Functional cereal pan-genomics: harnessing structural and regulatory variation for precision crop design

Area of Science:

• Genomics
• Plant Science
• Bioinformatics

Background:

• Traditional single-reference genomics limits the discovery of trait-associated variation in crops.
• Cultivated and wild cereal germplasm possess extensive genetic diversity crucial for crop improvement.

Purpose of the Study:

• To review the advancements and applications of cereal pan-genomics.
• To highlight how pan-genomics enables the discovery of novel trait-associated variations.
• To discuss the role of pan-genomics in accelerating crop design for enhanced resilience and yield.

Main Methods:

• Long-read sequencing technologies for comprehensive genome assembly.
• Multi-omics data integration (genomics, transcriptomics, epigenomics).
• Analysis of structural variants, regulatory elements, and adaptive alleles across diverse germplasm.

Main Results:

• Pan-genomics provides high-resolution maps of genetic variation, including structural variants and regulatory elements.
• Uncovers trait-associated variation previously inaccessible with single-reference methods.
• Enables haplotype-informed breeding, pathway engineering, and introgression of beneficial wild alleles.

Conclusions:

• Cereal pan-genomics is a foundational platform for predictive crop design.
• Facilitates the development of high-yielding, climate-resilient crop varieties.
• Offers actionable guidance for optimizing breeding strategies through comprehensive genetic insights.