Decoding genetic diversity and biochemical relationships in southern Kerala’s traditional Mango varieties using comprehensive marker analysis

This study explored the genetic diversity and relatedness of 34 mango accessions using 34 SSR markers, which were highly polymorphic and informative. The number of alleles per locus ranged from 2 to 7, with an average of 2.85, comparable to previous studies. The average PIC value was 0.502, underscoring the markers' suitability for genetic diversity assessment. The heterozygosity value averaged 0.473, indicating substantial genetic variability among the accessions. Unique fingerprints for five accessions were identified using seven SSR loci, demonstrating the markers' effectiveness in generating distinct genetic profiles. Additionally, specific SSR markers were significantly associated with biochemical traits, including glutamate synthase, catalase and peroxidase activities, highlighting their potential in trait-linked marker-assisted selection (MAS). Minimal Marker software indicated that 12 marker sets could distinguish all accessions, enhancing genotyping efficiency. Genome-wide association analysis found significant correlations between biochemical traits and specific SSR markers, with glutamate synthase, catalase and peroxidase activities associated with multiple SSR markers. These findings highlight the potential of SSR markers in identifying genomic regions linked to critical biochemical traits, aiding marker-assisted selection and breeding for stress tolerance and fruit quality. Genetic structure analysis revealed seven distinct clusters among the accessions, supported by UPGMA and FCA analyses, indicating moderate genetic differentiation. Jaccard pairwise similarity coefficients showed modest genetic diversity, consistent with previous studies. The UPGMA dendrogram categorized the accessions into seven major clusters, providing insights into their genetic relationships. This research offers valuable information for the genetic identification, characterization and conservation of mango accessions, supporting germplasm management, breeding programs and phylogenetic studies. These findings provide a foundation for marker-assisted breeding programs targeting stress tolerance and fruit quality traits in mango. The study also supports conservation efforts for Kerala’s traditional mango germplasm by identifying genetically unique accessions.