Pepper is among the most widely grown and consumed spice and one of the most important vegetable crops in Eritrea as well as the world. In Eritrea it is an ingredient in almost all traditional dishes of the country, thus it is characterized by its high demand throughout the year. Locally produced pepper is of low quality and low productivity which necessitates intervention for improving it. Thus this research aimed: To study the current status and opportunities of pepper production in Eritrea,the morphological and molecular characterization of locally available germ plasm and its relatedness to selected reference germ plasm from other countries and to evaluate the breeding potential of a local variety crossed with exotic varieties. Current status of pepper production in Eritrea was assessed using a participatory rural appraisal method,collection of secondary data, key informants interviews, focus group discussions and formal household survey The major constraints identified were unavailability of improved and quality seed, inputs and services, insect pests and diseases, small acreage and discouraging land tenure system, improper marketing chain, poor extension service and shortage of water.Opportunities were identified as availability of vast lands, favorable climate, domestic and export markets and high willingness of farmers to grow pepper. During the survey a total of 129 seed samples were collected from farmers and institutions for diversity studies. The collected germ plasm was evaluated at two sites;Hamelmalo and Asmaralocated in two different agro-climatic regions of Eritrea. A randomized complete block design was used in each evaluation. Data was collected on 39 quantitative and qualitative characters. Data were subjected to Analysis of variance, Principal Component Analysis, Principal Coordinate Analysis and Hierarchical clustering with Euclidean distance. Phonological attributes and fruit characteristics (number of fruits per plant, fruit weight, fruit wall thickness, calyx annular constriction and Fruit shape at both pedicel attachment and blossom end), were found to contribute most of the variation. Genotype and location had significant effect on majority of the characteristics evaluated; but the interaction between them was not.The highest Coefficient of Variation was related to fruit characteristics. xxBased on the combined data from the two sites the collections were grouped into four clusters. Cluster one was characterized by intermediate to erect growth habit, presence of calyx annular constriction, elongate fruit shape, mainly light red or dark red but sometimes orange red, light brown and brown mature fruit colourand neck at base of fruit was present or absent. Fruits of this group were relatively short, medium in fruit width and pericarp thickness and an average fruit weight of 15.06 g, number of fruits/plant of 45.28 and yield/plant of 419.68 g. Cluster two was characterized by mainly erect with intermediate growth habit, calyx annular constriction was rarely present, fruit shape was elongate, mature fruit colourwas usually light red but also dark red, brown and rarely light brown and neck at base of fruit was present or absent. Fruits were intermediate in length, slim andrelatively thin pericarp with an average fruit weight of 10.56g, number of fruits/plant of 62.63 and yield/plant 392.48. Cluster four was characterized by Erect or intermediate growth habit, calyx annular constriction was present but some times absent, triangular or elongate fruit shape, light red mature fruit colour, sometimes dark red and rarely brown and neck at base of fruit was usually absent but sometimes mixed. Fruits in this group were intermediate in length, wide and relatively thick pericarp withan average fruit weight of 25.46g, number of fruits/plant of 39.24 and yield/plant of 637.44g.A total of150 seed collectionwere evaluated using 28 SSR markers. The 28 polymorphic markers revealed existence of high genetic variation among Eritrea genotypes and that germplasmmaintained in situ by farmers are heterogeneous. Atotal of 352 alleleswere obtainedwith an average of 13 alleles per marker, Mean Polymorphic Information Content was0.62, mean Genetic Diversity was 0.65 and mean Observed Heterozygosity was0.4. Alarge number of rare alleleswere also observed. A PCoA analysis, neighbour joining clustering and the model based clustering (Structure) classified the collectionsinto 3 groups. However, in the model based clustering; increasing thenumber of populations to 4 (K=4 ) moved all the non-Eritrean genotypes in a separate cluster. This suggests thatthe Eritrean populationsare specificsince thecollections studiedhad a large number of private alleles.

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