Graph-based Pangenome Analysis Reveals the Genetic Control of Root Development in Cynanchum Species

Abstract The roots of three Cynanchum species—Cynanchum wilfordii (CW), C. auriculatum (CA), and C. rostellatum (CR)—are widely used for medicinal purposes in Northeast Asia. Unlike CW and CA, CR lacks storage roots and features long, slender roots. To explore these species' genomes and support breeding efforts, we assembled nearly complete pseudo-haploid reference genomes with centromere and telomere repeats for all three, along with 28 haplotype-resolved genomes from nine CW, three CA, and two CR accessions. Graph-based pangenome integration and association scans identified key genes involved in root diversity in CW. Additionally, the Cynanchum pangenome and expression data indicated lower abscisic acid (ABA) biosynthesis in CR due to structural variation in ABSCISIC ALDEHYDE OXIDASE 3. ABA deficiency hampers stomatal control, while extremely long roots likely adapt to water loss. Our findings offer insights into root development and aid genomics-based breeding of these valuable root crops.