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

Abstract

AbstractRice is an important crop and serves as a model for crop genomics and breeding studies. Here, we used Oxford Nanopore ultra-long sequencing and next-generation sequencing technologies to generate a chromosome-scale genome assembly of Huizhan, a disease-resistant and heat-tolerantindicarice variety. The final genome assembly was 395.20 Mb with a scaffold N50 of 31.87 Mb. We identified expanded gene families in Huizhan that are potentially associated with both organ growth and development, as well as stress responses. We observed that three functional rice blast resistance genes, includingPi2,PiaandPtr, and bacterial blight resistance geneXa27, likely contribute to disease resistance of Huizhan. In addition, integrated genomics and transcriptomics analyses show thatOsHIRP1,OsbZIP60, the SOD gene family, and various transcription factors are likely involved in heat tolerance of Huizhan. Results presented in this study will serve as a valuable resource for rice functional genomics studies and breeding.