVs discovery in 651 bulls of the Italian Brown Swiss breed using the Illumina Bovine SNP50 BeadChip data. Hidden Markov Model (HMM) of PennCNV and SVS7 software (Golden Helix) were used for the identification of the CNVs and Copy Number Variation Regions (CNVRs). A total of 5,099 and 1,289 CNVs were identified using PennCNV and SVS7 software, respectively. These were grouped at the population level into 1,101 (220 losses, 774 gains, 107 complex) and 277 (185 losses, 56 gains and 36 complex) CNVRs, covering 682 Mb (27.14%) and 33.7 Mb (1.35%) of the autosome, respectively. Ten of the selected CNVRs were experimentally validated with qPCR and the proportions of confirmed positive samples for each region varied from 50% to 100%. The GO and pathway analyses identified genes (false discovery rate corrected) in the CNVRs related to biological processes, cellular component, molecular function and metabolic pathways. Although there is variability in the CNVRs detection across methods, platforms, this study allowed the identification CNVRs in Italian Brown Swiss, overlapping those already detected in other breeds and finding additional ones
Histocompatibility genes and somatic cell count (SCC) in Italian Holstein Friesian
Full text linkGeni di istocompatibilità e conta delle cellule somatiche (SCC) nella Frisona Italiana –
Lo studio ha considerato l’effetto del Complesso Maggiore di Istocompatibilità (MHC) sulla mastite, clinica e subclinica, utilizzando l’Indice Genetico (I.G.) per la conta delle cellule somatiche: SCC (Somatic Cell Count). Su un totale di 302 tori di razza Frisona Italiana, valutati geneticamente per le cellule somatiche, sono stati analizzati il polimorfismo degli antigeni di istocompatibilità di classe I (test di microlinfocitotossicità locus BoLA-A) e di classe II (PCR/RFLP del locus DRB3 esone 2). L’effetto degli antigeni di istocompatibilità sugli indici genetici è stato valutato con un modello di sostituzione genica
Studio del gene NRAMP1 in relazione alla tubercolosi bovina
No full textDespite eradication programs, bovine tuberculosis is still a sanitary and economic problem in Italy. A different and interesting solution to the problem is the genetic approach, aimed to identify genetic susceptibility/resistance to the disease. As a candidate gene for bovine tuberculosis resistance we studied NRAMP1 gene, which encodes a protein thought to play some role in the priming of macrophages for activation, which in turn regulates the multiplication of a variety of intracellular pathogens, like M. bovis. To study NRAMP1 in cattle, we both sequenced part of the gene, and analysed three linked microsatellites. One of these markers, AR028 was found to be polymorphic with 7 alleles and a slight significant effect has been found for immunoglobulin production to M. bovis antigens
Quantitative Trait Loci affecting the somatic cell score on chromosome 4 and 26 in Italian Holstein cattle
Full text linkThis work aimed to confirm previously reported quantitative trait loci (QTL) affecting the somatic cell score (SCS) in dairy cattle on Bos taurus autosomes (BTA) 4 and 26. A granddaughter design with selective genotyping was implemented that included half-sib families from 12 male lines of Italian Holstein cattle. The animals were genotyped for 5 microsatellite markers each on regions of BTA 4 (average marker spacing 9.42 cM) and BTA 26 (average marker spacing 5.26 cM), previously reported by other authors as carrying QTL for somatic cell count. Quantitative trait loci analyses were performed using interval mapping by regressing sire breeding values for SCS onto genotype probabilities at 1-cM intervals along the 2 chromosome regions. Breeding values for SCS were estimated for the whole population using a test-day repeatability animal model. Results were not significant on a chromosome basis, but a possible QTL was found at BM4505 on BTA 26, confirming this region for further studies of QTL affecting SCS in the Italian Holstein population
Tursiops truncatus genetic analysis by DNA markers
No full textA recent law rules the captive breeding of Tursiops truncatus (T.t.) and prevents the introduction of new wild subjects in Italian delphinariums (D.M. n.469,6/12/2001). Microsatellite markers and D-loop mitochondrial polymorphism are widely used for identity/parentage control and analysis of the origin and genetic variability in several animal species. In the present work we characterized genetically the great part of the subjects of Tursiops truncatus ssp kept in captivity in Italy to get information to improve breeding programmes. Genomic and mitochondrial DNA from peripheral blood, blowhole mucosal swabs or necropsy tissues was extracted from 15 animals. Fourteen microsatellite loci informative in T.t. and 558bp of mitochondrial control region (Genbank#AF155161) were amplified by PCR and analyzed by fluorescent automatised methods. Mitochondrial sequences were aligned by Clustal W., genetic distance analysis calculated and a tree created by Phylip package using NEIGHBOR program and UPGMA option. Microsatellite markers allowed to genotype all the subjects and confirmed the parentage relationships. Mitochondrial control region analysis revealed 9 different haplotypes clustering in four different groups (Mediterranean Sea, Tenerife, Caribbean Sea and Mexican Gulf), according to the declared maternal origin of the capture areas. DNA polymorphism analysis clarified some genetic differences between the individuals of Tursiops truncates and suggests indication to orient mating plans and avoid the access of impreeding
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