Haplotype Analysis
A total of 17 haplotypes (27bp) (Supplementary Table S7 ) were
obtained based on six domains of matR markers (Figure 6A ). The
haplotype distribution of 35 populations showed their haplotype genetic
background (Figure 1 ), and the genetic association of all
haplotypes was shown in the TCS network (Figure 6B ). Hap-1
showed the most conservatism and occupies a dominant position in all
populations, suggesting hap-1 was the ancestral (dominant) haplotype,
followed by hap-2, which exists in most populations (10/35). Almost all
other haplotypes (13/17) were private haplotypes owned by a single
population. There was no special pattern of haplotype distribution in
the five groups, and the distribution patterns of haplotypes in
different populations provide limited available information for
plantation tracing (Figures 1&6B , Supplementary Table
S7 ).
A total of 68 haplotypes (34bp) (Supplementary Table S8 ) were
obtained based on six domains of the nad5-1 marker (Figure 6C ).
The different haplotype genetic backgrounds of 38 populations
(Figure 2 ) and the complex genetic relationships among 68
haplotypes (Figure 6D ) indicate the nad5-1 marker with a high
degree of variation. Hap-4, hap-6, and hap-11 exist in almost all
populations, especially hap-4, suggesting hap-4 was the ancestral
(dominant) haplotype, followed by hap-7、hap-3、hap-13, which exist in
most populations. Almost all other haplotypes (40/68) were private
haplotypes owned by a single population, and the relationship between 68
haplotypes showed a complicated network. There was a special pattern of
haplotype distribution in five groups, hap-4 and hap-11 were the
dominant haplotypes of SX*, HB*, and HB groups. The LN*, and LN groups
were dominated by Hap-7 and Hap-4. The diverse and regular haplotype
distribution structures of 38 populations provide a lot of valuable
information for the germplasm traceability of plantation forests
(Figures 2&6D , Supplementary Table S8 ).