Chromosome-level genome assembly of landrace ‘Huangzhou’ provides insights into high cellulose accumulation in radish

Abstract

<title>Abstract</title> Radish ( <italic>Raphanus sativus</italic> L.) is an important root vegetable crop with extensive morphological and nutritional diversity. The landrace radish, ‘Huangzhou’ (HZ) radish, origins in Huangzhou area, Hubei province of China, and characterized by a special subconical-shaped taproot and high dry matter content, making it particularly suitable for processing. However, the genetic basis underlying these agronomic traits remains largely unexplored due to the lack of a reference genome. In this study, we generated a high-quality haplotype-resolved genome assembly of HZ radish by integrating PacBio HiFi, Oxford Nanopore, and Hi-C sequencing technologies. Comparative analysis between the two haplotypes revealed substantial structural divergence and transposable elements (TEs) probably contributed to the differentiation of haplomes. Further population analysis with eight HZ radishes from different regions, as well as another 190 radish accessions identified 21,004 unique single nucleotide polymorphism sites (SNPs) in the HZ radishes, and those related genes were enriched in response to environmental pH and aluminum ion, suggesting local environmental adaptation. Phenotypic and cytological analyses demonstrated that the high dry matter content of HZ taproots was primarily associated with increased cellulose accumulation and thicker cell walls. Transcriptome analysis across four developmental stages of taproots showed that multiple cellulose synthase-related genes were consistently upregulated in HZ compared with the low-dry-matter cultivar ‘Dachangbai’. Collectively, our research provides new genetic resources for the radish genome research, and offers new insights into the genetic mechanisms underlying dry matter accumulation and cellulose biosynthesis in radish.