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Table 1 Factors for different scenarios in a simulation study

From: Impact of QTL minor allele frequency on genomic evaluation using real genotype data and simulated phenotypes in Japanese Black cattle

 

Scenario

Factor

1

2

3

4

MAFa

All, High, Low

All, High, Low

All, High, Low

All, High, Low

QTL heritability

0.2, 0.4, 0.8

0.4

0.4

0.4

Number of QTLs

500

50, 100, 300, 500, 1000, 2000

500

500

Distribution of QTL effectb

EquV

Gamma, EquV

EquV

EquV

SNP densityc

50 K

50 K

7 K, 50 K, 7K_to_HD, 50 K_to_HD, HD

50 K

Prediction modeld

Model (1) with GY

Model (1) with GY

Model (1) with GV, GY, and GS, Model (2)

Model (1) with GY

Size of reference set

1231

1231

1231

200, 400, 800, 1200

Size of test set

137

137

137

1168, 968, 568, 168

  1. aMAF, Minor allele frequency; All, 0.01 ≤ MAF ≤ 0.5; High, 0.05 < MAF ≤ 0.5; Low, 0.01 ≤ MAF ≤ 0.05
  2. bGamma, Gamma distribution model; EquV, Equal variance model
  3. c7K, 50 K and HD, Illumina infinium BovineLDv1.1, BovineSNP50v2, and BovineHD BeadChips, respectively; 7 K_to_HD and 50 K_to_HD, Imputations were performed from 7 K and 50 K to HD, respectively
  4. dGV, VanRaden's G matrix; GY, Yang's G matrix; GS, Speed's G matrix
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BMC Genomic Data

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