As expected, a top amount of macrocollinearity are noticed along side twelve LGs
Task out of homologous LGs
LGs that were homologous between F2 and you can G2F otherwise F2 and G2M maps had been understood on such basis as a beneficial subset from 198 and you may 240 well-known family genes, respectively. However, 15 instances of LG task otherwise buy discrepancies had been best dating sites Scottsdale identified, indicating either the clear presence of paralogous loci (that was obviously the fact for a couple of indicators mapped to various LGs into the G2 and you will F2 maps: AL750495 during the LG10_G2F and you can LG8_G2M, and you can CT577280 inside LG7_F2 and you will LG4_G2M) or a great linkage buying disease (that was the situation to have 13 low-altered indicators to present different chart metropolitan areas inside homologous linkage teams (BX678432 within the LG2_F2 and LG2_G2M, CR393801 in the LG4_F2 and you may LG4_G2F, CT580300 inside LG4_F2 and you will LG4_G2F, m26 from inside the LG4_F2 and you will LG4_G2F, AL749536 within the LG4_F2 and you can LG4_G2F, m592 for the LG4_F2 and you will LG4_G2F, m593 inside LG4_F2 and you can LG4_G2F, CT577468 inside LG4_F2 and you can LG4_G2F, FN256629 during the LG4_F and you can LG4_G2M, m738/m739/m740 (exact same contig) in the LG7_F2 and LG7_G2M, 384_LIM2 inside the LG7_F2 and LG7_G2M, BX250169 during the LG7_F2 and you will LG7_G2M, m590 in LG7_F2 and you may LG7_G2M). These types of fifteen family genes was indeed excluded regarding selection of point markers. And the point markers ranging from F2 and you can G2 maps, 25 testcross markers (that is, twenty-five contigs wherein one or two SNPs were polymorphic in either mother or father) were used to ensure the newest homology ranging from LGs on G2F and you can G2M maps.
An effective Chi 2 test try did for the about three maps to help you determine whether the number of family genes was evenly marketed within maritime pine chromosomes. What amount of indicators per cM (gene density) was discover in order to disagree notably of a great uniform shipments between the twelve linkage groups, in the 5% height getting G2F and you can F2 (P-worthy of G2F = 0.012, P-worthy of F2 = 0.00007), which improvement was only away from restrictions from mathematical value to have G2M (P-value G2M = 0.074). Towards every about three maps, there had been a lot fewer family genes in the LG 8 and more substantial number regarding genetics inside the LG 6 and you can LG12.
Issues 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 in the 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 instead 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).