Morphology and genic-SSRs-based diversity analysis and georeferencing of economic traits in natural populations of Jack (Artocarpus heterophyllus Lam.) from Eastern India

•Artocarpus heterophyllus (Jack) has immense potential to cater to the pharmaceutical/biomaterial, paint, agro-based, and several other product-specific sectors.•The breeding for cultivars suited for different end uses has mostly been overlooked until now.•We have collected and maintained 246 germplasm accessions for jack.•We analyzed the diversity in 110accessions of jack from Eastern India using morphological and genic-SSR markers. Moreover, we have geo-referenced a few valuable functional traits.•Our study provided an efficient tool for genetic analysis and opened up an avenue for more extensive future studies in the genus artocarpus. Jack (Artocarpus heterophyllus Lam.) is a medium-sized evergreen fruit tree. Its genetic improvement compromised due to limited understanding of available germplasm diversity. To address the gap, we report morphology (50 traits) and genic-SSRs (27)-based characterization of a germplasm collection of 110 accessions of Jack naturalized across diverse habitats in Eastern India and conserved in Field Gene Bank. Before analysis, the entire germplasm collection was divided into five sub-populations based on their naturalization sites. We observed a wide spectrum of diversity for qualitative (26) and quantitative (24) traits in the sub-populations. Principal component analysis using 24 quantitative traits explained 99.73% of the total variation through the first four-axis. Cluster analysis highlighted the dominance of vegetable purpose Jack in the sub-populations. Both morphological and genic-SSR markers revealed significant polymorphism (PIC = 0.12 to 0.46, polymorphism = 100%; PIC = 0.07 to 0.43, polymorphism = 100%) among the accessions. Morphological markers, namely leaf-blade margin, petiole shape, grooves on the petiole, fruit bracteole, and vivipary,exhibited the highest mean resolving power (1.0). Among the genic-SSR markers, JFSSR-4 exhibited the highest mean resolving power of 1.36. Overall, genic-SSR markers revealed higher genetic diversity at the species level (SI = 0.36, He = 0.23, P = 82.71%). Structure analysis using qualitative morphological markers, genic-SSR makers, and a combination of both marker types identified 2, 3 and 2 distinct groups, respectively,with frequent admixtures. The findings convincingly demonstrate that morphological and genic-SSR markers may together effectively explain complex biological diversity, particularly in perennial fruit trees like Jack.