Project of homologous LGs
LGs that have been homologous between F2 and G2F or F2 and G2M charts was indeed recognized based on an effective subset off 198 and you can 240 popular genes, respectively. However, 15 cases of LG assignment otherwise purchase discrepancies have been understood, indicating sometimes the clear presence of paralogous loci (which had been without a doubt the scenario for two markers mapped to several LGs for the G2 and you may F2 charts: AL750495 inside LG10_G2F and you will LG8_G2M, and you will CT577280 in the LG7_F2 and you will LG4_G2M) otherwise good linkage ordering problem (which had been the outcome for 13 non-distorted markers presenting other map cities from inside the homologous linkage communities (BX678432 in LG2_F2 and you can LG2_G2M, CR393801 during the LG4_F2 and you can LG4_G2F, CT580300 inside LG4_F2 and LG4_G2F, m26 inside LG4_F2 and you will LG4_G2F, AL749536 inside the LG4_F2 and LG4_G2F, m592 during the LG4_F2 and you can LG4_G2F, m593 during the LG4_F2 and LG4_G2F, CT577468 in the LG4_F2 and you can LG4_G2F, FN256629 inside the LG4_F and you will LG4_G2M, m738/m739/m740 (same contig) inside LG7_F2 and you can LG7_G2M, 384_LIM2 from inside the LG7_F2 and you can LG7_G2M, BX250169 inside LG7_F2 and you may LG7_G2M, m590 from inside the LG7_F2 and you will LG7_G2M). These 15 family genes was indeed excluded regarding the set of point markers. Along with the anchor markers ranging from F2 and G2 charts, twenty-five testcross indicators (which is, 25 contigs wherein a few SNPs was indeed polymorphic in a choice of moms and dad) were utilized to ensure the fresh new homology ranging from LGs on G2F and you can G2M charts.
Gene thickness
A Chi dos take to was did for the three maps so you can determine whether exactly how many genetics are evenly marketed involving the coastal oak chromosomes. The amount of indicators for every cM (gene density) is discover so you’re able to disagree somewhat off a beneficial consistent shipments between the twelve linkage communities, within 5% peak getting G2F and you may F2 (P-value G2F = 0.012, P-really worth F2 = 0.00007), hence variation was only outside the restrictions out of statistical benefits to possess G2M (P-worthy of G2M = 0.074). On the most of the around three maps, there have been fewer genes for the LG 8 and a larger count away from family genes in LG 6 and LG12.
Things affecting 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 rather than 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 free spanish chat F2 and between G2M and F2, with significant differences detected in both cases: P-value (F2 instead of G2F) = 0.0004 and P-value (F2 in place of 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).