3.5 PFAM, GO Term and Tandem Duplication Enrichment
The total number of genes present in the QTL intervals of each parental species was 174 on Chr04, 81 on Chr16, 161 on Chr10, 445 on Chr13, and 156 on Chr05 (Table 4). There were 40 PFAM domains enriched relative to the rest of the P. trichocarpa genome across all QTL intervals (alpha = 0.05; p-value threshold < 0.00014), and 25 PFAM domains enriched in the P. deltoides QTL intervals (alpha = 0.05, p-value < 0.000059) (Table S2). Additionally, there were 21 GO terms enriched in the P. trichocarpa intervals (alpha = 0.05, p-value < 0.000226) and 46 GO terms enriched in the P. deltoides intervals (alpha = 0.05, p-value < 0.000214) (Table S3). Finally seven of the genes in these intervals showed evidence of positive selection based on the ratio of nonsynonymous to synonymous nucleotide substitutions between the P. deltoides and P. trichocarpa orthologs (Table 5).
In total, there were 107 recent tandem duplicates in the P. trichocarpa intervals and 195 in the P. deltoides intervals for all biotic QTLs (Figure 6, Table 6). This includes 23 and 41 recent tandem duplicates for the Melampsora sp. intervals; 6 and 10 for the S. musiva intervals; 32 and 96 for the Phyllocolpa sp. intervals; and 47 and 46 for the M. vagabunda intervals, forP. trichocarpa and P. deltoides , respectively. The total number of recent tandem duplicates was significantly enriched relative to tandem counts for random intervals of the same size as the QTL intervals for the P. deltoides grandparent (p-value = 0.0118) but not for the P. trichocarpa grandparent (p-value = 0.1191).