GENETIC VARIATION IN COFFEE ACCESSIONS IN KENYA AND INTROGRESSION FROM ROBUSTA TO ARABICA USING RANDOM AMPLIFIED POLYMORPHIC DNA AND MICROSATELLITES

Coffee provides one of the most widely drunk beverages in the world, and is a very important source of foreign exchange income for many countries. In kenya, coffee production has a significant contribution to Kenya‟s economy for decades, and a high proportion of the coffee produced is considered the best quality coffee in the world. In coffee, morphological parameters are very often used to discriminate the varieties and hybrids. However, this exercise has some challenges that include the perennial nature of the plant that requires at least 5-7 years for attaining reproductive maturity for evaluation of both vegetative and reproductive characters. Therefore it is critical to identify suitable markers which can identify cultivars/hybrids at early stage of plant growth and at the same time discriminate between different coffee genotypes to fasclitate selection process and thereby speed up the coffee breeding program.Two molecular marker systems, RAPD (Random Amplified Polymorphic DNA) and SSR (Simple Sequence Repeats) were employed for identification of genetic relationship of 24 coffee accessions and to test for gene introgression from Coffea canephora into Coffea arabica with the objective of providing important information for improvement and in situ/ex situ conservation of this species. The total number of bands, the distribution of bands across all species, polymorphic bands, speciesspecific bands and average number of bands per primer calculated. Genetic dissimilarities was estimated using Pearson dissimilarity. Cluster analysis was performed using Un-weighted Pair Group Method with Arithmetic Averages (UPGMA) using STATSTICA software version 8. A total of 79 bands were detected by 10 RAPD and 50 bands were detected by 13 SSR primers.The polymorphism detected by both markers ranged from 33% to 100% for SSR and 50% to 100% for RAPD with average polymorphism of 65% and 81% respectively. The genetic dissimilarity index among the genotypes ranged from 0.06 to 1 for both SSR and RAPD primers. In this study, UPGMA analysis for RAPD and SSR markers showed some similarities; the 24 coffee accessions clustered according to the three different species namely C. eugenioides, C. canephora (Robusta) and C. arabica (Arabica). Considering that the coffee genotypes evaluated in this study originated from diferent countries, the similarities (for both SSR and RAPD results) observed among Arabica genotypes, attests to the narrow genetic diversity among Arabica coffee.This study confirmed the low genetic diversity in Arabica coffee genotypes evaluated with average dissimilarity index of 0.5 . The study also widened the information on genetic diversity of coffee germplasm available for breeding programmes in Kenya since previous work was biased to commercial cultivars and donors of resistance to diseases . Of the thirteen SSR markers employed in this study, only three markers were able to detect introgressed Canephora DNA fragments present in arabica genome (Sat 254, Sat 240 and Sat 172). The percentage of introgressed Canephora DNAfragments ranged from 9.1 % to 27.3 %. The results demonstrated that RAPD were suitable for genetic diversity studies in coffee while SSR were suitable for gene introgression studies in coffee.