Table 4.

Results^a of genomic prediction of the three traits using Bayesian BLUP or mixture models, according to number of main SNP effects

Main	Protein			Fertility			Mastitis
SNPs †	BLUP	4 mixture		BLUP	4 mixture		BLUP	4 mixture
1000	0.347 (-0.124)	0.396 (-0.181)		0.356 (0.060)	0.334 (0.040)		0.319 (0.028)	0.318 (0.085)
2000	0.376 (-0.115)	0.409 (-0.174)		0.364 (0.055)	0.333 (0.056)		0.333 (0.026)	0.346 (0.054)
3000	0.400 (-0.107)	0.413 (-0.171)		0.348 (0.016)	0.359 (0.008)		0.345 (0.009)	0.359 (0.033)
4000	0.410 (-0.107)	0.422 (-0.164)		0.359 (0.026)	0.370 (0.012)		0.348 (0.008)	0.368 (0.019)
5000	0.417 (-0.102)	0.426 (-0.160)		0.368 (0.035)	0.375 (0.022)		0.358 (0.002)	0.371 (0.012)
6000	0.422 (-0.102)	0.430 (-0.161)		0.367 (0.026)	0.376 (0.028)		0.358 (0.009)	0.373 (0.016)
7000	0.423 (-0.108)	0.435 (-0.155)		0.369 (0.031)	0.378 (0.034)		0.363 (0.006)	0.374 (0.006)
8000	0.426 (-0.106)	0.437 (-0.143)		0.373 (0.041)	0.384 (0.044)		0.366 (0.003)	0.378 (0.002)
9000	0.425 (-0.103)	0.440 (-0.136)		0.373 (0.035)	0.384 (0.037)		0.368 (0.008)	0.376 (0.009)
10 000	0.428 (-0.100)	0.441 (-0.137)		0.376 (0.040)	0.389 (0.054)		0.369 (0.006)	0.375 (0.011)
20 000	0.427 (-0.101)	0.446 (-0.122)		0.384 (0.048)	0.384 (0.033)		0.372 (0.012)	0.382 (0.003)
30 000	0.427 (-0.111)	0.448 (-0.116)		0.384 (0.048)	0.388 (0.048)		0.372 (0.018)	0.386 (0.006)
40 000	0.427 (-0.108)	0.446 (-0.114)		0.383 (0.043)	0.390 (0.043)		0.373 (0.008)	0.384 (0.003)
50 000	0.424 (-0.121)	0.447 (-0.115)		0.385 (0.051)	0.387 (0.044)		0.375 (0.008)	0.383 (0.006)
492 057	0.429 (-0.120)	0.447 (-0.127)		0.389 (0.057)	0.390 (0.057)		0.372 (0.005)	0.378 (0.005)
Indiv. SNP	0.423 (-0.122)	0.439 (-0.122)		0.384 (0.059)	0.383 (0.048)		0.368 (0.069)	0.373 (0.026)
approach

^avalues displayed as: reliability (prediction bias)

^†number of highest (absolute) SNP effects used to select haploblocks