EnvRtype: a software to interplay enviromics and quantitative genomics in agriculture
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 star...
| Main Authors: | , , , , |
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| Format: | Journal Article |
| Language: | Inglés |
| Published: |
Oxford University Press
2021
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| Subjects: | |
| Online Access: | https://hdl.handle.net/10568/164346 |
| _version_ | 1855513037766656000 |
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| author | Costa-Neto, Germano Galli, Giovanni Carvalho, Humberto Fanelli Crossa, José Fritsche-Neto, Roberto |
| author_browse | Carvalho, Humberto Fanelli Costa-Neto, Germano Crossa, José Fritsche-Neto, Roberto Galli, Giovanni |
| author_facet | Costa-Neto, Germano Galli, Giovanni Carvalho, Humberto Fanelli Crossa, José Fritsche-Neto, Roberto |
| author_sort | Costa-Neto, Germano |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | 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. |
| format | Journal Article |
| id | CGSpace164346 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2021 |
| publishDateRange | 2021 |
| publishDateSort | 2021 |
| publisher | Oxford University Press |
| publisherStr | Oxford University Press |
| record_format | dspace |
| spelling | CGSpace1643462025-01-24T14:11:46Z EnvRtype: a software to interplay enviromics and quantitative genomics in agriculture Costa-Neto, Germano Galli, Giovanni Carvalho, Humberto Fanelli Crossa, José Fritsche-Neto, Roberto genetics(clinical) genetics molecular biology 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. 2021-04-15 2024-12-19T12:53:45Z 2024-12-19T12:53:45Z Journal Article https://hdl.handle.net/10568/164346 en Open Access Oxford University Press Costa-Neto, Germano; Galli, Giovanni; Carvalho, Humberto Fanelli; Crossa, José and Fritsche-Neto, Roberto. 2021. EnvRtype: a software to interplay enviromics and quantitative genomics in agriculture. G3-Genes Genomes Genetics, Volume 11, no. 4; jkab040 (20 pages) |
| spellingShingle | genetics(clinical) genetics molecular biology Costa-Neto, Germano Galli, Giovanni Carvalho, Humberto Fanelli Crossa, José Fritsche-Neto, Roberto EnvRtype: a software to interplay enviromics and quantitative genomics in agriculture |
| title | EnvRtype: a software to interplay enviromics and quantitative genomics in agriculture |
| title_full | EnvRtype: a software to interplay enviromics and quantitative genomics in agriculture |
| title_fullStr | EnvRtype: a software to interplay enviromics and quantitative genomics in agriculture |
| title_full_unstemmed | EnvRtype: a software to interplay enviromics and quantitative genomics in agriculture |
| title_short | EnvRtype: a software to interplay enviromics and quantitative genomics in agriculture |
| title_sort | envrtype a software to interplay enviromics and quantitative genomics in agriculture |
| topic | genetics(clinical) genetics molecular biology |
| url | https://hdl.handle.net/10568/164346 |
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