cpSNP discovery and genotyping for a Pinus taeda breeding population with targeted comparison to related conifers

Pinus taeda (Loblolly pine) is the most important commercial tree species in the southern United States and a significant non-native plantation species in China. Its genetic improvement program has been implemented in South China for 30 years. In this study, the chloroplast (cp) genome of P. taeda was sequenced, assembled, and compared with other available chloroplast genomes of Pin aceae using BLAST. Codon usage among 33 species of Pinaceae was analyzed using the relative synonymous codon usage (RSCU) value. The results were then visualized using the pheatmap v1.0.10 in R. The rates of nonsynonymous (Ka) and synonymous (Ks) substitutions in the chloroplast genomes among five species of Pinus were estimated using the seqinr package in R. Additionally, selected single nucleotide polymorphisms (SNPs) were used to genotype 33 individuals from the P. taeda breeding population. The P. taeda cp genome is 121,530 bp, with certain regions (e.g., ycf1 and ycf2) showing lower sequence conservation compared to other Pinaceae species. Codon usage analysis revealed that codons ending in G or C were not prevalently used, with significant differences in natural selection pressure on chloroplast genes between three species (P. taiwanensis, P. thunbergii, and P. koraiensis) and the other 30 species. Phylogenomic analysis using 36 cp genomes (representing 25 species) resolved Pinus into two subgenera, with P. taeda clustered with P. rigida within the diploxylon pines. Notably, ycf1-based phylogenetic analysis recovered a topology highly congruent (normalized RF = 0.15) with whole-plastome phylogenies. This study validates the single-copy gene ycf1 as a robust and low-cost phylogenetic marker for conifer genus-level reconstruction. The identified SNPs provide valuable molecular markers for genotyping individuals in P. taeda breeding programs, supporting germplasm characterization and management.