Random amplified polymorphic DNA-based assessment of genetic variation in natural and cultivated allspice (Pimenta dioica (L.) Merr.) populations in Guatemala
Abstract
The fruit of the allspice tree (Pimenta dioica (L.) Merr.) is a valuable non-timber forest product traded for its flavour, oils and secondary metabolites. Intense selection pressure from traditional harvesting methods has favoured low-height, high-yield phenotypes, potentially impacting genetic diversity. Although phenotypic variations have been observed, no baseline molecular genetic assessments have been conducted in Guatemala to evaluate the impact of these practices. This study assessed the genetic diversity and structure of natural and cultivated populations of allspice in Guatemala using molecular markers. Seven populations from northern Guatemala, representing a range of ecological conditions, were analysed using 15 random amplified polymorphic DNA (RAPD) primers. A total of 126 amplified fragments, with 88.1 % polymorphism, were obtained. The RAPD markers showed high levels of polymorphism (Polymorphic information content (PIC) = 0.331), good discriminatory power (D = 0.907) and reasonable resolving power (Rp = 3.976). Estimates of genetic diversity, based on Nei’s gene diversity (He) and Shannon’s diversity index (H), were slightly higher in natural populations (He = 0.24–0.28; H = 0.35–0.40) than in cultivated populations (He = 0.17–0.22; H = 0.23–0.31), suggesting that natural populations maintain greater genetic variability, due to lower levels of human intervention. Population structuring methods, unweighted pair group method with arithmetic mean (UPGMA), discriminant analysis of principal components (DAPC), sparse non-negative matrix factorisation (sNMF)) revealed genetic similarity among most populations, with San Cristobal being the exception, showing significant differentiation (p < 0.05). These findings highlight the importance of implementing integrated conservation strategies (in situ, circa situ and ex situ methods), as well as sustainable management of naturally regenerated and cultivated populations, to preserve the Guatemalan gene pool of P. dioica.