Genomic and transcriptomic analyses of the elite rice variety Huizhan provide insight into disease resistance and heat tolerance

The indica rice variety Huizhan shows elite traits of disease resistance and heat tolerance. However, the underlying genetic basis of these traits is not fully understood due to limited genomic resources. Here, we used Nanopore long-read and next-generation sequencing technologies to generate a chromosome-scale genome assembly of Huizhan. Comparative genomics analysis uncovered a large chromosomal inversion and expanded gene families that are associated with plant growth, development and stress responses. Functional rice blast resistance genes, including Pi2, Pib and Ptr, and bacterial blight resistance gene Xa27, contribute to disease resistance of Huizhan. Furthermore, integrated genomics and transcriptomics analyses showed that OsHIRP1, OsbZIP60, the SOD gene family, and various transcription factors are involved in heat tolerance of Huizhan. The high-quality genome assembly and comparative genomics results presented in this study facilitate the use of Huizhan as an elite parental line in developing rice varieties adapted to disease pressure and climate challenges. •A chromosome-scale genome of Huizhan, a disease-resistant and heat-tolerant indica rice variety, was assembled.•The genome was analyzed and compared to the genomes of other rice varieties and wild relatives.•Rice blast resistance genes Pi2, Pib and Ptr and bacterial blight resistance gene Xa27 contribute to disease resistance.•OsHIRP1, OsbZIP60, the SOD gene family, and various transcription factors are involved in heat tolerance of Huizhan.