Chromosome-level genome assembly and characterization of Kaixuan 016: A high-oleic peanut variety with improved agronomic traits developed through gamma-radiation-assisted breeding

Abstract

High-oleic peanuts are increasingly valued in agricultural production and consumer markets. Nevertheless, limited genomic information hinders the integration of genetic analyses and modern breeding strategies. This study details a chromosome-level genome assembly of Kaixuan 016, a high-oleic peanut variety developed through gamma-radiation-assisted breeding, exhibiting enhanced agronomic traits. Utilizing PacBio long-read sequencing and Hi-C technology, the assembly encompasses 2532.9 Mb, with a contig N50 of 11.48 Mb, structured into 20 pseudochromosomes. Repetitive elements comprise 72.26 % of the genome. Of the 69,845 protein-coding genes, 97 % are annotated in public databases. Phylogenetic analysis reveals divergence times of approximately 0.3 million years ago (Mya) for the A subgenome and 0.2 Mya for the B subgenome, with their initial divergence occurring around 2.6 Mya. Additionally, our study includes enrichment analyses on species-specific genes, along with expanded, contracted, and positively selected gene families engaged in vital metabolic and biosynthetic pathways such as photosynthesis, linoleic acid metabolism, and fatty acid elongation—key processes for oleic acid accumulation in developing seeds. Comparative genomic analysis with the AT1–1 parent genome suggests that γ-radiation primarily induces structural variations in Kaixuan 016. Population analysis further differentiated Kaixuan 016 and its derivatives into two distinct clusters—Kainong and Jihua accessions, highlighting their superior agronomic traits. This high-quality genome assembly provides a vital resource for comparative genomic studies and facilitates the advancement of accelerated, genome-guided breeding efforts in high-oleic peanuts.