Estimating the effect of SNP genotype on quantitative traits from pooled DNA samples

Henshall, John M; Hawken, Rachel J; Dominik, Sonja; Barendse, William

doi:10.1186/1297-9686-44-12

Genetics Selection Evolution

Table 2 Hip height data, R² between parameters estimated using logistic regression and least squares regression

From: Estimating the effect of SNP genotype on quantitative traits from pooled DNA samples

			940 individuals		536 pools		268 pools		134 pools
	MAF	Breed	R²(α)	R²(MLP)	R²(α)	R²(MLP)	R²(α)	R²(MLP)	R²(α)	R²(MLP)
Concurrent estimation, contemporary groups with MAF < 0.01 excluded from analysis	> 0.20	both breeds	0.99	0.99	0.94	0.90	0.84	0.75	0.68	0.53
		Tropical composite	0.98	0.98	0.93	0.89	0.82	0.72	0.64	0.50
		Brahman	0.99	1.00	0.94	0.92	0.86	0.78	0.67	0.53
	> 0.05	both breeds	0.96	0.97	0.92	0.89	0.84	0.74	0.69	0.52
		Tropical composite	0.95	0.96	0.91	0.87	0.81	0.71	0.64	0.48
		Brahman	0.97	0.98	0.92	0.90	0.83	0.76	0.61	0.51
	> 0.01	both breeds	0.95	0.97	0.92	0.88	0.84	0.73	0.68	0.51
		Tropical composite	0.81	0.95	0.70	0.87	0.59	0.70	0.38	0.47
		Brahman	0.02	0.90	0.02	0.80	0.01	0.64	0.01	0.38
Pre-adjusted, all contemporary groups included in analysis	> 0.20	both breeds	0.96	0.99	0.91	0.90	0.80	0.74	0.65	0.53
		Tropical composite	0.99	1.00	0.93	0.89	0.81	0.71	0.64	0.50
		Brahman	0.99	1.00	0.94	0.91	0.86	0.79	0.67	0.54
	> 0.05	both breeds	0.97	0.99	0.92	0.90	0.83	0.73	0.69	0.53
		Tropical composite	0.98	0.99	0.93	0.89	0.82	0.71	0.66	0.50
		Brahman	0.97	0.99	0.93	0.91	0.86	0.79	0.69	0.54
	> 0.01	both breeds	0.97	0.99	0.91	0.89	0.83	0.73	0.71	0.53
		Tropical composite	0.84	0.98	0.80	0.88	0.71	0.70	0.59	0.49
		Brahman	0.00	0.76	0.00	0.68	0.00	0.59	0.00	0.41
Pre-adjusted, contemporary groups with MAF < 0.01 excluded from analysis	> 0.01	both breeds	0.97	0.99	0.93	0.90	0.85	0.73	0.72	0.53
		Tropical composite	0.95	0.99	0.92	0.89	0.82	0.71	0.65	0.50
		Brahman	0.93	0.90	0.78	0.62	0.80	0.62	0.45	0.18
Concurrent estimation, one random individual from each pool	> 0.20	both breeds	1.00	1.00	0.38	0.23	0.10	0.04	0.02	0.01
		Tropical composite	1.00	1.00	0.36	0.21	0.09	0.04	0.03	0.01
		Brahman	1.00	1.00	0.36	0.23	0.10	0.05	0.00	0.00
Adjustment for contemporary group before pooling	> 0.20	both breeds	0.95	0.91	0.74	0.62	0.74	0.61	0.30	0.17

Back to article page

ISSN: 1297-9686

Contact us

Submission enquiries: helene.hayes@inrae.fr
General enquiries: info@biomedcentral.com