Lina Zybartaitė Keturbriaunės Jonaţolės (Hypericum Maculatum Crantz)

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Lina Zybartaitė Keturbriaunės Jonaţolės (Hypericum Maculatum Crantz) VYTAUTO DIDŢIOJO UNIVERSITETAS GAMTOS MOKSLŲ FAKULTETAS BIOLOGIJOS KATEDRA LINA ZYBARTAITĖ KETURBRIAUNĖS JONAŢOLĖS (HYPERICUM MACULATUM CRANTZ) LIETUVOS POPULIACIJŲ GENETINĖ ĮVAIROVĖ Magistro baigiamasis darbas Biologijos studijų programa, valstybinis kodas 62401B107 Biologijos studijų kryptis Vadovas: prof. habil. dr. Eugenija Kupčinskienė ______ ______ (Mokls. laipsnis, vardas, pavardė) (Parašas) (Data) Apginta: prof. h.p. Algimantas Paulauskas ______ _____ (Fakulteto/studijų instituto dekanas/direktorius) (Parašas) (Data) Kaunas, 2011 Darbas atliktas: 2010–2011 m. Vytauto Didţiojo universitete, Biologijos katedroje, Paduvos universitete, Aplinkosauginės agronomijos ir augalininkystės mokslų katedroje Recenzentas: dr. Brigita Tamutė Darbas ginamas: viešame magistrų darbų gynimo komisijos posėdyje 2011 metų birţelio 2 d. Vytauto Didţiojo universitete, Biologijos katedroje, 801 auditorijoje. Adresas: Vileikos g. 8, LT-44404 Kaunas, Lietuva. Protokolo Nr. darbo vykdytojo pavardė ir parašas: ___________________________________ mokslinio vadovo(-ai) pavardė ir parašas: _______________________________ katedros, atsakingos uţ magistro darbo parengimą, Biologijos katedra pavadinimas, jos vedėjo pavardė ir parašas A. Sruoga __________________ 2 TURINYS SANTRUMPOS................................................................................................................................. 5 SANTRAUKA................................................................................................................................... 7 SUMMARY....................................................................................................................................... 8 ĮVADAS............................................................................................................................................ 9 1. LITERATŪROS APŢVALGA...................................................................................................... 11 1.1. Jonaţolės (Hypericum spp.) genties sistematinė, morfologinė-fiziologinė charakteristika........................................................................................................................ 11 1.2. Jonaţolių citogenetiniai poţymiai.................................................................................. 13 1.3. Jonaţolių antriniai metabolitai........................................................................................ 13 1.4. Jonaţolių genetiniai tyrimo metodai............................................................................... 16 1.4.1. Atsitiktinai pagausintos polimorfinės DNR metodo pritaikymas.................... 17 1.4.2. Numatytų sekų polimerazinės grandininės reakcijos metodas........................ 20 1.4.3. Amplifikuotų ir restrikcinių fragmentų ilgio polimorfizmo metodo pritaikymas................................................................................................................. 21 1.4.4. Mikrosatelitinių ţymenų metodo pritaikymas................................................. 23 1.4.5. Kiti metodai taikomi genetinės įvairovės tyrimuose....................................... 25 1.5. Jonaţolių genetinio profilio ryšys su antriniais junginiais............................................. 27 2. MEDŢIAGA IR METODIKA....................................................................................................... 29 2.1. Augalinės medţiagos rinkimo vietos.............................................................................. 29 2.2. DNR išskyrimas.............................................................................................................. 31 2.3. APPD analizės sąlygos................................................................................................... 32 2.4. Populiacijų APPD analizės sąlygos................................................................................ 33 2.5. AP-PGR analizės sąlygos............................................................................................... 34 2.6. AP-PGR produktų valymas............................................................................................ 35 2.7. PKS analizės sąlygos...................................................................................................... 36 2.8. DNR elektroforezė agarozės gelyje................................................................................ 38 2.9. PGR fragmento ekstrakcija iš agarozės gelio................................................................. 39 2.10. PGR fragmento pakartotinas pagausinimas.................................................................. 41 2.11. PGR fragmento klonavimo sąlygos.............................................................................. 