Shallot (Allium cepa L.) is a strategic horticultural commodity, facing considerable pressure from enhanced domestic demand and declining production in Indonesia. This research aimed to identify morphological traits, analyze genetic diversity, and identify the potential genotypes for promising parent selection. Shallot accessions totaled 57, evaluated for genetic diversity through 18 morphological traits and molecular analysis based on 17 inter-simple sequence repeat (ISSR) markers. Morphological characterization revealed broad diversity and grouped the bulb skin color into eight distinct colors, along with considerable variation in bulb diameter. The molecular analysis using 17 ISSR primers recognized the highest level of genetic diversity (91.70%). The analysis of molecular variance (AMOVA) showed most of the genetic variation (98%) appeared within populations, with a weak differentiation among populations (2%), which confirmed a high rate of gene flow among geographical regions. Based on phenotypic performance, the shallot accessions with the highest number of bulbs, heaviest bulb weight, and ideal bulb length were notably the promising parental genotypes. The optimal breeding strategy involves utilizing these high-yielding and genetically divergent accessions to optimize heterosis and enhance the adaptive stability in shallot. This research significantly contributes to optimizing the utilization of Indonesia’s local genetic resources to support national shallot seed security.
accessions, Allium cepa, gene flow, genetic diversity, ISSR markers, morphological traits
The highest level of morphological diversity within shallots (Allium cepa) supported in the identification of promising accessions. The ISSR marker analysis revealed the maximum genetic diversity among shallot accessions. However, the low genetic differentiation among the regions suggests the intensive gene flow across the geographical boundaries.