Sure enough, a high amount of macrocollinearity was observed along the 12 LGs

Task out of homologous LGs

LGs that were homologous between F2 and you can G2F or F2 and G2M charts were known on such basis as a subset out of 198 and you can 240 common genes, respectively. Although not, 15 instances of LG task otherwise order discrepancies was indeed understood, suggesting both the presence of paralogous loci (that has been without a doubt the actual situation for a few markers mapped to several LGs into G2 and F2 charts: chat room slovakian over 40 AL750495 in the LG10_G2F and you may LG8_G2M, and you will CT577280 inside the LG7_F2 and LG4_G2M) otherwise a good linkage buying state (that has been your situation to have 13 low-altered indicators presenting various other map locations for the homologous linkage groups (BX678432 into the LG2_F2 and you may LG2_G2M, CR393801 within the LG4_F2 and you will LG4_G2F, CT580300 within the LG4_F2 and you can LG4_G2F, m26 when you look at the LG4_F2 and LG4_G2F, AL749536 inside LG4_F2 and you may LG4_G2F, m592 inside LG4_F2 and LG4_G2F, m593 within the LG4_F2 and LG4_G2F, CT577468 from inside the LG4_F2 and you will LG4_G2F, FN256629 in the LG4_F and you will LG4_G2M, m738/m739/m740 (exact same contig) in the LG7_F2 and you may LG7_G2M, 384_LIM2 in LG7_F2 and you may LG7_G2M, BX250169 in the LG7_F2 and you will LG7_G2M, m590 inside the LG7_F2 and you can LG7_G2M). These types of 15 genes have been excluded on selection of point indicators. As well as the anchor markers ranging from F2 and G2 charts, twenty five testcross markers (which is, twenty five contigs whereby one or two SNPs had been polymorphic in both father or mother) were utilized to ensure the fresh new homology between LGs to the G2F and G2M charts.

Gene density

A beneficial Chi 2 test try did on the about three charts to see whether how many genetics are evenly delivered between the maritime oak chromosomes. Just how many markers for each cM (gene occurrence) is actually receive so you’re able to differ significantly off a good uniform shipment within several linkage organizations, from the 5% level to own G2F and F2 (P-worth G2F = 0.012, P-well worth F2 = 0.00007), and therefore huge difference was only outside of the restrictions out of analytical relevance getting G2M (P-value G2M = 0.074). For the all about three maps, there had been fewer genetics from inside the LG 8 and you may a larger number away from genes when you look at the LG 6 and you can LG12.

Factors 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 versus 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 in the place 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).