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Table 6 Accuracy of genomic prediction (SE) for a trait with a heritability of 0.30 based on single- and multi-breed reference populations (RP) obtained with 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

Single-breed

Multi-breed

RP = 200

RP = 400

RP = 400

T = 10

T = 50

SNP-BLUP

MixP

SNP-BLUP

MixP

SNP-BLUP

MixP

SNP-BLUP

MixP

45 QTL/Morgan

 WGS data

0.596 (0.015)

0.632 (0.018)

0.696 (0.014)

0.736 (0.017)

0.654 (0.013)

0.710 (0.015)

0.627 (0.013)

0.675 (0.019)

 data3000

0.578 (0.016)

0.598 (0.018)

0.681 (0.013)

0.719 (0.015)

0.578 (0.016)

0.602 (0.018)

0.571 (0.016)

0.592 (0.019)

 data2000

0.576 (0.014)

0.591 (0.015)

0.679 (0.013)

0.713 (0.014)

0.571 (0.015)

0.574 (0.016)

0.564 (0.016)

0.558 (0.017)

 data1000

0.564 (0.014)

0.579 (0.015)

0.668 (0.013)

0.697 (0.014)

0.552 (0.017)

0.551 (0.019)

0.546 (0.017)

0.549 (0.017)

 data200

0.473 (0.015)

0.484 (0.016)

0.566 (0.014)

0.576 (0.016)

0.424 (0.017)

0.406 (0.017)

0.428 (0.019)

0.423 (0.021)

132 QTL/Morgan

 WGS data

0.582 (0.014)

0.587 (0.014)

0.691 (0.011)

0.702 (0.012)

0.647 (0.011)

0.662 (0.011)

0.612 (0.014)

0.624 (0.014)

 data3000

0.575 (0.014)

0.579 (0.014)

0.681 (0.010)

0.688 (0.011)

0.569 (0.012)

0.573 (0.013)

0.573 (0.015)

0.576 (0.015)

 data2000

0.568 (0.014)

0.573 (0.014)

0.670 (0.012)

0.677 (0.012)

0.568 (0.012)

0.570 (0.013)

0.565 (0.015)

0.567 (0.015)

 data1000

0.555 (0.015)

0.562 (0.014)

0.654 (0.012)

0.665 (0.012)

0.537 (0.012)

0.536 (0.012)

0.542 (0.016)

0.521 (0.015)

 data200

0.468 (0.014)

0.465 (0.014)

0.568 (0.013)

0.563 (0.013)

0.427 (0.017)

0.416 (0.017)

0.430 (0.014)

0.411 (0.014)

  1. Accuracy of prediction was measured as the correlation between simulated true and predicted genetic value in the validation dataset