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Table 4 Genetic gain, \({R}_{GS}\), in the initial selection cycle of different breeding schemes with colony-based (CBS) and genomic preselection (GPS)

From: Simulation studies to optimize genomic selection in honey bees

Number of genotyped queens per year (\({{\varvec{n}}}_{{\varvec{g}}{\varvec{p}}{\varvec{y}}}\))

Proportion of DPQ selected by GPS compared to all DPQ deployed on mating stations (\({{\varvec{p}}}_{{\varvec{D}}{\varvec{P}}{\varvec{Q}}}\))

Selection intensity of GPS on DPQ (\({{\varvec{i}}}_{{\varvec{D}}{\varvec{P}}{\varvec{Q}}}^{{\varvec{G}}{\varvec{P}}{\varvec{S}}}\))

Proportion of BQ selected by GPS compared to all phenotyped BQ (\({{\varvec{p}}}_{{\varvec{B}}{\varvec{Q}}}\))

Selection intensity of GPS on BQ (\({{\varvec{i}}}_{{\varvec{B}}{\varvec{Q}}}^{{\varvec{G}}{\varvec{P}}{\varvec{S}}}\))

Number of BQ in the reference population (5 years in total)

Proportion of BQ in the reference population (\({{\varvec{p}}}_{{\varvec{r}}{\varvec{e}}{\varvec{f}}}\))

Breeding value estimation method

Genetic gain \({{\varvec{R}}}_{{\varvec{G}}{\varvec{S}}}\)

MOD

HGC

0

0

0

0

0

0

0

PBLUP

0.8751

0.5286

500

0.4

0.7979

0.15

0.2998

750

0.15

ssGBLUPBQ

0.9497

0.5715

500

0.46

0.7979

0.11

0.2998

550

0.11

ssGBLUPBQ

0.9492

0.5725

1000

1

0.7454

0.205

0.2998

1045

0.209

ssGBLUPDPQ+BQ

1.0909

0.6559

1000

1

0.8454

0.125

0.2998

625

0.125

ssGBLUPDPQ+BQ

1.0878

0.6567

1500

1

0.8454

0.46

0.4759

2330

0.466

ssGBLUPDPQ+BQ

1.2169

0.7344

1500

1

0.8889

0.5

0.2998

2500

0.5

ssGBLUPDPQ+BQ

1.2167

0.7353

2000

1

0.8889

0.785

0.4759

3930

0.786

ssGBLUPDPQ+BQ

1.3403

0.8091

2500

1

1.0324

1

0.4759

5000

1

ssGBLUPDPQ+BQ

1.4668

0.8831

3000

1

1.0908

1

0.7111

5000

1

ssGBLUPDPQ+BQ

1.5652

0.9391

3500

1

1.2322

1

0.7979

5000

1

ssGBLUPDPQ+BQ

1.6416

0.9828

4000

1

1.3401

1

0.872

5000

1

ssGBLUPDPQ+BQ

1.7026

1.0175

  1. Breeding queens and drone producing queens are referred to as BQ and DPQ, respectively
  2. Settings with a moderate negative genetic correlation (MOD), or a high negative genetic correlation (HGC) were simulated
  3. Pedigree-based BLUP and Single-Step-genomic-BLUP are referred to as PBLUP and ssGBLUP, respectively. The relationship matrix for ssGBLUP contained either exclusively BQ (ssGBLUPBQ) or BQ and DPQ (ssGBLUPDPQ+BQ)
  4. Genetic gain is given in the units of the selection criterion
  5. The standard deviations of the true breeding values \({\sigma }_{pW}\) (worker groups from year 8) and \({\sigma }_{uQ}\) (queens from year 9) are in Additional file 5
  6. Genetic gain,\({R}_{GS}\), was calculated according to Eqs. (18), (19), and (20)