Shipments of 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 dating spanish guys 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 off marker occurrence having linkage group #step three of the G2F, G2M and F2 charts, reflecting recombination coldspots and you will hotspots [find A lot more document 10 for your chart]. Marker thickness try influenced by moving forward this new period across the chart inside step one cM increments. Brand new horizontal traces suggest the reduced and you can upper thresholds identifying an effective gene people or a gap. x-axis: chart range over the whole linkage group (marker status is just as in the Even more file step 3, with preferred markers showcased into the eco-friendly (ranging from G2F and you may F2) and red (ranging from G2M and you may F2), and you can sealed for the squares to own indicators common so you’re able to G2F, G2M and F2). y-axis: level of family genes regarding the period. Groups prominent with the F2 map at least you to definitely G2 chart try conveyed by the tangerine groups linked because of the dotted tangerine lines. Clusters popular into the G2F and G2M charts try indicated by the black colored sectors connected of the dotted black colored contours. Groups noticed toward only 1 chart is actually conveyed because of the black colored groups.
Conversation
In this analysis, we build progressive genomic equipment (unigene set, SNP-selection and gene-dependent linkage maps) and you can used these to the fresh new identity out of an effective deleterious allele segregating during the an enthusiastic embryo stability locus, in order to degree of one’s the total amount and you may shipment of recombination with each other the latest chromosomes in addition to facts (sex, hereditary background) probably bookkeeping to possess variations.