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. 2022 May 20;13(5):916.
doi: 10.3390/genes13050916.

Identification of Pathogenicity Loci in Magnaporthe oryzae Using GWAS with Neck Blast Phenotypic Data

Nyein Nyein Aye Myint  1 , Siripar Korinsak  2 , Cattleya Chutteang  3 , Kularb Laosatit  3 , Burin Thunnom  2 , Theerayut Toojinda  2 , Jonaliza L Siangliw  2
Affiliations

Identification of Pathogenicity Loci in Magnaporthe oryzae Using GWAS with Neck Blast Phenotypic Data

Nyein Nyein Aye Myint et al. Genes (Basel). .

Abstract

Magnaporthae oryzae (M. oryzae) is the most destructive disease of rice worldwide. In this study, one hundred and two isolates of M. oryzae were collected from rice (Oryzae sativa L.) from 2001 to 2017, and six rice varieties with resistance genes Pizt, Pish, Pik, Pib, and Pi2 were used in a genome-wide association study to identify pathogenicity loci in M. oryzae. Genome-wide association analysis was performed using 5338 single nucleotide polymorphism (SNPs) and phenotypic data of neck blast screening by TASSEL software together with haplotype block and SNP effect analysis. Twenty-seven significant SNPs were identified on chromosomes 1, 2, 3, 4, 5, 6, and 7. Many predicted genes (820 genes) were found in the target regions of six rice varieties. Most of these genes are described as putative uncharacterized proteins, however, some genes were reported related to virulence in M. oryzae. Moreover, this study revealed that R genes, Pik, Pish, and Pi2, were broad-spectrum resistant against neck blast disease caused by Thai blast isolate. Haplotype analysis revealed that the combination of the favorable alleles causing reduced virulence of isolates against IRBLz5-CA carrying Pi2 gene contributes 69% of the phenotypic variation in pathogenicity. The target regions and information are useful to develop marker-specific genes to classify blast fungal isolates and select appropriate resistance genes for rice cultivation and improvement.

Keywords: GWAS; Magnaporthae oryzae; SNP; haplotype; neck blast.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Neck and panicle inoculated with conidia suspension. (Red arrows show neck blast infection with complete white head panicle).
Figure 2
Figure 2
Frequency distribution of blast isolates in six rice varieties showing disease score of 91 isolates in IRBLzt-T, 90 isolates in IRBLsh-S, 96 isolates in IRBLk-KA, 85 isolates in IRBLb-B, 84 isolates in LTH, and 91 isolates in IRBLz5-CA.
Figure 3
Figure 3
Linkage disequilibrium decay in blast isolates genome.
Figure 4
Figure 4
Principal component analysis of unrooted neighboring-joining clustering tree. Note: northeast—red; north—green; central—blue; south—purple; east—orange; west—black.
Figure 5
Figure 5
The Manhattan plots and Q−Q plots of genome-wide association study for six rice varieties inoculated with rice blast fungi using mixed linear model, 85 isolates in IRBLb-B, 96 isolates in IRBLk-KA, 90 isolates in IRBLsh-S, 91 isolates in IRBLz5-CA, 91 isolates in IRBLzt-T, and 84 isolates in LTH.
Figure 6
Figure 6
Haplotypes retained from multiple linear regression for the IRBLz5-CA. The first, second, third, and fourth allele in each combination were derived from MG2-5441644, MG3-1645410, MG6-703373, and MG6-957987 GWAS significant SNPs, respectively.
See this image and copyright information in PMC

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