Assignment away from homologous LGs
LGs that have been homologous anywhere between F2 and you will G2F otherwise F2 and G2M maps was in fact click here for info identified on the basis of good subset regarding 198 and you can 240 preferred genes, correspondingly. not, fifteen instances of LG assignment or order discrepancies had been identified, suggesting often the presence of paralogous loci (which was without a doubt the actual situation for 2 indicators mapped to different LGs towards G2 and you may F2 maps: AL750495 inside the LG10_G2F and LG8_G2M, and you will CT577280 from inside the LG7_F2 and LG4_G2M) otherwise good linkage buying problem (that has been happening for thirteen non-distorted markers to provide more chart metropolises in the homologous linkage teams (BX678432 in LG2_F2 and LG2_G2M, CR393801 inside LG4_F2 and you may LG4_G2F, CT580300 in LG4_F2 and you will LG4_G2F, m26 into the LG4_F2 and you can LG4_G2F, AL749536 in the LG4_F2 and you can LG4_G2F, m592 into the LG4_F2 and LG4_G2F, m593 into the LG4_F2 and LG4_G2F, CT577468 in the LG4_F2 and you will LG4_G2F, FN256629 during the LG4_F and LG4_G2M, m738/m739/m740 (same contig) within the LG7_F2 and LG7_G2M, 384_LIM2 for the LG7_F2 and you can LG7_G2M, BX250169 when you look at the LG7_F2 and you can LG7_G2M, m590 for the LG7_F2 and you may LG7_G2M). These types of 15 genes was indeed omitted regarding variety of anchor markers. Plus the anchor markers anywhere between F2 and you can G2 maps, 25 testcross indicators (that is, twenty five contigs wherein a few SNPs was polymorphic in either father or mother) were utilized to ensure brand new homology ranging from LGs for the G2F and G2M charts.
Gene thickness
A good Chi 2 attempt was performed on the about three charts so you can see whether the amount of family genes is uniformly delivered within maritime pine chromosomes. What number of markers for each cM (gene density) is actually discover so you can differ rather regarding a consistent delivery amongst the a dozen linkage teams, in the 5% top to have G2F and you may F2 (P-worthy of G2F = 0.012, P-really worth F2 = 0.00007), which variation was only beyond your limits from statistical benefit getting G2M (P-worth G2M = 0.074). On the all of the around three maps, there are fewer genes when you look at the LG 8 and more substantial amount away from family genes inside the LG six and LG12.
Affairs impacting recombination
We used the Wilcoxon signed rank test to test the hypothesis that ‘map lengths are equal between the three maps: G2F, G2M and F2.’ This hypothesis was not rejected for the comparison between G2F and G2M, P-value (G2F in place of G2M) = 0.78, indicating that sex had no significant effect on map length in this mapping population. The same test was applied for the comparisons between G2F and F2 and between G2M and F2, with significant differences detected in both cases: P-value (F2 as opposed to G2F) = 0.0004 and P-value (F2 versus G2M) = 0.005. We checked that the effect of genetic background on the frequency of recombination was not due to the presence of more markers on the F2 map than on the G2F and G2M maps, by carrying out a Wilcoxon signed rank test for all pair-wise recombinations between the common markers in each LG. This test clearly showed that the ‘genetic status’ (intra- versus interprovenance hybrids in our case) of the parental genotypes in which meiotic recombination occurred had a significant effect on the frequency of recombination, with nine LGs presenting significant differences between both F2 and G2F, and F2 and G2M, three LGs presenting a significant difference between F2 and G2F or F2 and G2M, and one LG presenting no effect [see Additional file 8]. Finally, a Z-test was applied to each pair-wise comparison, for the identification of significant pairs among those used to perform the Wilcoxon rank-test (highlighted in red in Figure 3). There was a clear trend toward a greater incidence of significant pair-wise recombination for the F2 map (interprovenance hybrid) than for the G2F or G2M maps (intraprovenance hybrids).
