An aspartic protease 47 causes quantitative recessive resistance to rice black‐streaked dwarf virus disease and southern rice black‐streaked dwarf virus disease

Abstract

Summary Rice black‐streaked dwarf virus disease (RBSDVD) and southern rice black‐streaked dwarf virus disease (SRBSDVD) are the most destructive viral diseases in rice. Progress is limited in breeding due to lack of resistance resource and inadequate knowledge on the underlying functional gene. Using genome‐wide association study (GWAS), linkage disequilibrium (LD) decay analyses, RNA‐sequencing, and genome editing, we identified a highly RBSDVD‐resistant variety and its first functional gene. A highly RBSDVD‐resistant variety W44 was identified through extensive evaluation of a diverse international rice panel. Seventeen quantitative trait loci (QTLs) were identified among which qRBSDV6‐1 had the largest phenotypic effect. It was finely mapped to a 0.8–1.2 Mb region on chromosome 6, with 62 annotated genes. Analysis of the candidate genes underlying qRBSDV6‐1 showed high expression of aspartic proteinase 47 (OsAP47) in a susceptible variety, W122, and a low resistance variety, W44. OsAP47 overexpressing lines exhibited significantly reduced resistance, while the knockout mutants exhibited significantly reduced SRBSDVD and RBSDVD severity. Furthermore, the resistant allele Hap1 of OsAP47 is almost exclusive to Indica, but rare in Japonica. Results suggest that OsAP47 knockout by editing is effective for improving RBSDVD and SRBSDVD resistance. This study provides genetic information for breeding resistant cultivars.

Plasmodesmata‐associated Flotillin positively regulates broad‐spectrum virus cell‐to‐cell trafficking

“…RDV‐borne N. cincticeps were collected from Zhejiang Province, China and maintained under experimental conditions for over 10 generations. Nonviruliferous S. furcifera or N. lugens nymphs were reared on SRBSDV‐infected or RRSV‐infected rice plants for 7 days and then transferred onto healthy rice seedlings for 8 days to allow the virus to pass through its circulation period before being used for virus transmission (Wang, Zhou et al ., 2022 ; Zhang et al ., 2018 ). The RGDV‐borne strain of R. dorsalis was established as described previously (Chen et al ., 2016 ).…”

A systematic review of southern rice black‐streaked dwarf virus in the age of omics

“…The ability of the virus to successfully infect susceptible hosts depends on the presence of proviral host factors and resources in the hosts necessary for its infection and movement. 74 Wang et al 75 showed that the rice aspartate protease 47 (OsAP47) could negatively regulate plant resistance to SRBSDV, and the OsAP47 overexpressing plants were more susceptible to SRBSDV infection, while knockout mutants showed noticeably higher resistance. 75 Nuclear factor Y (NF-Y) transcription factors (TFs) are important in rice growth and development, and can inhibit plant resistance to viruses.…”

“…74 Wang et al 75 showed that the rice aspartate protease 47 (OsAP47) could negatively regulate plant resistance to SRBSDV, and the OsAP47 overexpressing plants were more susceptible to SRBSDV infection, while knockout mutants showed noticeably higher resistance. 75 Nuclear factor Y (NF-Y) transcription factors (TFs) are important in rice growth and development, and can inhibit plant resistance to viruses. Tan et al 76 found a negative role of the rice NF-YA gene family against SRBSDV.…”

A Review of Vector-Borne Rice Viruses

“…Further haplotype analyses suggested that a candidate gene LOC_Os06g03150 is mainly associated with the differentiation of resistance within the Xian subgroup and LOC_Os06g31190 mainly explained the difference in the resistance between Xian and Geng . Using genome-wide association study (GWAS), linkage disequilibrium (LD) decay analyses, RNA-sequencing, and genome editing, a highly RBSDV-resistant variety and its first functional gene, Hap1, was identified [ 140 ]. Besides, multiple recessive resistance loci to RYMV have been mapped [ 141 , 142 ].…”