Genetics Selection Evolution

Table 4 Average (standard error) change of accuracy of MEBV for individuals in the evaluation population as affected by alternative simulation situations.

From: Sensitivity of methods for estimating breeding values using genetic markers to the number of QTL and distribution of QTL variance

Method	unequal QTL variance			equal QTL variance
	low QTL	int. QTL	high QTL	low QTL	int. QTL	high QTL
	sc. 1	sc. 2	sc. 3	sc. 4	sc. 5	sc. 6
h ² = 0.25
BM	-0.14 (< 0.01)	-0.16 (0.01)	-0.08 (0.01)	-0.12 (< 0.01)	-0.16 (< 0.01)	-0.18 (< 0.01)
LARS	-0.14 (< 0.01)	-0.16 (< 0.01)	-0.15 (< 0.01)	-0.15 (< 0.01)	-0.14 (< 0.01)	-0.14 (< 0.01)
PLSR	-0.10 (< 0.01)	-0.11 (< 0.01)	-0.11 (< 0.01)	-0.11 (< 0.01)	-0.12 (< 0.01)	-0.11 (< 0.01)
nTR = 1,000
BM	0.05 (< 0.01)	0.11 (0.01)	0.16 (0.01)	0.06 (< 0.01)	0.08 (< 0.01)	0.07 (< 0.01)
LARS	0.04 (< 0.01)	0.07 (< 0.01)	0.06 (< 0.01)	0.07 (< 0.01)	0.07 (< 0.01)	0.07 (< 0.01)
PLSR	0.07 (< 0.01)	0.06 (< 0.01)	0.06 (< 0.01)	0.06 (< 0.01)	0.06 (< 0.01)	0.07 (< 0.01)
MAF >0.1
BM	-0.03 (< 0.01)	-0.01 (< 0.01)	0.02 (0.01)	-0.03 (< 0.01)	-0.03 (< 0.01)	-0.04 (< 0.01)
LARS	-0.02 (< 0.01)	0.00 (< 0.01)	-0.01 (< 0.01)	0.00 (< 0.01)	0.00 (< 0.01)	0.00 (< 0.01)
PLSR	-0.02 (< 0.01)	-0.01 (< 0.01)	-0.01 (< 0.01)	-0.03 (< 0.01)	-0.02 (< 0.01)	-0.01 (< 0.01)

Simulated heritability was reduced from 0.5 to 0.25 (h² = 0.25); the size of the training population was increased from 500 to 1,000 individuals (nTR = 1,000); only markers with a MAF above 0.10 were used to fit the models (MAF > 0.1). The simulated number of QTL was low (low nQTL), intermediate (int. nQTL) or high (high nQTL). The simulated variance of every tenth QTL was 81 times larger than variance of remaining QTL (unequal QTL variance) or equal for all QTL (equal QTL variance). Methods BM, LARS and PLSR were used to calculate the MEBV. The averages and standard deviations were calculated using 60 replicated simulations.

Back to article page

ISSN: 1297-9686

Contact us

Submission enquiries: gse@inrae.fr
General enquiries: info@biomedcentral.com