Project regarding homologous LGs
LGs that have been homologous anywhere between F2 and you can G2F or F2 and you may G2M charts were understood on the basis of an effective subset away from 198 and you may 240 popular genetics, correspondingly. not, 15 cases of LG task otherwise purchase discrepancies had been understood, recommending both the presence of paralogous loci (which was without a doubt the actual situation for a couple of indicators mapped to various LGs to the G2 and you will F2 maps: AL750495 into the LG10_G2F and you will LG8_G2M, and you may CT577280 when you look at the LG7_F2 and you may LG4_G2M) otherwise a linkage purchasing state (which had been the truth for 13 non-altered indicators to present other chart places when you look at the homologous linkage groups (BX678432 when you look at the LG2_F2 and you can LG2_G2M, CR393801 inside the LG4_F2 and you will LG4_G2F, CT580300 when you look at the LG4_F2 and you will LG4_G2F, m26 for the LG4_F2 and you may LG4_G2F, AL749536 within the LG4_F2 and you can LG4_G2F, m592 inside the LG4_F2 and you can LG4_G2F, m593 in the LG4_F2 and you can LG4_G2F, CT577468 inside LG4_F2 and you may LG4_G2F, FN256629 within the LG4_F and you may LG4_G2M, m738/m739/m740 (same contig) in LG7_F2 and you may LG7_G2M, 384_LIM2 for the LG7_F2 and you can LG7_G2M, BX250169 from inside the LG7_F2 and you may LG7_G2M, m590 into the LG7_F2 and you can LG7_G2M). These types of fifteen genetics have been omitted regarding range of anchor markers. In addition to the anchor indicators anywhere between F2 and G2 maps, twenty-five testcross markers (that’s, twenty five contigs in which a couple of SNPs was polymorphic in a choice of moms and dad) were utilized to confirm the fresh homology between LGs into the G2F and you can G2M charts.
Gene thickness
A good Chi dos take to is performed toward around three maps to help you see whether exactly how many family genes was uniformly distributed amongst the coastal pine chromosomes. How many indicators per cM (gene occurrence) try found so you can differ rather away from a great uniform shipments between your 12 linkage teams, during the 5% height getting G2F and you may F2 (P-worth G2F = 0.012, P-value F2 = 0.00007), and this distinction was just outside of the limitations regarding statistical importance to have G2M San Antonio times lesbian dating apps (P-well worth G2M = 0.074). Into all three maps, there had been less genetics from inside the LG 8 and you can a bigger number from genetics inside LG six and you may LG12.
Points 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 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 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 versus 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).