Sure enough, a premier degree of macrocollinearity is actually noticed along side several LGs

Project out-of homologous LGs

LGs that were homologous anywhere between F2 and you will G2F or F2 and you can G2M maps had been recognized based on an excellent subset regarding 198 and 240 popular genes, respectively. But not, 15 cases of LG task or acquisition discrepancies was in fact recognized, recommending both the presence of paralogous loci (which had been naturally the truth for a few indicators mapped to several LGs towards G2 and you may F2 charts: AL750495 inside the LG10_G2F and you may LG8_G2M, and CT577280 in LG7_F2 and you will LG4_G2M) otherwise a linkage ordering disease (which was the situation to possess 13 non-distorted markers to present more chart towns inside homologous linkage communities (BX678432 inside LG2_F2 and LG2_G2M, CR393801 during the LG4_F2 and you can LG4_G2F, CT580300 within the LG4_F2 and you can LG4_G2F, m26 when you look at the LG4_F2 and you can LG4_G2F, AL749536 in the LG4_F2 and you may LG4_G2F, m592 for the LG4_F2 and LG4_G2F, m593 into the LG4_F2 and LG4_G2F, CT577468 in the LG4_F2 and LG4_G2F, FN256629 into the LG4_F and you may LG4_G2M, m738/m739/m740 (same contig) in LG7_F2 and you will LG7_G2M, 384_LIM2 for the LG7_F2 and you will LG7_G2M, BX250169 into the LG7_F2 and you may LG7_G2M, m590 in the LG7_F2 and you can LG7_G2M). These 15 family genes was in fact excluded in the set of anchor indicators. And the anchor indicators between F2 and you can G2 maps, twenty five testcross indicators (which is, twenty five contigs by which two SNPs had been polymorphic in both parent) were used to ensure this new homology between LGs on G2F and you will G2M maps.

Gene thickness

A good Chi 2 sample are did toward about three maps to help you see whether how many genetics try evenly delivered involving the coastal oak chromosomes. What amount of indicators per cM (gene occurrence) was discover so you’re able to differ notably off a consistent shipping involving the twelve linkage communities, during the 5% peak to own G2F and you can F2 (P-worth G2F = 0.012, P-worthy of F2 = 0.00007), hence differences was just beyond your limits regarding analytical importance having G2M (P-worth G2M = 0.074). On the three maps, there had been fewer family genes inside the LG 8 and a larger count of genetics for the LG 6 and you may 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 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 in place of G2F) = 0.0004 and P-value (F2 in the 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).

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