PhenoApp: A mobile tool for plant phenotyping to record field and greenhouse observations

Abstract

With the ongoing cost decrease of genotyping and sequencing technologies, accurate and fast phenotyping remains the bottleneck in the utilizing of plant genetic resources for breeding and breeding research. Although cost-efficient high-throughput phenotyping platforms are emerging for specific traits and/or species, manual phenotyping is still widely used and is a time- and money-consuming step. Approaches that improve data recording, processing or handling are pivotal steps towards the efficient use of genetic resources and are demanded by the research community. Therefore, we developed PhenoApp, an open-source Android app for tablets and smartphones to facilitate the digital recording of phenotypical data in the field and in greenhouses. It is a versatile tool that offers the possibility to fully customize the descriptors/scales for any possible scenario, also in accordance with international information standards such as MIAPPE (Minimum Information About a Plant Phenotyping Experiment) and FAIR (Findable, Accessible, Interoperable, and Reusable) data principles. Furthermore, PhenoApp enables the use of pre-integrated ready-to-use BBCH (Biologische Bundesanstalt für Land- und Forstwirtschaft, Bundessortenamt und CHemische Industrie) scales for apple, cereals, grapevine, maize, potato, rapeseed and rice. Additional BBCH scales can easily be added. The simple and adaptable structure of input and output files enables an easy data handling by either spreadsheet software or even the integration in the workflow of laboratory information management systems (LIMS). PhenoApp is therefore a decisive contribution to increase efficiency of digital data acquisition in genebank management but also contributes to breeding and breeding research by accelerating the labour intensive and time-consuming acquisition of phenotyping data.

Keywords: Android app; BBCH; FAIR principles; LIMS; digital data acquisition; plant phenotyping.

Figure 1.. General app view with a data-recording example for a BBCH (Biologische Bundesanstalt für Land- und Forstwirtschaft, Bundessortenamt und CHemische Industrie) growth stage of grapevine.

Figure 2.. Principal PhenoApp workflow.

A combined genotype-location and descriptor list is required as input. Post phenotyping, recorded data can be exported as a simple Microsoft Excel file. Minimal requirements are the PhenoApp on a mobile Android-based device and a computer with a spreadsheet software for data handling.

Figure 3.. Data capture and integration into the laboratory information management system (LIMS) infrastructure of the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK).

Figure 4.. Overview of the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) intern Apex (Oracle Application Express) application.

Here, users will find a compilation of the data already registered in the laboratory information management system (LIMS), i.e. given descriptors and scales of the genebank as well as additional information such as specific contact persons. This offers a wide range of applications and enables quick and clear access to existing data and information for the development of new experiments and routine work.