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Research article - Peer-reviewed, 2022

Genome-Based Genotype × Environment Prediction Enhances Potato (Solanum tuberosum L.) Improvement Using Pseudo-Diploid and Polysomic Tetraploid Modeling

Ortiz, Rodomiro; Crossa, Jose; Reslow, Fredrik; Pérez-Rodríguez, Paulino; Cuevas, Jaime


Potato breeding must improve its efficiency by increasing the reliability of selection as well as identifying a promising germplasm for crossing. This study shows the prediction accuracy of genomic-estimated breeding values for several potato (Solanum tuberosum L.) breeding clones and the released cultivars that were evaluated at three locations in northern and southern Sweden for various traits. Three dosages of marker alleles [pseudo-diploid (A), additive tetrasomic polyploidy (B), and additive-non-additive tetrasomic polyploidy (C)] were considered in the genome-based prediction models, for single environments and multiple environments (accounting for the genotype-by-environment interaction or G × E), and for comparing two kernels, the conventional linear, Genomic Best Linear Unbiased Prediction (GBLUP) (GB), and the non-linear Gaussian kernel (GK), when used with the single-kernel genetic matrices of A, B, C, or when employing two-kernel genetic matrices in the model using the kernels from B and C for a single environment (models 1 and 2, respectively), and for multi-environments (models 3 and 4, respectively). Concerning the single site analyses, the trait with the highest prediction accuracy for all sites under A, B, C for model 1, model 2, and for GB and GK methods was tuber starch percentage. Another trait with relatively high prediction accuracy was the total tuber weight. Results show an increase in prediction accuracy of model 2 over model 1. Non-linear Gaussian kernel (GK) did not show any clear advantage over the linear kernel GBLUP (GB). Results from the multi-environments had prediction accuracy estimates (models 3 and 4) higher than those obtained from the single-environment analyses. Model 4 with GB was the best method in combination with the marker structure B for predicting most of the tuber traits. Most of the traits gave relatively high prediction accuracy under this combination of marker structure (A, B, C, and B-C), and methods GB and GK combined with the multi-environment with G × E model.


genomic-enabled predictions; multi-environment trials; potato breeding; Solanum tuberosum; genetic gains in plant breeding

Published in

Frontiers in Plant Science
2022, volume: 13, article number: 785196

Authors' information

Ortiz, Rodomiro (Ortiz Rios, Rodomiro Octavio)
Swedish University of Agricultural Sciences, Plant breeding and Biotechnology
Crossa, Jose
International Maize and Wheat Improvment Centre (CIMMYT)
Swedish University of Agricultural Sciences, Department of Plant Breeding
Pérez-Rodríguez, Paulino
Colegio de Postgraduados, Montecillo
Cuevas, Jaime
University of Quintana Roo

Sustainable Development Goals

SDG2 Zero hunger

UKÄ Subject classification

Genetics and Breeding
Agricultural Science

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