CHARACTERISATION OF CHILLI PEPPER (Capsicum annuum L.) ACCESSIONS IN NORTHERN REGION OF GHANA USING AGRO-MORPHOLOGICAL TRAITS AND MOLECULAR MARKERS

Abstract

Ghana ranks among the top five pepper producers in Africa; however, there is inadequate research regarding farmer practices, morphological and genetic enhancement initiatives for this important crop. Understanding of variabilities in pepper (Capsicum species) will contribute to effective breeding efforts, especially in northern Ghana, where more than 60% of smallholder farmer income is from pepper. The focus of this study was to assess farmers’ knowledge and management practices in pepper cultivation, and to evaluate morphological and genetic variations among Capsicum annuum landraces cultivated in Northern region of Ghana. A cross-sectional survey was carried out using structured questionnaires and field observations to evaluate farmers’ knowledge and Capsicum annuum management practices; morphological characters at the seedling, vegetative, inflorescence and fruiting stages were evaluated using standard descriptors outline by IPGRI, AVRDC & CATIE under rainfed and irrigation conditions. Distinct genetic populations within a collection of 40 Capsicum annuum accessions using 24 simple sequence repeat (SSR) markers. The average acres allocated to pepper farming is 1.04 acres with majority of the farmers using farmer-saved seeds (67.3%). Generally, the farmer rating of improved pepper seeds was low, indicating that the local pepper varieties used in the study were comparable to the improved pepper varieties. A strong positive correlation was detected between days to 50% flowering and days to 50% fruiting for both the rainfed (r = 0.87) and irrigated (r = 0.73) conditions. In general, high performance of the genotypes at the vegetative and inflorescence stages was observed in the dry season, with low fruiting performance (number of fruits per plant, fresh weight, and dry weight). Multivariate analysis revealed that 60.54% (rainy season) and 54.63% (dry season) variations were explained by the first three principal components, respectively. Three main clusters were identified, with linear relationships and no distinct separation pattern based on the sample source. The SSR markers exhibited a polymorphic information content (PIC) below 0.50, with an average value of 0.11. A modest level of genetic diversity among the accessions (HE = 0.063) was observed, with marked genetic differentiation (FST = 0.57). Employing the admixture model based population structure analysis, set at a threshold of 60%, 29 pure genotypes from the 40 accessions used were identified. A phylogenetic analysis categorized the 40 Capsicum accessions into three primary clusters: Cluster I and Cluster II contained two individuals from the Capsicum annuum accession, while Cluster III was further subdivided into two subclusters. Overall, the study demonstrates that pepper production in northern Ghana is dominated by farmer-saved landraces with modest but structured genetic diversity, underscoring the need for location-specific management strategies and targeted breeding programmes to sustainably improve productivity and resilience.