Exploring the morphological and genetic diversity and relationship of elite jackfruit (Artocarpus heterophyllus Lam.) accessions in southern Kerala through comprehensive marker assay

Jackfruit (Artocarpus heterophyllus Lam.) is a highly nutritious and culturally significant fruit species native to tropical regions, yet its genetic and biochemical diversity remain underexplored. This study evaluates the morphological, genetic, and biochemical diversity among 30 elite jackfruit accessions from southern Kerala, India, using a comprehensive marker-assisted approach. Biochemical analyses revealed significant variation in key parameters, including acidity (0.13–1.57%), ascorbic acid (12.09–54 mg/100 g), reducing sugar (0.33–8.1%), total sugar (2.63–22.1%), and β-carotene (6.47–191.00 µg/100 g), underscoring the potential of the accessions for breeding in nutritional value. Genetic diversity analysis, performed using 38 polymorphic simple sequence repeat (SSR) markers, identified 142 putative alleles, with polymorphism information content (PIC) values ranging from 0.26 to 0.38 and mean heterozygosity of 0.35. Phylogenetic clustering grouped the accessions into three major clusters, corroborated by STRUCTURE analysis, which inferred three genetically distinct subpopulations with varying levels of admixture. Significant marker-trait associations were identified for key biochemical traits, such as β-carotene and total sugar, using genome-wide association analysis (GWAS), with genetic markers explaining up to 24.5% of the observed variance. These findings highlight the extensive genetic and biochemical diversity within jackfruit accessions, offering valuable insights for breeding programmes focused on enhancing nutritional quality, adaptability, and commercial viability.