Retrotransposon‐Based Molecular Profiling Reveals Genetic Diversity and Population Structure in Citrus Genotypes From Punjab, Pakistan

This study assessed genetic diversity and population structure among 23 citrus genotypes comprising 14 grapefruit ( Citrus paradisi ), seven pummelo ( Citrus maxima ) and two sweet orange ( Citrus sinensis ) genotypes using inter‐primer binding site (iPBS) markers. Twenty primers produced 425 amplified bands, of which 396 were polymorphic (93.18% overall). Primer‐specific polymorphism ranged from 86% to 100% and polymorphism information content (PIC) ranged from 0.21 to 0.35, indicating moderate marker informativeness. Species‐group diversity estimates were highest for C. paradisi (97.44% polymorphic loci), followed by C. maxima (84.62%); estimates for C. sinensis were substantially lower (25.65%) but should be interpreted cautiously because only two genotypes were sampled. The first two principal coordinates explained 32.06% of the molecular variation and showed partial, overlapping species‐associated structuring. Analysis of molecular variance (AMOVA) attributed 92% of the variation to differences within species groups and 8% to differences among groups (PhiPT = 0.080, p = 0.020). Bayesian analysis supported three major genetic components at K = 3; some genotypes were strongly assigned to one component, whereas others had mixed membership. These results provide a preliminary molecular baseline for citrus germplasm characterisation in Punjab and require confirmation through larger, balanced sampling and codominant or sequence‐based markers.