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Genetic Variation of the Genus Shorea (Dipterocarpaceae) in Indonesia

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Genetic Variation of the Genus Shorea (Dipterocarpaceae) in Indonesia Genetic variation of the genus Shorea (Dipterocarpaceae) in Indonesia Dissertation submitted in partial fulfilments of the requirements for the degree of Doctor of Forestry Science at the Faculty of Forest Sciences and Forest Ecology, Georg-August University of Göttingen by Cui-Ping Cao born in Gansu, China Göttingen 2006 Supervisor: Prof. Dr. Reiner Finkeldey Referees of the dissertation: Prof. Dr. Reiner Finkeldey Prof. Dr. Ursula Kües Date of oral examination: 20 February 2006 http://resolver.sub.uni-goettingen.de/purl/?webdoc-689 i Acknowledgements I would like to express my hearty gratitude to Prof. Dr. Reiner Finkeldey for accepting me as a Ph. D. candidate, his excellent supervision, valuable suggestion and support, great patience and encouragement during the conduction of this work. I am thankful to Prof. Dr. Ursula Kües for consenting to be the co-referee and to Prof. Dr. Gode Gravenhorst and Prof. Dr. Ralph Mitlöhner for their efforts as members of the examination committee. I am also grateful to Dr. Oliver Gailing for his valuable guidance, many helpful ideas and constructive discussions, and Iskandar Siregar for providing the experimental leaf material from Indonesia Thanks must be given to Prof. Dr. Martin Ziehe for his valuable advices in terms of data analysis, Prof. Dr. Hans H. Hattemer, Prof. Dr. Hans-Rolf Gregorius, Dr. Ludger Leinemann and Dr. Barbara Vornam and Dr. Elizabeth M. Gillet for their friendly behaviour and help in some way or another in all phases of my work. Special acknowledgements are given to the valuable technical assistance in laboratory work of Mr. Gerold Dinkel, Mr. Thomas Seliger, Mrs. Christine Radler, Ms. Olga Artes, Mrs . Alexandra Dolynska, and to secretarial work of Ms. Marita Schwahn. Gratitude is also extended to all other colleagues: Mr. Siegfried Krakuhn, Mr. August Capelle Mrs. Sigrid Schmaltz, Mrs. Sabine Fehrmann, Dr. Jörg Kleinschmit, Dr. Aki Höltken, Dr. Sapto Indrioko, Dr. Hong Truong Luu, Dr. Madhav Pandey, Mr. Valdir Marcos Stefenon, Mr. Martin Mottura, Mr. Alexandru Lucian Curtu, Mr. Abayneh Derero, Mr. Taye Bekele Ayele, Mr. Nicolas-George Eliade, Mr. Akindele Akinnagbe, Mr. Ekue Marius, Mr. Randy A. Villarin, Mrs. Yanti Rachmayanti and many others who could not be mentioned here for their readiness to help and creating a friendly atmosphere during my studying at the Institute of Forest Genetics and Forest Tree Breeding, Georg-August University of Göttingen in Germany. I sincerely thank the Deutsche Forschungsgemeinschaft Project (DFG) (Fi 569/4-1/2) for financial support, with which the completion of my Ph. D. work is possible. Last but not least, I express my thanks to my beloved son, Yuan Liu, for his understanding, support and obeying. I am often moved and encouraged by his love, intelligence, diligence and kindness. ii TABLE OF CONTENTS 1 Background and objectives of the study ........................................................................ 1 1.1 Background ................................................................................................................ 1 1.2 Objectives of the study............................................................................................... 1 2 Dipterocarpaceae and the genus Shorea ........................................................................ 2 2.1 Traditional taxonomy and natural distribution........................................................... 2 2.2 Ecological and economical significance .................................................................... 2 2.3 Reproductive biology................................................................................................. 4 3 Genetic markers ............................................................................................................... 5 3.1 AFLPs......................................................................................................................... 5 3.2 Interpretation of AFLP fingerprints ........................................................................... 6 3.3 Chloroplast DNA markers (PCR-RFLPs and cpSSRs).............................................. 6 4 Quantification of genetic variation ................................................................................. 7 4.1 Basic genetic parameters............................................................................................ 7 4.2 Measurement of genetic variation within populations ............................................... 8 4.3 Measurement of genetic variation among populations............................................... 9 5 Summary of results ........................................................................................................ 