Cross-species transferability and genetic diversity analysis in Linum species using microsatellite markers

The genus Linum comprises over 230 species, with L. usitatissimum valued for linen and oil, yet crop wild relatives (CWRs) remain underutilized due to limited availability and poor molecular characterization. In this study, 96 accessions representing 16 wild and one cultivated species were evaluated using 49 SSR markers to assess genetic diversity and cross-species transferability (CST). A total of 473 alleles were detected, with allelic richness ranging from 1 to 22 alleles per locus and polymorphic information content (PIC) values reaching up to 0.91, underscoring the discriminatory power of the markers. High genetic diversity parameters, including Shannon's index (up to 1.296), revealed substantial allelic variation in species such as L. bienne and L. lewisii. Population structure analysis indicated moderate differentiation (global Fst = 0.186) and the presence of admixed individuals, reflecting complex evolutionary histories shaped by multiple gene flow events and introgression. Cluster analysis proved effective for uncovering pedigree relationships among genotypes and offered advantages over PCoA, while CST rates ranged from 45.45 to 100% across species. The high CST observed within sections (Linum, Dasylinum) highlights conserved genomic regions, whereas variable amplification in Linastrum points to divergent evolutionary trajectories. Together, these findings demonstrate that SSR markers not only capture allelic richness and population structure but also illuminate evolutionary processes such as speciation, introgression, and lineage divergence. The study establishes a valuable foundation for integrating Linum CWRs into breeding programs, thereby broadening the genetic base in cultivated linseed. These findings can enhance the scope and effectiveness of future breeding initiatives, particularly where such markers are lacking.