Procjena i usporedba raznolikosti različitih populacija kokoši putem genomske informacije

master's thesis

• Title (english): Estimation and comparation of the diversity of different chicken populations through genomic information
• Author: Tea Jurić
• Mentor: Maja Ferenčaković (mentor)
• Committee member: Maja Ferenčaković (predsjednik povjerenstva)
• Committee member: Vlatka Čubrić Čurik (član povjerenstva)
• Committee member: Zlatko Janječić (član povjerenstva)
• Granter: University of Zagreb; Faculty of Agriculture; (Animal Science); Zagreb
• Defense date and country: 2020-09-30, Croatia
• Scientific / art field, discipline and subdiscipline: BIOTECHNICAL SCIENCES; Agronomy

Abstract

Kokoši i njihovi proizvodi čine važan udio u prehrani ljudi, a isto tako su pogodan organizam za istraživanje. Postoji velik broj pasmina kokoši koje su rasprostranjene po cijelom svijetu. Današnja tehnologija, SNP-ovi velike gustoće i dostupnost genomske informacije omogućuju lakša i točnija istraživanja genoma. U ovom radu procijenjeni su genetski parametri bitni za procjenu ugroženosti populacije, a to su: inbreeding, efektivna veličina populacije i heterozigotnost. Analiza je napravljena na 37 tradicionalnih nizozemskih pasmina. Za analizu su korišteni programski paketi SAS, R, PLINK, cgaTOH i SNeP. Heterozigotnost varira između pasmina. Od pasmine eikenburger kod koje iznosi 0.016±0.020, do pasmine sumatra 0.559±0.006. Najveće vrijednosti FROH imamo kod izvedenica iz velikih u patuljaste pasmine tzv. „neo-bantams“. Za preciznije izračune heterozigotnosti, FIS koeficijenta i efektivne veličine populacije potrebno je povećati veličinu uzorka za svaku populaciju na 20 jedinki. Procjena FROH zahtijeva prilagodbu zbog specifičnosti genoma kokoši.

Abstract (english)

Chickens and their products make up an important part of human nutrition and are also a suitable organism for research. There are many breeds of chickens that are widespread throughout the world. Today’s technology, high-density SNPs, and the availability of genomic information allow for easier and more accurate genome research. In this paper, the genetic parameters important for the assessment of population vulnerability were assessed, namely: inbreeding, effective population size and heterozygosity. The analysis was made on 37 traditional Dutch breeds. The software packages SAS, R, PLINK, cgaTOH and SNeP were used for the analysis. Heterozygosity varies between breeds. From the Eikenburger breed, which is 0.016 ± 0.020, to the Sumatra breed, it is 0.559 ± 0.006. We have the highest values of FROH in derivatives from large to dwarf breeds, the so-called "Neo-bantams". For more accurate calculations of heterozygosity, FIS coefficient, and effective population size, it is necessary to increase the sample size for each population to 20 individuals. The assessment of FROH requires adjustment due to the specificity of the chicken genome.

• Keywords: kokoši; SNP; inbreeding; efetivna veličina populacije; heterozigotnost
• Keywords (english): Chicken; SNP; inbreeding; effectiv population size; heterozigosity
• Language: croatian
• URN:NBN: urn:nbn:hr:204:884806
• 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: 2020-10-30 11:00:28