Table 3.

Average estimated heritabilities of QTL with different properties

Sc.	Nb HF 1	Nb J 2	RANDOM			VAR
			Moderately low MAF 3	Very low MAF 3	Extremely low MAF 3	Moderately low MAF 3	Very low MAF 3	Extremely low MAF 3
1	2000	2000	0.78 (0.003)	0.77 (0.002)	0.72 (0.011)	0.60 (0.001)	0.44 (0.002)	0.21 (0.002)
2	2000	500	0.76 (0.004)	0.75 (0.006)	0.70 (0.023)	0.54 (0.002)	0.38 (0.004)	0.18 (0.001)
3	2000	100	0.75 (0.005)	0.75 (0.007)	0.70 (0.027)	0.54 (0.002)	0.36 (0.004)	0.18 (0.002)
4	2000	0	0.75 (0.005)	0.75 (0.007)	0.70 (0.029)	0.54 (0.002)	0.37 (0.004)	0.18 (0.002)
5	500	2000	0.79 (0.004)	0.78 (0.002)	0.70 (0.008)	0.64 (0.001)	0.47 (0.002)	0.22 (0.006)
6	100	2000	0.78 (0.007)	0.76 (0.005)	0.62 (0.017)	0.62 (0.001)	0.44 (0.002)	0.19 (0.004)
7	0	2000	0.78 (0.008)	0.76 (0.006)	0.58 (0.025)	0.61 (0.002)	0.42 (0.002)	0.17 (0.004)

Average heritabilities (standard errors across replicates) estimated with a model including a random across-breed animal effect and a within-breed animal effect and using 606 384 SNPs to calculate the genomic relationship matrix using different reference populations, different average minor allele frequencies (MAF) of the 100 QTL that underlie the trait and using simulated allele substitution effects randomly sampled from a gamma distribution (RANDOM) or with each QTL explaining an equal proportion of the genetic variance (VAR).

Sc. = scenarios; ¹Nb HF = number of Holstein-Friesian animals; ²Nb J = number of Jersey animals; ³MAF = minor allele frequency.