Shipping 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 scottish women dating sites 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.
Symbolization off marker thickness having linkage class #step three of G2F, G2M and you can F2 charts, showing recombination coldspots and you will hotspots [find Most file ten for your chart]. Marker density is influenced by shifting the fresh new interval across the chart into the step 1 cM increments. The newest lateral outlines mean the low and you can top thresholds identifying a beneficial gene class otherwise a space. x-axis: chart distance along the entire linkage classification (marker reputation is really as from inside the Most file step 3, that have popular markers highlighted when you look at the eco-friendly (between G2F and F2) and red (anywhere between G2M and you may F2), and sealed into the squares getting indicators well-known to help you G2F, G2M and you can F2). y-axis: amount of genes regarding interval. Groups preferred on F2 chart as well as minimum that G2 map is shown because of the tangerine groups connected from the dotted tangerine traces. Groups preferred to the G2F and you will G2M maps is shown of the black colored groups linked from the dotted black colored lines. Groups seen on only 1 map is conveyed because of the black colored groups.
Talk
Within research, i arranged modern genomic tools (unigene set, SNP-number and you may gene-centered linkage maps) and you may used these to the latest identity out-of a beneficial deleterious allele segregating on an enthusiastic embryo stability locus, and to studies of the the quantity and you will shipping away from recombination along brand new chromosomes while the issues (gender, genetic history) potentially accounting getting differences.