A genome-wide association study of panicle blast resistance to Magnaporthe oryzae in rice

IF 2.6 3区农林科学 Q1 AGRONOMY Molecular Breeding Pub Date : 2024-07-11 DOI:10.1007/s11032-024-01486-5

Hu Jinlong, Zhang Yu, Wang Ruizhi, Wang Xiaoyu, Feng Zhiming, Xiong Qiangqiang, Zhou Nianbing, Zhou Yong, Wei Haiyan, Zhang Hongcheng, Zhu Jinyan

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Abstract

Rice blast, caused by Magnaporthe oryzae (M. oryzae), is one of the most serious diseases worldwide. Developing blast-resistant rice varieties is an effective strategy to control the spread of rice blast and reduce the reliance on chemical pesticides. In this study, 477 sequenced rice germplasms from 48 countries were inoculated and assessed at the booting stage. We found that 23 germplasms exhibited high panicle blast resistance against M. oryzae. Genome-wide association analysis (GWAS) identified 43 quantitative trait loci (QTLs) significantly associated (P < 1.0 × 10⁻⁴) with resistance to rice panicle blast. These QTL intervals encompass four genes (OsAKT1, OsRACK1A, Bsr-k1 and Pi25/Pid3) previously reported to contribute to rice blast resistance. We selected QTLs with -Log10 (P-value) greater than 6.0 or those detected in two-year replicates, amounting to 12 QTLs, for further candidate gene analysis. Three blast resistance candidate genes (Os06g0316800, Os06g0320000, Pi25/Pid3) were identified based on significant single nucleotide polymorphisms (SNP) distributions within annotated gene sequences across these 12 QTLs and the differential expression levels among blast-resistant varieties after 72 h of inoculation. Os06g0316800 encodes a glycine-rich protein, OsGrp6, an important component of plant cell walls involved in cellular stress responses and signaling. Os06g0320000 encodes a protein with unknown function (DUF953), part of the thioredoxin-like family, which is crucial for maintaining reactive oxygen species (ROS) homeostasis in vivo, named as OsTrxl1. Lastly, Pi25/Pid3 encodes a disease resistance protein, underscoring its potential importance in plant biology. By analyzing the haplotypes of these three genes, we identified favorable haplotypes for blast resistance, providing valuable genetic resources for future rice blast resistance breeding programs.

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水稻抗穗瘟的全基因组关联研究

由 Magnaporthe oryzae（M. oryzae）引起的稻瘟病是全球最严重的病害之一。培育抗稻瘟病的水稻品种是控制稻瘟病蔓延、减少对化学农药依赖的有效策略。本研究对来自 48 个国家的 477 个水稻测序种质进行了接种，并在抽穗期进行了评估。我们发现，有 23 个种质表现出对 M. oryzae 的高抗稻瘟病性。全基因组关联分析（GWAS）发现 43 个数量性状位点（QTLs）与稻穗瘟的抗性显著相关（P < 1.0 × 10-4）。这些 QTL 区间包含四个基因（OsAKT1、OsRACK1A、Bsr-k1 和 Pi25/Pid3），以前曾报道它们对稻瘟病抗性有贡献。我们选择了-Log10（P-值）大于 6.0 或在两年重复中检测到的 QTLs（共 12 个 QTLs）进行进一步的候选基因分析。根据这 12 个 QTLs 的注释基因序列中显著的单核苷酸多态性（SNP）分布以及抗瘟品种在接种 72 小时后的不同表达水平，确定了三个抗瘟候选基因（Os06g0316800、Os06g0320000 和 Pi25/Pid3）。Os06g0316800 编码富含甘氨酸的蛋白 OsGrp6，它是植物细胞壁的重要组成部分，参与细胞胁迫反应和信号转导。Os06g0320000 编码一个功能未知的蛋白质（DUF953），属于类硫氧还蛋白家族，对维持体内活性氧（ROS）平衡至关重要，命名为 OsTrxl1。最后，Pi25/Pid3编码一种抗病蛋白，突出了其在植物生物学中的潜在重要性。通过分析这三个基因的单倍型，我们发现了对稻瘟病抗性有利的单倍型，为未来的稻瘟病抗性育种计划提供了宝贵的遗传资源。

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来源期刊

Molecular Breeding 农林科学-农艺学

CiteScore

5.60

自引率

6.50%

发文量

审稿时长

1.5 months

期刊介绍： Molecular Breeding is an international journal publishing papers on applications of plant molecular biology, i.e., research most likely leading to practical applications. The practical applications might relate to the Developing as well as the industrialised World and have demonstrable benefits for the seed industry, farmers, processing industry, the environment and the consumer. All papers published should contribute to the understanding and progress of modern plant breeding, encompassing the scientific disciplines of molecular biology, biochemistry, genetics, physiology, pathology, plant breeding, and ecology among others. Molecular Breeding welcomes the following categories of papers: full papers, short communications, papers describing novel methods and review papers. All submission will be subject to peer review ensuring the highest possible scientific quality standards. Molecular Breeding core areas: Molecular Breeding will consider manuscripts describing contemporary methods of molecular genetics and genomic analysis, structural and functional genomics in crops, proteomics and metabolic profiling, abiotic stress and field evaluation of transgenic crops containing particular traits. Manuscripts on marker assisted breeding are also of major interest, in particular novel approaches and new results of marker assisted breeding, QTL cloning, integration of conventional and marker assisted breeding, and QTL studies in crop plants.