Shipping out of 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 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.

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Representation from marker occurrence to possess linkage class #step three of the G2F, G2M and you will F2 charts, reflecting recombination coldspots and you may hotspots [select Most document ten for the whole map]. Marker occurrence are dependent on progressing the new period over the map in step 1 cM increments. The latest lateral contours imply the reduced and you can higher thresholds defining a gene people otherwise a space. x-axis: map distance across the whole linkage category (marker position is really as in A lot more file 3, which have common indicators showcased inside eco-friendly (anywhere between G2F and you will F2) and you will green (anywhere between G2M and you can F2), and you can sealed in squares getting indicators popular to help you G2F, G2M and you may F2). y-axis: quantity of genetics on the interval. Groups prominent on F2 chart at the very least you to G2 chart is indicated from the lime circles linked from the dotted orange lines. Clusters common to the G2F and you will G2M charts is conveyed from the black groups connected of the dotted black colored contours. Groups noticed on the singular map is conveyed of the black colored sectors.

Discussion

Contained in this studies, i install modern genomic equipment (unigene put, SNP-range and you may gene-built linkage charts) and you can used these to the identification out of a good deleterious allele segregating in the an enthusiastic embryo stability locus, also to knowledge of the amount and shipping from recombination collectively the fresh new chromosomes as well as the affairs (gender, genetic background) possibly accounting for variations.