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An Ecogeographic Analysis of Oryza Series Sativae in Asia and the Pacific

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An Ecogeographic Analysis of Oryza Series Sativae in Asia and the Pacific An ecogeographic analysis of An ecogeographic analysis of Oryza series Sativae in Asia and the Pacific Oryza Maria Celeste N. Banaticla-Hilario series Sativae in Asia and the Pacific in Maria Celeste N. Banaticla-Hilario An ecogeographic analysis of Oryza series Sativae in Asia and the Pacific Maria Celeste N. Banaticla-Hilario Thesis committee Promoter Prof.dr. M.S.M. Sosef Professor of Biosystematics Wageningen University / Naturalis Biodiversity Center Co-promoters Dr. R.G. van den Berg Associate Professor, Biosystematics Group Wageningen University Dr. K.L. McNally Senior Scientist, T.T. Chang Genetic Resources Center International Rice Research Institute, Los Baños, Philippines Other members Prof.dr. B.J. Zwaan, Wageningen University Dr.ir. T.J.L. van Hintum, Centre for Genetic Resources, Wageningen Dr. M.J.M. Smulders, Plant Research International, Wageningen Dr. H. Duistermaat, Leiden University This research was conducted under the auspices of the Graduate School of Experimental Plant Sciences. An ecogeographic analysis of Oryza series Sativae in Asia and the Pacific Maria Celeste N. Banaticla-Hilario Thesis submitted in fulfillment of the requirements for the degree of doctor at Wageningen University by the authority of the Rector Magnificus Prof. dr. M.J. Kropff, in the presence of the Thesis Committee appointed by the Academic Board to be defended in public on Wednesday 24 October 2012 at 11 a.m. in the Aula. Maria Celeste N. Banaticla-Hilario An ecogeographic analysis of Oryza series Sativae in Asia and the Pacific PhD thesis, Wageningen University, NL (2012) With references, with summaries in English, Dutch and Filipino ISBN 978-94-6173-378-8 CONTENTS Chapter 1: General Introduction 7 Chapter 2: Morphological variation patterns between and within Oryza nivara and O. rufipogon 31 Chapter 3: Local differentiation amidst extensive allele sharing in Oryza nivara and O. rufipogon 79 Chapter 4: Crossability patterns in Asia Pacific Oryza series Sativae 149 Chapter 5: Resolving the taxonomic ambiguity of Oryza nivara 189 Chapter 6: General Discussion 207 Summary 221 Samenvatting (Summary in Dutch) 225 Kabuuran (Summary in Filipino) 229 Acknowledgements 233 Curriculum vitae 235 Education statement 237 CHAPTER 1 General Introduction 8 | Chapter 1 The genus Oryza L. It was Linnaeus who, back in 1753, first formally published the genus name Oryza L. in his famous Species Plantarum. More than 250 years later, a wealth of information about this grass genus has been and is still being discovered. Oryza is defined by its oblique spikelets having two rudimentary glumes whose function is taken over by two small sterile lemmas that are acuminate to setiform, and the single fertile lemma being generally awned and crustaceous or rarely chartaceous-coriaceous (Tateoka 1964; Duistermaat 1987). Since its first publication, the circumscription of the genus Oryza expanded from a single species Oryza sativa (Linnaeus 1753), to more than 20 species found in different regions of the tropics. Tateoka (1962) classified the genus into species complexes: groups of closely related species. Vaughan (1989) adapted Tateoka`s system and modified it by adding O. glumaepatula, O. granulata, O. meridionalis, O. nivara and O. rhizomatis to the species list, and removing members that are now relegated to the genus Leersia. Lu (1999) reviewed the taxonomic history of Oryza and compared the different subgeneric classifications published by Roschevics (1931), Chevalier (1932), Ghose et al. (1965), Sharma and Shastry (1965, 1972), Tateoka (1963), Oka (1988) and Vaughan (1989). He then proposed his own scheme applying the section and series categories used by Sharma and Shastry (1965). In 2001, Lu et al. modified this classification by combining O. meyeriana with O. granulata and reviving the species status of O. malampuzhaensis and O. schweinfurthiana. Vaughan et al. (2003) also revised the species list, synonymizing O. nivara with O. rufipogon and recognizing O. malampuzhaensis as a distinct species. The most current taxonomic systems of Lu et al. (2001) and Vaughan et al. (2003) are presented in Table 1, together with the classification scheme used in the taxonomic database of the Germplasm Resources Information Network (GRIN Taxonomy) (USDA, ARS, National Genetic Resources Program 2012). GRIN Taxonomy is an online system that provides a standard reference for the classification and nomenclature of economically important plants and their wild and weedy relatives. It has been widely adopted by the genebank community. Taxonomic information in this database is derived from standard botanical literature, recent taxonomic revisions and specialist consultation (USDA, ARS, National Genetic Resources Program 2012). Table 1. Species of genus Oryza as classified by Lu et al. (2001), Vaughan et al. (2003) and the Germplasm Resources Information Network (USDA, ARS, National Genetic Resources Program 2012). Genome Lu et al. (2001) Vaughan et al. (2003) GRIN (2012) Distribution group I. Section Padia (Zoll. & Moritzi) I. Section Padia (Zoll. & Moritzi) Baill. Baill. 