Integrating genomic prediction and genotype specific parameter estimation in ecophysiological models: overview and perspectives
Pratishtha Poudel, Bryan Naidenov, Charles Chen, Phillip D. Alderman, Stephen M. Welch
Abstract
Abstract The Genome-to-Phenome (G2P) problem is one of the highest-priority challenges in applied biology. Ecophysiological crop models (ECM) and genomic prediction (GP) models are quantitative algorithms, which, when given information on a genotype and environment, can produce an accurate estimate of a phenotype of interest. In this article, we discuss how the GP algorithms can be used to estimate genotype-specific parameters (GSPs) in ECMs to develop robust prediction methods. In this approach, the numerical constants (GSPs) that ECMs use to distinguish and characterize crop cultivars/varieties are treated as quantitative traits to be predicted by genomic prediction models from underlying genetic information. In this article we provide information on which GP methods appear favorable for predicting different types of GSPs, such as vernalization sensitivity or potential radiation use efficiency. For each example GSP, we assess a number of GP methods in terms of their suitability using a set of three criteria grounded in genetic architecture, computational requirements, and the use of prior information. In general, we conclude that the most useful algorithms were dependent on both the nature of the particular GSP and the GP methods considered.