10 5.1 Genetic variation at AFLPs for the Dipterocarpaceae and its relation to molecular phylogenies and taxonomic subdivisions (see part 1).............................................. 10 5.2 Genetic diversity within and among populations of Shorea leprosula Miq. and S. parvifolia Dyer (Dipterocarpaceae) in Indonesia detected by AFLPs (see part 2).. 11 5.3 Genetic variation in nine Shorea species in Indonesia revealed by AFLPs (see part 3) .................................................................................................................................. 11 6 References ....................................................................................................................... 13 Part 1 ....................................................................................................................................... 19 Part 2 ....................................................................................................................................... 31 Part 3 ....................................................................................................................................... 58 Appendix 1: List of publication ............................................................................................... 80 Appendix 2: Protocol of AFLP ................................................................................................ 82 Appendix 3: Sequences of adaptors and primers used............................................................. 84 Appendix 4: PCR-RFLP analysis............................................................................................. 85 iii Appendix 5: Chloroplast simple sequence repeat (cpSSR) analysis........................................ 87 Appendix 6: Species, size in bp and presence and absence of diagnostic markers (from part 1) .......................................................................................................................................... 88 Appendix 7: Frequency distribution of AFLP markers in Shorea leprosula and S. parvifolia and genetic Differentiation ( Gst ) among populations at each locus generated with POPGENE ver 1.31 (Yeh et al. 1999) (from part 2)........................................................ 89 Appendix 8: AFLP marker distribution in populations of Shorea leprosula and S. parvifolia (from part 2) ..................................................................................................................... 92 Appendix 9: AFLP diagnostic markers (primer E35M63, from part 2)................................... 95 Appendix 10: Genetic differentiation between Shorea leprosula and S. parvifolia at each locus obtained using POPGENE ver 1.31 (Yeh et al. 1999) (from part 2)................................ 96 Appendix 11: Genetic diversity and differentiation for Shorea leprosula at each locus obtained using POPGENE ver 1.31 (Yeh et al. 1999) (from part 2)................................ 98 Appendix 12: Genetic diversity and differentiation for Shorea parvifolia at each locus obtained using POPGENE ver 1.31 (Yeh et al. 1999) (from part 2).............................. 100 Appendix 13: Frequency distribution of AFLP markers in Shorea species and genetic Differentiation (Gst ) among populations at each locus generated with POPGENE ver 1.31 (Yeh et al. 1999) (from part 3) ....................................................................................... 102 Appendix 14: AFLP marker distribution in Shorea species (from part 3)............................. 106 Appendix 15: AFLP diagnostic markers (primer E35M63, from part 3)............................... 111 Appendix 16: Genetic diversity and differentiation for Shorea species in Nanjak Makur Sumatra at each locus obtained using POPGENE ver 1.31 (Yeh et al. 1999) (from part 3) ........................................................................................................................................ 112 Appendix 17: Genetic diversity and differentiation for Shorea species in Sumalindo Borneo at each locus obtained using POPGENE ver 1.31 (Yeh et al. 1999) (from part 3)............ 114 Appendix 18: Genetic diversity and differentiation for Shorea species in Nanjak Makur Sumatra and Sumalindo Borneo at each locus obtained using POPGENE ver 1.31 (Yeh et al. 1999) (from part 3) ................................................................................................ 116 Summary .............................................................................................................................. 118 Zusammenfassung ............................................................................................................... 122 1 1 Background and objectives of the study 1.1 Background The analysis of genetic diversity is a primary concern of population
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