Metode procjene genomskog inbridinga

master's thesis

• Title (english): Methods of estimating genomic inbreeding
• Author: Filip Čavlović
• Mentor: Maja Ferenčaković (mentor)
• Committee member: Maja Ferenčaković (predsjednik povjerenstva)
• Committee member: Ino Čurik (član povjerenstva)
• Committee member: Vlatka Čubrić Čurik (član povjerenstva)
• Granter: University of Zagreb; Faculty of Agriculture; (Animal Science); Zagreb
• Defense date and country: 2021-09-23, Croatia
• Scientific / art field, discipline and subdiscipline: BIOTECHNICAL SCIENCES; Agronomy

Abstract

Parenje jedinki u srodstvu, odnosno inbreeding dugi je niz godina predmet istraživanja mnogih radova. Inbreeding se mjeri pomoću koeficijenta inbreedinga do čijeg se izračuna može doći korištenjem podataka iz rodoslovlja ili preko genomskih podataka. Procjena stupnja inbreedinga iz pedigrea ima određene nedostatke, a razvoj molekularnih markera doveo je do razvoja niza metoda procjene koeficijenta inbreedinga iz genomskih podataka. Procjena inbreeding koeficijenta iz podataka SNP-ova i dalje je najčešće korištena metoda no pojava NGS sekvenciranja donosi veću količinu i kvalitetu podataka te ima potencijal postati prvi izbor kod procjene inbreeding koeficijenta. Međutim, s dobrim stranama iskazali su se i određeni problemi kao što su cijena, pohrana, mogućnost analize odnosno nedostatak adekvatnih softvera i pitanje privatnosti. Iako se cijena NGS analiza drastično snizila i dalje je financijski nepristupačna mnogim znanstvenicima, osobito ako se istraživanje bazira na većem broju jedinki. Postojeći problemi sa pohranom podataka WGS analiza su i dalje neriješeni, iako su predložena neka djelomična rješenja, većinom sa sobom donose neka ograničenja ili rizike. U radu sažeto su prikazane neke od metoda procjene inbreedinga iz genomskih podataka kao i trenutne limitacije te moguća buduća rješenja.

Abstract (english)

Mating of related organisms, also known as inbreeding, has been the topic of many studies. Inbreeding is measured by coefficient of inbreeding which is calculated either by using pedigree data or by the usage of genomic data. Estimation of inbreeding coefficient from pedigree has certain disadvantages and development of molecular markers has led to creation of several methods to estimate inbreeding coefficient from genomic data. Estimation of inbreeding coefficient from SNP data is still the most often used method but development of NGS sequencing brings more data and better quality. However, with beneficial sides of NGS, some problems have also arisen. Problems like price, data storing, data processing and the question of privacy. Although the price has drastically dropped it is still not affordable to most researchers, especially if the research is based on a large number of samples. Existing problems with data storage are still not solved and even though some part solutions have been suggested, they come with certain limitations and risks. This thesis summarizes some of the methods for estimating inbreeding from genomic data as well as current limitations and possible future solutions.

• Keywords: inbreeding; koeficijent inbreedinga; NGS
• Keywords (english): inbreeding; inbreeding coefficient; NGS
• Language: croatian
• URN:NBN: urn:nbn:hr:204:976278
• 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: 2021-12-10 08:30:09