Challenges in Bringing Pangenome Research Into Breeding: A Case Study in Rice

Area of Science:

• Genomics
• Crop Science
• Bioinformatics

Background:

• Pangenomics offers a comprehensive view of genetic diversity beyond single reference genomes.
• Rice pangenome resources have identified structural variations (SVs) and novel genes impacting agronomic traits.

Purpose of the Study:

• To review advancements in rice pangenome research for trait discovery and molecular breeding.
• To highlight the transition of pangenome resources from research to practical breeding tools.

Main Methods:

• Review of rice pangenome research encompassing cultivated and wild species.
• Analysis of trait discovery for yield, disease resistance, and stress tolerance.
• Examination of molecular breeding strategies enabled by pangenomics.

Main Results:

• Rice pangenome research has advanced discovery of key agronomic traits.
• Pangenomics enables new molecular breeding strategies for crop improvement.
• Significant challenges hinder routine integration of pangenomic data into breeding pipelines.

Conclusions:

• The rice pangenome is a pivotal advance for sustainable agriculture and global food security.
• Overcoming data complexity, variant detection, and tool development barriers is crucial.
• Interdisciplinary collaboration and breeder-focused innovations are needed for pangenomic adoption.