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Table 1 Experimental variables and genetic parameter estimates for IHNV resistance in rainbow trout

From: Genome-wide association analysis and accuracy of genome-enabled breeding value predictions for resistance to infectious hematopoietic necrosis virus in a commercial rainbow trout breeding population

IHNV resistance phenotypea

Methodb

Number of families

Phenotyped fish

Genotypedc

Sliding 1-Mb windows

Genetic parameterf

SNPsd

Fishd

\(\sigma_{g}^{2}\)

\(\sigma_{f/d}^{2}\)

\(\sigma_{e}^{2}\)

\(h^{2}\)

DAYS

PBLUP

100

4987

n.a.e

n.a.

n.a.

9.44 ± 3.22

1.77 ± 1.05

17.06 ± 1.67

0.33 ± 0.10

ssGBLUP

100

4987

35,397

1044

1414

6.35 ± 1.25

2.40 ± 0.77

18.58 ± 0.72

0.23 ± 0.04

STATUS

PBLUP

100

4987

n.a.

n.a.

n.a.

2.22 ± 17.41

0.29 ± 1.16

1.00 ± 0.04

0.28 ± 0.14

ssGBLUP

100

4987

35,397

1044

1414

0.81 ± 0.23

0.19 ± 0.07

1.00 ± 0.03

0.25 ± 0.07

  1. Offspring from year-class 2016 families from the nucleus breeding population of Clear Springs Foods, Inc.
  2. aIHNV resistance phenotypes: survival days after disease challenge (DAYS) and binary survival status (STATUS)
  3. bVariance components analysis was performed using pedigree-based BLUP (PBLUP) and PBLUP with genomics data (ssGBLUP)
  4. cSampled fish were genotyped with the 57 K SNP array (Chip)
  5. dEffective number of genotyped SNPs and fish after data quality control, respectively; the initial raw dataset had 1044 fish (sires = 52; offspring = 992) genotyped with 42,045 SNPs
  6. en.a. indicates that data are not available; the PBLUP model uses only pedigree and phenotype records in the analysis
  7. fGenetic parameter estimate (± standard error): \(\sigma_{g }^{2}\) is the additive genetic variance; \(\sigma_{f/d}^{2}\) is the variance due to nested effects of families within challenge date; \(\sigma_{e}^{2}\) is the residual error; and \(h^{2}\) is the estimated narrow-sense heritability. For the binary STATUS, the heritability estimated on the underlying scale of liability was transformed to the observed scale of disease survival