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Table 1 Minor allele frequencies (MAF) of QTL and SNPs and the level of historical linkage disequilibrium (LD) in the base population of simulated scenarios

From: Contributions of linkage disequilibrium and co-segregation information to the accuracy of genomic prediction

Scenario

Common QTL\(^{\mathrm{a}}\)

Rare QTL\(^{\mathrm{b}}\)

High LD\(^{\mathrm{c}}\)

No LD\(^{\mathrm{d}}\)

High LD

No LD

MAF of QTL

0.01–0.5

0.01–0.06

MAF of SNPs

0.06–0.5

LD between QTL and SNPs

>0

=0

≈0

=0

LD between SNPs

>0

=0

>0

=0

  1. \(^{\mathrm{a}}\) The scenario with MAF of QTL between 0.01 and 0.50, and MAF of SNPs between 0.06 and 0.50
  2. \(^{\mathrm{b}}\) The scenario with MAF of QTL between 0.01 and 0.06, and MAF of SNPs between 0.06 and 0.50
  3. \(^{\mathrm{c}}\) The scenario with high LD in the base population created by historical generations
  4. \(^{\mathrm{d}}\) The scenario with linkage equilibrium in the base population by independently sampling genotypes of QTL and SNPs
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Genetics Selection Evolution

ISSN: 1297-9686