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Identification and fine-mapping of Xo2, a novel rice bacterial leaf streak resistance gene

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Abstract

Key message

A novel rice resistance gene, Xo2, influencing pathogenesis of the bacterial leaf streak disease, has been identified, and candidate genes for Xo2 in the fine mapping region have been shown to be involved in bacterial leaf streak resistance.

Abstract

Rice (Oryza sativa) bacterial leaf streak, caused by Xanthomonas oryzae pv. oryzicola (Xoc), is one of the most serious rice bacterial diseases. The deployment of host resistance genes is an effective approach for controlling this disease. The cultivar BHADOIA 303 (X455) from Bangladesh is resistant to most of Chinese Xoc races. To identify and map the resistance gene(s) involved in Xoc resistance, we examined the association between phenotypic and genotypic variations in two F2 populations derived from crosses between X455/Jingang 30 and X455/Wushansimiao. The segregation ratios of the F2 progeny were consistent with the action of a single dominant resistance gene, which was designated as Xo2. Based on rice SNP chip (GSR40K) assays of X455, Jingang 30, and resistant and susceptible pools thereof, we mapped Xo2 to the region from 10 Mb to 12.5 Mb on chromosome 2. The target gene was further finely mapped between the markers RM12941 and D6-1 within an approximately 110-kb region. The de novo sequencing and gene annotation of X455 and Jingang 30 revealed nineteen predicted genes within the target region. RNA-seq and expression analysis showed that four candidate genes, including Osa002T0115800, encoding an NLR resistance protein, were distinctly upregulated. Differential sequence and synteny analysis between X455 and Jingang 30 suggested that Osa002T0115800 is likely the functional Xo2 gene. This study lays a foundation for marker-assisted selection resistance breeding against rice bacterial leaf streak and the further cloning of Xo2.

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Data availability

The datasets generated and/or analysed during the current study are available from the corresponding author upon reasonable request.

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Acknowledgements

This work is supported by the "14th Five-Year Plan" New Discipline Team Building Project of Guangdong Academy of Agricultural Sciences (202116TD), the Special Fund for Modern Agricultural Industry Technology System (CARS-01-35; 2021KJ105), the "Jin Ying Zhi Guang" Training Program for Young and Middle-aged Academic Leaders of Guangdong Academy of Agricultural Sciences (R2020PY-JG007), the Project of Collaborative Innovation Center of GDAAS (XT202211), the Jiangsu Province Key Research and Development Program (Modern Agriculture) Sub project (BE2020318-3), the Natural Science Foundation of Guangdong Province (2021A1515012497), and the Science and Technology Plan Project of Guangzhou (202002030001).

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The data sets supporting the results of this article are included within the article and its additional files.

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Authors and Affiliations

  1. Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute of Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China

    Shen Chen, Aiqing Feng, Congying Wang, Jinqi Feng, Bing Chen, Jianyuan Yang, Wenjuan Wang, Meiying Zhang, Kailing Chen, Weiqin Chen, Jing Su & Xiaoyuan Zhu

  2. Rice Research Institute and Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China

    Junliang Zhao & Bin Liu

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  1. Shen Chen
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Contributions

SC carried out the development of the mapping population, genetic analysis, primer design, and gene mapping and drafted the manuscript. AQF and CYW participated in the phenotypic selection and data assays for molecular mapping. JQF and JYY contributed to the isolation and culture of virulent strains of Xoc used in this study. BC and MYZ were involved in phenotypic selection for the fine-mapping and data mining of candidates. JLZ and BL were responsible for sequencing data assembly and analysis. JS and WJW performed RNA-seq and candidate gene transcription data analysis. KLC and WQC were responsible for plant cultivation and pathogen inoculation. XYZ designed and coordinated the study, assisted with genetic analyses, and drafted the manuscript. All authors read and approved the final manuscript.

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Correspondence to Xiaoyuan Zhu.

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The authors declare that the study complies with the current laws of China.

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Communicated by Mingliang Xu.

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Chen, S., Feng, A., Wang, C. et al. Identification and fine-mapping of Xo2, a novel rice bacterial leaf streak resistance gene. Theor Appl Genet 135, 3195–3209 (2022). https://doi.org/10.1007/s00122-022-04179-9

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