Efficient Genomic Prediction of Yield and Dry Matter in Hybrid Potato

There is an ongoing endeavor within the potato breeding sector to rapidly adapt potato from a clonal polyploid crop to a diploid hybrid potato crop. While hybrid breeding allows for the efficient generation and selection of parental lines, it also increases breeding program complexity and results in longer breeding cycles. Over the past two decades, genomic prediction has revolutionized hybrid crop breeding through shorter breeding cycles, lower phenotyping costs, and better population improvement, resulting in increased genetic gains for genetically complex traits. In order to accelerate the genetic gains in hybrid potato, the proper implementation of genomic prediction is a crucial milestone in the rapid improvement of this crop. The authors of this paper set out to test genomic prediction in hybrid potato using current genotyped material with two alternative models: one model that predicts the general combining ability effects (GCA) and another which predicts both the general and specific combining ability effects (GCA+SCA). Using a training set comprising 769 hybrids and 456 genotyped parental lines, we found that reasonable a prediction accuracy could be achieved for most phenotypes with both zero common parents (ρ=0.36−0.61) and one (ρ=0.50−0.68) common parent between the training and test sets. There was no benefit with the inclusion of non-additive genetic effects in the GCA+SCA model despite SCA variance contributing between 9% and 19% of the total genetic variance. Genotype-by-environment interactions, while present, did not appear to affect the prediction accuracy, though prediction errors did vary across the trial’s targets. These results suggest that genomically estimated breeding values on parental lines are sufficient for hybrid yield prediction.

[1]  Jeffrey B. Endelman,et al.  Genomic selection and genome‐wide association studies in tetraploid chipping potatoes , 2023, The plant genome.

[2]  Jiming Jiang,et al.  Diploid Potatoes as a Catalyst for Change in the Potato Industry , 2022, American Journal of Potato Research.

[3]  R. Ortiz,et al.  Modeling genotype × environment interaction for single and multitrait genomic prediction in potato (Solanum tuberosum L.) , 2022, bioRxiv.

[4]  F. V. van Eeuwijk,et al.  Little heterosis found in diploid hybrid potato: The genetic underpinnings of a new hybrid crop , 2022, G3.

[5]  P. Pérez-Rodríguez,et al.  Genome-Based Genotype × Environment Prediction Enhances Potato (Solanum tuberosum L.) Improvement Using Pseudo-Diploid and Polysomic Tetraploid Modeling , 2022, Frontiers in Plant Science.

[6]  J. Bradshaw A Brief History of the Impact of Potato Genetics on the Breeding of Tetraploid Potato Cultivars for Tuber Propagation , 2022, Potato Research.

[7]  P. Struik,et al.  Transplanting Hybrid Potato Seedlings at Increased Densities Enhances Tuber Yield and Shifts Tuber-Size Distributions , 2021, Potato Research.

[8]  R. Visser,et al.  Understanding the Effectiveness of Genomic Prediction in Tetraploid Potato , 2021, Frontiers in Plant Science.

[9]  C. Bachem,et al.  Neofunctionalisation of the Sli gene leads to self-compatibility and facilitates precision breeding in potato , 2021, Nature Communications.

[10]  W. J. Lucas,et al.  A nonS-locus F-box gene breaks self-incompatibility in diploid potatoes , 2021, Nature Communications.

[11]  Dawei Li,et al.  Genome design of hybrid potato , 2021, Cell.

[12]  D. Podlich,et al.  Back to the future: implications of genetic complexity for the structure of hybrid breeding programs , 2021, G3.

[13]  J. Rutkoski,et al.  Heterosis and Hybrid Crop Breeding: A Multidisciplinary Review , 2021, Frontiers in Genetics.

[14]  Zhenliang Zhang,et al.  Using genomic data to improve the estimation of general combining ability based on sparse partial diallel cross designs in maize , 2020 .

[15]  R. Bernardo Reinventing quantitative genetics for plant breeding: something old, something new, something borrowed, something BLUE , 2020, Heredity.

[16]  P. Struik,et al.  Contribution and Stability of Yield Components of Diploid Hybrid Potato , 2020, Potato Research.

[17]  D. Milbourne,et al.  Genome-Wide Association and Genomic Prediction for Fry Color in Potato , 2020, Agronomy.

[18]  D. Gianola,et al.  Deep Kernel and Deep Learning for Genome-Based Prediction of Single Traits in Multienvironment Breeding Trials , 2019, Front. Genet..

[19]  Yusheng Zhao,et al.  Reciprocal recurrent genomic selection: an attractive tool to leverage hybrid wheat breeding , 2018, Theoretical and Applied Genetics.

