Multi-trait, multi-environment genomic prediction of durum wheat with genomic best linear unbiased predictor and deep learning methods

Although durum wheat (Triticum turgidum var. durum Desf.) is a minor cereal crop representing just 5-7% of the world's total wheat crop, it is a staple food in Mediterranean countries, where it is used to produce pasta, couscous, bulgur and bread. In this paper, we cover multi-trait prediction of grain yield (GY), days to heading (DH) and plant height (PH) of 270 durum wheat lines that were evaluated in 43 environments (country-location-year combinations) across a broad range of water regimes in the Mediterranean Basin and other locations. Multi-trait prediction analyses were performed by implementing a multi-trait deep learning model (MTDL) with a feed-forward network topology and a rectified linear unit activation function with a grid search approach for the selection of hyper-parameters. The results of the multi-trait deep learning method were also compared with univariate predictions of the genomic best linear unbiased predictor (GBLUP) method and the univariate counterpart of the multi-trait deep learning method (UDL). All models were implemented with and without the genotype x environment interaction term. We found that the best predictions were observed without the genotype x environment interaction term in the UDL and MTDL methods. However, under the GBLUP method, the best predictions were observed when the genotype x environment interaction term was taken into account. We also found that in general the best predictions were observed under the GBLUP model; however, the predictions of the MTDL were very similar to those of the GBLUP model. This result provides more evidence that the GBLUP model is a powerful approach for genomic prediction, but also that the deep learning method is a practical approach for predicting univariate and multivariate traits in the context of genomic selection.

Bibliographic Details

Main Authors:	Montesinos-Lopez, O.A., Montesinos-Lopez, A., Tuberosa, R., Maccaferri, M., Sciara, G., Ammar, K., Crossa, J.
Format:	Article biblioteca
Language:	English
Published:	Frontiers 2019
Subjects:	HARD WHEAT, MARKER-ASSISTED SELECTION, AGRONOMIC CHARACTERS,
Online Access:	https://hdl.handle.net/10883/20598
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