Usporedba metoda procjene inbreedinga iz DNA ROH segmenata kod kokoši

master's thesis

• 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; (Department of Animal Science I); 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: kokoši; ROH segmenti; FROH; PLINK; cgaTOH; RZooROH
• Keywords (english): chicken; ROH segments; FROH; PLINK; cgaTOH; RZooROH
• 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
• Created on: 2020-11-19 11:37:34