Genomics and Phenomics of Plant Diversity

In contrast to subject areas focusing on genetic improvement or plant–environment interactions, this field centers on the discovery, characterization, and understanding of genetic and phenotypic diversity itself, as the foundation for future breeding, domestication, and adaptation. Domestication and modern plant breeding significantly narrowed the genetic base of many crops, increasing their susceptibility to pests, diseases, and environmental stresses, challenges further intensified by climate change. To counteract this genetic erosion and ensure resilient food- and biobased systems, it is essential to characterize and utilize the rich genetic diversity found across crops, landraces, old cultivars, crop wild relatives, feral populations and breeding germplasm. This is a critical research area dedicated to characterizing the broad genetic variation and uncovering traits that support crop adaptation, resilience, and sustainability. These efforts are especially important for plant breeders working to improve crops in the Northern Hemisphere, where climate change presents a complex array of challenges—including rising temperatures, shifting precipitation patterns, the need for adaptation to long-day growing conditions and seasonal cues, and increased pressure from pests and diseases.

This subject area focuses on generating foundational knowledge and developing tools to investigate genetic and phenotypic diversity across diverse germplasm collections. It provides the knowledge base and data resources that feed into plant genetic improvement, by identifying and characterizing the diversity that breeding programs can later exploit. By bridging classical approaches with cutting-edge technologies, such as population/quantitative genetics, genomics, high-throughput phenotyping and computational analytics, we aim to identify valuable traits and genetic resources across both cultivated and wild materials for future crop improvement. This includes developing predictive tools, such as genomic selection models and breeding simulations to unlock the genetic potential of diverse

populations and guide data-driven decisions in deploying genetic resources for crop improvement. However, the emphasis remains on understanding the underlying diversity and trait architecture rather than on optimization or selection per se. These approaches also enable de novo domestication, where novel or underutilized species are transformed into viable crops through targeted trait selection supported by integrated genomics and phenomics.

Investigating crop evolution, including genomic and phenotypic changes associated with domestication and diversification, represents a central research focus of this subject area. This aims to elucidate the emergence of key traits and their potential introduction or reintroduction to modern agricultural and horticultural systems. Research in this area contributes to long-term agricultural resilience, sustainability and food security by unlocking the potential of plant genetic resources.

Key focus areas

• Genetic diversity: Exploration and analysis of allelic and transcriptional variation inter and intra-population levels across a wide range of plant materials to understand and preserve the breadth of plant genetic resources.

• Trait discovery and Heritability: Identification of valuable traits related to stress resilience, nutritional quality, environmental stability, adaptation, and estimation of their heritability using tools from quantitative and population genetics.

• Phenomics and Artificial Intelligence (AI): Development and usage of high-throughput phenotyping technologies and AI-based data analysis pipelines for efficient trait screening and characterization across diverse germplasm collections.

• Crop evolution and Domestication: Investigation of genetic and phenotypic changes associated with domestication, diversification, and re-domestication processes. This includes exploring the evolutionary history of crops as well as supporting the domestication of novel or underutilized species by identifying key traits and alleles that can contribute to future resilient and sustainable cropping systems.

• Genomic tools- & resources, and Predictive frameworks: Design and application of genomic resources including markers, reference genomes, and analytical pipelines alongside genomic prediction models and breeding simulations aimed at evaluating genetic potential within diverse populations. These tools primarily serve to describe and make accessible plant diversity as a strategic resource.