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Table 4 Average estimated heritabilities using different marker densities to calculate the genomic relationship matrix

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

Sc. Nb HF 1 Nb J 2 RANDOM VAR
    600 k 60 k 600 k + QTL 60 k + QTL 600 k 60 k 600 k + QTL 60 k + QTL
1 2000 2000 0.78 (0.003) 0.77 (0.003) 0.80 (0.002) 0.84 (0.001) 0.59 (0.001) 0.58 (0.001) 0.61 (0.001) 0.64 (0.001)
2 2000 500 0.76 (0.004) 0.74 (0.004) 0.78 (0.003) 0.82 (0.003) 0.54 (0.003) 0.53 (0.003) 0.57 (0.003) 0.59 (0.003)
3 2000 100 0.75 (0.005) 0.73 (0.005) 0.77 (0.004) 0.80 (0.005) 0.54 (0.004) 0.53 (0.004) 0.57 (0.004) 0.59 (0.004)
4 2000 0 0.75 (0.005) 0.73 (0.005) 0.77 (0.004) 0.81 (0.005) 0.55 (0.004) 0.54 (0.004) 0.58 (0.004) 0.60 (0.004)
5 500 2000 0.79 (0.004) 0.78 (0.005) 0.80 (0.003) 0.83 (0.002) 0.61 (0.006) 0.60 (0.005) 0.63 (0.005) 0.66 (0.005)
6 100 2000 0.78 (0.007) 0.77 (0.007) 0.80 (0.006) 0.82 (0.005) 0.58 (0.006) 0.58 (0.006) 0.60 (0.006) 0.63 (0.005)
7 0 2000 0.78 (0.008) 0.77 (0.008) 0.79 (0.007) 0.82 (0.006) 0.56 (0.006) 0.55 (0.006) 0.57 (0.005) 0.60 (0.005)
  1. Average heritabilities (standard errors across replicates) estimated with a model including a random across-breed animal effect and a within-breed animal effect using different reference populations, 100 QTL underlying the trait with on average a moderately low minor allele frequency 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). The genomic relationship matrix was calculated using 606 384 SNPs (600 k), 60 000 SNPs (60 k), 606 384 SNPs plus all sampled QTL (600 k + QTL), or 60 000 SNPs plus all sampled QTL (60 k + QTL).
  2. Sc. = scenarios; 1Nb HF = number of Holstein Friesian animals; 2Nb J = number of Jersey animals.