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Link to original content: https://www.ncbi.nlm.nih.gov/pubmed/26092719
Selection on Optimal Haploid Value Increases Genetic Gain and Preserves More Genetic Diversity Relative to Genomic Selection - PubMed Skip to main page content
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. 2015 Aug;200(4):1341-8.
doi: 10.1534/genetics.115.178038. Epub 2015 Jun 19.

Selection on Optimal Haploid Value Increases Genetic Gain and Preserves More Genetic Diversity Relative to Genomic Selection

Hans D Daetwyler  1 , Matthew J Hayden  2 , German C Spangenberg  2 , Ben J Hayes  2
Affiliations

Selection on Optimal Haploid Value Increases Genetic Gain and Preserves More Genetic Diversity Relative to Genomic Selection

Hans D Daetwyler et al. Genetics. 2015 Aug.

Abstract

Doubled haploids are routinely created and phenotypically selected in plant breeding programs to accelerate the breeding cycle. Genomic selection, which makes use of both phenotypes and genotypes, has been shown to further improve genetic gain through prediction of performance before or without phenotypic characterization of novel germplasm. Additional opportunities exist to combine genomic prediction methods with the creation of doubled haploids. Here we propose an extension to genomic selection, optimal haploid value (OHV) selection, which predicts the best doubled haploid that can be produced from a segregating plant. This method focuses selection on the haplotype and optimizes the breeding program toward its end goal of generating an elite fixed line. We rigorously tested OHV selection breeding programs, using computer simulation, and show that it results in up to 0.6 standard deviations more genetic gain than genomic selection. At the same time, OHV selection preserved a substantially greater amount of genetic diversity in the population than genomic selection, which is important to achieve long-term genetic gain in breeding populations.

Keywords: GenPred; doubled haploid; genetic diversity; genetic gain; genomic selection; haplotype; shared data resource.

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Figures

Figure 1
Figure 1
An example of applying optimal haplotype value (OHV) to develop a new wheat variety. Two heterozygous parents are crossed, each offspring is genotyped, and haplotype values (HV) and OHV are calculated in silico, leading to selection of elite individuals from which to produce doubled haploids. All doubled haploids are genotyped, their genomic breeding values are predicted, and the doubled haploid with highest genetic value is the new elite individual. Note that the line with the highest OHV may not be the plant with the highest average genomic breeding value.
Figure 2
Figure 2
Generic genomic breeding program design, where DH is doubled haploid, and n is number of generations. Selection was on either optimal haploid or genomic estimated breeding value. Elite doubled haploids can be cycled back into the breeding population in the second generation after creation.
Figure 3
Figure 3
(A–D) Difference in genetic gain (Genetic_Gain) in base genetic SD between optimal haploid value (OHV) selection and genomic selection (GS), when (A) varying the number of offspring per outbred cross (nOff, SE < 0.21), (B) varying the number of doubled haploids produced per elite plant (nDH, SE < 0.08), (C) varying the number of elite doubled haploids cycled back into the breeding program (nDHcycled, SE < 0.15), and (D) varying the number of elite individuals taken to doubled haploid production (nEliteInd, SE < 0.23).
Figure 4
Figure 4
Difference in genetic gain (Genetic_Gain) in base genetic SD (blue line) and proportion (green bars) between optimal haploid value (OHV) selection and genomic selection (GS), when continuing the DEFAULT scenario for 20 generations (nGen, SE < 0.10).
Figure 5
Figure 5
The true genetic variance in each generation when selection was on optimal haploid value (OHV) or genomic breeding values (GS) for DEFAULT and nDH500 scenarios (SE < 3.64).
Figure 6
Figure 6
(A and B) Difference in genetic gain (Genetic_Gain) between OHV and GS when (A) the number of QTL is varied (nQTL, SE < 0.21) or (B) the number of haplotype segments per chromosome is varied (nSeg, SE < 0.17).
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References

    1. Akhunov E. D., Goodyear A. W., Geng S., Qi L.-L., Echalier B., et al. , 2003. The organization and rate of evolution of wheat genomes are correlated with recombination rates along chromosome arms. Genome Res. 13: 753–763. - PMC - PubMed
    1. Cavanagh, C. R., S. Chao, S. Wang, B. E. Huang, S. Stephen et al., 2013 Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars. Proc. Natl. Acad. Sci. USA 110: 8057–8062. - PMC - PubMed
    1. Cole J. B., VanRaden P. M., 2010. Visualization of results from genomic evaluations. J. Dairy Sci. 93: 2727–2740. - PubMed
    1. Cole J. B., VanRaden P. M., 2011. Use of haplotypes to estimate Mendelian sampling effects and selection limits. J. Anim. Breed. Genet. 128: 446–455. - PubMed
    1. Cooper M., Messina C. D., Podlich D., Totir L. R., Baumgarten A., et al. , 2014. Predicting the future of plant breeding: complementing empirical evaluation with genetic prediction. Crop Pasture Sci. 65: 311–336.