PHENOTYPIC CHARACTERIZATION AND MOLECULAR STUDIES OF KENYAN PASSION FRUI ) ' ( Passiflora edulis ( Sims » GENOTYPES BASED ON SSR MARKERS

Passion fruit (Passiflora edulis) was introduced to Kenya in the 1920s by European farmers. The fruit is a significant income earner for the country from both local and international markets. There are increased research activities on variety improvement and development of new varieties with the hall marker of this research being the KPFs 4, 11, 12 by KALRO. The KPFs are hybrids developed through natural crosses of the coastal yellow varieties and purple variety. Despite these gains in breeding, there is little information of both phenotypic and molecular variability of these new cultivars as well as the existing ones. The present study aimed at evaluating the molecular and phenotypic variation in the hybrid and parent varieties. Phenotypic characterization was done by targeting 7 morpho-agronomic descriptors with three biological replicates. Analysis was done using MINITAB 16 software, for description principle components and construction of a dendrogram using the Eucledian distance tool. The first principal component alone accounted for 51.3% variance, while the first two components accounted for cumulative variance of 74.3%. Molecular characterization was done using SSR markers. Eleven (11) markers were polymorphic while one marker; PE 20 was monomorphic. Calculation of genetic distance, PIC, allele number as well as gene diversity was done using Powermarker® version 3.25 while phylogeny reconstruction was done using DARWIN version 6. On the other hand, AMOV A was calculated using GenAlex 6.502. The PIC ranged from 0.2929 (PE 04) to 0.6179 (PE 90) with a mean of 0.3909 indicating that marker PE 90 was highly informative and other markers were reasonably informative. The mean PIC of 0.3909 indicated that generally, all the 11 polymorphic markers were informative and as such can be utilized for further analysis of Passiflora edulis genome. The dissimilarity matrix indicated that KRC-2 and KRP-2 had the highest level of dissimilarity, confirming the known molecular variation that exists between the yellow and purple varieties where the respective genotypes belong to. Several genotypes had a dissimilarity of 0% and indication that they shared closer ancestry compared to other genotypes. The phylogenetic tree discriminated the samples into three main clusters with several sub-clusters carrying different fruit populations, indicating genetic relatedness among members of the same population. From the phylogenetic tree, genetic variability was highest between genotype KRC-2 and KRP-4 which are coastal and purple varieties respectively. This corroborates the findings of dissimilarity matrix where they had a dissimilarity of 76%. The AMOVA indicated intra-population variation of 91 % while inter-population variation was 9%. From the results, Molecular and phenotypic characterization proved to be useful tools for discrimination of various genotypes of Passiflora edulis. The results from this study will enable better detection and management of genetic variability that could hinder adoption of the KPF as an alternative crop for the semi-arid agro-ecologies. % °C III ADP AFLP AMOVA ANOVA AP-PCR Bp CAPS CTAB DAF DNA EDTA EST EU FAO g GoK Ha HCDA HDC ISSR KALRO KAPAP Kg KHCP KPF mM MoA NAFIS NCBI PCA PCR QTL RAPD RFLP RNA RPM SNP SSR STS TBE TE XI ABBREVIATIONS AND ACRONYMS Percent Degree Celcius Micro litre Adenosine Diphosphate Amplified Fragment length Polymorphism Analysis of Molecular Variance Analysis of Variance Arbitrarily primed Polymerase Chain Reaction Base pair Cleaved Amplified Polymorphic Sequence Cetyltrimethylammonium bromide DNA Amplification Fingerprinting Deoxyribonucleic Acid Ethylenediaminetetraacetic acid Expressed Sequence Tag European Union Food and Agricultural Organization Gram Government of Kenya Hectare Horticultural Crops Development Authority Horticulture Development Centre Inter Simple Sequence Repeats Kenya Agricultural and Livestock Research Organization Kenya Agricultural Productivity and Agribusiness Project. Kilogram Kenya Horticultural Competitiveness Program Kenya Passion Fruit Milimolar Ministry of Agriculture National Farmers Information Services National Center for Biotechnology Information Principal Component Analysis Polymerase Chain Reaction Quantitative Trait Loci Random Amplified Polymorphic DNA Restriction Fragment Length Polymorphism Ribonucleic Acid Rotation per Minute Single Nucleotide Polymorphism Simple Sequence Repeats Sequence-Tagged Sites Tris-Borate-EDTA Tris-EDTA CHAPTER ONE INTRODUCTION 1.1 Background information Kenya relies mainly on agriculture, which accounts for 24% of the GDP and hence invests in this sector (MoA, 2010). According to OoK (2007), approximately 5 million smallholders in rural areas rely on farming as a source of livelihood; through production of food, cash and horticultural crops both for subsistence and commercial purposes. Kenyan horticultural exports sustain the livelihoods of approximately 1.20 million people and are an important source of foreign exchange. The horticultural exports account for 14% of total export earnings (HCDA, 2011). In 2010, Kenya earned Kshs. 77.70 billion from horticultural exports with passion fruit contributing Kshs. 1.9 billion which translated to 1.19% of the domestic value of the total horticultural produce (Republic of Kenya, 2010; HCDA, 2011). Approximately 80% of horticultural producers are small holder farmers, with a large portion (96%) of horticultural produce being consumed locally, thus sold in the local markets (Namu, 2007; Kibet et al., 20 I Ia). In 2010, passion fruit was ranked third (8%) after avocado (62%) and mango (26%) in Kenya in terms of foreign exchange earnings for the country (HCDA, 2011). Kenya is considered the market leader of fruit juice exports in East Africa and is also listed among the large producers of passion fruit globally (KHCP, 2011). The major regional market for passion fruit produced'