EnvRtype: A software to interplay enviromics and quantitative genomics in agriculture

Authors

Germano Costa-Neto, Universidade de São Paulo
Giovanni Galli, Universidade de São Paulo
Humberto Fanelli Carvalho, Universidade de São Paulo
Jose Crossa, Centro Internacional de Mejoramiento de Maiz y Trigo
Roberto Fritsche-Neto, Universidade de São Paulo

Document Type

Article

Publication Date

4-1-2021

Abstract

Envirotyping is an essential technique used to unfold the nongenetic drivers associated with the phenotypic adaptation of living organisms. Here, we introduce the EnvRtype R package, a novel toolkit developed to interplay large-scale envirotyping data (enviromics) into quantitative genomics. To start a user-friendly envirotyping pipeline, this package offers: (1) remote sensing tools for collecting (get_weather and extract_GIS functions) and processing ecophysiological variables (processWTH function) from raw environmental data at single locations or worldwide; (2) environmental characterization by typing environments and profiling descriptors of environmental quality (env_typing function), in addition to gathering environmental covariables as quantitative descriptors for predictive purposes (W_matrix function); and (3) identification of environmental similarity that can be used as an enviromic-based kernel (env_typing function) in whole-genome prediction (GP), aimed at increasing ecophysiological knowledge in genomic best-unbiased predictions (GBLUP) and emulating reaction norm effects (get_kernel and kernel_model functions). We highlight literature mining concepts in fine-tuning envirotyping parameters for each plant species and target growing environments. We show that envirotyping for predictive breeding collects raw data and processes it in an eco-physiologically smart way. Examples of its use for creating global-scale envirotyping networks and integrating reaction-norm modeling in GP are also outlined. We conclude that EnvRtype provides a cost-effective envirotyping pipeline capable of providing high quality enviromic data for a diverse set of genomic-based studies, especially for increasing accuracy in GP across untested growing environments.

Publication Source (Journal or Book title)

G3: Genes, Genomes, Genetics

Recommended Citation

Costa-Neto, G., Galli, G., Carvalho, H., Crossa, J., & Fritsche-Neto, R. (2021). EnvRtype: A software to interplay enviromics and quantitative genomics in agriculture. G3: Genes, Genomes, Genetics, 11 (4) https://doi.org/10.1093/g3journal/jkab040