On the G2F and you can G2M maps, recombination coldspots were recognized as a group with a minimum of 7 indicators (P

Shipment of recombination along 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; P_G2M = 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 https://datingranking.net/local-hookup/charlottetown/ (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.

Image out-of marker thickness to own linkage group #3 of one’s G2F, G2M and you may F2 maps, reflecting recombination coldspots and you may hotspots [see More file 10 for the whole chart]. Marker density is actually influenced by progressing the fresh new interval across the chart inside the 1 cM increments. The new horizontal contours suggest the low and upper thresholds identifying a beneficial gene people or a space. x-axis: map length along side whole linkage group (marker condition is as within the More document step 3, with well-known markers emphasized when you look at the eco-friendly (ranging from G2F and you can F2) and you can red (anywhere between G2M and you can F2), and sealed in the squares to have indicators popular to help you G2F, G2M and you may F2). y-axis: quantity of family genes regarding the period. Groups common for the F2 map as well as minimum you to G2 chart is indicated from the tangerine circles linked by the dotted tangerine lines. Groups popular to the G2F and you can G2M charts was conveyed of the black groups linked by dotted black outlines. Groups observed into the only 1 chart was shown by the black colored groups.

Discussion

In this studies, i install modern genomic systems (unigene set, SNP-variety and you may gene-centered linkage maps) and you will used them to the fresh identification out of a deleterious allele segregating within a keen embryo viability locus, and studies of your own extent and you may shipment of recombination along the newest chromosomes while the points (gender, hereditary history) potentially bookkeeping having variations.