[20]  P. Lindhout,et al.  Hybrid potato breeding for improved varieties , 2018, Achieving sustainable cultivation of potatoes Volume 1.

[21]  Ea Høegh Riis Sundmark,et al.  The Value of Expanding the Training Population to Improve Genomic Selection Models in Tetraploid Potato , 2018, Front. Plant Sci..

[22]  G. de los Campos,et al.  Genomic Selection for Late Blight and Common Scab Resistance in Tetraploid Potato (Solanum tuberosum) , 2018, G3: Genes, Genomes, Genetics.

[23]  G. C. Yencho,et al.  Genetic Variance Partitioning and Genome-Wide Prediction with Allele Dosage Information in Autotetraploid Potato , 2018, Genetics.

[24]  A. Bentley,et al.  A Two‐Part Strategy for Using Genomic Selection to Develop Inbred Lines , 2017 .

[25]  B. Hayes,et al.  Improving Genetic Gain with Genomic Selection in Autotetraploid Potato , 2016, The plant genome.

[26]  P. Muñoz,et al.  AGHmatrix: R Package to Construct Relationship Matrices for Autotetraploid and Diploid Species: A Blueberry Example , 2016, The plant genome.

[27]  R. Bernardo Bandwagons I, too, have known , 2016, Theoretical and Applied Genetics.

[28]  Jiming Jiang,et al.  Reinventing potato as a diploid inbred line-based crop , 2016 .

[29]  G. Covarrubias-Pazaran Genome-Assisted Prediction of Quantitative Traits Using the R Package sommer , 2016, PloS one.

[30]  J. Gopal Challenges and Way-forward in Selection of Superior Parents, Crosses and Clones in Potato Breeding , 2015, Potato Research.

[31]  M. Mette,et al.  Genomic selection in hybrid breeding , 2015 .

[32]  C. Gebhardt Bridging the gap between genome analysis and precision breeding in potato. , 2013, Trends in genetics : TIG.

[33]  M. Lund,et al.  Estimating Additive and Non-Additive Genetic Variances and Predicting Genetic Merits Using Genome-Wide Dense Single Nucleotide Polymorphism Markers , 2012, PloS one.

[34]  A. Melchinger,et al.  Genomic prediction of hybrid performance in maize with models incorporating dominance and population specific marker effects , 2012, Theoretical and Applied Genetics.

[35]  R. Visser,et al.  Towards F1 Hybrid Seed Potato Breeding , 2011, Potato Research.

[36]  P. This,et al.  Novel measures of linkage disequilibrium that correct the bias due to population structure and relatedness , 2011, Heredity.

[37]  M. Sorrells,et al.  Plant Breeding with Genomic Selection: Gain per Unit Time and Cost , 2010 .

[38]  H. Piepho,et al.  Comparison of Spatial Models for Sugar Beet and Barley Trials , 2010 .

[39]  H. Piepho,et al.  Comparison of Weighting in Two‐Stage Analysis of Plant Breeding Trials , 2009 .

[40]  B. S. Dhillon,et al.  Molecular marker-based prediction of hybrid performance in maize using unbalanced data from multiple experiments with factorial crosses , 2009, Theoretical and Applied Genetics.

[41]  P. VanRaden,et al.  Efficient methods to compute genomic predictions. , 2008, Journal of dairy science.

[42]  D. Gianola,et al.  Reproducing Kernel Hilbert Spaces Regression Methods for Genomic Assisted Prediction of Quantitative Traits , 2008, Genetics.

[43]  M. Stephens,et al.  Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. , 2003, Genetics.

[44]  M. Goddard,et al.  Prediction of total genetic value using genome-wide dense marker maps. , 2001, Genetics.

[45]  Rajendra Bhatia,et al.  A Better Bound on the Variance , 2000, Am. Math. Mon..

[46]  Brian R. Cullis,et al.  Genotype by Environment Variance Heterogeneity in a Two-Stage Analysis , 1997 .

[47]  D. Douches,et al.  Assessment of potato breeding progress in the USA over the last century , 1996 .

[48]  N. Pallais True Potato Seed: Changing Potato Propagation from Vegetative to Sexual , 1991 .

[49]  Sanwen Huang,et al.  Acquisition of deleterious mutations during potato polyploidization. , 2019, Journal of integrative plant biology.

[50]  White Paper SeqSNP targeted GBS as alternative for array genotyping in routine breeding programs , 2019 .

[51]  R Core Team,et al.  R: A language and environment for statistical computing. , 2014 .

[52]  A. Haverkort Ecology of potato cropping systems in relation to latitude and altitude. , 1990 .

[53]  Stefan E. Wilson Statistical considerations for applying genomic prediction to potato , 2022 .