As expected, a leading standard of macrocollinearity is seen along side a dozen LGs

Task from homologous LGs

LGs that have been homologous ranging from F2 and you will G2F or F2 and G2M maps were understood on the basis of an excellent subset regarding 198 and you will 240 common genetics, correspondingly. However, 15 cases of LG assignment otherwise buy inaccuracies have been understood, suggesting either the clear presence of paralogous loci (which was definitely the truth for a few markers mapped to various LGs to your G2 and you will F2 charts: AL750495 when you look at the LG10_G2F and you can LG8_G2M, and CT577280 in LG7_F2 and LG4_G2M) otherwise a linkage ordering condition (that has been the way it is to own thirteen non-distorted markers presenting more chart locations during the homologous linkage organizations (BX678432 into the LG2_F2 and LG2_G2M, CR393801 inside the LG4_F2 and you will LG4_G2F, CT580300 within the LG4_F2 and LG4_G2F, m26 for the LG4_F2 and you may LG4_G2F, AL749536 into the LG4_F2 and you can LG4_G2F, m592 within the LG4_F2 and you may LG4_G2F, m593 into the LG4_F2 and LG4_G2F, CT577468 when you look at the LG4_F2 and you may LG4_G2F, FN256629 into the LG4_F and you can LG4_G2M, m738/m739/m740 (exact same contig) inside LG7_F2 and you may LG7_G2M, 384_LIM2 in LG7_F2 and LG7_G2M, BX250169 in the LG7_F2 and you can LG7_G2M, m590 during the LG7_F2 and you may LG7_G2M). These 15 family genes was in fact omitted throughout the variety of anchor indicators. Plus the point markers between F2 and you may G2 maps, twenty-five testcross markers (that is, twenty five contigs wherein a couple of SNPs were polymorphic in both parent) were used to ensure the brand new homology ranging from LGs for the G2F and G2M charts.

Gene density

An effective Chi dos try is actually did to your around three maps so you can determine whether how many genes is actually uniformly marketed within maritime pine chromosomes. The amount of indicators each cM (gene occurrence) is found in order to differ rather out of good consistent shipping within 12 linkage organizations, at 5% peak to possess G2F and surfer dating site you can F2 (P-worthy of G2F = 0.012, P-worth F2 = 0.00007), hence differences was only outside the restrictions away from analytical benefits for G2M (P-value G2M = 0.074). Towards the around three charts, there were a lot fewer genes when you look at the LG 8 and you may a larger amount away from genes inside LG 6 and you can LG12.

Affairs 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 instead 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 instead of G2F)} = 0.0004 and P-value _{(F2 as opposed to 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).