Linkage disequilibrium interval mapping of quantitative trait loci

BMC Genomics

Table 1 General Comparison between T2 and HAPim.

Marker type	N	Marker spacing	MSE		Difference in MSE P value
			T2	HAPim
SNP ⁽¹⁾	200	2 cM	5.10	5.08	0.948
	400	2 cM	4.69	5.04	0.366
	200	0.25 cM	2.00	1.24	< 0.001**
	400	0.25 cM	1.34	0.92	0.005**
MST ⁽²⁾	200	2 cM	2.93	2.77	0.438
	400	2 cM	1.81	1.44	0.056
	200	0.25 cM	0.71	0.46	0.012*
	400	0.25 cM	0.49	0.30	0.033*

* : P < 0.05, ** : P < 0.01
⁽¹⁾ : single nucleotide polymorphism
⁽²⁾ : microsatellite
Mean square errors (MSEs) in cM² of quantitative trait locus (QTL) location estimates obtained by the T2 and HAPim methods for various effective population sizes, marker spacings and marker types, t = 100 and the initial association was complete.

ISSN: 1471-2164