Sequencing and population structure
A total of 78,198 possible SNPs were generated and filtered down to
13,534 independent SNPs, with 8,824 SNPs mapped to the 11Eucalyptus chromosomes. The number of SNPs per chromosome varied
from 599 to 1,083, with a mean of 802 SNPs per chromosome. Of the
remaining SNPs, 477 fell on unspecified scaffolds and 4,233 on regions
that could not be aligned to the E. grandis genome (unknown
location). Population differentiation was
low (globalFST = 0.04) and similar to that identified in a
previous RFLP analysis of variation (FST = 0.034;
Wheeler et al., 2003) with population pairwiseFST values ranging from 0.011 to 0.18. The
cross‐entropy analysis estimated that the optimal number of clusters
(k ‐value) was 6 (Figure S1). SNMF analysis with six clusters
revealed substantial admixture in populations. Five of the clusters
could be geographically described (Figure 2, S2), one cluster was
primarily located in the southern area, one in the central area and two
in the northern area, where one cluster was dominant in populations
along the coast. A fifth cluster occurred in the outlier population
(JIL; blue colour), and the sixth cluster was present in four
individuals (two individuals from BRA and BOO). The LES population
displays mixed affinity, being similar to both southern (green) and
northern (yellow and red) populations.