Genotipizacija navadne (Fagopyrum esculentum) in tatarske ajde (Fagopyrum tataricum) z mikrosatelitnimi označevalci

Fabjan, Primož (author), Luthar, Zlata (mentor)

Navadna (Fagopyrum esculentum Moench) in tatarska ajda (Fagopyrum tataricum Gaertn.) sta gospodarsko manj pomembni poljščini, vendar v zadnjem času zaradi ugodih vplivov na zdravje zanimanje zanju narašča. Poznavanje diverzitete in genetske strukture genskih virov predstavlja osnovo za njihovo ohranjanje in uporabo v žlahtniteljskih programih. Zato smo se odločili, da bomo z mikrosatelitnimi markerji genotipizirali izbrane akcesije navadne in tatarske ajde iz genske banke na Biotehniški fakulteti Univerze v Ljubljani. Večino akcesij so predstavljale lokalne populacije, nekaj je bilo tudi tujih akcesij in standardnih sort. S PCR reakcijo smo pri obeh vrstah preizkusili 31 mikrosatelitnih označevalcev oz. markerjev. S programom GeneMapper smo ovrednotili rezultate kapilarne elektroforeze. Pri navadni ajdi se je uspešno pomnožilo 17 markerjev, pri tatarski pa 22. Pri navadni ajdi je bilo od 10 izbranih markerjev variabilnih 6, pri tatarski jih je bilo od 11 izbranih variabilnih 8. Prenosljivost markerjev med obema vrstama je znašala 31,5 %. S programom Cervus smo za njih izračunali parametre variabilnosti. Povprečno število pomnoženih alelov na akcesijo je pri navadni ajdi znašalo 27,2 in pri tatarski 10,3. Povprečna vrednost PIC je bila pri navadni ajdi 0,678, pri tatarski 0,394.. Vsi parametri variabilnosti so bili pri navadni ajdi večji kot pri tatarski. S programom DARwin smo izrisali dendrograme, kjer so prikazani filogenetski odnosi med vzorci. S pomočjo faktorialne analize smo ocenili variabilnost in grupiranje akcesij. Pri navadni ajdi je bila variabilnost znotraj akcesij zelo visoka, akcesije pa so si bile genetsko zelo podobne. Pri tatarski ajdi smo ravno nasprotno ugotovili zelo nizko variabilnost znotraj akcesij, ki pa so se zelo razlikovale med seboj. Za nadaljnje raziskave priporočamo uporabo večjega seta polimorfnih markerjev, s katerimi bo mogoče natančneje določiti filogenetske povezave med akcesijami in njihovo variabilnostjo.

• Language: Slovenian
• Keywords: navadna ajda, tatarska ajda, genotipizacija, mikrosatelitni označevalci, lokus, alel, dendrogram, faktorialna analiza
• Work type: Master's thesis/paper
• Typology: 2.09 - Master's Thesis
• Organization: BF - Biotechnical Faculty
• Year: 2023
• PID: 20.500.12556/RUL-150345
• COBISS.SI-ID: 164798723
• Publication date in RUL: 16.09.2023

Secondary language

• Language: English
• Title: Genotyping of common (Fagopyrum esculentum) and Tartary buckwheat (Fagopyrum tataricum) using microsatellite markers

Abstract

Common buckwheat (Fagopyrum esculentum Moench) and Tartary buckwheat (Fagopyrum tataricum Gaertn.) are two minor crops. However, their significance has been growing in recent years. Understanding the diversity and genetic structure of genetic resources is crucial for their conservation and utilization in breeding programs. Here, we genotyped selected accessions of common and Tartary buckwheat using microsatellite markers from the gene bank at the Biotechnical Faculty, University of Ljubljana. Most of the accessions were local populations, a few were foreign accessions and standard varieties. We used PCR to test 31 microsatellite markers in both species. 17 markers successfully amplified fragments in common buckwheat and 22 markers in Tartary buckwheat. Out of 10 selected markers, 6 exhibited variability in common buckwheat, while in Tartary buckwheat, 8 out of 11 selected markers were variable. The transferability rate of markers was 31.5%. We evaluated capillary electrophoresis results with GeneMapper software. We used Cervus software to calculate variability parameters for the polymorphic markers. Average number of alleles per accession was 27,2 and 10,3 in common and Tartary buckwheat, respectively. Average PIC (Polymorphic Information Content) value for common and Tartary buckwheat was 0,678 and 0,394, respectively. All variability parameters were higher for common buckwheat than Tartary buckwheat. We used DARwin software to construct dendrograms depicting phylogenetic relationships among samples. Additionally, we used factorial analysis to assess variability and grouping of accessions. In common buckwheat we observed very high variability within accessions and low genetic differentiation between accessions. In Tartary buckwheat we observed low variability within accessions and high genetic differentiation among accessions. For future research we recommend using a larger set of polymorphic markers that will allow for a more precise determination of phylogenetic relationships among the accessions and their variability.

• Keywords: common buckwheat, Tartary buckwheat, genotypization, microsatellite markers, locus, allele, dendrogram, factorial analysis