Genetic Parameter and Hyper-Parameter Estimation Underlie Nitrogen Use Efficiency in Bread Wheat

Author:

Sadeqi Mohammad Bahman1ORCID,Ballvora Agim1ORCID,Dadshani Said2ORCID,Léon Jens1ORCID

Affiliation:

1. INRES-Plant Breeding, Rheinische Friedrich-Wilhelms-Universität Bonn, 53113 Bonn, Germany

2. INRES-Plant Nutrition, Rheinische Friedrich-Wilhelms-Universität Bonn, 53113 Bonn, Germany

Abstract

Estimation and prediction play a key role in breeding programs. Currently, phenotyping of complex traits such as nitrogen use efficiency (NUE) in wheat is still expensive, requires high-throughput technologies and is very time consuming compared to genotyping. Therefore, researchers are trying to predict phenotypes based on marker information. Genetic parameters such as population structure, genomic relationship matrix, marker density and sample size are major factors that increase the performance and accuracy of a model. However, they play an important role in adjusting the statistically significant false discovery rate (FDR) threshold in estimation. In parallel, there are many genetic hyper-parameters that are hidden and not represented in the given genomic selection (GS) model but have significant effects on the results, such as panel size, number of markers, minor allele frequency, number of call rates for each marker, number of cross validations and batch size in the training set of the genomic file. The main challenge is to ensure the reliability and accuracy of predicted breeding values (BVs) as results. Our study has confirmed the results of bias–variance tradeoff and adaptive prediction error for the ensemble-learning-based model STACK, which has the highest performance when estimating genetic parameters and hyper-parameters in a given GS model compared to other models.

Publisher

MDPI AG

Subject

Inorganic Chemistry,Organic Chemistry,Physical and Theoretical Chemistry,Computer Science Applications,Spectroscopy,Molecular Biology,General Medicine,Catalysis

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