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Table 3 Average estimated heritabilities of QTL with different properties

From: Impact of QTL properties on the accuracy of multi-breed genomic prediction

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