Shipment out of recombination along side 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 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; PG2M = 1.4 ? 10 -26 ). trucker dating apps 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.
Icon regarding marker occurrence to have linkage class #step three of one’s G2F, G2M and you can F2 charts, highlighting recombination coldspots and you will hotspots [come across More document ten for the entire chart]. Marker density are influenced by progressing the period along side map from inside the step one cM increments. The latest lateral contours indicate the lower and you will higher thresholds identifying good gene class or a space. x-axis: chart range over the whole linkage group (marker standing is really as in More document 3, which have common markers highlighted for the environmentally friendly (ranging from G2F and you may F2) and red (ranging from G2M and you may F2), and you can sealed into the squares for markers popular so you’re able to G2F, G2M and F2). y-axis: level of genes throughout the interval. Clusters preferred with the F2 map and at the very least you to definitely G2 map was indicated because of the lime circles linked from the dotted lime contours. Groups common towards the G2F and you may G2M charts try shown by the black colored circles connected because of the dotted black colored outlines. Clusters seen for the only one chart is conveyed from the black groups.
Discussion
Inside studies, i create progressive genomic tools (unigene place, SNP-number and you can gene-established linkage maps) and applied these to the newest character out-of good deleterious allele segregating at an enthusiastic embryo viability locus, and also to education of one’s extent and shipments off recombination collectively the brand new chromosomes and points (gender, genetic background) probably bookkeeping having variations.