Application of Artificial Neural Networks to Predict Genotypic Values of Soybean Derived from Wide and Restricted Crosses for Relative Maturity Groups

Abstract

The primary objective of soybean-breeding programs is to develop cultivars that offer both high grain yield and a maturity cycle tailored to the specific soil and climatic conditions of their cultivation. Therefore, predicting the genetic value is essential for selecting and advancing promising genotypes. Among the various analytical approaches available, deep machine learning emerges as a promising choice due to its capability to predict the genetic component of phenotypes assessed under field conditions, thereby enhancing the precision of breeding decisions. This study aimed to determine the efficiency of artificial neural networks (ANNs) in predicting the genetic values of soybean genotypes belonging to populations derived from crosses between parents of different relative maturity groups (RMGs). We characterized populations with broad and restricted genetic bases for RMG traits. Data from three soybean populations, evaluated over three different agricultural years, were used. Genetic values were predicted using the multilayer perceptron (MLP) artificial neural network and compared to those obtained using the best unbiased linear prediction from variance components using restricted maximum likelihood (RR-BLUP). The MLP neural network efficiently predicted genetic values for the relative maturity group trait for genotypes belonging to populations of broad and restricted crosses, with an R2 of 0.999 and root-mean-square error (RMSE) of 0.241, and for grain yield, there was an R2 of 0.999 and an RMSE of 0.076. While the percentage of coincident superior genotypes remained relatively consistent, a significant difference was observed in their ranking order. The genetic gain with selection estimated using MLP was higher by 30–110% compared to RR-BLUP for the relative maturity group trait and 90–500% for grain yield. Artificial neural networks (ANNs) showed higher efficiency than RR-BLUP in predicting the genetic values of the soybean population. Local selection at intermediate latitudes is conducive to developing lines adaptable for regions at higher and lower latitudes.

Keywords

• variance components
• <i>Glycine max</i>
• machine learning
• mixed models
• REML/BLUP