Erratum to: Theor Appl Genet (2013) 126:2699–2716 DOI 10.1007/s00122-013-2166-x
Unfortunately, the original publication of this paper contained error in the presentation of Fig. 5.
The ratio of genetic position to physical position (shown on the y-axis of Fig. 5) was incorrectly plotted as cumulative cM to cumulative Mb. As a result, this figure does not show an estimate of local recombination, as the authors intended, but rather the averaging of genetic recombination along the length of the chromosome, i.e., at the beginning of the chromosome, no averaging takes place, but by the end of the x-axis, the recombination rate has converged to the genome-wide average.
To obtain an estimate of local recombination rate, a Gaussian kernel (Python3 scipy.ndimage.filters.gaussianfilter) was used to obtain arrays of smoothed genetic distance and smoothed physical distance for the 30,984 post-imputation, post-error correction GBS SNPs—note that the SSR data were insufficiently dense to map local recombination, so corrected Fig. 5 shows results using the GBS SNPs only. Three levels of sigma (σ = 50, 100, and 200), roughly equivalent to window-size/two in a ‘rolling windows’ algorithm, were used. Smaller values of sigma allow the visualization of greater detail but also include more noise, while larger values result in greater smoothing and less noisy models. The smoothed genetic position was then divided by the smoothed physical position and plotted versus physical position using pylab (Python3 matplotlib.pyplot).
In the corrected Fig. 5, the authors highlight that recombination rates ranged substantially from as high as four times the genome-wide average to rates half the genome average, excluding centromeric regions. Thus the results still supports the original conclusion that there is benefit to saturating a genetic map of a biparental cross with GBS SNPs as variation in local recombination means that placing one marker per cM will not ensure genetic linkage between every QTL and at least one marker. The authors also note that in the corrected figure, recombination is suppressed around the centromeres, as is typically expected.
The online version of the original article can be found under doi:10.1007/s00122-013-2166-x.
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Spindel, J., Wright, M., Chen, C. et al. Erratum to: Bridging the genotyping gap: using genotyping by sequencing (GBS) to add high-density SNP markers and new value to traditional bi-parental mapping and breeding populations. Theor Appl Genet 129, 201–202 (2016). https://doi.org/10.1007/s00122-015-2618-6