Distribution away from 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 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 https://datingranking.net/local-hookup/atlanta/ 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.
Symbol away from marker thickness for linkage group #step three of the G2F, G2M and you may F2 charts, reflecting recombination coldspots and you can hotspots [look for More document ten for the entire chart]. Marker density was determined by moving on new period across the chart during the step 1 cM increments. The fresh lateral outlines suggest the low and you can upper thresholds defining a beneficial gene class otherwise a gap. x-axis: chart distance along the entire linkage classification (marker position can be inside the Even more document step three, with common indicators emphasized inside green (between G2F and you will F2) and you will red (between G2M and you can F2), and you can enclosed when you look at the squares to own indicators preferred in order to G2F, G2M and you will F2). y-axis: level of family genes on the interval. Clusters prominent on F2 map as well as the very least you to G2 map was expressed by orange circles connected of the dotted tangerine outlines. Clusters common toward G2F and you can G2M maps was shown by black colored groups linked by the dotted black contours. Groups noticed into the only one map try indicated because of the black circles.
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Within this investigation, i build modern genomic devices (unigene set, SNP-variety and gene-based linkage maps) and you will applied these to the brand new character away from a good deleterious allele segregating during the an embryo viability locus, and education of your the amount and you may shipping away from recombination with each other the chromosomes and also the activities (gender, genetic record) probably bookkeeping getting differences.