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

Table 1 Characteristics of different classes of variants used to simulate QTL

Characteristic per class	Holstein-Friesian	Jersey	Total
Moderately low average MAF ^1,2
Segregating variants	63 119	55 363	65 920
Number of breed-specific variants	10 557	2801	13 358
Percentage of breed-specific variants	16.0	4.2	20.3
Average MAF¹ of the 65 920 segregating variants (± standard deviation)	0.130 ± 0.169	0.115 ± 0.168	0.122 ± 0.146
Very low average MAF ^1,3
Segregating variants	61 302	49 473	67 097
Number of breed-specific variants	17 624	5795	23 419
Percentage of breed-specific variants	26.3	8.6	34.9
Average MAF¹ of the 67 097 segregating variants (± standard deviation)	0.082 ± 0.146	0.072 ± 0.142	0.077 ± 0.127
Extremely low average MAF ^1,4
Segregating variants	1804	1245	2142
Number of breed-specific variants	897	338	1235
Percentage of breed-specific variants	41.9	15.8	57.7
Average MAF¹ of the 2142 segregating variants (± standard deviation)	0.017 ± 0.067	0.015 ± 0.066	0.016 ± 0.059

¹MAF = minor allele frequency; ²annotated as synonymous mutations; ³annotated as missense mutations; ⁴annotated as premature stop codon mutations.

ISSN: 1297-9686