Procjena strukture populacija goveda na temelju polimorfizma mitogenoma

master's thesis

• Title (english): Estimation of bovine population structure based on mitogenom polymorphisms
• Author: Katarina Turkalj
• Mentor: Ino Čurik (mentor)
• Committee member: Ino Čurik (predsjednik povjerenstva)
• Committee member: Vlatka Čubrić Čurik (član povjerenstva)
• Committee member: Vladimir Brajković (član povjerenstva)
• Granter: University of Zagreb; Faculty of Agriculture; (Animal Science); Zagreb
• Defense date and country: 2021-09-27, Croatia
• Scientific / art field, discipline and subdiscipline: BIOTECHNICAL SCIENCES; Agronomy

Abstract

Domestikacija goveda promijenila je društveni i ekonomski život čovjeka te pridonijela postupnom prijelazu iz lovaca-sakupljača u poljoprivrednike sa stalnim naseljima. No, procesi domestikacije goveda su složeniji nego što se mislilo te još uvijek postoje neodgovorena pitanja, pa tako i kada govorimo o rijetkim haplogrupama i mitogenomu goveda. Informacije mitogenoma mogle bi potencijalno biti od koristi prilikom određivanja struktura populacija, a nekolicina komercijalnih SNP čipova koji se koriste mogu pružiti informacije o mutacijama, bolestima ili svojstvima od interesa. Stoga, u suradnji s NEOGEN Genomics odlučili smo implementirati određene SNP-ove mtDNA. Cilj rada je bio identificirati haplogrupe i zabilježiti raznolikost putem metoda analitičke vizualizacije i klasteriranja koristeći uzorak od 264 jedinke 20 pasmina goveda i 317 SNP-ova. Uočene su značajnosti u nadopunjavanju metoda i implementiranju SNP-ova mitogenoma na GGP 100K. Za precizniju i pouzdaniju analizu potrebno je povećati uzorak te poduprijeti analizu s nukleusnom informacijom.

Abstract (english)

The domestication of cattle changed the social and economic life of people and contributed to the gradual transition from gatherers and hunters to farmers with permanent settlements. However, the processes of cattle domestication are more complex than previously thought and there are still unanswered questions, especially when we talk about rare haplogroups and cattle mitogenome. Mitogenome information can be potentially useful to determine population structure. Several commercial SNP Chips can be used to provide information on mutations, diseases, or traits of interest. Therefore, in collaboration with company NEOGEN Genomics, we decided to use specific mtDNA SNPs. The objective of the study was to identify haplogroups and capture diversity through the method of analytical visualization and clustering using samples of 264 individuals from 20 cattle breeds and 317 SNPs. It was found that the addition of method and implementation of SNP mitogenomes in GGP 100K are significant. For a more accurate and reliable analysis, it is necessary to increase the sample size and support the analysis with nuclear information.

• Keywords: struktura populacije; mtDNA; SNP; govedo; GGP 100K
• Keywords (english): population structure; mtDNA; SNP; cattle; GGP 100K
• Language: croatian
• URN:NBN: urn:nbn:hr:204:124128
• 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: Access restricted to students and staff of home institution
• Created on: 2021-12-06 12:24:26