High density marker panels, SNPs prioritizing and accuracy of genomic selection

BMC Genomic Data

Table 2 Preselected SNPs based on different cutoff values for the FST scores and different simulation scenarios

Panel density	QTL effects¹	Quantile	F_ST Score³	Selected SNPs⁴
		99.5	0.02	935
	Gamma⁵	99.0	0.01	1956
		97.5	0.004	4932
200 K
		99.5	0.009	1076
	Predefined⁶	99.0	0.007	2171
		97.5	0.005	5620
		99.5	0.015	2078
	Gamma	99.0	0.009	3586
		97.5	0.004	10,178
400 K
		99.5	0.009	2036
	Predefined	99.0	0.007	4646
		97.5	0.004	10,651

¹Distribution used for the simulation of the QTL effects, ²quantiles of the F_ST score distribution, ³cutoff point for the fixation index (F_ST), ⁴number of selected SNPs based on the F_ST score cutoff, ⁵Gamma distribution with shape parameter equal 0.4, and ⁶QTL effects pre-defined to explain at least 0.5% of genetic variance each

ISSN: 2730-6844