Ming-Hao Liu, Houxiang Kang, Yucheng Xu, Ye Peng, Dan Wang, Lijun Gao, Xuli Wang, Yuese Ning, Jun Wu, Wende Liu, Chengyun Li, Bin Liu, Guo-Liang Wang

Plant Biotechnol Journal; 2020 Jun;18(6):1376-1383.  doi: 10.1111/pbi.13300. Epub 2019 Dec 15.

Abstract

Because of the frequent breakdown of major resistance (R) genes, identification of new partial R genes against rice blast disease is an important goal of rice breeding. In this study, we used a core collection of the Rice Diversity Panel II (C-RDP-II), which contains 584 rice accessions and are genotyped with 700 000 single-nucleotide polymorphism (SNP) markers. The C-RDP-II accessions were inoculated with three blast strains collected from different rice-growing regions in China. Genome-wide association study identified 27 loci associated with rice blast resistance (LABRs). Among them, 22 LABRs were not associated with any known blast R genes or QTLs. Interestingly, a nucleotide-binding site leucine-rich repeat (NLR) gene cluster exists in the LABR12 region on chromosome 4. One of the NLR genes is highly conserved in multiple partially resistant rice cultivars, and its expression is significantly up-regulated at the early stages of rice blast infection. Knockout of this gene via CRISPR-Cas9 in transgenic plants partially reduced blast resistance to four blast strains. The identification of this new non-strain specific partial R gene, tentatively named rice blast Partial Resistance gene 1 (PiPR1), provides genetic material that will be useful for understanding the partial resistance mechanism and for breeding durably resistant cultivars against blast disease of rice.

See: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7206997/

Figure 3: The SNPs and synteny of the genomic sequences of the ~ 200‐kb region at the LABR12 locus. (a) Manhattan plots of SNPs at LABR12. The x‐axis indicates the distance (kb), and the y‐axis indicates the association score of each SNP. The score represents a transformed P value, −log₁₀ P. The blue and red dots indicate SNPs with a LOD score < 4.0 and ≥ 4.0, respectively. (b) Synteny analysis of the LABR12 locus between the Nipponbare and the 9311 genomes. The blue bars link the homologous genes between the genomes. The red polygons represent the NBS‐LRR‐type R genes. The red arrow indicates the PiPR1 gene(Os04g53050).