Phenotypic Selection, Genetic Variation, and Genome-Wide SNP Fingerprinting of Typhoon-Surviving Candidate Individuals in Casuarina equisetifolia

Casuarina equisetifolia L. is a key pioneer tree species for coastal shelterbelt plantations in tropical and subtropical regions. However, long-term reliance on a limited number of superior clones has narrowed its genetic base and reduced stress resistance, which necessitates the selection of elite individuals and the construction of molecular identities to support precise germplasm identification. In this study, 108 ten-year-old half-sib families from 23 provenances were evaluated for four traits: tree height (H), diameter at breast height (DBH), volume (V), and wind-throw resistance grade (WTRG). Highly significant variation was detected among blocks, families, and block-by-family interactions for all traits (p < 0.001). Phenotypic and genotypic coefficients of variation ranged from 47.52–81.55% and 9.43–14.89%, respectively. Using combined selection, 29 elite individuals were identified, achieving genetic gains of 6.02%, 11.30%, 34.44%, and 3.84% for H, DBH, V, and WTRG, respectively. Whole-genome resequencing of these 29 individuals generated high-quality data, yielding 3,533,880 high-confidence SNP loci after initial filtering. After stringent quality control, 379 core SNP markers were retained, with a mean polymorphic information content (PIC) of 0.366 and a minor allele frequency (MAF) of 0.420, indicating their potential utility for individual discrimination. Based on these core SNPs, a DNA fingerprint database was constructed and integrated with QR code technology to create digital identity tags for each elite individual. Our results indicate that the tested C. equisetifolia population harbors considerable genetic variation and exhibits potential for genetic improvement. The established SNP-based fingerprinting system, together with the QR-code-enabled digital tagging platform, provides technical support for precise identification and germplasm management of elite genotypes.