The pangenome of hexaploid bread wheat

Area of Science:

• Plant Genomics
• Crop Science
• Bioinformatics

Background:

• Gene presence-absence variation significantly impacts heritability of agronomic traits in crops.
• Intensive breeding in hexaploid wheat has reduced genetic diversity in elite cultivars.
• Existing reference genomes may not fully capture the diversity within modern wheat cultivars.

Purpose of the Study:

• To build an improved reference genome for Chinese Spring wheat.
• To explore gene diversity and pangenome structure across 18 elite wheat cultivars.
• To identify genes associated with agronomic traits through functional annotation of variable gene sets.

Main Methods:

• Construction of an improved reference genome assembly for Chinese Spring.
• Pangenome analysis across 18 diverse wheat cultivars.
• Functional annotation of the predicted wheat pangenome and identification of single nucleotide polymorphisms (SNPs).

Main Results:

• Predicted a wheat pangenome size of 140,500 ± 102 genes and a core genome of 81,070 ± 1631 genes.
• Identified an average of 128,656 genes per cultivar, with a substantial variable gene set.
• Discovered over 36 million intervarietal single nucleotide polymorphisms (SNPs) across the pangenome.
• Functional annotation indicated enrichment of variable genes potentially linked to agronomic traits.

Conclusions:

• The wheat pangenome analysis provides crucial insights into genome diversity within elite wheat.
• Understanding gene presence-absence variation and SNPs is fundamental for genomics-based crop improvement.
• The developed wheat pangenome resources (GBrowse and downloadable data) will aid future research and breeding efforts.