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Table 2 Accuracy of genomic prediction (±SE) for a trait with a heritability of 0.30 for population A based on SNP-BLUP or MixP using the different datasets

From: Within- and across-breed genomic prediction using whole-genome sequence and single nucleotide polymorphism panels

Dataset

45 QTL/Morgan

132 QTL/Morgan

Accuracy

% decrease

Accuracy

% decrease

SNP-BLUP

 WGS data

0.596 (±0.015)

 

0.582 (±0.014)

 

 data3000

0.578 (±0.016)

3.0

0.575 (±0.014)

1.2

 data2000

0.576 (±0.014)

3.4

0.568 (±0.014)

2.4

 data1000

0.564 (±0.014)

5.4

0.555 (±0.015)

4.6

 data200

0.473 (±0.015)

20.0

0.468 (±0.014)

19.6

MixP

 WGS data

0.632 (±0.018)

 

0.587 (±0.014)

 

 data3000

0.598 (±0.018)

5.4

0.579 (±0.014)

1.4

 data2000

0.591 (±0.015)

6.5

0.573 (±0.014)

2.4

 data1000

0.579 (±0.015)

8.4

0.562 (±0.015)

4.3

 data200

0.484 (±0.016)

23.4

0.465 (±0.014)

20.8

  1. Accuracy of prediction was measured as the correlation between simulated true and predicted genetic values in the validation dataset
  2. % decrease in accuracy of prediction relative to that obtained with WGS data