Impact of rare and low-frequency sequence variants on reliability of genomic prediction in dairy cattle

Table 5 Reliabilities of genomic prediction for one random replicate in each simulation scenario and different strategies for selection of rare and low-frequency variants (RLFV)

Scenarios	SQTN	MQTN	LQTN
50 k	35.7	43.0	38.0
50 k + all simulated QTN	42.5	46.4	43.6
50 k + simulated QTN and RLFV from 10 random selected genes from each chromosome	41.3	44.1	37.9
50 k + RLFV in mapped genes	39.7	44.3	40.1

SQTN corresponds to the scenario with RLFV in seven to ten genes per chromosome simulated as causal variants; MQTN corresponds to the scenario with RLFV in one gene per chromosome simulated as causal variants; LQTN corresponds to the scenario with RLFV in nine randomly selected genes across the whole genome simulated as causal variants. Reliabilities are presented on a scale from 0 to 100%. Accuracies, i.e. the square roots of the reliabilities, ranged from 0.597 to 0.681 on a scale from 0 to 1, while the corresponding standard errors ranged from 0.010 to 0.012

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