Leaf margin phenotype and the genetic diversity of collected pineapple germplasm: a validation of the P locus on Spiny/Pipe leaf phenotype

Pineapple ( Ananas comosus (L.) Merr.) is a commercially important tropical fruit, with global production exceeding 28 million metric tons. Breeding programs require the assessment of genetic diversity and trait-specific markers across diverse germplasms. This study evaluated 60 pineapple accessions, including cultivars, mutants, and breeding lines, using 20 SSR markers and investigated the relationship between leaf spine traits and the presence of the P locus. The SSR analysis revealed moderate genetic diversity, with an average of 2.65 alleles per locus and a mean polymorphism information content (PIC) of 0.70. Clustering analysis revealed distinct groupings based on genetic background. A strong negative correlation (rho = -0.848, p value < 2.2e-16) was observed between the presence of the P locus and the leaf spiny phenotype, supported by a significant Wilcoxon rank sum test ( p value = 7.667e-11), which suggested an inverse relationship. These results validate the P locus control of the spine/pipe leaf phenotype and demonstrate the utility of SSR markers and the P locus in marker-assisted selection, providing insights into the genetic control of spineless leaf traits in pineapple.