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Genomic selection (GS) is transforming plant and animal breeding, but its practical implementation for complex traits and multi-environmental trials remains challenging. To address this issue, this study investigates the integration of environmental information with genotypic information in GS. The study proposes the use of two feature selection methods (Pearson’s correlation and Boruta) for the integration of environmental information. Results indicate that the simple incorporation of environmental covariates may increase or decrease prediction accuracy depending on the case. However, optimal incorporation of environmental covariates using feature selection significantly improves prediction accuracy in four out of six datasets between 14.25% and 218.71% under a leave one environment out cross validation scenario in terms of Normalized Root Mean Squared Error, but not relevant gain was observed in terms of Pearson´s correlation. In two datasets where environmental covariates are unrelated to the response variable, feature selection is unable to enhance prediction accuracy. Therefore, the study provides empirical evidence supporting the use of feature selection to improve the prediction power of GS. [ABSTRACT FROM AUTHOR]

Genomic selection (GS) is transforming plant and animal breeding, but its practical implementation for complex traits and multi-environmental trials remains challenging. To address this issue, this study investigates the integration of environmental information with genotypic information in GS. The study proposes the use of two feature selection methods (Pearson’s correlation and Boruta) for the integration of environmental information. Results indicate that the simple incorporation of environmental covariates may increase or decrease prediction accuracy depending on the case. However, optimal incorporation of environmental covariates using feature selection significantly improves prediction accuracy in four out of six datasets between 14.25% and 218.71% under a leave one environment out cross validation scenario in terms of Normalized Root Mean Squared Error, but not relevant gain was observed in terms of Pearson´s correlation. In two datasets where environmental covariates are unrelated to the response variable, feature selection is unable to enhance prediction accuracy. Therefore, the study provides empirical evidence supporting the use of feature selection to improve the prediction power of GS.

The assessment of cassava clones across multiple environments is often carried out at the uniform yield trial, a late evaluation stage, before variety release. This is to assess the differential response of the varieties across the testing environments, a phenomenon referred to as genotype-by-environment interaction (GEI). This phenomenon is considered a critical challenge confronted by plant breeders in developing crop varieties. This study used the data from variety trials established as randomized complete block design (RCBD) in three replicates across 11 locations in different agro-ecological zones in Nigeria over four cropping seasons (2016-2017, 2017-2018, 2018-2019, and 2019-2020). We evaluated a total of 96 varieties, including five checks, across 48 trials. We exploited the intricate pattern of GEI by fitting variance-covariance structure models on fresh root yield. The goodness-of-fit statistics revealed that the factor analytic model of order 3 (FA3) is the most parsimonious model based on Akaike Information Criterion (AIC). The three-factor loadings from the FA3 model explained, on average across the 27 environments, 53.5% [FA (1)], 14.0% [FA (2)], and 11.5% [FA (3)] of the genetic effect, and altogether accounted for 79.0% of total genetic variability. The association of factor loadings with weather covariates using partial least squares regression (PLSR) revealed that minimum temperature, precipitation and relative humidity are weather conditions influencing the genotypic response across the testing environments in the southern region and maximum temperature, wind speed, and temperature range for those in the northern region of Nigeria. We conclude that the FA3 model identified the common latent factors to dissect and account for complex interaction in multi-environment field trials, and the PLSR is an effective approach for describing GEI variability in the context of multi-environment trials where external environmental covariables are included in modeling. [ABSTRACT FROM AUTHOR]

Clustering genotype × environment (GE) interactions and understanding the causes of GE interactions are among the most important tasks in crop breeding programs. Pattern analysis (cluster and ordination techniques) was applied to analyze GE interactions for grain yield of 24 durum wheat (Triticum turgidum L. var. durum) genotypes (breeding lines and old and new cultivars) along with a popular bread wheat (Triticum aestivum) cultivar grown in 21 different rainfed environments during the 2010–2013 cropping seasons. To investigate the causes of GE interaction, several genotypic and environmental covariables were used. In a combined ANOVA, environment was the predominant source of variation, accounting for 81.2% of the total sum of squares (TSS), and the remaining TSS due to the GE interaction effect was almost seven times that of the genetic effect. Cluster analysis separated the environments into four groups with similar discriminating ability among genotypes, and genotypes into five groups with similar patterns in yield performance. Pattern analysis confirmed two major environmental clusters (cold and warm), and allowed the discrimination and characterization of genotype adaptation. Within the cold-environment cluster, several subclusters were identified. The breeding lines were most adapted to moderate and warm environments, whereas the old varieties were adapted to cold environments. The results indicated that winter rainfall and plant height were among the environmental and genotypic covariables, respectively, that contributed most to GE interaction for grain yield in rainfed durum wheat.

There are different methods for predicting streamflow, and, recently machine learning has been widely used for this purpose. This technique uses a wide set of covariables in the prediction process that must undergo a selection to increase the precision and stability of the models. Thus, this work aimed to analyze the effect of covariable selection with Recursive Feature Elimination (RFE) and Forward Feature Selection (FFS) in the performance of machine learning models to predict daily streamflow. The study was carried out in the Piranga river basin, located in the State of Minas Gerais, Brazil. The database consisted of an 18-year-old historical series (2000–2017) of streamflow data at the outlet of the basin and the covariables derived from the streamflow of affluent rivers, precipitation, land use and land cover, products from the MODIS sensors, and time. The highly correlated covariables were eliminated and the selection of covariables by the level of importance was carried out by the RFE and FFS methods for the Multivariate Adaptive Regression (EARTH), Multiple Linear Regression (MLR), and Random Forest (RF) models. The data were partitioned into two groups: 75% for training and 25% for validation. The models were run 50 times and had their performance evaluated by the Nash Sutcliffe efficiency coefficient (NSE), Determination coefficient (R2), and Root of Mean Square Error (RMSE). The three models tested showed satisfactory performance with both covariable selection methods, however, all of them proved to be inaccurate for predicting values associated with maximum streamflow events. The use of FFS, in most cases, improved the performance of the models and reduced the number of selected covariables. The use of machine learning to predict daily streamflow proved to be efficient and the use of FFS in the selection of covariables enhanced this efficiency. • The Forward Feature Selection (FFS) was more advantageous for selecting covariables. • In most cases, the FFS selected fewer covariables to predict daily streamflow. • The machine learning models with covariable selection were efficient in predicting streamflow. • The most important covariable was the streamflow of affluent rivers lagged in time. [ABSTRACT FROM AUTHOR]