Genetic Characterization and nutritional analysis of Eastern and South African Cleome Gynandra (spider plant) accessions Ann K. Munene BSc. Biotechnology (University of Nairobi) A thesis submitted in partial fulfillment of the requirement for the award of Master of Science Degree in Plant Breeding and Biotechnology Department of Plant Science and Crop Protection, College of Agriculture and Veterinary Sciences University of Nairobi 2017 DECLARATION This thesis is my original work and it has not been presented for a degree in any other university. Ann Kangai Munene Signed………………………………….. Date……………………… This thesis is submitted for examination with our approval as the University supervisors: Dr. Felister Nzuve Department of Plant Science and Crop Protection University of Nairobi (UoN) P.O. Box 29053 – 00625 Nairobi, Kenya Signed……………………………………. Date………………………………… Dr. Jane L. Ambuko Department of Plant Science and Crop Protection University of Nairobi (UoN) P.O. Box 29053 – 00625 Nairobi, Kenya Signed…………………………………. Date………………………………… Dr. Damaris Achieng Odeny ICRISAT – NAIROBI P.O Box 39063, NAIROBI Signed…………………………………. Date……………………… ii DEDICATION This thesis is dedicated to my family for their unwavering all rounded support, true love and patience during my study years. iii ACKNOWLEDGEMENTS I am highly indebted to Almighty God, for making everything a success in my life. My deep gratitude goes to the University of Nairobi for offering me an opportunity to pursue my postgraduate studies. Special thanks to the National Commission for Science, Technology and Innovation (NACOSTI) and the National Research Foundation (NRF) for sponsoring this research study. I appreciate the gene banks of Kenya and South Africa for providing the study accessions. I greatly acknowledge my supervisors Dr. Felister Nzuve, Dr. Jane L. Ambuko and Dr. Damaris A. Odeny of ICRISAT for their constant advice, guidance, encouragement and proof reading of my thesis throughout my study period. Special Thanks to Jescar and the staff Biochemistry and Food Science and Technology (FST) department, JKUAT, for their assistance during my nutrition analysis. I express my deepest gratitude to my hubby Emmanuel, my strong pillar for his unlimited support in every aspect, instilling a sense of inspiration and hope in my work. Sincerely, you gave me additional strength to work towards achieving this dream. Not forgetting my doting daughters, Janelle, Jewel and Jenny my stars, that brightened my path throughout the study period. To my colleagues and friends for standing with me, I thank you. iv ABBREVIATIONS ALVs African leafy vegetables ANOVA Analysis of variance DARwin Dissimilarity analysis representation for windows FAO Food and Agriculture Organization of the United Nations GBK Genebank of Kenya GDP Gross domestic product GMATo Genome wide Microsatellite Analyzing Tool HCD Horticultural Crops Directorate ITC International Trade Centre JKUAT Jomo Kenyatta university of Agriculture and Technology KARI Kenya Agricultural Research Institute KEPHIS Kenya plant health inspectorate service MOA Ministry of Agriculture MT Metric tonnes NCBI National Center for Biotechnology Information PCR Polymerized chain reaction SPAD Soil Plant Analysis Development SSRs Simple sequence repeats UPGMA Unweighted pair-group method using arithmetic averages v TABLE OF CONTENTS DECLARATION ............................................................................................................................ ii DEDICATION ............................................................................................................................... iii ACKNOWLEDGEMENTS ........................................................................................................... iv ABBREVIATIONS ........................................................................................................................ v TABLE OF CONTENTS ............................................................................................................... vi LIST OF TABLES .......................................................................................................................... x LIST OF FIGURES ....................................................................................................................... xi LIST OF APPENDICES ............................................................................................................... xii ABSTRACT ................................................................................................................................. xiii CHAPTER 1 ................................................................................................................................... 1 INTRODUCTION .......................................................................................................................... 1 1.1 Background information ................................................................................................................... 1 1.2 Problem statement ............................................................................................................................. 3 1.3 Justification ....................................................................................................................................... 4 1.4 Objectives ......................................................................................................................................... 5 1.4.1 Specific objectives .............................................................................................................. 6 1.4.2 Hypothesis .............................................................................................................................. 6 LITERATURE REVIEW ............................................................................................................... 7 2.1 Botany of spider plant ....................................................................................................................... 7 2.2 Origin and distribution ...................................................................................................................... 8 2.3 Ecologicalrequirement ...................................................................................................................... 8 2.4 Cultivation and utilization ................................................................................................................. 9 2.5 Constrains to spider plant production in Kenya and South Africa ..................................................... 9 2.6 Germplasm collection ..................................................................................................................... 11 2.7 Characterization of spider plant ...................................................................................................... 12 vi 2.8 Phenotypic variation ....................................................................................................................... 14 2.8.1 Analysis of morphological and agronomic variation in cleome gynandra ............................... 16 2.8.2 Measures of genetic diversity ................................................................................................... 22 2.8. 3 Heritability of nutrition and yield related traits ....................................................................... 23 2.9 Nutrition composition ..................................................................................................................... 24 2.9.1 Genetic diversity and its effect on the quality of vegetables..................................................... 27 2.10 Genotypic characterization of Simple sequence repeats. ............................................................... 27 CHAPTER 3 ................................................................................................................................. 30 PHENOTYPIC CHARACTERIZATION OF EAST AND SOUTH AFRICAN CLEOME GYNANDRA ACCESSIONS ........................................................................................................ 30 3.1 Abstract ........................................................................................................................................... 30 3.2 Introduction ..................................................................................................................................... 31 3.3 Materials and methods .................................................................................................................... 33 3.3.1 Germplasm assembly and collection ........................................................................................ 33 3.3.2 Study site.................................................................................................................................. 37 3.3.3 Experimental design and crop husbandry ................................................................................. 37 3.4 Data collection ................................................................................................................................ 39 3.4.1 Qualitative traits ....................................................................................................................... 39 3.4.2 Quantitative traits ..................................................................................................................... 40 3.4.3 Phenotypic characterization ....................................................................................................