Unveiling genetic diversity and population structure in jackfruit (Artocarpus heterophyllus) through SNP markers for enhanced breeding and conservation

Jackfruit (Artocarpus heterophyllus Lam) is a vital tropical fruit species extensively cultivated across South and Southeast Asia, including Bangladesh and India. Renowned for its highly nutritious, large fruit, valuable timber, and medicinal properties, jackfruit demonstrates resilience across diverse climatic conditions. Its inherent highly heterozygous nature, resulting from cross-pollination, leads to extensive genetic diversity. While this makes jackfruit an excellent candidate for improvement through molecular breeding, comprehensive genomic studies to identify SNPs (single-nucleotide polymorphisms) within the jackfruit genome have been lacking until this study. This study is aimed to characterize the genetic variation and population structure of jackfruit using SNP markers. A total of 37 jackfruit accessions were collected from three regional stations of the Bangladesh Agricultural Research Institute and two local farmers’ fields. Morphological traits, including fruit size, color, number of bulbs per fruit, seed weight, seed size, bulb weight, and brix (%), were recorded during the 2023–24 growing season. Genomic DNA was extracted, and Genotyping-by-Sequencing libraries were prepared using a two-enzyme protocol, followed by sequencing on the NovaSeq Illumina platform. After stringent quality control, trimming, and bioinformatics processing, 23,795 high-quality biallelic SNP markers were identified by filtering for minor allele frequency > 0.01 and missing data < 20%. These SNP markers were then utilized to comprehensively characterize genetic variation and population structure among the accessions. Population structure analysis of 37 jackfruit accessions identified five genetic clusters, reflecting both shared ancestry and distinct divergent lineages (e.g., GK9/GK9.1, AK005/AK008, BK1/PD19.1, GK2/GK4). The results demonstrate the efficacy of SNP markers for genetic diversity studies, providing crucial information for parental selection and supporting advanced breeding and conservation strategies. This study significantly contributes valuable insights into jackfruit’s genetic diversity, establishing a foundation for genomic-assisted breeding and conservation initiatives for food security.