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Possible coding of the genotype design matrix for autotetraploid potato.

 
Cultivar genotype Pseudo diploid Additive autotetraploid Full autotetraploid, including nonadditive
Number of effects per marker 1 1 1 2 3 4 5
AAAA 0 0 1 0 0 0 0
AAAB 1 1 0 1 0 0 0
AABB 1 2 0 0 1 0 0
ABBB 1 3 0 0 0 1 0
BBBB 2 4 0 0 0 0 1



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Number of lines in each generation of potato, estimates of cumulative inbreeding, rate of inbreeding, and effective population size (Ne) for 0.0 and 0.25 double reduction (DR).

 
Generation Number of lines Inbreeding
Inbreeding rate
Ne
No DR 0.25 DR No DR 0.25 DR No DR 0.25 DR
1 97 NA† 0.25 NA NA NA NA
2 196 0 0.319 0.000 0.092 NA NA
3 1797 0.029 0.366 0.029 0.069 17.2 7.2
4 1218 0.034 0.376 0.005 0.016 97.1 31.7
5 396 0.042 0.384 0.008 0.013 60.4 39.0
Total 3704
NA, Not available



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Predicted accuracy of genomic selection for four traits of potato, in which BVP is breeders’ visual preference, h2 is narrow-sense heritability, Acc BLUP is the prediction accuracy of pedigree best linear unbiased prediction, and Np is the reference population size.

 
Trait h2 Acc BLUP Np = 500 Np = 1000 Np = 2000 Np = 5000
BVP 0.23 0.33 0.19 0.27 0.37 0.53
Yield 0.56 0.19 0.29 0.40 0.52 0.70
Boiling color 0.73 0.44 0.33 0.44 0.57 0.74
Maturity 0.86 0.78 0.36 0.47 0.61 0.77
Data from Slater et al. (2014b).
Data from Slater et al. (2014b), reflecting the fact that only a subset of the pedigree was phenotyped for some traits.



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Comparison of the cost of potato breeding under three selection regimes with two genomic selection models.

 
Generation Details Intense Moderate Mild GS 5000¶ GS 2000¶
G0 No. of seedlings† 100,000 20,000 6,667 5,000 2,000
Seedling tuber production $300,000 $60,000 $20,001 $15,000 $6,000
G0 selection rate 0% 0% 0% 50% 50%
G1 No. of seedlings 100,000 20,000 6,667 2,500 1,000
G1 cost‡ $164,731 $32,946 $10,983 $32,946 $10,983
G1 selection rate 2% 10% 30% 80% 80%
G2 No. of genotypes 2,000 2,000 2,000 2,000 800
G2 cost§ $119,552 $119,552 $119,552 $119,552 $47,821
Total cost $633,040 $257,248 $194,618 $138,671 $55,468
Cost savings with GS 5000 489,453 117,668 55,705
Breakeven genotyping cost per genotype 98 24 11
Cost savings with GS 2000 572,656 200,870 138,908
Breakeven genotyping cost per genotype 286 100 69
The number of seedlings varies because the selection intensity applied at G1 to arrive at 2000 genotypes in the G2 generation apart from the GS 2000 model.
The G1 trial cost (in Australian dollars) is based on the cost per hectare taken from Slater et al. (2013).
§The G2 trial cost (in Australian dollars) is based on the cost per hectare taken from Slater et al. (2013).
GS = genomic selection seedling population size.