Discriminatory Power of Retrotransposon-Based iPBS Markers for Assessing Genetic Diversity and Population Structure in Loquat (Eriobotrya japonica) Genotypes

Abstract

Genetic relationships and population structure of loquat (Eriobotrya japonica) germplasm maintained in northern Pakistan have received limited molecular assessment. We genetically characterized 37 genotypes collected at six sites in Punjab and Khyber Pakhtunkhwa (KPK) using 22 inter-primer binding site (iPBS) markers. The iPBS markers generated 289 scorable bands, all of which were polymorphic (mean = 13.14 bands per primer). Across primers, mean polymorphic information content (PIC), resolving power (Rp; genotype-discrimination capacity) and marker index (MI; combined informativeness and multiplex capacity) were 0.36, 7.01 and 4.69, respectively. Primer 2079 recorded the highest Rp, effective multiplex ratio (EMR) and MI, while primer 2243 had the highest PIC. Within the sampled material, expected heterozygosity, Shannon’s information index and the percentage of polymorphic loci were higher in KPK than in Punjab. The first two principal coordinate analysis (PCoA) coordinates accounted for 15.14% of the variation, and samples from the two provinces overlapped. A locus-resampled, bootstrap-supported neighbor-joining (NJ) tree recovered several relationships among genotypes from different localities. Analysis of molecular variance (AMOVA) assigned 96% of the variation within the two sampled provincial groups and 4% between them (PhiPT = 0.04, p = 0.001). Bayesian analysis indicated two principal genetic backgrounds with mixed membership across locations. Together, the analyses identify informative iPBS primers, show that molecular variation is concentrated within the two sampled provincial groups, and highlight differentiated genotypes for conservation and replicated phenotypic evaluation.