[Posted on August 25, 2025]

Quick Summary by GrainGenes: Zhang et al., Nature Genetics, 2025 (corresponding authors: Zhizhong Gong, Qiang He, and Huilong Du) constructed a genus-level Avena "super-pangenome," which consists of 35 genome assemblies--14 cultivated and 21 wild oat species. The study integrates phylogenetic, structural variations, and transcriptomic analyses under abiotic stress conditions. Notably, it revealed that "26.62% and 59.93% specific genes and haplotypes in wild species," underscoring wild species' critical role as reservoirs of genetic diversity for breeders. This work stands as one of the most comprehensive and up-to-date genomic studies in oat research.

Title: Super-pangenome analyses across 35 accessions of 23 Avena species highlight their complex evolutionary history and extensive genomic diversity

Abstract: Common oat, belonging to the genus Avena with 30 recognized species, is a nutritionally important cereal crop and high-quality forage worldwide. Here, we construct a genus-level super-pangenome of Avena comprising 35 high-quality genomes from 14 cultivated oat accessions and 21 wild species. The fully resolved phylogenomic analysis unveils the origin and evolutionary scenario of Avena species, and the super-pangenome analysis identifies 26.62% and 59.93% specific genes and haplotypes in wild species. We delineate the landscape of structural variations (SVs) and the transcriptome profile based 1,401 RNA-sequencing (RNA-seq) samples from diverse abiotic stress treatments in oat. We highlight the crucial role of SVs in modulating gene expression and shaping adaptation to diverse stresses. Further combining SV-based genome-wide association studies (GWASs), we characterize 13 candidate genes associated with drought resistance such as AsARF7, validated by transgenic oat lines. Our study provides unprecedented genomic resources to facilitate genomic, evolution and molecular breeding research in oat.

Reference link: https://www.nature.com/articles/s41588-025-02294-z

Pubmed link: https://pubmed.ncbi.nlm.nih.gov/40835889/