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However, reducing the sampling frequency did have a profound effect on likelihood intervals for (N, s).
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Our BTxSP mapping population [ 29] and Shiringani et al., [ 28] each suggested two overlapping QTL likelihood intervals on Sb04, 57.98 Mb-64.93 Mb and 48.80 Mb-58.58 Mb, to contribute to plant height (Additional file 2: Figure S11).
Our findings lead to the prediction that the likelihood intervals on chromosome Sb01, Sb03, Sb04 and Sb06 identified by QTL mapping should bear the signature of selection, and may encode important variants with low/rare frequency for plant height and flowering time.
Finally, correspondence between sorghum and rice QTL was evaluated based on the proportions of sorghum QTL likelihood intervals within rice QTL intervals vs. outside rice QTL intervals.
In particular, two 2010 seed mass hotspots determined on chromosome Sb06 each correspond to QTL likelihood intervals (Table S2).
Some discrepancy between the association peak and the likelihood interval on chromosome Sb07 may be due to statistical limitations of QTL mapping or uneven coverage of genetic maps.
As illustrated in Figure 4 for one simulated data set with s = 0.5, the 95% likelihood interval based on the delta method widened considerably when the sampling frequency was reduced fourfold.
The corresponding profile likelihood interval based on the diffusion approximation was also much wider at (0.258, 1.062).
20 We used Epicure software for parameter estimation and tests, 24 and we based significance tests and 95% confidence intervals on likelihood profiles.
Odds-ratios with 95% confidence intervals based on likelihood ratio statistics are reported.
Odds-ratios (OR) with 95% confidence intervals based on likelihood ratio statistics were reported.
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