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Characterization of Novel Rice Germplasm from West CORE Metadata, citation and similar papers at core.ac.uk Provided by Texas A&M Repository CHARACTERIZATION OF NOVEL RICE GERMPLASM FROM WEST AFRICA AND GENETIC MARKER ASSOCIATIONS WITH RICE COOKING QUALITY A Dissertation by KARIM TRAORE Submitted to the Office of Graduate Studies of Texas A&M University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY August 2005 Major Subject: Plant Breeding CHARACTERIZATION OF NOVEL RICE GERMPLASM FROM WEST AFRICA AND GENETIC MARKER ASSOCIATIONS WITH RICE COOKING QUALITY A Dissertation by KARIM TRAORE Submitted to the Office of Graduate Studies of Texas A&M University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Approved by: Co-Chairs of Committee, Anna M. McClung William L. Rooney Committee Members, Lloyd W. Rooney Edwin C. Price Robert G. Fjellstrom Head of Department, C.Wayne Smith August 2005 Major Subject: Plant Breeding iii ABSTRACT Characterization of Novel Rice Germplasm from West Africa and Genetic Marker Associations with Rice Cooking Quality. (August 2005) Karim Traore, B.S., Institut Polytechnique Rural de Katibougou; M.S., University of Nebraska-Lincoln Co-Chairs of Advisory Committee: Dr. Anna M. McClung Dr. William L. Rooney Genetic resource enhancement is the foundation of any good breeding program. Landraces from West Africa, interspecifics between Oryza sativa and Oryza glaberrima and improved lines from the West African Rice Development Association and other research centers were introduced to the Beaumont Rice Research center for in situ evaluation and characterization. Beside the introduction of seeds, milled samples were also introduced for grain chemistry analysis. Field evaluation combined with physico- chemical and molecular characterization revealed unique characteristics among African germplasm. New rice for Africa (NERICA) lines performed well in the USA environment. Varieties like Nerica 2, Nerica 3, Nerica 4, and Nerica 5 need more attention because of their superior performance in yield and grain quality. Landraces did not perform well due to their height and late maturity and their resulting problems with lodging. The rapid visco analyzer RVA profiles showed that the cultivar Jaya has unusually strong paste viscosity features. Comparing West Africa samples grown in Cote d’Ivoire with those grown in Texas, parameters like AA, ASV, Hot, Cool, and CT were not stongly affected by the environment. According to the Stbk value, cultivars iv grown in Cote d’Ivoire will cook softer than when they were grown in Texas. The lack of the environmental effect is somewhat surprising considering the difference in latitude, soil types, weather patterns, and management practices between the two locations. Apparent amylose is a key element to characterize a rice cultivar; however certain varieties like Cocodrie and Dixiebelle have similar apparent amylose content but dramatically different functional qualities. A population derived from Cocodrie and Dixiebelle was developed for genotypic and phenotypic analysis of grain chemistry traits that affect functionality. It was concluded that the amount of soluble amylose in the grain had a significant effect on flour pasting properties, even when total apparent amylose content did not vary. Marker association studies revealed that the Waxy microsatellite and the Waxy exon 10 SNP markers were associated with soluble amylose content and RVA characteristics. These markers will speed up the development of new rice cultivars with desirable quality characteristics in West Africa and in the USA. v DEDICATION To my father vi ACKNOWLEDGMENTS I wish to express my sincere gratitude to Dr. Anna M. McClung, my co-chair, for her assistance and sharing with me her numerous experiences. Sincere thanks to Dr. William L. Rooney, my co-chair, for his assistance and daily advice. I will never forget your help in solving the administrative protocols at the university. Sincere thanks to Dr. Edwin Price, member of my committee, who started helping me even before I came to Texas A&M University. I will never forget your interest in all my academic and private life issues. I am thankful to Dr. Lloyd W. Rooney, member, with whom I used to work in the national program of Mali. I will always need your constructive adviice. Many thanks to Dr. Robert G. Fjellstrom, member, who helped me to understand basic knowledge in biotechnology. I am greatly indebted to the Rockefeller Foundation and the West Africa Rice Development Association (WARDA) for providing funds for my study. Special mention is hereby made of Soil and Crop Sciences and USDA-ARS staff at Beaumont for all their support. Many thanks to the International Agriculture program’s staff at Texas A&M for their help and assistance. I am thankful to Ms. Cook and her staff at the sponsored student’s office for their daily help and assistance. Many thanks to the international student office for all the administrative work. I am grateful to all my fellow graduate students at the Heep center for sharing with me many ideas during my stay in the USA. For their help and patience, I would like to thanks my parents in Mali. Special thanks to my wife, Aminata Traore Guindo, Assitan and Fatima, my daughters, and Abdoulaye, my son. I am proud of you. vii TABLE OF CONTENTS Page ABSTRACT................................................................................................................. iii DEDICATION ............................................................................................................. v ACKNOWLEDGMENTS............................................................................................ vi TABLE OF CONTENTS............................................................................................. vii LIST OF FIGURES...................................................................................................... x LIST OF TABLES ....................................................................................................... xii 1. INTRODUCTION.................................................................................................... 1 2. LITERATURE REVIEW......................................................................................... 5 2.1. Rice in Africa ............................................................................................ 5 2.1.1. History of Oryza glaberrima in Africa ...................................... 5 2.1.2. History of Oryza sativa in Africa............................................... 6 2.1.3. Importance of Rice in Africa...................................................... 7 2.2. Rice Ecosystems in Africa ........................................................................ 12 2.2.1. Dryland Ecosystem .................................................................... 12 2.2.2. Lowland/Hydromorphic Ecosystem........................................... 13 2.2.3. Mangrove Swamps Ecosystem................................................... 14 2.2.4. Irrigated Ecosystem.................................................................... 14 2.2.5. Deepwater/Floating Rice Environment...................................... 15 2.3. Principal Constraints to Rice Cultivation in Africa .................................. 15 2.3.1. Water/Drought............................................................................ 16 2.3.2. Weeds ......................................................................................... 17 2.3.3. Blast Disease .............................................................................. 17 2.3.4. Insects......................................................................................... 18 2.3.5. Grain Quality.............................................................................. 20 2.4. Parameters Which Define Rice Grain Quality .......................................... 21 2.4.1. Rice Market Classes ................................................................... 21 2.4.2. Components of Quality .............................................................. 22 2.4.2.1. Hull and Bran Color .................................................... 22 2.4.2.2. Grain Dimensions, Weight and Uniformity ................ 22 viii Page 2.4.2.3. General Appearance .................................................... 22 2.4.2.4. Milling Yield............................................................... 23 2.4.2.5. Rice Cooking and Eating Quality................................ 24 2.4.2.6. Amylose Content......................................................... 24 2.4.2.7. Gel Consistency........................................................... 36 2.4.2.8. Gelatinization Temperature......................................... 37 2.4.2.9. Starch Pasting Properties............................................. 44 2.4.2.10. Correlation Studies Among Starch Properties .......... 51 2.4.2.11. Aroma in Cooked Rice.............................................. 54 2.4.2.12. Protein ....................................................................... 56 2.4.2.13. Lipids......................................................................... 59 3. MATERIALS AND METHODS............................................................................. 63 3.1. Origin of the Experimental Material ......................................................... 63 3.2. Description of the Experimental Field Sites ............................................. 65 3.2.1. Beaumont, Texas.......................................................................
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