| Literature DB >> 29448946 |
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
Descriptive statistics of simulation schemes
| Historical Population (HP) | |
|---|---|
| Number of generation | 315 |
| Mutation rate for markers | 1.0*10− 4 |
| Mutation rate for QTL | 1.0* |
| Founder Population (G0) | |
| Number of generation | 3 |
| Number of male | 1500 |
| Number of female | 15,000 |
| Selection Population (G3) | |
| Number of chromosomes | 10 |
| Length per chromosome (cM) | 100 |
| Number of markers per generation | 200,000 / 400,000 |
| Marker distribution | Evenly spaced |
| Number of QTL per generation | 100 |
| QTL distribution | Randomly distributed |
| QTL effect | Sampled from gamma with shape 0.4 |
| Heritability | 0.4 |
| Genetic variance | 0.4 |
| Residual variance | 0.6 |
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 | |||||
|---|---|---|---|---|---|---|---|---|
| Gamma | Predefined | Gamma | Predefined | Gamma | Predefined | Gamma | Predefined | |
| 200 K marker density | ||||||||
| # SNP | 20 K | 20 K | 10 K | 10 K | 4 K | 4 K | 2 K | 2 K |
| Tagged QTL3 | 76 | 97 | 61 | 96 | 53 | 94 | 46 | 91 |
| % GV4 | 88.84 | 97.66 | 86.56 | 97.53 | 86.30 | 95.74 | 85.76 | 93.32 |
| Acc_P5 | 0.453 | 0.451 | 0.467 | 0.459 | 0.484 | 0.477 | 0.496 | 0.493 |
| (0.019) | (0.009) | (0.019) | (0.009) | (0.018) | (0.008) | (0.018) | (0.008) | |
| Acc_G6 | 0.769 | 0.751 | 0.791 | 0.766 | 0.821 | 0.794 | 0.842 | 0.821 |
| (0.017) | (0.009) | (0.018) | (0.008) | (0.018) | (0.009) | (0.018) | (0.006) | |
|
| ||||||||
| # SNP | 40K | 40K | 20 K | 20 K | 8 K | 8 K | 4 K | 4 K |
| Tagged QTL | 85 | 99 | 68 | 98 | 53 | 97 | 48 | 95 |
| % GV | 92.05 | 98.97 | 91.59 | 98.37 | 90.98 | 96.95 | 90.16 | 95.81 |
| Acc_P | 0.444 | 0.441 | 0.456 | 0.447 | 0.472 | 0.459 | 0.485 | 0.472 |
| (0.013) | (0.017) | (0.013) | (0.017) | (0.014) | (0.017) | (0.014) | (0.018) | |
| Acc_G | 0.754 | 0.740 | 0.773 | 0.749 | 0.802 | 0.769 | 0.824 | 0.791 |
| (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