Distribution away from recombination across 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 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.
Icon regarding marker density to own linkage group #step three of your own G2F, G2M and F2 maps, reflecting recombination coldspots and hotspots [discover Extra document ten for the whole chart]. Marker density are influenced by progressing the fresh new interval along side map within the step one cM increments. The lateral lines imply the lower and higher thresholds determining good gene group otherwise a gap. x-axis: chart distance along side entire linkage classification (marker reputation can be within the Even more document step 3, with prominent indicators emphasized from inside the eco-friendly (between G2F and you will F2) and you will green (ranging from G2M and F2), and sealed for the squares getting markers preferred so you can G2F, G2M and you may F2). y-axis: number of family genes in the interval. Groups well-known on F2 chart at minimum you to G2 chart is shown from the tangerine circles connected by the dotted lime outlines. Groups common on the G2F and you may G2M charts is shown by the black colored groups linked by dotted black traces. Groups chat room serbian seen towards only 1 map is conveyed by the black colored sectors.
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Inside data, i build modern genomic gadgets (unigene place, SNP-array and you will gene-mainly based linkage charts) and used them to the fresh character regarding good deleterious allele segregating within an enthusiastic embryo viability locus, in order to training of your own the amount and shipment regarding recombination with each other this new chromosomes therefore the facts (gender, genetic record) potentially bookkeeping for differences.
