GWAS analysis reveals the genetic basis of blast resistance associated with heading date in rice

Seung Young Lee, Gileung Lee, Jiheon Han, Su-Kyung Ha, Chang-Min Lee, Kyeongmin Kang, Mina Jin, Jung-Pil Suh, Ji-Ung Jeung, Youngjun Mo, Hyun-Sook Lee

Front Plant Sci; 2024 May 21: 15:1412614. doi: 10.3389/fpls.2024.1412614. 

Abstract

Rice blast is a destructive fungal disease affecting rice plants at various growth stages, significantly threatening global yield stability. Development of resistant rice cultivars stands as a practical means of disease control. Generally, association mapping with a diversity panel powerfully identifies new alleles controlling trait of interest. On the other hand, utilization of a breeding panel has its advantage that can be directly applied in a breeding program. In this study, we conducted a genome-wide association study (GWAS) for blast resistance using 296 commercial rice cultivars with low population structure but large phenotypic diversity. We attempt to answer the genetic basis behind rice blast resistance among early maturing cultivars by subdividing the population based on its Heading date 1 (Hd1) functionality. Subpopulation-specific GWAS using the mixed linear model (MLM) based on blast nursery screening conducted in three years revealed a total of 26 significant signals, including three nucleotide-binding site leucine-rich repeat (NBS-LRR) genes (Os06g0286500, Os06g0286700, and Os06g0287500) located at Piz locus on chromosome 6, and one at the Pi-ta locus (Os12g0281300) on chromosome 12. Haplotype analysis revealed blast resistance associated with Piz locus was exclusively specific to Type 14 hd1 among japonica rice. Our findings provide valuable insights for breeding blast resistant rice and highlight the applicability of our elite cultivar panel to detect superior alleles associated with important agronomic traits.

See https://pubmed.ncbi.nlm.nih.gov/38835858/

Figure 3: Manhattan and quantile-quantile (Q-Q) plots resulting from the GWAS for blast resistance in Korean rice cultivars using MLM. GWAS for blast resistance in (A) Whole population (n=296). (B) Functional Hd1 group (n=183). (C) Nonfunctional hd1 group (n=113). The x- and y-axis represent SNPs along each chromosome and −log₁₀ (P) for the association, respectively. SNP positions in red indicate significant signals annotated as NBS-LRR.