Results
Combining the outcomes off most of the crosses we detected a maximum of thirty-two,511 CO occurrences which were always make large-solution CO maps during the D. melanogaster (Shape 1). Considering the increased density away from indicators and few away from CO occurrences per chromosome and you can genotyped travel, per CO was supported by of a lot contiguous indicators at either side and is all of our presumption that people has actually recognized all COs. The entire genetic map size to have D. melanogaster received in our crosses is 287.step 3 cM, closely coordinating classical strategies (282 cM ). A low-resolution approximation towards shipment out-of CO rates (c) with each other chromosome hands predicated on all want Vietnamese dating reviews of our studies (Figure S2) recovers an equivalent general, large-level delivery because the past charts predicated on visible markers –, , –. Affirmed, c was dramatically quicker close telomeres and you will centromeres, so we discover zero CO occurrences regarding small fourth (dot) chromosome that proceeds so you’re able to meiotic segregation instead chiasmata .
Rate off crossing over (c) considering study off the crosses and you can conveyed inside the centimorgans (cM) for each megabase (Mb) for each girls meiosis (red line). c try found along chromosomes to own 100-kb screen and you can a motion ranging from adjacent window away from 50 kb. Bluish lines mean ninety% confidence interval to have c at each windows.
Our detailed maps deepen the recent appreciation for intra-chromosomal variation in 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 variation when you look at the CO terrain
The analysis away from crosses out-of pure D. melanogaster stresses allowed me to make and you can evaluate seven CO charts once controlling getting type of this situations that may alter CO costs during the Drosophila such decades, temperature, amount of matings otherwise eating –. To increase statistical stamina i focused on variations certainly one of crosses at the the dimensions away from 250-kb collectively chromosomes. New eight CO charts reveal a high standard of intra-certain version, having form of crosses that have nations having exceptionally large pricing (>40-fold) relative to possibly surrounding regions or to other crosses (Contour dos). Sure enough, crosses revealing that parental filters do have more equivalent maps than crosses not discussing parental stresses nevertheless full magnitude of the correlation ranging from such crosses, albeit high, is pretty short (Spearman’s Roentgen = +0.451). Which observation reinforces the idea of an incredibly polygenic and polymorphic cause 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.