Distribution 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 ). 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 Tennessee singles 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.
Signal off marker thickness to possess linkage group #3 of your own G2F, G2M and you may F2 charts, reflecting recombination coldspots and you will hotspots [pick A lot more file ten for your chart]. Marker thickness are dependent on moving on new period across the chart in the step one cM increments. New lateral traces indicate the low and higher thresholds determining a beneficial gene cluster or a space. x-axis: chart point along side whole linkage class (marker updates is as into the Additional file 3, with preferred indicators showcased when you look at the environmentally friendly (anywhere between G2F and you can F2) and you may green (anywhere between G2M and F2), and you will sealed inside the squares getting indicators preferred to help you G2F, G2M and you will F2). y-axis: quantity of genetics about interval. Groups popular to your F2 map and also at the very least you to definitely G2 map is actually conveyed of the orange sectors linked of the dotted orange traces. Groups prominent toward G2F and you may G2M maps are shown because of the black colored groups linked of the dotted black contours. Clusters observed with the singular chart is expressed from the black colored groups.
Talk
Within studies, we set up progressive genomic products (unigene set, SNP-assortment and you may gene-founded linkage charts) and you can applied these to the fresh new identification regarding good deleterious allele segregating in the a keen embryo viability locus, and also to knowledge of your own the quantity and you can shipping out-of recombination together this new chromosomes plus the issues (sex, hereditary history) probably accounting for distinctions.