Author: André Eggen, Director, Agrigenomics Global, Illumina Inc.
Plant breeding is experiencing a transformative era, one driven by data, molecular insight, and the need for rapid, resilient innovation. As agriculture confronts climate variability, pest and disease pressures, soil constraints, and rising global food demand, breeding programs must navigate unprecedented complexity. Agrigenomics has become central to these efforts, giving breeders the ability to uncover genetic diversity, predict performance, and accelerate selection cycles.
For more than 15 years, Illumina has supported plant researchers and breeders worldwide, providing robust genomic technologies that have reshaped how modern breeding is conducted. From the earliest SNP arrays to today’s sequencing-driven applications, Illumina tools have enabled trait discovery, association studies, germplasm management, and reliable genomic selection across nearly every major crop species.
The rising complexity of crop improvement
Plant breeders increasingly work on traits governed by intricate interactions between genes, regulatory mechanisms, development, environment, and stress. Drought resilience, nitrogen efficiency, disease resistance, and nutritional quality all depend on multilayered biological pathways that cannot be fully explained by genotype alone. This growing complexity demands technologies that reveal not just genetic variation, but also how plants regulate, express, and deploy that variation across tissues and conditions.
Illumina technologies powering today’s agrigenomics
Illumina’s contributions to plant breeding have been built around delivering scalable, accurate molecular data that breeding programs can trust. Current technologies include high‑density and mid‑density SNP arrays for genomic selection and diversity management, whole-genome and low-pass sequencing for variant discovery and haplotype reconstruction, and RNA sequencing for exploring gene expression under stress or developmental transitions.
These tools remain the foundation for many successful genomic breeding programs, enabling faster decision cycles and improved prediction accuracy. Yet the future of agrigenomics requires going beyond single-layer data to capture the full biological complexity behind important agronomic traits.
Expanding into multiomics: the new frontier in plant science
To address the need for deeper biological insight, Illumina is expanding its multiomics capabilities, first developed and proven in human research, to integrate genomic, transcriptional, epigenetic, and spatial data in ways that will also enable a unified and more comprehensive understanding of plant biology.
One powerful addition is single‑cell transcriptomics, which allows researchers to examine gene expression at cellular resolution. This opens new possibilities for studying developmental regulation, cell-type differentiation, stress responses, and plant–microbe interactions in unprecedented detail. Understanding how individual cells respond to biotic or abiotic challenges provides breeders with new targets and a clearer view of trait formation.
Complementing this, spatial transcriptomics, soon available for human and other species, will enable scientists to map gene activity directly within intact tissues. By visualizing expression patterns in sit, across leaves, roots, embryos, meristems, or infection sites, researchers can better understand how molecular programs are organized within the plant and how they influence phenotype. Spatial insights will be essential for linking gene networks to structure, physiology, and developmental context.
A key part of this multiomic evolution is the ability to capture both genetic and epigenetic information simultaneously. Illumina’s 5‑base sequencing, already available, supports the combined analysis of standard genomic variation and DNA methylation. Because methylation plays a crucial role in flowering time, vernalization, environmental memory, and stress adaptation, integrating these signals helps researchers uncover regulatory layers that directly influence agronomic performance.
With these capabilities, all delivered on the same NGS instrument, genomics, gene expression, single‑cell profiling, spatial mapping, and epigenetic readouts, Illumina aims to help plant scientists build richer, more predictive models of how plants grow, adapt, and perform under real‑world conditions.
Driving a renewed vision for predictive breeding
The long-term vision for agrigenomics is to translate molecular signals into reliable predictions of crop performance. By integrating multiomic data with high‑throughput phenotyping and environmental information, breeding programs can more accurately anticipate how varieties will behave across diverse contexts. Machine learning and AI are accelerating this shift, but their success depends on the quality and depth of the molecular data they consume.
Illumina’s platforms, spanning sequencing, expression profiling, and emerging multiomic modalities, provide the comprehensive datasets needed to power next‑generation predictive breeding.
A continued commitment to the plant breeding community
Illumina remains dedicated to enabling innovation in plant science by delivering technologies that match the scale, diversity, and complexity of modern agricultural challenges. Whether supporting foundational genotyping, advanced sequencing, or cutting‑edge multiomics, our goal is to empower breeders and researchers to accelerate the development of resilient, high‑performing crops that can support global food security.
As agriculture moves deeper into the era of integrated biology, Illumina is committed to walking alongside the community, helping transform molecular insight into real-world agricultural impact.
