Application of RAD Sequencing to Assess Genetic Diversity in the Understudied Plant Persicaria odorata

Persicaria odorata is an underutilized aromatic plant with limited genomic resources available to support its conservation and genetic improvement. This study employed restriction site-associated DNA sequencing (RAD-seq) to assess the genetic diversity and relationships among 20 P. odorata accessions. A total of 524,967 single-nucleotide polymorphisms (SNPs) were initially identified. After excluding SNPs with missing genotype calls, 191,231 complete SNPs were retained. Further removal of 13,836 monomorphic SNPs and 37,400 SNPs with a minor allele frequency (MAF) below 0.05 yielded a final dataset of 139,995 high-quality polymorphic SNPs. The retained SNPs exhibited a mean MAF of 0.244 and mean expected heterozygosity of 0.326, indicating moderate genetic variation within the germplasm. The mean observed heterozygosity across accessions was 0.402, ranging from 0.371 in MKSM020 to 0.415 in MKSM014. Principal component analysis (PCA), conducted using 129,835 variable biallelic SNPs, showed that the first two principal components explained 29.25% and 19.08% of the total genetic variation, respectively, with a cumulative contribution of 48.32%. Both PCA and hierarchical clustering consistently separated the accessions into three major genetic clusters comprising six, two and 12 accessions. Pairwise genetic similarity ranged from approximately 67.24% to 89.79%. MKSM003 and MKSM014 were identified as the most genetically similar pair, whereas MKSM011 and MKSM020 were the most genetically distinct. Overall, RAD-seq successfully generated informative genome-wide SNP markers and revealed considerable genetic structure among the evaluated P. odorata accessions. These findings provide valuable genomic information to support germplasm conservation, accession identification and the selection of genetically divergent parentalRAD-seq, single-nucleotide polymorphism, genetic diversity, materials for future breeding programmes.