Rice Yellow Mottle Virus resistance by genome editing of the Oryza sativa L. ssp. japonica nucleoporin gene OsCPR5.1 but not OsCPR5.2

Rice yellow mottle virus (RYMV) causes one of the most devastating rice diseases in Africa.
Management of RYMV is challenging. Genetic resistance provides the most effective and environment-
friendly control. The recessive resistance locus rymv2 (OsCPR5.1) had been identified
in African rice (O. glaberrima), however, introgression into O. sativa ssp. japonica and
indica remains challenging due to crossing barriers. Here, we evaluated whether CRISPR/Cas9
genome editing of the two rice nucleoporin paralogs OsCPR5.1 (RYMV2) and OsCPR5.2 can
be used to introduce RYMV resistance into the japonica variety Kitaake. Both paralogs had
been shown to complement the defects of the Arabidopsis atcpr5 mutant, indicating partial
redundancy. Despite striking sequence and structural similarities between the two paralogs,
only oscpr5.1 loss-of-function mutants were fully resistant, while loss-of-function oscpr5.2
mutants remained susceptible, intimating that OsCPR5.1 plays a specific role in RYMV susceptibility.
Notably, edited lines with short in-frame deletions or replacements in the N-terminal
domain (predicted to be unstructured) of OsCPR5.1 were hypersusceptible to RYMV. In contrast
to mutations in the single Arabidopsis AtCPR5 gene, which caused severely dwarfed
plants, oscpr5.1 and oscpr5.2 single knockout mutants show neither substantial growth defects
nor symptoms indicative of programmed cell death, possibly reflecting functional redundancy
of the isoforms regarding other important functions. The specific editing of OsCPR5.1, while
maintaining OsCPR5.2 activity, provides a promising strategy for generating RYMV-resistance
in elite Oryza sativa lines as well as for effective stacking with other RYMV resistance genes
or other traits.