Unified crop-specific standards and protocols for PGR phenotype and agronomic evaluation

Unified, crop-specific standards and protocols for the evaluation of the phenotypes and agronomic characteristics of PGR, incorporating the ECPGR, MIAPPE, Crop Ontology, EMPHASIS and final user recommendations and methodologies

The phenotype encompasses the structural, physiological and performance-related traits of a genotype within a specific environment. Plant phenotyping quantifies these traits to understand their structures, functions and interrelationships. Traditionally, phenotyping relied on visual observations and simple instrumental measures of the whole plants and their parts. It has pivotal importance in breeding activities for producing varietal innovations with superior traits such as higher yield, disease and pest resistance and adaptation to abiotic stresses.

Recent technological advances have introduced high-throughput phenotyping, significantly transforming the field and giving rise to phenomics, which complements genome sequencing by fully characterizing phenotypes encoded by a genome. However, this progress has introduced the challenge of standardizing protocols and methods to ensure data comparability and interoperability.

Over time, an ecosystem of resources has been developed for phenotyping aiming to standardize descriptor measurements and ensuring that data are FAIR (Findable, Accessible, Interoperable and Reusable).

Deliverable D4.1 aimed to review and map in detail the current initiatives in plant phenotyping and related ontologies and propose a unified crop-specific standardization of protocol methods for the evaluation and valorization of plant genetic resources (PGR).

The project focused on PGR across four groups: fruit trees, fruit vegetables, leafy vegetables and grains (cereals and legumes). The targeted traits included those more relevant for breeding, such as yield, quality characteristics, resistance to biotic stresses, tolerance to abiotic stresses, and plant and root architecture.

The analysis carried out in D4.1 highlighted gaps in unified standards and protocols for evaluating PGR phenotypes and agronomic characteristics. Challenges included heterogeneity in phenotypic descriptors, redundancy in descriptor catalogues, and lack of interoperability. Many catalogues are outdated, difficult to access and not machine-actionable, hindering data comparison and reuse. Moreover, metadata about phenotyping conditions are often missing, which is essential for understanding genotype-by-environment (GxE) effects.

To standardize the evaluation and valorization of PGR phenotypes and agronomic characteristics, it is essential to:

1. Include recommended metadata for phenotyping experiments as per MIAPPE guidelines.

2. Harmonize descriptors using trait and crop ontologies, with reference scientists overseeing the guidelines.

3. Ensure data management practices align with FAIR principles.

These steps will facilitate the development of robust standards and protocols, aiding the future GRACE-RI in achieving standardized phenotyping of PGRs.

Deliverable D4.1 was led by INRAE in collaboration with CREAENEA, ECPGR/IPGRI, UPV, KIS

For more information, download the Deliverable report.