Usporedba metoda procjene inbreedinga iz DNA ROH segmenata kod kokoši

Bošković, Boško

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master's thesis

Usporedba metoda procjene inbreedinga iz DNA ROH segmenata kod kokoši

Zagreb: University of Zagreb, Faculty of Agriculture, 2020. urn:nbn:hr:204:197528

Bošković, Boško

University of Zagreb
Faculty of Agriculture
Animal Science

Cite this document

APA 6th Edition

Bošković, B. (2020). Usporedba metoda procjene inbreedinga iz DNA ROH segmenata kod kokoši (Master's thesis). Zagreb: University of Zagreb, Faculty of Agriculture. Retrieved from https://urn.nsk.hr/urn:nbn:hr:204:197528

MLA 8th Edition

Bošković, Boško. "Usporedba metoda procjene inbreedinga iz DNA ROH segmenata kod kokoši." Master's thesis, University of Zagreb, Faculty of Agriculture, 2020. https://urn.nsk.hr/urn:nbn:hr:204:197528

Chicago 17th Edition

Harvard

Bošković, B. (2020). 'Usporedba metoda procjene inbreedinga iz DNA ROH segmenata kod kokoši', Master's thesis, University of Zagreb, Faculty of Agriculture, accessed 19 September 2024, https://urn.nsk.hr/urn:nbn:hr:204:197528

Vancouver

Bošković B. Usporedba metoda procjene inbreedinga iz DNA ROH segmenata kod kokoši [Master's thesis]. Zagreb: University of Zagreb, Faculty of Agriculture; 2020 [cited 2024 September 19] Available at: https://urn.nsk.hr/urn:nbn:hr:204:197528

IEEE

B. Bošković, "Usporedba metoda procjene inbreedinga iz DNA ROH segmenata kod kokoši", Master's thesis, University of Zagreb, Faculty of Agriculture, Zagreb, 2020. Available at: https://urn.nsk.hr/urn:nbn:hr:204:197528

Cite this item: https://urn.nsk.hr/urn:nbn:hr:204:197528

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Metadata

Title	Usporedba metoda procjene inbreedinga iz DNA ROH segmenata kod kokoši
Title (english)	Comaparison of inbreeding estimating methods from DNA ROH in chicken
Author	Boško Bošković
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	ROH segmenti (Runs of homozygosity) su dugi neprekinuti nizovi homozigotnosti u genomu na osnovu kojih je moguće procijeniti razinu inbreedinga u populaciji. Iako je genom kokoši jedan od prvih koji je sekvenciran, zbog specifičnosti u odnosu na genom sisavaca nema mnogo radova u kojima se procjenjuje inbreeding kokoši korištenjem genomske informacije. U ovom radu uspoređene su tri različite metode procjene inbreedinga upotrebom programskih paketa: cgaTOH (koristi metodu prebrojavanja), PLINK (metoda klizećeg prozora) i RZooROH (HMM – skriveni Markovljev model). Genomski podaci 40 različitih pasmina kokoši, sedam ekotipova afričkih seoskih kokoši i dvije podvrste divlje kokoši preuzeti su sa online repozitorija. U analizu je ušlo 551 866 SNP-ova. Statistička obrada i vizualizacija dobivenih podataka izvršene su u programskim paketima SAS 9.4 i JMP14. Za utvrđivanje statističke značajnosti korišten je Tukey-Kramer HSD test. Nakon usporedbe dobivenih rezultata zaključuje se da je pri općenitoj procjeni inbreedinga bolje koristiti cgaTOH ili PLINK tj. metode prebrojavanja i klizećeg prozora jer su brže i jednostavnije. Ukoliko je cilj istraživanja ustanoviti dob inbreedinga RZooROH metoda temeljena na skrivenom Markovljevom modelu daje preciznije rezultate pri detektiranju inbreedinga koji se dogodio u bliskoj prošlosti, dok cgaTOH i PLINK preciznije detektiraju manje ROH segmente koji upućuju na inbreeding koji se dogodio davno. RZooROH općenito bolje procjenjuje varijabilnost u odnosu na ostale programske pakete.
Abstract (english)	Runs of homozygosity are long continous stretches of homozygous genome that are used as a tool in calculating population inbreeding level. Although chicken genome was one of the first to be sequenced it's peculiarities in compare to mammalian genome caused that not much research has been done with calculating inbreeding level in chicken using genomic information. In this thesis three different methods were compared using cgaTOH, PLINK and RZooROH program. Genomic data from 40 different breeds, 7 ecotypes of african village chickens and two subspecies of red jungle fowl were downloaded from online repository. 551,866 SNPs were included in the analysis. Statistical processing and visualization of the obtained data were performed in the software packages SAS 9.4 and JMP14. The Tukey-Kramer HSD test was used to determine statistical significance. After comparing the obtained results, it is concluded that it is better to use cgaTOH or PLINK, ie counting and sliding window methods, in the general assessment of inbreeding, because they are faster and simpler. If the aim of the research is to establish the age of inbreeding, the RZooROH method based on the hidden Markov model gives more accurate results in detecting inbreeding that occurred in the recent past, while cgaTOH and PLINK more accurately detect smaller ROH segments indicating inbreeding that occurred long ago. RZooROH generally estimates variability better than other software packages.
Keywords
Keywords (english)
Language	croatian
URN:NBN	urn:nbn:hr:204:197528
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
Terms of use
Repository	Repository Faculty of Agriculture University of Zagreb
Created on	2020-11-19 11:37:34