Population Genetic Structure and Diversity of Camellia oleifera: Insights from Comparative Chloroplast Genomics and Development of Molecular Markers

This study aimed to develop chloroplast sequence markers through comparative plastome analysis and evaluate their application in haplotype identification and genetic diversity assessment in sampled Camellia oleifera populations. Three newly assembled chloroplast genomes of Camellia sect. Oleifera ranged from 156,918 to 157,003 bp and retained the typical quadripartite structure. Comparative analyses of these genomes and 13 reference plastomes identified 605 long repeats and 3315 SSRs. The three new plastomes shared 29 preferred sense codons, 28 ending in A/U. Sliding-window nucleotide diversity highlighted eight candidate variable regions, with a maximum π of 0.01397. Among 324 individuals from 37 sampling populations, the 1772-bp concatenated alignment contained 38 variable sites and 55 haplotypes (Hd = 0.8052; π = 0.002183). Thirty-six haplotypes were singletons, while H003 occurred in 133 individuals across 35 populations. Sequence PCA and exploratory ADMIXTURE described broad variation. K = 2 had the lowest cross-validation error among the values shown for K = 2–10, and its two components were interpreted descriptively. These results document chloroplast sequence diversity and population structure in the sampled C. oleifera material and provide molecular resources for germplasm characterization and conservation sampling.