Genetic Diversity, Genetic Structure and Haplotype Characteristics of Five Groups
Both matR and nad5-1 sites were neutral loci (Supplementary Table S2&S3 ), it was accords with the conservative variation of mtDNA (Held and Patel, 2020), which could brought the reliable results for our research. There were similarities in the genetic diversity comparison of five groups at these two loci (Figure 3 ), considering there was a higher variant conservatism at matR site, we taken the genetic diversity of matR site as the reference, which showed: HB*> HB> SX*, LN> SX*> LN* (Pi) (Figure 3A ). This was similar to our previous results (HB>HB*>SX*, LN*>LN>SX*) based on SSR markers (Zhou et al., 2022), the common point was HB> SX* and LN> SX*, shown that HB and LN plantations own the higher genetic variation once again.
The results of AMOVA, NJ tree, PCoA, and STRUCTURE were consistently showed the differences in the genetic background of all populations at these two loci were nad5-1>matR (Figure 4&5 ). The NJ tree shown the stationary ancestral status relationship of 5 groups (Figure 4A ), suggesting SX* natural populations with an identity of core position in northern China, which confirmed our previous results (Zhou et al., 2022). 38 populations of Chinese pine were divided into 4 clusters based on matR and nad5-1 loci (Figure 4E&5E ), which was not consistent with the results based on SSR markers (6 clusters), the consistent contents were as follows: SX* and LN had large differences in genetic structure within groups, while those of HB had little differences in genetic structure (Figure 4&5 ). The genetic structure of SX*, LN varies greatly within groups, which indicated that the genetic background of natural forests of different mountain lines in Shanxi was quite different (Wu et al., 2018; Zhou et al., 2022), and the germplasm sources of LN were more complex, which was not a single germplasm source. There was a small difference of genetic structure within the group of HB, which indicated that the germplasm sources of HB were relatively simple.
The results of haplotype analysis also showed that there were several dominant haplotypes in different populations in SX* and LN groups, and the haplotype structure of HB group was uniform, which was consistent with the results of genetic structure (Figure 1,2,5 ). We firmly believed that there was great difference in the genetic background of Chinese pine natural forest in different geographical mountains of Shanxi, the germplasm sources of SX* and LN were more complex, and the germplasm sources of HB were relatively simple.