The genome of the rice variety LTH provides insight into its universal susceptibility mechanism to worldwide rice blast fungal strains

Lei Yang; Mengfei Zhao; Gan Sha; Qiping Sun; Qiuwen Gong; Qun Yang; Kabin Xie; Meng Yuan; Jenny C Mortimer; Weibo Xie; Tong Wei; Zhensheng Kang; Guotian Li

doi:10.1016/j.csbj.2022.01.030

The genome of the rice variety LTH provides insight into its universal susceptibility mechanism to worldwide rice blast fungal strains

Comput Struct Biotechnol J. 2022 Feb 10:20:1012-1026. doi: 10.1016/j.csbj.2022.01.030. eCollection 2022.

Authors

Lei Yang¹, Mengfei Zhao¹, Gan Sha¹, Qiping Sun¹, Qiuwen Gong¹, Qun Yang¹, Kabin Xie², Meng Yuan², Jenny C Mortimer³, Weibo Xie², Tong Wei⁴, Zhensheng Kang⁵, Guotian Li¹

Affiliations

¹ State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, the Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430070, China.
² National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China.
³ School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, Australia.
⁴ Department of Plant Pathology and the Genome Center, University of California, Davis, CA 95616, USA.
⁵ State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China.

Abstract

The widely used rice variety Lijiangxintuanheigu (LTH) shows a universal susceptibility to thousands of Magnaporthe oryzae isolates, the causal agent of devastating rice blast, making LTH an ideal line in resistance (R) gene cloning. However, the underlying genetic mechanism of the universal susceptibility has not been fully revealed because of the lack of a high-quality genome. Here, we took a genomic approach together with experimental assays to investigate LTH's universal susceptibility to rice blast. Using Nanopore long reads, we assembled a chromosome-level genome. Millions of genomic variants were detected by comparing LTH with 10 other rice varieties, of which large-effect variants could affect plant immunity. Gene family analyses show that the number of R genes and leucine-rich repeat receptor-like protein kinase (LRR-RLK)-encoding genes decrease significantly in LTH. Rice blast resistance genes called Pi genes are either absent or disrupted by genomic variations. Additionally, residual R genes of LTH are likely under weak pathogen selection pressure, and other plant defense-related genes are weakly induced by rice blast. In contrast, the pattern-triggered immunity (PTI) of LTH is normal, as demonstrated by experimental assays. Therefore, we conclude that weak effector-trigger immunity (ETI)-mediated primarily by Pi genes but not PTI results in the universal susceptibility of LTH to rice blast. The attenuated ETI of LTH may be also associated with reduced numbers of R genes and LRR-RLKs, and minimally functional residual defense-related genes. Finally, we demonstrate the use of the LTH genome by rapid cloning of the Pi gene Piak from a resistant variety.

Keywords: Genome assembly; LTH; Nanopore; Oryza sativa; Plant immunity; Resistance gene.