Analiza varijanti u broju kopija u genomu paške ovce

master's thesis

• Title (english): Analysis of copy number variants in the genome of Pag Island sheep
• Author: Iva Šefček
• Mentor: Maja Ferenčaković (mentor)
• Committee member: Maja Ferenčaković (predsjednik povjerenstva)
• Committee member: Vlatka Čubrić Čurik (član povjerenstva)
• Committee member: Ino Čurik (član povjerenstva)
• Granter: University of Zagreb; Faculty of Agriculture; (Animal Science); Zagreb
• Defense date and country: 2024-09-30, Croatia
• Scientific / art field, discipline and subdiscipline: BIOTECHNICAL SCIENCES; Agronomy

Abstract

Varijante broja kopija (engl. Copy Number Variants, CNVs) predstavljaju jedan od najčešćih oblika genetske varijacije, kako u smislu brzine mutacije, tako i udjela genoma koji obuhvaćaju. Ove varijacije mogu značajno utjecati na različite fenotipske osobine i imaju ključnu ulogu u prilagodbi, zdravlju i proizvodnim karakteristikama životinja. Paška ovca je poznata po svojoj prilagodljivosti te visokokvalitetnom mesu i mlijeku, s osobitostima poput visoke masnoće u mlijeku i specifične, finije vune. Ciljevi ovog rada bili su detektirati CNV-ove i CNV regije (CNVR-ove) specifične za populaciju paške ovce, povezati CNVR-ove s genima i njihovim funkcijama, te identificirati QTL regije koje se preklapaju s CNVR-ovima. U istraživanju su korišteni genotipovi (Ovine Infinium® HD SNP BeadChip) 25 jedinki paške ovce te 75 jedinki drugih pasmina (istarska ovca, dalmatinska pramenka i dubrovačka ruda). Pomoću bioinformatičkih alata za detekciju CNV-ova i njihovo povezivanje s funkcionalnim genima, ukupno je identificirano 955 CNVR-ova, od kojih je 18 bilo jedinstveno za pašku ovcu. Ove regije sadrže gene koji su ključni za osobine poput otpornosti na vanjske uvjete, metabolizma hranjivih tvari i reprodukcije. Također, prisutni su u biološkim putevima koji pružaju uvid u genetske osnove prilagodljivosti paške ovce na specifične okolišne uvjete. Dodatno, identificirani su QTL-ovi povezani s finoćom vune, koagulacijskim svojstvima mlijeka i proizvodnjom mesa. Ova saznanja mogu značajno doprinijeti daljnjem unapređenju uzgojnih programa, optimizaciji prehrane i postizanju veće produktivnosti, osiguravajući visoku kvalitetu proizvoda poput mlijeka i sira, po kojima je paška ovca nadaleko poznata.

Abstract (english)

Copy number variants (CNVs) are one of the most common forms of genetic variation, both in terms of mutation rate and the proportion of the genome they cover. These variations can significantly affect various phenotypic traits and play a crucial role in the adaptation, health and production traits of animals. The Pag Island sheep is known for its adaptability as well as for its high-quality meat and milk with specific traits such as high milk fat content and fine wool. The objectives of this study were to detect CNVs and CNV regions (CNVRs) in the Pag Island sheep genome that are specific to the population, to map CNVRs to genes and their functions, and to identify QTL regions that overlap with CNVRs. Genotypes (Ovine Infinium® HD SNP BeadChip) of 25 Pag Island sheep and 75 individuals of other breeds (Istrian sheep, Dalmatian Pramenka and Dubrovnik Ruda) were used for the study. Using bioinformatics tools to detect CNVs and functional gene association, a total of 955 CNVRs were discovered, 18 of which were unique to the Pag Island sheep. These regions contain genes critical for traits such as resistance to environmental conditions, nutrient metabolism and reproduction, and are present in biological pathways that provide insights into the genetic basis of the Pag sheep's adaptation to specific environmental conditions. In addition, QTLs associated with wool fineness, milk coagulation traits and meat production have been identified. These findings can make an important contribution to further improvements in breeding programs, optimizing nutrition and achieving higher productivity, thus ensuring the high quality of products such as milk and cheese for which the Pag Island sheep is known.

• Keywords: Varijante broja kopija (CNV-ovi); regije varijanti broja kopija (CNVR-ovi); paška ovca; genetska osnova prilagodljivosti
• Keywords (english): Pag Island sheep; Copy number variants (CNV); CNV regions (CNVR); genetic basis of adaptability
• Language: croatian
• URN:NBN: urn:nbn:hr:204:987088
• Study programme: Title: Animal Genetics and Breeding; Study programme type: university; Study level: graduate; Academic / professional title: magistar/ magistra inženjer/inženjerka genetike i oplemenjivanja životinja (magistar/ magistra inženjer/inženjerka genetike i oplemenjivanja životinja)
• Type of resource: Text
• File origin: Born digital
• Access conditions: Open access
• Created on: 2024-11-04 10:25:25