Uncovering Disease Resistance Gene Diversity in Sorghum Through High-Quality Assemblies and Full-Length Transcriptomics

Authors: CHOUGULE, KAPEEL - Cold Spring Harbor Laboratory; WEI, SHARON - Cold Spring Harbor Laboratory; LU, ZHENYUAN - Cold Spring Harbor Laboratory; OLSON, ANDREW - Cold Spring Harbor Laboratory; TRESSEL, LYDIA - Cold Spring Harbor Laboratory; Gladman, Nicholas; Ware, Doreen

Submitted to: CONFERENCE ON THE BIOLOGY OF GENOMES
Publication Type: Abstract Only
Publication Acceptance Date: 5/5/2026
Publication Date: 5/5/2026
Citation: Chougule, K., Wei, S., Lu, Z., Olson, A., Tressel, L., Gladman, N.P., Ware, D. 2026. Uncovering Disease Resistance Gene Diversity in Sorghum Through High-Quality Assemblies and Full-Length Transcriptomics. CONFERENCE ON THE BIOLOGY OF GENOMES. Conference on the Biology of Genomes.

Interpretive Summary:

Technical Abstract: Sorghum (Sorghum bicolor) is a vital cereal crop for food security, livestock feed, and bioenergy, grown worldwide under challenging climates. However, its productivity is continually threatened by pathogens and pests, including anthracnose, grain mold, and more recently the sugarcane aphid, which since 2013 has caused devastating losses across the U.S. sorghum belt. Breeding for durable resistance depends on identifying and deploying natural resistance (R) genes, yet these genes are among the most difficult to annotate due to their rapid sequence diversification, structural clustering, and the limitations of conventional genome annotation methods. High-quality reference assemblies are essential to resolve complex R-gene regions, which often contain large structural insertions, tandem duplications, and copy number variation. Resources such as SorghumBase now host assemblies and annotations for diverse sorghum accessions, including many lines with disease resistance traits. Building on this genomic foundation, we leveraged the growing diversity of sorghum accessions sequenced with long-read technologies to systematically characterize R-genes at pangenome scale. We first conducted genome-wide scans using the NLR-Annotator tool across 72 sorghum assemblies, identifying >350 candidate NLR loci. To complement this, we applied PlantNLR, a protein-based pipeline that detects canonical NLRs as well as NLRs with integrated domains (NLR-IDs), which may act as decoys to trap pathogen effectors. Integration of both methods revealed substantial overlap while also uncovering unique candidates from each. Comparative genomics using NB-ARC gene trees from SorghumBase then enabled the classification of NLR families, highlighting clear lineage-specific expansions and contractions that shape sorghum’s immune diversity. To improve structural accuracy, we incorporated long-read full-length transcript sequencing (PacBio Kinnex and Revio platforms). Across resistant accessions, these data refined splice junctions and UTR boundaries, enhanced sensitivity of detection, and revealed extensive alternative splicing, intron retention, and antisense transcription at NLR loci. These transcriptomic insights not only improve annotation quality but also provide functional evidence for diversification among closely related paralogs. Together, these results demonstrate that the combination of high-quality assemblies, pan-genomic analyses, and full-length transcriptomics is essential for capturing the true diversity of sorghum disease resistance genes. This integrative framework lays the groundwork for identifying novel R-gene variants, understanding adaptive mechanisms, and accelerating the breeding of cultivars with durable resistance.