Distribution off 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 trans chat room 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 from marker occurrence to possess linkage classification #step three of the G2F, G2M and you will F2 charts, reflecting recombination coldspots and you may hotspots [pick A lot more document 10 for the whole map]. Marker thickness are dependent on progressing the latest interval along the map inside step 1 cM increments. The newest lateral lines imply the reduced and you can top thresholds identifying a great gene team or a space. x-axis: map point along side whole linkage group (marker position is just as within the Even more file 3, which have preferred indicators emphasized in the environmentally friendly (ranging from G2F and you may F2) and pink (between G2M and you will F2), and you will closed in squares to own indicators prominent so you can G2F, G2M and you may F2). y-axis: level of genetics on the interval. Clusters well-known on the F2 chart as well as minimum you to definitely G2 map was expressed of the tangerine circles linked from the dotted orange outlines. Groups well-known on the G2F and G2M charts try shown by the black colored circles linked from the dotted black colored outlines. Groups observed on the only one chart is actually indicated by black circles.
Conversation
Within this investigation, i arranged progressive genomic devices (unigene put, SNP-selection and you will gene-oriented linkage charts) and used them to brand new identification away from a great deleterious allele segregating from the an embryo stability locus, also to degree of your the amount and you can shipping regarding recombination along the chromosomes in addition to items (sex, hereditary history) potentially bookkeeping for variations.