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Chromosome-level genome assembly of landrace ‘Huangzhou’ provides insights into high cellulose accumulation in radish
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DOI：10.1186/s12870-026-09729-7.png)
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Abstract
En 中文
Radish (Raphanus sativus L.) is an important root vegetable crop with extensive morphological and nutritional diversity. ‘Huangzhou’ (HZ) is a traditional landrace originating from the Huangzhou region in Hubei Province, China, that is characterized by a distinctive subconical taproot and high dry-matter content, making it exceptionally suited for food processing. However, the genetic basis underlying these valuable agronomic traits remains largely unexplored due to the lack of a high-quality reference genome. In this study, we generated a haplotype-resolved, chromosome-level genome assembly of the HZ radish by integrating PacBio HiFi, Oxford Nanopore, and Hi-C sequencing technologies. Comparative analysis between the two haplotypes revealed substantial structural variation, with transposable element activity likely driving haplotype differentiation. Population genomic analysis comparing eight regional HZ accessions against 190 diverse radish accessions identified 21,004 HZ-specific single nucleotide polymorphisms (SNPs). Genes harboring these unique SNPs were significantly enriched in pathways related to environmental pH and aluminum ion responses, suggesting localized environmental adaptation. Phenotypic and cytological evaluations demonstrated that the high dry matter content of HZ taproots is driven primarily by elevated cellulose accumulation and thicker cell walls. Furthermore, longitudinal transcriptome profiling across four taproot developmental stages revealed consistent upregulation of multiple cellulose synthase-related genes in HZ compared to ‘Dachangbai,’ a low-dry-matter cultivar. Collectively, our results provide a valuable genomic resource for radish breeding and offer fundamental insights into the genetic mechanisms governing cellulose biosynthesis and dry-matter accumulation in root crops.
Keywords:
Genome assembly
Landrace radish
Dry matter
Cellulose
Taproot
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