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

Table 4 Characteristics for one random replicate of each simulation scenario

Characteristics	SQTN	MQTN	LQTN
Number of genes	7–10 per chr	1 per chr	9
Number of genic RLFV simulated as QTN	21,468	1348	235
Number of RLFV from 10 random selected genes from each chromosome	29,166	27,290	28,308
Number of RLFV from mapped genes	78,080	81,010	80,999

Chr = chromosome
RLFV refer to rare and low-frequency variants and QTN refer to quantitative trait nucleotides. 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. The simulated total variances for the QTN in SQTN, MQTN and LQTN were 10% of the estimate of variance explained by 50 k markers for fertility index

ISSN: 1297-9686