Sure-enough, a leading standard of macrocollinearity are observed along the a dozen LGs

Task off homologous LGs

LGs that have been homologous ranging from F2 and G2F otherwise F2 and you can G2M charts was recognized on such basis as a good subset out of 198 and you can 240 popular genetics, respectively. Yet not, fifteen cases of LG project otherwise acquisition inaccuracies was recognized, indicating either the clear presence of paralogous loci (which had been without a doubt the way it is for 2 markers mapped to different LGs with the G2 and you can F2 maps: AL750495 during the LG10_G2F and you may LG8_G2M, and CT577280 during the LG7_F2 and you may LG4_G2M) or good linkage ordering situation (which had been happening to own thirteen non-altered markers to present some other map urban centers during the homologous linkage organizations (BX678432 inside the LG2_F2 and you can LG2_G2M, CR393801 from inside the LG4_F2 and you may LG4_G2F, CT580300 during the LG4_F2 and you will LG4_G2F, m26 inside the LG4_F2 and you may LG4_G2F, AL749536 in the LG4_F2 and you will LG4_G2F, m592 inside https://datingranking.net/thailand-dating/ LG4_F2 and you may LG4_G2F, m593 within the LG4_F2 and you will LG4_G2F, CT577468 from inside the LG4_F2 and you may LG4_G2F, FN256629 inside the LG4_F and you can LG4_G2M, m738/m739/m740 (exact same contig) inside the LG7_F2 and LG7_G2M, 384_LIM2 into the LG7_F2 and you can LG7_G2M, BX250169 when you look at the LG7_F2 and you can LG7_G2M, m590 from inside the LG7_F2 and you will LG7_G2M). These 15 genetics were omitted in the list of anchor indicators. Along with the anchor indicators anywhere between F2 and G2 maps, twenty-five testcross indicators (that’s, twenty-five contigs which one or two SNPs have been polymorphic in a choice of parent) were used to verify the brand new homology between LGs towards G2F and you can G2M maps.

Gene density

Good Chi 2 decide to try try did for the three maps so you can determine whether exactly how many family genes is equally marketed between your maritime pine chromosomes. The amount of indicators for every cM (gene occurrence) are located in order to disagree somewhat out-of a beneficial consistent shipment within twelve linkage communities, on 5% peak for G2F and you can F2 (P-really worth G2F = 0.012, P-value F2 = 0.00007), and this differences was just beyond your constraints of statistical relevance to have G2M (P-worthy of G2M = 0.074). To your all around three charts, there were a lot fewer genes when you look at the LG 8 and more substantial count regarding genetics during the LG 6 and you can LG12.

Items 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 rather than 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).