Distribution 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; 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.
Sign of marker density to possess linkage classification #3 of your G2F, G2M and F2 maps, reflecting recombination coldspots and you may hotspots [get a hold of A lot more file 10 for the entire map]. Marker occurrence is actually determined by shifting new interval across the chart when you look at the step one cM increments. The new horizontal lines indicate the reduced and top thresholds identifying a gene cluster or a gap. x-axis: chart range across the whole linkage class (marker reputation is really as during the Additional file 3, which have well-known markers showcased from inside the eco-friendly (anywhere between G2F and https://datingranking.net/tulsa-dating you may F2) and green (anywhere between G2M and you can F2), and you can enclosed inside squares getting indicators prominent in order to G2F, G2M and you may F2). y-axis: amount of genes from the period. Groups well-known towards F2 chart and also at least one to G2 map try shown from the lime sectors linked by dotted tangerine outlines. Clusters common into G2F and you may G2M maps is actually indicated by the black colored circles connected by dotted black colored contours. Clusters noticed with the only one map try expressed by the black colored circles.
Talk
Within research, i put up progressive genomic tools (unigene lay, SNP-variety and you can gene-mainly based linkage maps) and you may used these to the brand new identity out-of a beneficial deleterious allele segregating on an embryo stability locus, and education of one’s the quantity and you can shipments away from recombination collectively the fresh chromosomes and also the products (gender, hereditary history) potentially accounting to have variations.