Genetic Diversity Analysis and Core Marker Identification of Shanlan Upland Rice Landraces Using Highly Informative InDel Markers

Shanlan upland rice is a unique genetic resource from the mountainous regions of Hainan, China, yet its genetic diversity and agronomic potential remain poorly characterized. This study systematically evaluated 114 Shanlan upland rice landraces using phenotypic assessment and 38 genome-wide Insertion/Deletion (InDel) markers. Significant phenotypic variability was observed in key agronomic traits, including plant height, tiller number, and yield components. The molecular analysis revealed a moderate level of genetic diversity (average PIC = 0.43) and consistently grouped the landraces into three distinct genetic subpopulations. To facilitate efficient germplasm management, we developed a DNA fingerprinting system using a reduced set of 19 core InDel markers, which was integrated with a phenotypic QR code database. Furthermore, a network-based strategy identified a core collection of 54 accessions, streamlining the resource for future breeding and conservation efforts. These findings provide a robust molecular framework for the conservation and genetic improvement of Shanlan upland rice.