Literature DB >> 29448946

Correction to: High density marker panels, SNPs prioritizing and accuracy of genomic selection.

Ling-Yun Chang1, Sajjad Toghiani2, Ashley Ling2, Sammy E Aggrey3,4, Romdhane Rekaya2,4.   

Abstract

CORRECTION TO: BMC GENETICS (2018) 19:4 DOI: 10.1186/S12863-017-0595-2: The original version of this article [1], published on 5 January 2018, contained 3 formatting errors. In this Correction the affected parts of the article are shown. The original article has been updated.

Year:  2018        PMID: 29448946      PMCID: PMC5815195          DOI: 10.1186/s12863-018-0598-7

Source DB:  PubMed          Journal:  BMC Genet        ISSN: 1471-2156            Impact factor:   2.797


Correction to: BMC Genetics (2018) 19:4 DOI: 10.1186/s12863-017-0595-2

The original version of this article [1], published on 5 January 2018, contained 3 formatting errors. In this Correction the affected parts of the article are shown. The original article has been updated. Table 1 contained a formatting error. The correct version of Table 1 is shown below and the corrected entry is marked in bold:0 Descriptive statistics of simulation schemes Table 5 contained a formatting error. The correct version of Table 5 is shown below and the corrected entry is marked in bold: Number of selected SNPs, number of tagged QTL, percentage of genetic variance explained, and accuracies of genomic and phenotype prediction under different π values, sampling distribution for the QTL effects and density of the marker panel using BayesC method. Standard errors of accuracies are listed between parentheses 1QTL effects sampled from a Gamma distribution, 2 QTL effects pre-defined to explain at least 0.5% of genetic variance (GV), 3 QTL with r2 > 0.7 with at least one selected SNP, 4 GV = Genetic Variance, 5 accuracy of phenotype prediction, 6 accuracy of genomic prediction The first equation contained formatting errors. The correct version of this equation is shown below: with H = 2 ∗ p ∗ q, , and H = 2 ∗ p ∗ q
Table 1

Descriptive statistics of simulation schemes

Historical Population (HP)
 Number of generation315
 Mutation rate for markers1.0*10− 4
 Mutation rate for QTL1.0*10−4
Founder Population (G0)
 Number of generation3
 Number of male1500
 Number of female15,000
Selection Population (G3)
 Number of chromosomes10
 Length per chromosome (cM)100
 Number of markers per generation200,000 / 400,000
 Marker distributionEvenly spaced
 Number of QTL per generation100
 QTL distributionRandomly distributed
 QTL effectSampled from gamma with shape 0.4
 Heritability0.4
 Genetic variance0.4
 Residual variance0.6
Table 5

Number of selected SNPs, number of tagged QTL, percentage of genetic variance explained, and accuracies of genomic and phenotype prediction under different π values, sampling distribution for the QTL effects and density of the marker panel using BayesC method. Standard errors of accuracies are listed between parentheses

(1-π) =0.90(1-π) =0.95(1-π) =0.98(1-π) =0.99
GammaPredefinedGammaPredefinedGammaPredefinedGammaPredefined
200 K marker density
# SNP20 K20 K10 K10 K4 K4 K2 K2 K
Tagged QTL37697619653944691
% GV488.8497.6686.5697.5386.3095.7485.7693.32
Acc_P50.4530.4510.4670.4590.4840.4770.4960.493
(0.019)(0.009)(0.019)(0.009)(0.018)(0.008)(0.018)(0.008)
Acc_G60.7690.7510.7910.7660.8210.7940.8420.821
(0.017)(0.009)(0.018)(0.008)(0.018)(0.009)(0.018)(0.006)
400 K marker density
# SNP40K40K20 K20 K8 K8 K4 K4 K
Tagged QTL8599689853974895
% GV92.0598.9791.5998.3790.9896.9590.1695.81
Acc_P0.4440.4410.4560.4470.4720.4590.4850.472
(0.013)(0.017)(0.013)(0.017)(0.014)(0.017)(0.014)(0.018)
Acc_G0.7540.7400.7730.7490.8020.7690.8240.791
(0.017)(0.011)(0.017)(0.011)(0.017)(0.012)(0.016)(0.012)

1QTL effects sampled from a Gamma distribution, 2 QTL effects pre-defined to explain at least 0.5% of genetic variance (GV), 3 QTL with r2 > 0.7 with at least one selected SNP, 4 GV = Genetic Variance, 5 accuracy of phenotype prediction, 6 accuracy of genomic prediction

  1 in total

1.  High density marker panels, SNPs prioritizing and accuracy of genomic selection.

Authors:  Ling-Yun Chang; Sajjad Toghiani; Ashley Ling; Sammy E Aggrey; Romdhane Rekaya
Journal:  BMC Genet       Date:  2018-01-05       Impact factor: 2.797

  1 in total

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