Phenotypic diversity, core collections and trait associations in Coffea stenophylla based on agro-morphological markers

Abstract

Coffea stenophylla is a wild coffee species of growing interest in West Africa due to its resilience and potential for crop improvement. Understanding its phenotypic diversity and trait relationships is critical for conservation and breeding programmes. This study assessed phenotypic diversity, generated a representative core collection and determined trait associations in C. stenophylla accessions using agro-morphological markers. A total of 179 accessions were assessed across 21 morphological traits. Principal component analysis (PCA), factor analysis (FA) and Unweighted Pair Group Method with Arithmetic Mean (UPGMA) dendrogram were used to unravel variability and clustering patterns. Core Hunter 3 software was applied to select the core subsets. Traits that discriminated the most between the genotypes included: leaf length, leaf width, leaf area, circumference, plant height, stem diameter, length of longest primary branch, angle of primary branches, length of primary branch, pair number of plagiotropic branch per plant, number of orthotropic shoot internode, number of internodes on longest primary branch, internode length of plagiotropic branch and internode length of orthotropic stem. FA had seven factors, which explained 63.35% of the total genetic variation in the dependence structure. A putative core set of 18 accessions was identified. The contributions by the communalities were fairly high, with nine traits exhibiting higher communality over the specificity (12 traits). Factor 5 had the highest negative associations (15 traits); whereas factor 6 had the least (9 traits). This study revealed wide genetic diversity in coffee genotypes grown in Sierra Leone, which could be used to breed high yielding genotypes and other desired traits such as resistance to local pests and diseases.