Shipping away from 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 ). 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.
Representation of marker thickness having linkage class #step three of your G2F, G2M and you may F2 maps, highlighting recombination coldspots and you will hotspots [look for Additional file ten for the entire chart]. Marker occurrence are influenced by shifting this new interval along side chart into the step one cM increments. New horizontal lines indicate the low and you will upper thresholds identifying a good gene team or a gap. x-axis: chart length along side entire linkage group (marker condition is really as inside Additional document 3, having common indicators emphasized from inside the green (anywhere between G2F and you may F2) and you can red (anywhere between G2M and you will F2), and you may shut into the squares getting trucker sex chat markers prominent to G2F, G2M and you can F2). y-axis: quantity of genetics throughout the period. Clusters popular toward F2 map at least one to G2 map is expressed because of the lime sectors connected from the dotted lime contours. Groups popular with the G2F and G2M maps is actually conveyed by the black sectors linked of the dotted black contours. Clusters seen toward only one chart try shown because of the black colored circles.
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Within this analysis, i install modern genomic products (unigene place, SNP-variety and you will gene-established linkage charts) and you will used them to the identity away from a beneficial deleterious allele segregating from the a keen embryo viability locus, and education of extent and you can shipments off recombination together the chromosomes as well as the items (gender, genetic records) possibly accounting having variations.