41 2.12. Plazmidţių išskyrimas iš ląstelių.................................................................................. 43 2.13. Kapiliarinė elektroforezė ir DNR sekoskaita................................................................ 44 3 2.14. Statistinė duomenų analizė........................................................................................... 44 3. TYRIMŲ REZULTATAI IR JŲ APTARIMAS........................................................................... 46 3.1. DNR išskyrimo iš keturbriaunės jonaţolės metodo parinkimas..................................... 46 3.2. APPD metodo sąlygų optimizavimas keturbriaunės jonaţolės genetinės įvairovės tyrimams................................................................................................................................ 46 3.2.1. APPD PGR mišinio sudėties parinkimas........................................................... 46 3.2.2. APPD DNR pagausinimo programos sąlygų optimizavimas............................. 46 3.3. AP-PGR metodo sąlygų optimizavimas keturbriaunės jonaţolės genetinės įvairovės tyrimams................................................................................................................................ 48 3.4. PKS metodo sąlygų optimizavimas keturbriaunės jonaţolės genetinės įvairovės tyrimams................................................................................................................................ 56 3.4.1. Mikrosatelitinių pradmenų kūrimas.................................................................... 56 3.4.2. PKS metodo PGR mišinio sudėties parinkimas................................................. 57 3.4.3. PKS metodo pagausinimo programos sąlygų optimizavimas............................ 58 3.4.4. PGR fragmento klonavimas................................................................................ 59 3.5. Keturbriaunės jonaţolės populiacijų genetinės įvairovė, įvertinta APPD metodu....... 61 IŠVADOS.......................................................................................................................................... 72 LITERATŪROS SĄRAŠAS............................................................................................................. 74 PADĖKA........................................................................................................................................... 80 MOKSLINĖS PUBLIKACIJOS IR PRANEŠIMAI......................................................................... 81 PRIEDAI............................................................................................................................................ 83 4 SANTRUMPOS AFIP – amplifikuotų fragmentų ilgio polimorfizmas (angl. Amplified Fragment Length Polymorphism) AMOVA – molekulinės genetinės įvairovės analizė (angl. Analysis of Molecular Variance) AOX – alternatyvios oksidazės genas (angl. Alternative oxidase gene) APPD – atsitiktinai pagausinta polimorfinė DNR (angl. Random Amplified Polymorphic DNA, RAPD) AP-PGR – numatytų sekų polimerazinė grandininė reakcija (angl. Arbitrarily Primed Polymerase Chain Reaction – AP-PCR) bp – bazių pora (angl. base pair) CTAB – cetiltrimetilamonio bromidas (angl. Cetyltrimethylammonium bromide) DNR – deoksiribonukleorūgštis (angl. Deoxyribonucleic acid, DNA) dNTP – deoksiribonukleotidai FCSS – srovės citometrinis sėklų įvertinimas (angl. Flow Cytometric Seed Screen, FCSS) GDxy – genetinis atstumas tarp x ir y genotipų (angl. Genetic Distance) Gst – genetinės diferenciacijos koeficientas (Nei, 1973) H – genetinė įvairovė (Nei, 1973) I – Šenono (Shannon‟o) informacinis indeksas ITS – transkriptų vidiniai skirtukai (angl. Internal Transcribed Spacer, ITS) IVNP – introno vieno nukleotido polimorfizmas (angl. Intron Single Nucleotide Polymorphism, ISNP) LC-MS/MS – skystinė chromatografija, masių spektrometrija Na – stebimas alelių skaičius lokuse NCBI – nacionalinis biotechnologinės informacijos centras (angl. National Center for Biotechnology Information) Ne – efektyvių alelių skaičius lokuse Nm – genų srautas tarp populiacijų (angl. Gene flow) P – polimorfinių lokusų procentas PGR – polimerazinė grandininė reakcija (angl. Polymerase Chain Reaction, PCR) PKA – principinių koordinačių analizė (angl. Principal Coordinates Analysis, PCA) PKS – paprastosios kartotinės sekos (angl. Simple Sequence Repeat, SSR) PPSI – paprastųjų pasikartojančių sekų intarpai (angl. Inter-Simples Sequence Repeats, ISSR) RFIP – restrikcijos fragmentų ilgio polimorfizmas (angl. Restriction Fragment Length Polymorphism, RFLP) SDS – natrio dodecilsulfatas (angl. Sodium dodecyl sulphate) 5 UPGMA – porų grupavimo pagal aritmetinius vidurkius metodas su vienodais svoriais (angl. Unweighted Pair-Group Method of arithmetic Averages) ΦPT – fiksacijos indekso FST analogas, populiacijų diferenciacijos
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