Identification of Blast Disease Resistance-related Genes by Genomic Sequence Comparison of Rice Variety Ziyu 44 and Jiangnanxiangnuo

doi:10.16819/j.1001-7216.2020.9066

Abstract

Abstract:

【Objective】 Ziyu 44 is indigenous japonica rice from Yunnan Province of China with durable broad-spectrum resistance to M. oryzae. In order to identify novel candidate rice blast resistance-related genes from Ziyu 44, 【Method】 we performed the whole genome sequencing of Ziyu 44 and susceptible variety Jiangnanxiangnuo(JNXN). Then we checked and summarized SNPs/InDels of high-throughput sequencing data by software GATK(3.4-46), and screened out disease resistance-related genes with SNPs/InDels polymorphic loci at DNA level of Ziyu 44 and JNXN.【Result】4 118 170 045 bp and 2 995 054 509 bp genomic data of Ziyu 44 and Jiangnanxiangnuo were respectively produced using Hiseq X10 PE150 platform. The alignment rates to the reference genomes (Ensembl release 31) were 98.56% and 98.30%, respectively. A total of 922 resistance-related differential genes were identified between Ziyu 44 and JNXN. Further, combined with the result of gene mapping, we identified a new blast resistance candidate gene in Ziyu 44. 【Conclusion】Our results provide valuable information for cloning of new rice blast resistance new genes, and lay an important foundation for exploring the molecular mechanism of durable broad-spectrum resistance to rice blast in Ziyu 44.

Key words: rice, rice blast, genome sequencing, resistance-related genes

摘要：

【目的】子预44是一具有广谱持久稻瘟病抗性的云南地方粳稻品种。为了鉴定子预44中候选稻瘟病抗性相关基因,【方法】本研究利用高通量测序技术（High-throughput sequencing）对子预44和感病水稻江南香糯进行了全基因组测序。而后使用软件GATK(3.4-46)对高质量测序结果进行SNP和InDel的检测和统计,进一步筛选出子预44和江南香糯DNA水平存在SNPs/InDels多态性抗病相关基因。【结果】通过Hiseq X10 PE150平台分别获得了4 118 170 045 bp和2 995 054 509 bp子预44和江南香糯的基因组数据,比对到参考基因组（Ensembl release 31）的比对率分别为98.56％和98.30％。在抗病水稻子预44和感病水稻江南香糯之间鉴定了922个纯合突变的差异抗病相关基因。结合基因定位结果,在子预44中鉴定了一个新的抗稻瘟病候选基因。【结论】研究结果为子预44中抗稻瘟病新基因的克隆提供了参考,对子预44广谱持久抗瘟分子机制的研究奠定了基础。

关键词: 水稻, 稻瘟病, 基因组测序, 抗病相关基因

CLC Number:

Jinlu LI, Hui ZHANG, Zeyu JIAO, Jianyu LIU, Guangyu HAN, Xiaoxuan ZHUO, Qiong LUO. Identification of Blast Disease Resistance-related Genes by Genomic Sequence Comparison of Rice Variety Ziyu 44 and Jiangnanxiangnuo[J]. Chinese Journal OF Rice Science, 2020, 34(1): 8-16.

李金璐, 张慧, 焦泽宇, 刘剑宇, 韩光煜, 卓晓轩, 罗琼. 水稻子预44和江南香糯基因组比较鉴定稻瘟病抗性相关基因[J]. 中国水稻科学, 2020, 34(1): 8-16.

Figures/Tables 8

Table 1 Summary of the sequence data for Ziyu 44 and Jiangnanxiangnuo.

样品Sample		高质量Reads数 HQ clean reads number	读长 Reads length/bp	碱基数 Base number/bp	Q30(%)
子预44 Ziyu 44	41 021 044	101/101	4 118 170 045	3 928 449 674(95.39%)
江南香糯基因Jiangnanxiangnuo	29 931 088	101/101	2 995 054 509	2 840 051 178(94.82%)

Fig. 1. Distribution of resistance related genes on rice chromosomes.

Fig. 2. Polymorphisms of disease resistance-related genes between Ziyu 44 and Jiangnanxiangnuo.

Table 2 Nonsynonymous mutation of SNP/InDel.

突变类型 Mutant type	终止缺失/获得 Stop loss/gain	非同义SNP Non-synonymous SNPs	非移码InDel Non-frame shift InDels	移码InDel Frame shift InDels
数量 Number	90	4732	144	97

Fig. 3. Nonsynonymous mutation of SNP/InDel between Ziyu 44 and Jiangnanxiangnuo. Frameshift InDel, Insertion deletion mutation of amino acid coding frameshift; Nonframeshift InDel, Insertion deletion mutation of amino acid coding nonframeshift; Nonsynonymous SNP, Single nucleotide polymorphisms causing amino acid differences; Stoploss/gain, Single nucleotide polymorphisms (SNP)/Insertion deletion mutation (InDel) causing premature termination or not end of amino acid translation.

Fig. 4. Distribution of 922 resistance-related genes on rice chromosomes.

Fig. 5. Comparison of the nucleotide and amino acid sequences of LOC_Os06g18820 from nine rice varieties. ZY44, Ziyu 44; ZH11, Zhonghua 11; JNXN, Jiangnanxiangnuo; Nip, Nipponbare; LTH, Lijiangxintuoheigu; TP309, Taipei 309.

Fig. 6. Symptoms of nine rice varieties inoculated with M. oryzae LP174. ZY44, Ziyu 44; ZH11, Zhonghua 11; JNXN, Jiangnanxiangnuo; Nip, Nipponbare; LTH, Lijiangxintuoheigu; TP309, Taipei 309.

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