With the G2F and G2M maps, recombination coldspots was indeed recognized as a group with a minimum of seven indicators (P

Shipment from recombination over the chromosomes

We also investigated whether the distribution of recombination along the maritime pine chromosomes was affected by the genetic background in which meiotic recombination occurred, by kernel density function analysis. This approach made it possible to set appropriate band widths (per map and go to website per LG) for gene counts, rather than having to fix an arbitrary interval, as in most methods. Based on a comparative analysis of observed and expected marker distributions, we first determined the upper and lower thresholds defining recombination hotspots (larger gaps between markers than expected and coldspots (tightly linked markers), respectively [see Additional file 9]. An analysis of the F2 map showed that a cluster of at least 10 markers (P = 3 ? 10 -9 ) could be considered to constitute a recombination coldspot, whereas a cluster of no more than three markers (P = 3.6 ? 10 -10 ) could be interpreted as a recombination hotspot. _G2F = 0.002; P _G2M = 4.5 ? 10 -25 ), whereas hotspots were defined as a cluster of no more than two markers (P _G2F = 0.002; P_G2M = 1.4 ? 10 -26 ). A plot of gene density over each linkage group, generated by sliding (every 1 cM) an interval corresponding to the predetermined bandwidth, revealed the presence of significant gene clusters or gaps in the three maps (Figure 4 and Additional file 10). By aligning homologous linkage groups, we were able to compare the numbers and locations of recombination coldspots and hotspots between the three maps obtained for the different genotypes (two intraprovenance hybrids for the G2 population and one interprovenance hybrid for the F2 population). We detected a mean of 2.8 coldspots and 5.6 hotspots of recombination per chromosome, respectively. Most (67%) of the hotspots were common to at least two genotypes (27% being common to all three genotypes), but only 48% of the coldspots were common to at least two genotypes (only 7.5% were common to all three genotypes). This result suggests that the spatial structure of recombination is genetically variable, with some recombination hotspots and coldspots specific to a given genotype. Based on the number of shared and specific recombination coldspots and hotspots (Venn diagram in Additional file 10), we calculated a Jaccard index to assess the similarity between the three maps (three pair-wise comparisons). Surprisingly, the recombination patterns of the G2F and G2M maps were found to be more similar to that of the F2 map than to each other.

Image away from marker density to possess linkage group #3 of one’s G2F, G2M and F2 maps, reflecting recombination coldspots and you will hotspots [find Even more document 10 for the whole chart]. Marker density is determined by progressing the fresh new period across the chart into the step one cM increments. Brand new lateral outlines imply the lower and you will higher thresholds determining a beneficial gene group otherwise a gap. x-axis: chart length over the entire linkage class (marker reputation can be as inside the Extra document step 3, with well-known indicators showcased inside the eco-friendly (between G2F and F2) and you may pink (anywhere between G2M and you will F2), and you may sealed during the squares for indicators prominent to help you G2F, G2M and you can F2). y-axis: level of genes throughout the period. Clusters preferred with the F2 map as well as least one to G2 chart is actually expressed by orange groups connected from the dotted lime traces. Clusters prominent to the G2F and you will G2M charts was expressed by the black sectors linked by the dotted black colored traces. Clusters observed on just one map is actually shown by the black sectors.

Discussion

Contained in this study, we install modern genomic systems (unigene put, SNP-selection and you will gene-dependent linkage charts) and you may applied them to the identification of a deleterious allele segregating during the a keen embryo stability locus, in order to knowledge of the the total amount and you may delivery out of recombination together new chromosomes and the situations (sex, hereditary history) possibly accounting having variations.