Comparative genome-wide characterization of simple sequence repeats in coriander (Coriandrum sativum) and related Apiaceae

Background Simple sequence repeats (SSRs) are among the most informative molecular markers for plant genetics, yet their genome-wide distribution and marker potential in coriander ( Coriandrum sativum ) and related Apiaceae remain poorly characterized. Here we surveyed and compared SSRs in the publicly available whole-genome sequences of five Apiaceae species: coriander, carrot ( Daucus carota ), celery ( Apium graveolens ), gotu kola ( Centella asiatica ) and fennel ( Foeniculum vulgare ). Results A total of 569,531 perfect microsatellites were recovered in the 2,118.68 Mbp coriander assembly, an overall density of 268.8 SSRs/Mbp that places coriander at the low-density end of the family. Tetranucleotides were the most abundant repeat type in coriander, celery and fennel, while dinucleotides predominated in carrot and gotu kola; across all genomes exons were consistently depleted in SSRs and enriched in frame-preserving trinucleotides and AG-type motifs, a shift consistent with selection against frame-disrupting repeats in coding sequence. From the coriander loci we designed 1,806 primer pairs and assessed their transferability in silico across the family; requiring a predicted amplicon within 50 bp of the expected size, verified transferability was low and strongly dependent on the mismatch tolerance applied, ranging from 2.2 to 7.6% in carrot, 4.3 to 15.6% in celery, 2.8 to 11.0% in fennel and 0.2 to 4.2% in gotu kola across thresholds of one to three mismatches per primer, whereas a homology-only screen of the same primers returned 74.9 to 98.0%, indicating that homology screening substantially overstates cross-genus transferability. Comparison of repeat number at 552 orthologous motifs, of which 191 had sufficient locus support for analysis, showed that length change was nearly universal, with expansions and contractions roughly balanced across repeat types and stable loci essentially absent, while repeat number was positively correlated with allele-length divergence (Spearman's ρ = 0.53 to 0.86), pointing to replication slippage as the dominant process. Applied to 14 coriander accessions of diverse origin, six polymorphic loci resolved 26 alleles (mean 4.3 per locus; mean PIC = 0.68) and revealed limited diversity with weak population structure, in line with the narrow genetic base of the crop. Conclusions This work delivers the first genome-wide SSR catalogue for coriander and a set of cross-genus primer pairs that can serve as practical anchors for comparative genomics, mapping and marker-assisted breeding across Apiaceae.