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Table 3 Accuracy of genomic prediction (±SE) for a trait with a heritability of 0.07 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

0.413 (±0.024)

 

0.347 (±0.019)

 

 data3000

0.400 (±0.023)

3.1

0.332 (±0.019)

4.3

 data2000

0.394 (±0.021)

4.6

0.326 (±0.019)

6.1

 data1000

0.377 (±0.023)

8.7

0.326 (±0.019)

6.1

 data200

0.326 (±0.021)

20.6

0.273 (±0.016)

21.1

MixP

 WGS data

0.431 (±0.028)

 

0.348 (±0.019)

 

 data3000

0.407 (±0.025)

5.6

0.333 (±0.019)

4.3

 data2000

0.404 (±0.023)

6.3

0.327 (±0.019)

6.0

 data1000

0.382 (±0.024)

11.4

0.328 (±0.019)

5.7

 data200

0.338 (±0.023)

21.6

0.276 (±0.016)

20.7

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