Results
Consolidating the outcome off all crosses we perceived a maximum of thirty two,511 CO situations which were used to make higher-quality CO maps within the D. melanogaster (Figure 1). As a result of the raised density away from indicators therefore the small number out of CO occurrences for each chromosome and you can genotyped travel, for each and every CO is actually backed by of many contiguous markers during the each side and is our expectation that we provides observed every COs. The full genetic map duration to have D. melanogaster acquired in our crosses are 287.step 3 cM, closely matching ancient actions (282 cM ). A reduced-solution approximation into shipment away from CO pricing (c) along chromosome hands centered on our study (Profile S2) recovers an identical standard, large-measure shipment just like the earlier charts predicated on noticeable indicators –, , –. Sure-enough, c is greatly shorter near telomeres and you may centromeres, and in addition we detect no CO situations regarding brief 4th (dot) chromosome one proceeds to meiotic segregation without chiasmata .
Rate regarding crossing-over (c) according to investigation off all the crosses and conveyed into the centimorgans (cM) each megabase (Mb) for each and every women meiosis (red line). c are revealed with each other chromosomes to own a hundred-kb screen and you can a motion between adjoining window regarding 50 kb. Bluish outlines imply 90% rely on interval getting c at each windows.
Our detailed maps deepen the recent appreciation for intra-chromosomal variation in hot Over 50 dating CO rates in Drosophila , , and outline this heterogeneity at a much finer scale across the whole genome. Heterogeneity in CO rates along each chromosome is significant at all physical scales analyzed, from 100 kb to 10 Mb, even after removing centromeric and telomeric regions with visibly reduced rates (P<0.0001 in all cases; see Materials and Methods). All chromosome arms (except the fourth chromosome) show 15-to-20-fold variation within regions traditionally labeled as regions of non-reduced recombination rates based on low-resolution maps. This heterogeneity in CO rates is highly punctuated, with intense short-distance variation and several adjacent 100-kb windows differing by 15-to-20-fold (eg., region 15.9-16.1 Mb in the X chromosome) thus defining hot- and coldspots for CO in D. melanogaster. Most coldspots are 100-kb regions embedded in larger regions with non-reduced recombination, but we also detect several larger regions that show consistently low CO rates (e.g., a region around position15.8 Mb along chromosome arm 2R) in addition to centromeric/telomeric sequences.
Intraspecific version for the CO landscapes
The analysis out of crosses out-of sheer D. melanogaster strains allowed us to generate and you may contrast seven CO charts shortly after handling to possess type associated with points that will change CO pricing inside Drosophila eg decades, temperature, number of matings otherwise food –. To increase analytical fuel i worried about differences certainly crosses from the the dimensions away from 250-kb with each other chromosomes. The fresh seven CO charts tell you a high amount of intra-particular adaptation, that have brand of crosses having places which have excessively higher rates (>40-fold) relative to either surrounding regions or to other crosses (Shape dos). As expected, crosses revealing that adult strain have significantly more comparable maps than just crosses maybe not sharing parental challenges however the full magnitude of your correlation anywhere between this type of crosses, albeit tall, is rather brief (Spearman’s R = +0.451). So it observance reinforces the idea of a very polygenic and you can polymorphic basis for CO distribution collectively chromosomes.
To quantify variation in CO rates among the eight CO maps we estimated the variance to mean ratio (Index of Dispersion; RCO) and tested whether the different number of CO events at a given region can be explained by a Poisson process. Moreover, we focused on variation in the distribution of CO rates along chromosomes and therefore we took into account the number of total events for each chromosome (see Materials and Methods for details). Our study of RCO along chromosomes reveals many regions (107 or 22% of all non-overlapping 250-kb regions across the genome) with a variance among crosses larger than expected (overdispersion) and this pattern is observed in all chromosomes (Figure 3). The magnitude of this excess variance is highest for chromosome arm 2L while notably reduced for the chromosome arm 3L. Significant overdispersion of CO rates among crosses is also detected when we study larger genomic regions. At a physical scale of 1 Mb, more than half of the genomic regions exhibit excess variance, thus suggesting that regions with variable CO rates are frequent enough across the D. melanogaster genome to be playing a detectable role in a large fraction of these longer sequences.