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

Publicated to:G3-Genes Genomes Genetics. 11 (4): - 2021-04-01 11(4), DOI: 10.1093/g3journal/jkab040

Authors: Costa-Neto G; Galli G; Carvalho HF; Crossa J; Fritsche-Neto R

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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.

Keywords

environmentenvironmental characterizationenvirotypinggenotypeimpacttemperaturetrialsyieldEnabled predictionEnvironmental characterizationEnvirotypingGxe: genotype x environment interactionG_e: genotype _ environment interaction

Quality index

Bibliometric impact. Analysis of the contribution and dissemination channel

The work has been published in the journal G3-Genes Genomes Genetics due to its progression and the good impact it has achieved in recent years, according to the agency Scopus (SJR), it has become a reference in its field. In the year of publication of the work, 2021, it was in position , thus managing to position itself as a Q1 (Primer Cuartil), in the category Medicine (Miscellaneous).

From a relative perspective, and based on the normalized impact indicator calculated from World Citations from Scopus Elsevier, it yields a value for the Field-Weighted Citation Impact from the Scopus agency: 4.01, which indicates that, compared to works in the same discipline and in the same year of publication, it ranks as a work cited above average. (source consulted: ESI Nov 14, 2024)

This information is reinforced by other indicators of the same type, which, although dynamic over time and dependent on the set of average global citations at the time of their calculation, consistently position the work at some point among the top 50% most cited in its field:

  • Field Citation Ratio (FCR) from Dimensions: 23.06 (source consulted: Dimensions Jun 2025)

Specifically, and according to different indexing agencies, this work has accumulated citations as of 2025-06-01, the following number of citations:

  • WoS: 12
  • Scopus: 69
  • OpenCitations: 68

Impact and social visibility

From the perspective of influence or social adoption, and based on metrics associated with mentions and interactions provided by agencies specializing in calculating the so-called "Alternative or Social Metrics," we can highlight as of 2025-06-01:

  • The use, from an academic perspective evidenced by the Altmetric agency indicator referring to aggregations made by the personal bibliographic manager Mendeley, gives us a total of: 136.
  • The use of this contribution in bookmarks, code forks, additions to favorite lists for recurrent reading, as well as general views, indicates that someone is using the publication as a basis for their current work. This may be a notable indicator of future more formal and academic citations. This claim is supported by the result of the "Capture" indicator, which yields a total of: 133 (PlumX).

With a more dissemination-oriented intent and targeting more general audiences, we can observe other more global scores such as:

  • The Total Score from Altmetric: 6.1.
  • The number of mentions on the social network Facebook: 3 (Altmetric).
  • The number of mentions on the social network X (formerly Twitter): 10 (Altmetric).

It is essential to present evidence supporting full alignment with institutional principles and guidelines on Open Science and the Conservation and Dissemination of Intellectual Heritage. A clear example of this is:

  • The work has been submitted to a journal whose editorial policy allows open Open Access publication.

Leadership analysis of institutional authors

This work has been carried out with international collaboration, specifically with researchers from: Brazil; Mexico; Philippines.