Affirmed, a premier standard of macrocollinearity are seen across the a dozen LGs

Affirmed, a premier standard of macrocollinearity are seen across the a dozen LGs

Project from homologous LGs

LGs which were homologous ranging from F2 and G2F or F2 and G2M charts have been recognized on such basis as a good subset out-of 198 and you can 240 popular genetics, correspondingly. But not, 15 cases of LG project otherwise purchase inaccuracies were understood, indicating sometimes the current presence of paralogous loci (which was however the case for a couple of indicators mapped to various LGs towards G2 and you will F2 maps: AL750495 inside the LG10_G2F and you may LG8_G2M, and you may CT577280 when you look at the LG7_F2 and you will LG4_G2M) or a linkage buying disease (that was the truth for 13 non-distorted indicators to present more map metropolises into the homologous linkage groups (BX678432 during the LG2_F2 and you will LG2_G2M, CR393801 inside the LG4_F2 and you will LG4_G2F, CT580300 into the LG4_F2 and LG4_G2F, m26 in the LG4_F2 and you will LG4_G2F, AL749536 in LG4_F2 and you may LG4_G2F, m592 in the LG4_F2 and you can LG4_G2F, m593 when you look at the LG4_F2 and you may LG4_G2F, CT577468 in the LG4_F2 and you can LG4_G2F, FN256629 during the LG4_F and you may LG4_G2M, m738/m739/m740 (same contig) inside LG7_F2 and LG7_G2M, 384_LIM2 inside LG7_F2 and you will LG7_G2M, BX250169 in LG7_F2 and you can LG7_G2M, m590 within the LG7_F2 and LG7_G2M). These 15 genetics have been excluded throughout the list of anchor markers. In addition to the point indicators between F2 and G2 charts, twenty-five testcross indicators (that’s, twenty five contigs whereby one or two SNPs was basically polymorphic in either father or mother) were used to ensure the fresh new homology anywhere between LGs to the G2F and G2M maps.

Gene thickness

Good Chi dos shot was did to the three charts so you’re able to determine whether just how many genes try uniformly marketed involving the coastal pine chromosomes. What amount of markers each cM (gene thickness) is discovered so you can disagree somewhat away from an excellent consistent delivery involving the a dozen linkage teams, at the 5% top to have G2F and you may F2 (P-well worth G2F = 0.012, P-really worth F2 = 0.00007), and this improvement was just away from limits out-of analytical relevance to own G2M (P-worthy of G2M = 0.074). With the the about three charts, there have been fewer genes from inside the LG 8 and more substantial count away from family genes from inside 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 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 versus G2F) = 0.0004 and P-value (F2 as opposed to 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 https://datingranking.net/local-hookup/ballarat/ 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).