1. Series Meyerianae Sharma & O. granulata complex 1. Series Meyerianae Sharma Shastry & Shastry O. granulata Nees & Arn ex O. granulata Nees & Arn ex O. meyeriana (Zoll. & GG South and Southeast Wall. (syn: O. meyeriana ) Wall. Moritzi) Baill. var. granulata Asia (Nees & Arn ex Wall.) Duist. O. meyeriana (Zoll. & Moritzi) O. meyeriana var. meyeriana GG Southeast Asia Baill. (syn: O. neocaledonica) (Zoll. & Moritzi) Baill. O. meyeriana (Zoll. & GG Andaman and Moritzi) Baill. var. Nicobar Isl. inandamanica (J.L. Ellis) Veldkamp General IntroductionGeneral O. neocaledonica Morat O. neocaledonica Morat GG New Caledonia 2. Series Ridleyanae Sharma & O. ridleyi complex 2. Series Ridleyanae Sharma & Shastry Shastry O. longiglumis Jansen O. longiglumis Jansen O. longiglumis Jansen HHJJ New Guinea | General Intro General 9 duction | 9 Table 1. (Continued) Species of genus Oryza as classified by Lu et al. (2001), Vaughan et al. (2003) and the Germplasm Resources 10 Information Network (USDA, ARS, National Genetic Resources Program 2012). | Chapter 1 Chapter Genome Lu et al. (2001) Vaughan et al. (2003) GRIN (2012) Distribution group O. ridleyi Hook.f. O. ridleyi Hook.f. O. ridleyi Hook.f. HHJJ South Asia 3. Series Schlechterianae Sharma 3. Series Schlechterianae & Shastry Sharma & Shastry O. schlechteri Pilger O. schlechteri Pilger O. schlechteri Pilger Unknown New Guinea II. Section Brachyantha B.R.Lu II. Section Brachyantha B.R.Lu 4. Series Brachyanthae Sharma & 4. Series Brachyanthae Sharma Shastry & Shastry O. brachyantha Chev. & O. brachyantha Chev. & Roehr. O. brachyantha Chev. & FF Africa Roehr. Roehr. III. Section Oryza III. Section Oryza 5. Series Sativae Sharma & O. sativa complex 5. Series Oryza Shastry O. barthii A.Chev. O. barthii A.Chev. O. barthii A.Chev. AA Africa O. glaberrima Steud. O. glaberrima Steud. O. glaberrima Steud. AA West Africa Table 1. (Continued) Species of genus Oryza as classified by Lu et al. (2001), Vaughan et al. (2003) and the Germplasm Resources Information Network (USDA, ARS, National Genetic Resources Program 2012). Genome Lu et al. (2001) Vaughan et al. (2003) GRIN (2012) Distribution group O. glumaepatula Steud. O. glumaepatula Steud. O. glumipatula Steud. AA South and Central America O. longistaminata Chev. & O. longistaminata Chev. & O. longistaminata Chev. & AA Africa Roehr. Roehr. Roehr. O. meridionalis N.Q.Ng O. meridionalis N.Q.Ng O. meridionalis N.Q.Ng AA New Guinea and tropical Australia O. sativa L. O. sativa L. O. sativa L. AA Cultivated worldwide O. rufipogon Griff. O. rufipogon Griff. O. rufipogon Griff. AA Tropical and (syn: O. nivara) subtropical Asia, tropical Australia O. nivara Sharma & Shastry O. nivara Sharma & Shastry AA Tropical and subtropical Asia General IntroductionGeneral 6. Series Latifoliae Sharma & O. officinalis complex 6. Series Latifoliae Sharma & Shastry Shastry O. alta Swallen O. alta Swallen O. alta Swallen CCDD South and Central America | General Intro General 11 duction | 11 Table 1. (Continued) Species of genus Oryza as classified by Lu et al. (2001), Vaughan et al. (2003) and the Germplasm Resources 12 Information Network (USDA, ARS, National Genetic Resources Program 2012). | Chapter 1 Chapter Genome Lu et al. (2001) Vaughan et al. (2003) GRIN (2012) Distribution group O. eichingeri Peter O. eichingeri Peter O. eichingeri Peter CC South Asia and East Africa O. grandiglumis (Döll) O. grandiglumis (Döll) O. grandiglumis (Döll) CCDD South and Central Prodoehl. Prodoehl. Prodoehl. America O. latifolia Desv. O. latifolia Desv. O. latifolia Desv. CCDD South and Central America O. malampuzhaensis Krish. & O. malampuzhaensis Krish. & O. malampuzhaensis Krish. BBCC India Chandr. Chandr. & Chandr. O. minuta J.Presl & C.Presl O. minuta J.Presl & C.Presl O. minuta J.Presl & C.Presl BBCC Philippines and Papua New Guinea O. officinalis Wall. ex Watt O. officinalis Wall. ex Watt O. officinalis Wall. ex Watt CC Tropical and subtropical Asia, tropical Australia O. rhizomatis Vaughan O. rhizomatis Vaughan O. rhizomatis Vaughan CC Sri Lanka O. punctata Kotschy ex Steud. O. punctata Kotschy ex Steud. O. punctata Kotschy ex BB, BBCC Africa (syn: O. schweinfurthiana) Steud. O. schweinfurthiana Prodoehl O. schweinfurthiana BBCC Africa Prodoehl Table 1. (Continued) Species of genus Oryza as classified by Lu et al. (2001), Vaughan et al. (2003) and the Germplasm Resources Information Network (USDA, ARS, National Genetic Resources Program 2012). Genome Lu
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