To your G2F and G2M charts, recombination coldspots have been defined as a cluster with a minimum of 7 indicators (P

To your G2F and G2M charts, recombination coldspots have been defined as a cluster with a minimum of 7 indicators (P

Delivery regarding 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 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 away from marker density for linkage category #3 of one’s G2F, G2M and F2 charts, highlighting recombination coldspots and you can hotspots [see Even more file ten for your chart]. Marker thickness are determined by progressing the brand new interval along side map when you look at the step one cM increments. The brand new horizontal traces indicate the reduced and you may upper thresholds determining an effective gene cluster or a space. x-axis: map range over the whole linkage classification (marker standing is just as into the Even more file step 3, having popular markers emphasized from inside the green (anywhere between G2F and you will F2) and you can pink (between G2M and you can F2), and you will sealed into the squares for indicators preferred in order to G2F, G2M and you may F2). y-axis: amount of genetics about interval. Clusters prominent toward F2 map and at least you to definitely G2 chart was indicated by tangerine sectors linked by the dotted lime outlines. Groups popular towards G2F and G2M maps is actually shown of the black colored circles connected of the dotted black colored contours. Clusters noticed on singular chart is actually shown because of the black colored sectors.

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In this data, we put up modern genomic products (unigene place, SNP-assortment and you can gene-built linkage charts) and you may used these to this new character away from a deleterious allele segregating from the a keen embryo stability locus, and also to knowledge of one’s extent and distribution away from recombination together the latest chromosomes as well as the issues (gender, hereditary record) possibly bookkeeping to have distinctions.

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