Genetic identification of Pid3-1 and its regulatory role in promoting blast resistance in rice

Junhua Liu, Niqing He, Zhaoping Cheng, Shaojun Lin, Shiyuan Fu, Mingmin Wang, Fenghuang Huang, Salah F Abou-Elwafa, Nora M Al Aboud, Chengzhi Huang, Dewei Yang

G3 (Bethesda); 2026 Apr 1; 16(4):jkag027. doi: 10.1093/g3journal/jkag027.

Abstract

Rice blast is a destructive rice disease caused by the fungus Magnaporthe oryzae. Here, we identified a resistance gene from the rice cultivar Wanhui 66 which is resistant to the rice blast Guy11 isolate. Genetic mapping positioned a blast resistance locus to chromosome 6. Employing map-based cloning approach ultimately mapped the novel blast resistance locus to a genomic region of 117 kb that contains the Pid3 gene. Candidate gene prediction and cDNA sequencing indicate that the target resistance gene in the Wanhui 66 is allelic to Pid3, thus it was designated Pid3-1. Further analysis showed that the Pid3-1 has 3 nucleotide substitutions, resulting in 3 amino acid substitutions in the Pid3-1 protein, which significantly affect the structure of the Pid3-1 protein as indicated by the 3D structure simulation. The CRISPR/Cas9 system was employed to generate a Pid3-1 knockout mutants that confirmed that the Wanhui 66 resistant phenotype is controlled by Pid3-1. A molecular marker, Indel-6-34, cosegregates with Pid3-1 was identified that could have a great impact on rice breeding against blast disease resistance.

See https://pubmed.ncbi.nlm.nih.gov/41655242/

Fig. 2. Genetic and physical maps of the Pid3-1 gene. (a) Primary mapping of the resistance gene; the Pid3-1 gene was identified between markers RM3330 and RM3207. (b) Further genetic mapping positioned the Pid3-1 gene between the Indel-6-5 and Indel-6-7 markers. (c) Fine mapping of the resistance gene; the Pid3-1 gene was identified between the Indel-6-20 and Indel-6-21 markers. (d) High-resolution mapping eventually mapped the Pid3-1 gene to a 113 kb region between the Indel-6-32 and Indel-6-37 markers. (e) Sixteen genes were annotated in the 117 kb region.