Genetic and epigenetic landscapes of spontaneus genome rearrangements in grapevine

master's thesis

• Title (croatian): Genetička i epigenetička obilježja spontanih rearanžmana genoma vinove loze
• Author: Dominik Noršić
• Mentor: Detlef Weigel (mentor)
• Mentor: Dunja Leljak-Levanić (sumentor)
• Committee member: Dunja Leljak-Levanić (predsjednik povjerenstva)
• Committee member: Nenad Malenica (član povjerenstva)
• Committee member: Biljana Balen (član povjerenstva)
• Committee member: Željka Vidaković-Cifrek (član povjerenstva)
• Granter: University of Zagreb; Faculty of Science; (Department of Biology); Zagreb
• Defense date and country: 2022-02-22, Croatia
• Scientific / art field, discipline and subdiscipline: NATURAL SCIENCES; Biology

Abstract

Grapevine cultivars (Vitis vinifera ssp. vinifera), depending on the color of their berries, can be divided into black, white and red. White cultivars lack functional copies of the VviMybA1 and VviMybA2 genes that regulate the accumulation of anthocyanins in grape skin, whose level determines the color of the berry. The focus of this study was to characterize genetic and epigenetic processes that result in natural grape color somatic variants. Two genome structural variation events were bioinformatically identified previously as the cause of the white berry phenotype in ‘Garnacha Blanca’ derivative cultivar. These two structural variation events were validated here by polymerase chain reaction and were confirmed as the likely only two independent origins for this cultivar after genotyping a collection of clonal accessions. Samples of the ancestral black-berried ‘Garnacha Tinta’ cultivar were also genotyped for the same structural variations, identifying one likely epidermal cell monolayer chimera mutant. To characterize the genetic origin of mutants with altered berry color, Oxford Nanopore target enrichment sequencing using UNCALLED method was tested. Among others, the region harbouring VviMybA1 gene was targeted in a color re-gain somatic variant of the white-berried cultivar Alvarinho, confirming that a Gret1 transposable element excision from VviMybA1 promoter is the cause of color recovery.

Abstract (croatian)

Kultivari vinove loze (Vitis vinifera ssp. vinifera), ovisno o boji bobica, mogu se podijeliti na crne, bijele i crvene. Bijelim sortama nedostaju funkcionalne kopije gena VviMybA1 i VviMybA2 koji reguliraju nakupljanje antocijana u kožici grožđa, čija razina određuje boju bobica. Fokus ovog istraživanja bio je karakterizirati genetičke i epigenetičke procese koji rezultiraju prirodnim somatskim varijantama boje grožđa. Dva događaja strukturne varijacije genoma prethodno su bioinformatički identificirana kao uzrok fenotipa bijele bobice u sorti 'Garnacha Blanca'. Ova dva događaja strukturne varijacije ovdje su potvrđena metodom lančane reakcije polimeraze i potvrđena su kao vjerojatno jedina dva nezavisna podrijetla za ovu sortu nakon genotipizacije zbirke klonskih akcesija. Uzorci sorte 'Garnacha Tinta' s crnom bobicom također su genotipizirani za iste strukturne varijacije, identificirajući jednu kimeru vjerojatnu mutantnu u sloju stanica kože. Kako bi se okarakteriziralo genetsko podrijetlo mutanata s promijenjenom bojom bobica, testirana je metoda sekvenciranja Oxford Nanopore pomoću programa UNCALLED koja omogućuje selektivno ciljanje i obogaćenje specifičnih regija genoma. Između ostalih, regija u kojoj se nalazi gen VviMybA1 bila je ciljana u somatskoj varijanti sa povraćenom bojom bobice kultivara 'Alvarinho', potvrđujući da je izrezivanje transpozabilnog elementa Gret1 iz VviMybA1 promotora uzrok oporavka boje.

• Keywords: structural variation; Vitis vinifera; MYBA genes; anthocyanins; grapevine berry color; nanopore; transposable elements
• Keywords (croatian): strukturna varijacija; Vitis vinifera; geni MYBA; antocijani; boja bobica grožđa nanopore; transpozabilni elementi
• Language: english
• URN:NBN: urn:nbn:hr:217:976183
• Study programme: Title: Molecular Biology; Study programme type: university; Study level: graduate; Academic / professional title: magistar/magistra molekularne biologije (magistar/magistra molekularne biologije)
• Type of resource: Text
• File origin: Born digital
• Access conditions: Open access
• Created on: 2022-03-16 10:48:44