Morphological and Molecular Assessment of Beta maritima Populations over an Environmental Gradient: A Comparative Analysis Utilizing ISSR and SRAP Markers

Sea beet (Beta vulgaris subsp. maritima (L.) Arcang.) is the primary gene pool of breeding programs for sugar beet and cultivated beets (B. vulgaris subsp. vulgaris L.). It mainly inhabits the Mediterranean region, where anthropogenic activities and climate change threaten this globally significant genetic resource. The present study aims to (i) assess the phenotypic and molecular diversity within the sea beet across its geographic gradients, including both wild and crop–weed populations, and (ii) explore the correlations between the phenotypic and molecular diversity and the environmental factors. The morphological diversity of seven populations representing their geographic range in Egypt was studied. This research used 59 quantitative and 39 qualitative traits to assess the phenotypic plasticity within sea beet. UPGMA cluster analysis grouped these populations into two clusters. Canonical correspondence analysis (CCA) evaluated relationships between variation in morphological traits among populations and 18 soil and climatic parameters. Further molecular investigation was conducted using ISSR and SRAP markers. The study found a higher polymorphism rate with SRAP markers compared to ISSR markers. Diverse molecular diversity indices were observed with the two markers (ISSR, SRAP), revealing molecular differentiation among populations. Mantel and partial Mantel analyses showed that environmental factors rather than molecular ones mainly influence morphological divergence. The suitability of the markers used for assessing the molecular profiles of Beta populations was evaluated using six polymorphism indices for each marker. Overall, the current study suggests that the classical coastal–wild prostrate hairy (var. pilosa) and inland crop–weed erect glabrous (var. glabra) sea beet forms in Egypt represent an environmentally induced phenotypic gradient rather than distinct genetic lineages. However, as this clear phenotypic divergence did not correlate with the molecular variation detected by the surveyed ISSR and SRAP loci, further testing with high-density, genome-wide markers remains necessary to definitively confirm the absence of subtle genetic differentiation.