Identification and genetic diversity analysis of Paeonia lactiflora Pall. populations based on the chloroplast genes rpoB and psbK-psbI

Abstract Paeonia lactiflora Pall. is a species with significant medicinal and economic value. In this study, five complete chloroplast genome sequences of P. lactiflora samples originating from different regions in China were sequenced using the Illumina NovaSeq 4000 platform. All five P. lactiflora chloroplasts had a typical cyclic tetrameric structure with 130 genes annotated. Comparative genomic analysis indicated that rpoB and psbK-psbI function as potential specific DNA barcodes for intraspecific identification of P. lactiflora. PCR amplification of rpoB and psbK-psbI was performed on 246 samples from 7 production areas, achieving 100% amplification efficiency. Sequence analysis revealed that 5 and 10 haplotypes were identified based on rpoB and psbK-psbI, respectively. The joint analysis of two sequences identified 15 haplotypes named Hap1ཞHap15. Hap5 emerged as the most prevalent and geographically widespread haplotype across China. Haplotypic diversity (Hd) was 0.786, and nucleotide diversity was 0.00281, suggesting that P. lactiflora had high genetic diversity at the species level. The Neighbor-Joining tree showed that the 15 haplotypes were clustered into two branches, indicating extensive genetic exchange between clusters. The introduction of new individuals or rare genes into different clusters through gene flow increased genetic variation within clusters, enriching P. lactiflora genetic diversity. This study provides a foundation for identifying P. lactiflora, protecting and utilizing germplasm resources, and supporting molecular breeding efforts.