A sorghum pangenome reference improves global crop trait discovery.

Area of Science:

• Plant genetics
• Crop science
• Bioinformatics

Background:

• Global food security relies on diverse, locally-adapted crops from smallholder farms, not just industrialized agriculture.
• Sorghum, a vital grain and bioenergy crop, possesses significant genetic diversity crucial for improvement.
• Breeding efforts are often limited by highly specialized traits and breeding targets.

Purpose of the Study:

• To construct a comprehensive sorghum pangenome reference and diversity panel.
• To investigate the genetic diversity, historical adaptation, and structural variations within sorghum cultivars and landraces.
• To demonstrate pangenome-accelerated trait discovery by linking genetic variation to phenotypic traits.

Main Methods:

• Construction of a 33-member pangenome reference and a diversity panel (1,984 cultivars/landraces).
• Analysis of structural variants, particularly in the SHATTERING1 domestication gene.
• Application of landscape genomics to study gene flow and adaptation.
• Correlation of structural variation in biosynthetic gene clusters with dhurrin concentration.

Main Results:

• Identification of multiple nested and deeply diverged structural variants in SHATTERING1, supporting sorghum's multicentric origin.
• Uncovering the complex genetic mosaic in contemporary breeding networks shaped by gene flow and secondary contact.
• Demonstrated a link between structural variation in biosynthetic gene clusters and dhurrin levels in sorghum leaves.

Conclusions:

• The developed pangenome and diversity panel are valuable resources for sorghum genetic improvement.
• Understanding structural diversity is key to unlocking the potential of crop genetic resources.
• This framework accelerates breeding and trait discovery, applicable to other crop species.