The total linkage drag (combined homozygous and heterozygous types) was 8.53%, which is more than half of the total donor component on carrier chromosomes (Table 3).
The common markers spanned 81.1 cM on 10B and 75.0 cM on 10A, accounting for 75.7% and 68.0% of the total linkage group length, respectively.
No linkage group arms were syntenic with more than a single stickleback chromosome, and marker coverage to infer homologies is still largely incomplete in the salmonids as synteny blocks on seven linkage groups spanned less than 10% of the total linkage group length (i.e., AC-1, -3, -5, -15+2, -22, -31, and -37).
Since the inverted chromosome segments accounted for nearly 30% of the total linkage groups' lengths and 36.0% (9 out of 25) of the total putative orthologous markers in both A and B genomes, there could be an inverted chromosome segment between 5A and 5B, which also has not been detected from previous reports.
Out of the 913 total linkages, we find 173 that share at least 1 compound, significantly more than expected by chance (85.95 ± 7.90, p < 0.0001).
Hierarchical cluster analysis was performed using the WECCA program, with the parameter total linkage [ 18].
The estimated total linkage length for each chromosome, also shown in Table 1, was estimated as its cM length in the second-generation linkage map, divided by the estimated proportion of chromosome covered by that linkage map (Wang et al. unpublished).
In the previous linkage QTL mapping studies, approximately 120 and 30 QTLs have been identified for SW [ 20, 21, 24, 25, 27- 29, 37] and SL [ 20, 21, 25, 26], respectively, which were distributed on all and 16 of the 19 total linkage groups.
Although not detectable in wild-type plants, these substructures constituted 11% of the total lignin linkages, similar to the 12% observed in COMT-deficient Arabidopsis[ 19], and 10% in COMT antisense Populus[ 18].
Figure 6 shows the total backward linkage index and the total forward linkage index in the year 2000 and the year 2011 (Miller and Blair 2009).
