Partial least squares enhance multi-trait genomic prediction of potato cultivars in new environments

Rodomiro Ortiz; Fredrik Reslow; Abelardo Montesinos-López; José Huicho; Paulino Pérez-Rodríguez; Osval A. Montesinos-López; José Crossa

doi:10.1038/s41598-023-37169-y

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Partial least squares enhance multi-trait genomic prediction of potato cultivars in new environments

Journal article

Open access

Peer reviewed

Partial least squares enhance multi-trait genomic prediction of potato cultivars in new environments

Rodomiro Ortiz, Fredrik Reslow, Abelardo Montesinos-López, José Huicho, Paulino Pérez-Rodríguez, Osval A. Montesinos-López and José Crossa

Scientific reports, Vol.13(1), 9947

2023

DOI: https://doi.org/10.1038/s41598-023-37169-y

PMID: 37336933

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Abstract

Genetics

Heritable quantitative trait

Quantitative trait loci

It is of paramount importance in plant breeding to have methods dealing with large numbers of predictor variables and few sample observations, as well as efficient methods for dealing with high correlation in predictors and measured traits. This paper explores in terms of prediction performance the partial least squares (PLS) method under single-trait (ST) and multi-trait (MT) prediction of potato traits. The first prediction was for tested lines in tested environments under a five-fold cross-validation (5FCV) strategy and the second prediction was for tested lines in untested environments (herein denoted as leave one environment out cross validation, LOEO). There was a good performance in terms of predictions (with accuracy mostly > 0.5 for Pearson’s correlation) the accuracy of 5FCV was better than LOEO. Hence, we have empirical evidence that the ST and MT PLS framework is a very valuable tool for prediction in the context of potato breeding data.

Details

Title: Partial least squares enhance multi-trait genomic prediction of potato cultivars in new environments
Authors/Creators: Rodomiro Ortiz - P.O. Box 190, SE 23436 Lomma, Sweden
Fredrik Reslow - Swedish University of Agricultural Sciences
Abelardo Montesinos-López - Departamento de Matemáticas, Centro Universitario de Ciencias Exactas e Ingenierías (CUCEI), 44430 Guadalajara, México
José Huicho - Centro Internacional de Mejoramiento de Maíz Y Trigo
Paulino Pérez-Rodríguez - 56230 Montecillos, Edo. de México México
Osval A. Montesinos-López - 28040 Colima, México
José Crossa - Carretera México-Veracruz Km. 45, El Batán, 56237 Texcoco, Edo. de México México 56230 Montecillos, Edo. de México México Murdoch, Australia
Publication Details: Scientific reports, Vol.13(1), 9947
Publisher: Nature Publishing Group UK
Identifiers: 991005585960907891
Murdoch Affiliation: Centre for Crop and Food Innovation
Language: English
Resource Type: Journal article

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Collaboration types: Domestic collaboration; International collaboration
Citation topics: 3 Agriculture, Environment & Ecology; 3.51 Dairy & Animal Sciences; 3.51.115 Livestock Reproduction
Web Of Science research areas: Genetics & Heredity
ESI research areas: Agricultural Sciences